Lecture notes on ridge regression

Version 0.30, January 18, 2020.

arXiv:1509.09169v5 [stat.ME] 18 Jan 2020

Wessel N. van Wieringen1,2

1
Department of Epidemiology and Biostatistics,
Amsterdam Public Health research institute, Amsterdam UMC, location VUmc
P.O. Box 7057, 1007 MB Amsterdam, The Netherlands
2
Department of Mathematics, VU University Amsterdam
De Boelelaan 1111, 1081 HV Amsterdam, The Netherlands
Email: [email protected]

License
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Disclaimer
This document is a collection of many well-known results on ridge regression. The current status of the document
is ‘work-in-progress’ as it is incomplete (more results from literature will be included) and it may contain incon-
sistencies and errors. Hence, reading and believing at own risk. Finally, proper reference to the original source
may sometimes be lacking. This is regrettable and these references – if ever known to the author – will be included
in later versions.
Acknowledgements
Many people aided in various ways to the construction of these notes. Mark A. van de Wiel commented on various
parts of Chapter 2. Jelle J. Goeman clarified some matters behind the method described in Section 6.4.3. Paul
H.C. Eilers pointed to helpful references for Chapter 4 and provided parts of the code used in Section 4.3.
Small typo’s or minor errors, that have – hopefully – been corrected in the latest version, were pointed out by
(among others): Rikkert Hindriks, Micah Blake McCurdy, José P. González-Brenes, and numerous students from
the High-dimensional data analysis- and Statistics for high-dimensional data-courses taught at Leiden University
and the VU University Amsterdam, respectively.
Contents

1 Ridge regression 2
1.1 Linear regression 2
1.2 The ridge regression estimator 5
1.3 Eigenvalue shrinkage 9
1.3.1 Principal components regression 10
1.4 Moments 10
1.4.1 Expectation 10
1.4.2 Variance 11
1.4.3 Mean squared error 14
1.5 Constrained estimation 16
1.6 Degrees of freedom 19
1.7 Efficient calculation 19
1.8 Choice of the penalty parameter 20
1.8.1 Information criterion 20
1.8.2 Cross-validation 21
1.8.3 Generalized cross-validation 22
1.9 Simulations 23
1.9.1 Role of the variance of the covariates 23
1.9.2 Ridge regression and collinearity 25
1.9.3 Variance inflation factor 27
1.10 Illustration 29
1.10.1 MCM7 expression regulation by microRNAs 29
1.11 Conclusion 33
1.12 Exercises 34

2 Bayesian regression 36
2.1 A minimum of prior knowledge on Bayesian statistics 36
2.2 Relation to ridge regression 37
2.3 Markov chain Monte Carlo 40
2.4 Empirical Bayes 45
2.5 Conclusion 46
2.6 Exercises 46

3 Generalizing ridge regression 47

3.1 Moments 48
3.2 The Bayesian connection 49
3.3 Application 50
3.4 Generalized ridge regression 52
3.5 Conclusion 53
3.6 Exercises 53

4 Mixed model 55
4.1 Link to ridge regression 60
4.2 REML consistency, high-dimensionally 61
4.3 Illustration: P-splines 63
5 Ridge logistic regression 67
5.1 Logistic regression 67
5.2 Ridge estimation 69
5.3 Moments 71
5.4 The Bayesian connection 73
5.5 Penalty parameter selection 74
5.6 Application 74
5.7 Conclusion 76
5.8 Exercises 76

6 Lasso regression 79
6.1 Uniqueness 80
6.2 Analytic solutions 82
6.3 Sparsity 85
6.3.1 Maximum number of selected covariates 87
6.4 Estimation 88
6.4.1 Quadratic programming 88
6.4.2 Iterative ridge 89
6.4.3 Gradient ascent 90
6.4.4 Coordinate descent 92
6.5 Moments 92
6.6 The Bayesian connection 93
6.7 Comparison to ridge 95
6.7.1 Linearity 95
6.7.2 Shrinkage 95
6.7.3 Simulation I: Covariate selection 96
6.7.4 Simulation II: correlated covariates 97
6.8 Pandora’s box 97
6.8.1 Elastic net 97
6.8.2 Fused lasso 99
6.8.3 The (sparse) group lasso 101
6.8.4 Adaptive lasso 102
6.8.5 The ℓ0 penalty 103
6.9 Exercises 103
1 Ridge regression

High-throughput techniques measure many characteristics of a single sample simultaneously. The number of
characteristics p measured may easily exceed ten thousand. In most medical studies the number of samples n
involved often falls behind the number of characteristics measured, i.e: p > n. The resulting (n × p)-dimensional
data matrix X:
   
X1,∗ X1,1 . . . X1,p
   .. 
X = (X∗,1 | . . . | X∗,p ) =  ...  =  ... ..
. . 
Xn,∗ Xn,1 . . . Xn,p

from such a study contains a larger number of covariates than samples. When p > n the data matrix X is said to
be high-dimensional.
In this chapter we adopt the traditional statistical notation of the data matrix. An alternative notation would be
X⊤ (rather than X), which is employed in the field of (statistical) bioinformatics. In X⊤ the rows comprise the
samples rather than the covariates. The case for the bioinformatics notation stems from practical arguments. A
spreadsheet is designed to have more rows than columns. In case p > n the traditional notation yields a spreadsheet
with more columns than rows. When p > 10000 the conventional display is impractical. In this chapter we stick
to the conventional statistical notation of the data matrix as all mathematical expressions involving X are then in
line with those of standard textbooks on regression.
The information contained in X is often used to explain a particular property of the samples involved. In
applications in molecular biology X may contain microRNA expression data from which the expression levels of
a gene are to be described. When the gene’s expression levels are denoted by Y = (Y1 , . . . , Yn )⊤ , the aim is to
find the linear relation Yi = Xi,∗ β from the data at hand by means of regression analysis. Regression is however
frustrated by the high-dimensionality of X (illustrated in Section 1.2 and at the end of Section 1.5). These notes
discuss how regression may be modified to accommodate the high-dimensionality of X. First, however, ‘standard’
linear regression is recaputilated.

1.1 Linear regression

Consider an experiment in which p characteristics of n samples are measured. The data from this experiment are
denoted X, with X as above. The matrix X is called the design matrix. Additional information of the samples
is available in the form of Y (also as above). The variable Y is generally referred to as the response variable.
The aim of regression analysis is to explain Y in terms of X through a functional relationship like Yi = f (Xi,∗ ).
When no prior knowledge on the form of f (·) is available, it is common to assume a linear relationship between
X and Y. This assumption gives rise to the linear regression model:

Yi = Xi,∗ β + εi (1.1)
= β1 Xi,1 + . . . + βp Xi,p + εi .

In model (1.1) β = (β1 , . . . , βp )⊤ is the regression parameter. The parameter βj , j = 1, . . . , p, represents

the effect size of covariate j on the response. That is, for each unit change in covariate j (while keeping the
other covariates fixed) the observed change in the response is equal to βj . The second summand on the right-
hand side of the model, εi , is referred to as the error. It represents the part of the response not explained by the
functional part Xi,∗ β of the model (1.1). In contrast to the functional part, which is considered to be systematic
(i.e. non-random), the error is assumed to be random. Consequently, Yi1 ,∗ need not equal Yi2 ,∗ for i1 6= i2 , even
if Xi1 ,∗ = Xi2 ,∗ . To complete the formulation of model (1.1) we need to specify the probability distribution of
1.1 Linear regression 3

εi . It is assumed that εi ∼ N (0, σ 2 ) and the εi are independent, i.e.:


σ2 if i1 = i2 ,
Cov(εi1 , εi2 ) =
0 if i1 6= i2 .

The randomness of εi implies that Yi is also a random variable. In particular, Yi is normally distributed, because
εi ∼ N (0, σ 2 ) and Xi,∗ β is a non-random scalar. To specify the parameters of the distribution of Yi we need to
calculate its first two moments. Its expectation equals:

E(Yi ) = E(Xi,∗ β) + E(εi ) = Xi,∗ β,

while its variance is:

Var(Yi ) = E{[Yi − E(Yi )]2 } = E(Yi2 ) − [E(Yi )]2

= E[(Xi,∗ β)2 + 2εi Xi,∗ β + ε2i ] − (Xi,∗ β)2
= E(ε2i ) = Var(εi ) = σ 2 .

Hence, Yi ∼ N (Xi,∗ β, σ 2 ). This formulation (in terms of the normal distribution) is equivalent to the formulation
of model (1.1), as both capture the assumptions involved: the linearity of the functional part and the normality of
the error.
Model (1.1) is often written in a more condensed matrix form:

Y = X β + ε, (1.2)

where ε = (ε1 , ε2 , . . . , εn )⊤ and distributed as ε ∼ N (0p , σ 2 Inn ). As above model (1.2) can be expressed as a
multivariate normal distribution: Y ∼ N (X β, σ 2 Inn ).
Model (1.2) is a so-called hierarchical model. This terminology emphasizes that X and Y are not on a par,
they play different roles in the model. The former is used to explain the latter. In model (1.1) X is referred as the
explanatory or independent variable, while the variable Y is generally referred to as the response or dependent
variable.
The covariates, the columns of X, may themselves be random. To apply the linear model they are temporarily
assumed fixed. The linear regression model is then to be interpreted as Y | X ∼ N (X β, σ 2 Inn )

Example 1.1 Methylation of a tumor-suppressor gene

Consider a study which measures the gene expression levels of a tumor-suppressor genes (TSG) and two methy-
lation markers (MM1 and MM2) on 67 samples. A methylation marker is a gene that promotes methylation.
Methylation refers to attachment of a methyl group to a nucleotide of the DNA. In case this attachment takes
place in or close by the promotor region of a gene, this complicates the transcription of the gene. Methylation
may down-regulate a gene. This mechanism also works in the reverse direction: removal of methyl groups may
up-regulate a gene. A tumor-suppressor gene is a gene that halts the progression of the cell towards a cancerous
state.
The medical question associated with these data: do the expression levels methylation markers affect the
expression levels of the tumor-suppressor gene? To answer this question we may formulate the following linear
regression model:

Yi,tsg = β0 + βmm1 Xi,mm1 + βmm2 Xi,mm2 + εi ,

with i = 1, . . . , 67 and εi ∼ N (0, σ 2 ). The interest focusses on βmm1 and βmm2 . A non-zero value of at least one
of these two regression parameters indicates that there is a linear association between the expression levels of the
tumor-suppressor gene and that of the methylation markers.
Prior knowledge from biology suggests that the βmm1 and βmm2 are both non-positive. High expression levels
of the methylation markers lead to hyper-methylation, in turn inhibiting the transcription of the tumor-suppressor
gene. Vice versa, low expression levels of MM1 and MM2 are (via hypo-methylation) associated with high
expression levels of TSG. Hence, a negative concordant effect between MM1 and MM2 (on one side) and TSG
(on the other) is expected. Of course, the methylation markers may affect expression levels of other genes that in
turn regulate the tumor-suppressor gene. The regression parameters βmm1 and βmm2 then reflect the indirect effect
of the methylation markers on the expression levels of the tumor suppressor gene. 
4 Ridge regression

The linear regression model (1.1) involves the unknown parameters: β and σ 2 , which need to be learned from
the data. The parameters of the regression model, β and σ 2 are estimated by means of likelihood maximization.
Recall that Yi ∼ N (Xi,∗ β, σ 2 ) with corresponding density: fYi (yi ) = (2 π σ 2 )−1/2 exp[−(yi − Xi∗ β)2 /2σ 2 ].
The likelihood thus is:
n
Y 1
L(Y, X; β, σ 2 ) = √ exp[−(Yi − Xi,∗ β)2 /2σ 2 ],
i=1
2πσ

in which the independence of the observations has been used. Because of the concavity of the logarithm, the
maximization of the likelihood coincides with the maximum of the logarithm of the likelihood (called the log-
likelihood). Hence, to obtain maximum likelihood (ML) estimates of the parameter it is equivalent to find the
maximum of the log-likelihood. The log-likelihood is:
√ 1 Xn
L(Y, X; β, σ 2 ) = log[L(Y, X; β, σ 2 )] = −n log( 2 π σ) − 2 (yi − Xi,∗ β)2 .
2σ i=1
Pn
After noting that i=1 (Yi − Xi,∗ β)2 = kY − X βk22 = (Y − X β)⊤ (Y − X β), the log-likelihood can be
written as:
√ 1
L(Y, X; β, σ 2 ) = −n log( 2 π σ) − 2 kY − X βk22 .
2σ
In order to find the maximum of the log-likelihood, take its derivate with respect to β:
∂ 1 ∂ 1
L(Y, X; β, σ 2 ) = − kY − X βk22 = 2 X⊤ (Y − X β).
∂β 2σ 2 ∂ β σ
Equate this derivative to zero gives the estimating equation for β:

X⊤ X β = X⊤ Y. (1.3)

Equation (1.3) is called to the normal equation. Pre-multiplication of both sides of the normal equation by
(X⊤ X)−1 now yields the ML estimator of the regression parameter: β̂ = (X⊤ X)−1 X⊤ Y, in which it is as-
sumed that (X⊤ X)−1 is well-defined.
Along the same lines one obtains the ML estimator of the residual variance. Take the partial derivative of the
log-likelihood with respect to σ 2 :
∂ n 1
L(Y, X; β, σ 2 ) = − + 3 kY − X βk22 .
∂σ σ σ
1
Equate the right-hand side to zero and solve for σ 2 to find σ̂ 2 = n kY − X βk22 . In this expression β is unknown
and the ML estimate of β is plugged-in.

With explicit expressions of the ML estimators at hand, we can study their properties. The expectation of the
ML estimator of the regression parameter β is:

E(β̂) = E[(X⊤ X)−1 X⊤ Y] = (X⊤ X)−1 X⊤ E[Y] = (X⊤ X)−1 X⊤ X β = β.

Hence, the ML estimator of the regression coefficients is unbiased.

The variance of the ML estimator of β is:

Var(β̂) = E{[β̂ − E(β̂)][β̂ − E(β̂)]⊤ }

= E{[(X⊤ X)−1 X⊤ Y − β] [(X⊤ X)−1 X⊤ Y − β]⊤ }
= (X⊤ X)−1 X⊤ E{Y Y⊤ } X (X⊤ X)−1 − β β ⊤
= (X⊤ X)−1 X⊤ {X β β ⊤ X⊤ + Σ} X (X⊤ X)−1 − β β ⊤
= β β ⊤ + σ 2 (X⊤ X)−1 − β β ⊤ = σ 2 (X⊤ X)−1 ,

in which we have used that E(YY⊤ ) = X β β ⊤ X⊤ + σ 2 Inn . From Var(β̂) = σ 2 p (X⊤ X)−1 , one obtains an
estimate of the variance of the estimate of the j-th regression coefficient: σ̂ 2 (β̂j ) = σ̂ 2 [(X⊤ X)−1 ]jj . This may
be used to construct a confidence interval for the estimates or test the hypothesis H0 : βj = 0. In the latter σ̂ 2
1.2 The ridge regression estimator 5

should not be the maximum likelihood estimator, as it is biased. It is then to be replaced by the residual sum-of-
squares divided by n − p rather than n.

The prediction of Yi , denoted Ybi , is the expected value of Yi according the linear regression model (with its pa-
rameters replaced by their estimates). The prediction of Yi thus equals E(Yi ; β̂, σ̂ 2 ) = Xi,∗ β̂. In matrix notation
the prediction is:
b
Y = X β̂ = X (X⊤ X)−1 X⊤ Y := HY,

where H is the hat matrix, as it ‘puts the hat’ on Y. Note that the hat matrix is a projection matrix, i.e. H2 = H
for

H2 = X (X⊤ X)−1 X⊤ X (X⊤ X)−1 X⊤ = X (X⊤ X)−1 X⊤ .

b is an orthogonal projection of Y onto the space spanned by the columns of X.

Thus, the prediction Y
b
With β available, an estimate of the errors ε̂i , dubbed the residuals are obtained via:

ε̂ b = Y − X β̂ = Y − X (X⊤ X)−1 X⊤ Y = [I − X (X⊤ X)−1 X⊤ ] Y.

= Y−Y

Thus, the residuals are a projection of Y onto the orthogonal complement of the space spanned by the columns of
X. The residuals are to be used in diagnostics, e.g. checking of the normality assumption by means of a normal
probability plot.

For more on the linear regression model confer the monograph of Draper and Smith (1998).

1.2 The ridge regression estimator

If the design matrix is high-dimensional, the covariates (the columns of X) are super-collinear. Recall collinearity
in regression analysis refers to the event of two (or multiple) covariates being strongly linearly related. Conse-
quently, the space spanned by collinear covariates is then a lower-dimensional subspace of the parameter space. If
the design matrix X, which contains the collinear covariates as columns, is (close to) rank deficient, it is (almost)
impossible to separate the contribution of the individual covariates. The uncertainty with respect to the covariate
responsible for the variation explained in Y is often reflected in the fit of the linear regression model to data by a
large error of the estimates of the regression parameters corresponding to the collinear covariates.
Example 1.2
The flotillins (the FLOT-1 and FLOT-2 genes) have been observed to regulate the proto-oncogene ERBB2 in vitro
(Pust et al., 2013). One may wish to corroborate this in vivo. To this end we use gene expression data of a breast
cancer study, available as a Bioconductor package: breastCancerVDX. From this study the expression levels
of probes interrogating the FLOT-1 and ERBB2 genes are retrieved. For clarity of the illustration the FLOT-2
gene is ignored. After centering, the expression levels of the first ERBB2 probe are regressed on those of the four
FLOT-1 probes. The R-code below carries out the data retrieval and analysis.
Listing 1.1 R code
# load packages
library(Biobase)
library(breastCancerVDX)

# ids of genes FLOT1

idFLOT1 <- which(fData(vdx)[,5] == 10211)

# ids of ERBB2
idERBB2 <- which(fData(vdx)[,5] == 2064)

# get expression levels of probes mapping to FLOT genes

X <- t(exprs(vdx)[idFLOT1,])
X <- sweep(X, 2, colMeans(X))

# get expression levels of probes mapping to FLOT genes

6 Ridge regression

Y <- t(exprs(vdx)[idERBB2,])
Y <- sweep(Y, 2, colMeans(Y))

# regression analysis
summary(lm(formula = Y[,1] ˜ X[,1] + X[,2] + X[,3] + X[,4]))

# correlation among the covariates

cor(X)

Prior to the regression analysis, we first assess whether there is collinearity among the FLOT-1 probes through
evaluation of the correlation matrix. This reveals a strong correlation (ρ̂ = 0.91) between the second and third
probe. All other cross-correlations do not exceed the 0.20 (in an absolute sense). Hence, there is collinearity
among the columns of the design matrix in the to-be-performed regression analysis.

Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 0.0000 0.0633 0.0000 1.0000
X[, 1] 0.1641 0.0616 2.6637 0.0081 **
X[, 2] 0.3203 0.3773 0.8490 0.3965
X[, 3] 0.0393 0.2974 0.1321 0.8949
X[, 4] 0.1117 0.0773 1.4444 0.1496
---
Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1

Residual standard error: 1.175 on 339 degrees of freedom

Multiple R-squared: 0.04834,Adjusted R-squared: 0.03711
F-statistic: 4.305 on 4 and 339 DF, p-value: 0.002072

The output of the regression analysis above shows the first probe to be significantly associated to the expression
levels of ERBB2. The collinearity of the second and third probe reveals itself in the standard errors of the effect
size: for these probes the standard error is much larger than those of the other two probes. This reflects the un-
certainty in the estimates. Regression analysis has difficulty to decide to which covariate the explained proportion
of variation in the response should be attributed. The large standard error of these effect sizes propagates to the
testing as the Wald test statistic is the ratio of the estimated effect size and its standard error. Collinear covariates
are thus less likely to pass the significance threshold. 

The case of two (or multiple) covariates being perfectly linearly dependent is referred as super-collinearity. The
rank of a high-dimensional design matrix is maximally equal to n: rank(X) ≤ n. Consequently, the dimension of
subspace spanned by the columns of X is smaller than or equal to n. As p > n, this implies that columns of X
are linearly dependent. Put differently, a high-dimensional X suffers from super-collinearity.

Example 1.3 Super-collinearity

Consider the design matrix:
 
1 −1 2
 1 0 1 
X = 
 1

2 −1 
1 1 0

The columns of X are linearly dependent: the first column is the row-wise sum of the other two columns. The
rank (more correct, the column rank) of a matrix is the dimension of space spanned by the column vectors. Hence,
the rank of X is equal to the number of linearly independent columns: rank(X) = 2. 

Super-collinearity of an (n × p)-dimensional design matrix X implies∗ that the rank of the (p × p)-dimensional
matrix X⊤ X is smaller than p, and, consequently, it is singular. A square matrix that does not have an inverse is
called singular. A matrix A is singular if and only if its determinant is zero: det(A) = 0.

∗ If the (column) rank of X is smaller than p, there exists a non-trivial v ∈ Rp such that Xv = 0 . Multiplication of this inequality by
p
X⊤ yields X⊤ Xv = 0p . As v 6= 0p , this implies that X⊤ X is not invertible.
1.2 The ridge regression estimator 7

Example 1.4 Singularity

Consider the matrix A given by:
 
1 2
A =
2 4

Clearly, det(A) = a11 a22 − a12 a21 = 1 × 4 − 2 × 2 = 0. Hence, A is singular and its inverse is undefined. 

As det(A) is equal to the product of the eigenvalues νj of A, the matrix A is singular if

Pone (or more) of the
eigenvalues of A is zero. To see this, consider the spectral decomposition of A: A = pj=1 νj vj vj⊤ , where
corresponding to νj . To obtain the inverse of A it requires to take the reciprocal of the
vj is the eigenvectorP
p
eigenvalues: A−1 = j=1 νj−1 vj vj⊤ . The right-hand side is undefined if νj = 0 for any j.
Example 1.4 (Singularity, continued)
Revisit Example 1.4. Matrix A has eigenvalues ν1 = 5 and ν2 = 0. According to the spectral decomposition,
the inverse of A is: A−1 = 51 v1 v1⊤ + 01 v2 v2⊤ . This expression is undefined as we divide by zero in the second
summand on the right-hand side. 

In summary, the columns of a high-dimensional design matrix X are linearly dependent and this super-collinearity
causes X⊤ X to be singular. Now recall the ML estimator of the parameter of the linear regression model:
β̂ = (X⊤ X)−1 X⊤ Y. This estimator is only well-defined if (X⊤ X)−1 exits. Hence, when X is high-dimensional
the regression parameter β cannot be estimated.

Above only the practical consequence of high-dimensionality is presented: the expression (X⊤ X)−1 X⊤ Y cannot
be evaluated numerically. But the problem arising from the high-dimensionality of the data is more fundamental.
To appreciate this, consider the normal equations: X⊤ Xβ = X⊤ Y. The matrix X⊤ X is of rank n, while β is a
vector of length p. Hence, while there are p unknowns, the system of linear equations from which these are to be
solved effectively comprises n degrees of freedom. If p > n, the vector β cannot uniquely be determined from
this system of equations. To make this more specific let U be the n-dimensional space spanned by the columns
of X and the p − n-dimensional space V be orthogonal complement of U , i.e. V = U ⊥ . Then, Xv = 0p for all
v ∈ V . So, V is the non-trivial null space of X. Consequently, as X⊤ Xv = X⊤ 0p = 0n , the solution of the
normal equations is:

β̂ = (X⊤ X)− X⊤ Y + v for all v ∈ V,

where A− denotes the Moore-Penrose inverse of the matrix A, which is defined as:
Xp
A− = νj−1 I{νj 6=0} vj vj⊤ .
j=1

The solution of the normal equations is thus only determined up to an element from a non-trivial space V , and
there is no unique estimator of the regression parameter.
To arrive at a unique regression estimator for studies with rank deficient design matrices, the minimum least
squares estimator may be employed.
Definition 1.1 (Ishwaran and Rao, 2014)
The minimum least squares estimator of regression parameter minimizes the sum-of-squares criterion and is of
minimum length. Formally, β̂MLS = arg minβ∈Rp kY − Xβk22 such that kβ̂MLS k22 < kβk for all β that minimize
kY − Xβk22 .

If X is of full rank, the minimum least squares regression estimator coincides with the least squares/maximum
likelihood one as the latter is a unique minimizer of the sum-of-squares criterion and, thereby, automatically also
the minimizer of minimum length. When X is rank deficient, β̂MLS = (X⊤ X)− X⊤ Y. To see this recall from
above that kY − Xβk22 is minimized by (X⊤ X)− X⊤ Y + v for all v ∈ V . The length of these minimizers is:

k(X⊤ X)− X⊤ Y + vk22 = k(X⊤ X)− X⊤ Yk22 + 2Y⊤ X(X⊤ X)− v + kvk22 ,

which, by the orthogonality of V and the space spanned by the columns of X, equals k(X⊤ X)− X⊤ Yk22 + kvk22 .
Clearly, any nontrivial v, i.e. v 6= 0p , results in k(X⊤ X)− X⊤ Yk22 + kvk22 > k(X⊤ X)− X⊤ Yk22 and, thus,
β̂MLS = (X⊤ X)− X⊤ Y.
8 Ridge regression

An alternative (and related) estimator of the regression parameter β that avoids the use of the Moore-Penrose
inverse and is able to deal with (super)-collinearity among the columns of the design matrix is the ridge regres-
sion estimator proposed by Hoerl and Kennard (1970). It essentially comprises of an ad-hoc fix to resolve the
(almost) singularity of X⊤ X. Hoerl and Kennard (1970) propose to simply replace X⊤ X by X⊤ X + λIpp with
λ ∈ [0, ∞). The scalar λ is a tuning parameter, henceforth called the penalty parameter for reasons that will
become clear later.

Example 1.3 (Super-collinearity, continued)

Recall the super-collinear design matrix X of Example 1.3. Then, for (say) λ = 1:
 
5 2 2
X⊤ X + λIpp =  2 7 −4  .
2 −4 7

The eigenvalues of this matrix are 11, 7, and 1. Hence, X⊤ X + λIpp has no zero eigenvalue and its inverse is
well-defined. 

With the ad-hoc fix for the singularity of X⊤ X, Hoerl and Kennard (1970) proceed to define the ridge regression
estimator:

β̂(λ) = (X⊤ X + λIpp )−1 X⊤ Y, (1.4)

for λ ∈ [0, ∞). Clearly, this is – for λ strictly positive – a well-defined estimator, even if X is high-dimensional.
However, each choice of λ leads to a different ridge regression estimate. The set of all ridge regression estimates
{β̂(λ) : λ ∈ [0, ∞)} is called the solution or regularization path of the ridge estimator.

Example 1.3 (Super-collinearity, continued)

Recall the super-collinear design matrix X of Example 1.3. Suppose that the corresponding response vector
is Y = (1.3, −0.5, 2.6, 0.9)⊤. The ridge regression estimates for, e.g. λ = 1, 2, and 10 are then: β̂(1) =
(0.614, 0.548, 0.066)⊤, β̂(2) = (0.537, 0.490, 0.048)⊤, and β̂(10) = (0.269, 0.267, 0.002)⊤. The full solution
path of the ridge estimator is shown in the left-hand side panel of Figure 1.1.

Ridge solution path

^
β1(λ)
^
β2(λ)
^
β3(λ)
Y
0.6
ridge estimate

0.4

X2
X2
0.2

^
Y
0.0

Y(
)
^

−5 0 5 10

log(λ)

X1

Figure 1.1: Left panel: the regularization path of the ridge estimator for the data of Example 1.3. Right panel:
the ‘maximum likelihood fit’ Yb and the ‘ridge fit’ Yb (λ) (the dashed-dotted red line) to the observation Y in the
(hyper)plane spanned by the covariates.
1.3 Eigenvalue shrinkage 9

With an estimate of the regression parameter β available one can define the fit. For the ridge regression estimator
the fit is defined analogous to the ML case:

b
Y(λ) = Xβ̂(λ) = X(X⊤ X + λIpp )−1 X⊤ Y := H(λ)Y.

For the ML regression estimator the fit could be understood as a projection of Y onto the subspace spanned by
the columns of X. This is depicted in the right panel of Figure 1.1, where Yb is the projection of the observation
Y onto the covariate space. The projected observation Yb is orthogonal to the residual ε = Y − Yb . This means
the fit is the point in the covariate space closest to the observation. Put differently, the covariate space does not
contain a point that is better in explaining the observation. Compare this to the ‘ridge fit’ which is plotted as a
dashed-dotted red line in the right panel of Figure 1.1. The ‘ridge fit’ is a line, parameterized by {λ : λ ∈ R≥0 },
where each point on this line matches to the corresponding intersection of the regularization path β̂(λ) and the
vertical line x = λ. The ‘ridge fit’ Yb (λ) runs from the ML fit Yb = Yb (0) to the an intercept-only fit in which the
covariates do not contribute to the explanation of the observation. From the figure it is obvious that for any λ > 0
the ‘ridge fit’ Yb (λ) is not orthogonal to the observation Y . In other words, the ‘ridge residuals’ Y − Yb (λ) are not
orthogonal to the fit Yb (λ) (confer Exercise 1.4b). Hence, the ad-hoc fix of the ridge regression estimator resolves
the non-evaluation of the estimator in the face of super-collinearity but yields a ‘ridge fit’ that is not optimal in
explaining observation. Mathematically this is due to the fact that the fit Yb (λ) corresponding to the ridge estimator
is not a projection of Y onto the covariate space (confer Exercise 1.4a).

1.3 Eigenvalue shrinkage

The effect of the ridge penalty may also studied from the perspective of singular values. Let the singular value
decomposition of the (n × p)-dimensional design matrix X be:

X = Ux Dx Vx⊤ ,

where Dx an (n × n)-dimensional diagonal matrix with the singular values, Ux an (n × n)-dimensional matrix
with columns containing the left singular vectors (denoted ui ), and Vx a (p×n)-dimensional matrix with columns
containing the right singular vectors (denoted vi ). The columns of Ux and Vx are orthogonal: U⊤ x Ux = Inn =
Vx⊤ Vx .
The OLS estimator can then be rewritten in terms of the SVD-matrices as:

β̂ = (X⊤ X)−1 X⊤ Y = (Vx Dx U⊤ ⊤ −1

x Ux Dx Vx ) Vx Dx U⊤
xY
= (Vx D2x Vx⊤ )−1 Vx Dx U⊤ −2 ⊤ ⊤
x Y = Vx Dx Vx Vx Dx Ux Y
−2 ⊤
= Vx Dx Dx Ux Y,

where D−2x Dx is not simplified further to emphasize the effect of the ridge penalty. Similarly, the ridge estimator
can be rewritten in terms of the SVD-matrices as:

β̂(λ) = (X⊤ X + λIpp )−1 X⊤ Y

= (Vx Dx U⊤ ⊤
x Ux Dx Vx + λIpp )
−1
Vx Dx U⊤
xY
= (Vx D2x Vx⊤ + λVx Vx⊤ )−1 Vx Dx U⊤
xY
2 −1 ⊤ ⊤
= Vx (Dx + λInn ) Vx Vx Dx Ux Y
= Vx (D2x + λInn )−1 Dx U⊤
x Y. (1.5)

Combining the two results and writing (Dx )jj = dx,jj we have: d−1 2
x,jj ≥ dx,jj (dx,jj + λ)
−1
for all λ > 0.
Thus, the ridge penalty shrinks the singular values.

Return to the problem of the super-collinearity of X in the high-dimensional setting (p > n). The super-
collinearity implies the singularity of X⊤ X and prevents the calculation of the OLS estimator
Pp of the regression
coefficients. However, X⊤ X+λIpp is non-singular, with inverse: (X⊤ X+λIpp )−1 = j=1 (d2x,jj +λ)−1 vj vj⊤ .
The right-hand side is well-defined for λ > 0.

From the ‘spectral formulation’ of the ridge regression estimator (1.5) the λ-limits can be deduced. The lower
10 Ridge regression

λ-limit of the ridge regression estimator β̂(0+ ) = limλ↓0 β̂(λ) coincides with the minimum least squares estima-
tor. This is immediate when X is of full rank. In the high-dimensional situation, when the dimensional p exceeds
the sample size n, it follows from the limit:
 −1
djj djj if djj 6= 0
lim 2 =
λ↓0 djj + λ 0 if djj = 0

Then, limλ↓0 β̂(λ) = β̂MLS . Similarly, the upper λ-limit is evident from the fact that limλ→∞ djj (d2jj + λ)−1 = 0,
which implies limλ→∞ β̂(λ) = 0p . Hence, all regression coefficients are shrunken towards zero as the penalty
parameter increases. This also holds for X with p > n. Furthermore, this behaviour is not strictly monotone in λ:
λa > λb does not necessarily imply |β̂j (λa )| < |β̂j (λb )|. Upon close inspection this can be witnessed from the
ridge solution path of β3 in Figure 1.1.

1.3.1 Principal components regression

Principal component regression is a close relative to ridge regression that can also be applied in a high-dimensional
context. Principal components regression explains the response not by the covariates themselves but by linear
combinations of the covariates as defined by the principal components of X. Let UDV⊤ be the singular value
decomposition of X. The i-th principal component of X is then Xvi , henceforth denoted zi . Let Zk be the
matrix of the first k principal components, i.e. Zk = XVk where Vk contains the first k right singular vectors as
columns. Principal components regression then amounts to regressing the response Y onto Zk , that is, it fits the
model Y = Zk γ + ε. The least squares estimator of γ then is (with some abuse of notation):
γ̂ = (Z⊤
k Zk ) Zk Y = (Vk⊤ X⊤ XVk )−1 Vk⊤ X⊤ Y
−1 ⊤

= (Vk VDU⊤ UDV⊤ Vk )−1 Vk⊤ VDU⊤ Y

⊤

= (Ikn D2 Ink )−1 Ikn DU⊤ Y

= D−2 De k U⊤ Y = D e −1 U⊤ Y,
k k

where Dk and D e k are submatrices of D. The matrix Dk is obtained from D by removal of the last n − p rows
and columsn, while for D e k only the last n − k rows are dropped. Similarly, Ikn and Ink are obtained from Inn by
removal of the last n − k rows and columns, respectively. The principal component regression estimator of β then
e −1 U⊤ Y. When k is set equal to the column rank of X, and thus to the rank of X⊤ X, the principal
is β̂pcr = Vk D k
component regression estimator β̂pcr = (X⊤ X)− X⊤ Y, where A− denotes the Moore-Penrose inverse of matrix
A.
The relation between ridge and principal component regression becomes clear when their corresponding esti-
mators are written in terms of the singular value decomposition of X:
β̂pcr = Vx (Ink Dx Ikn )−1 U⊤
x Y,
β̂(λ) = Vx (D2x + λInn )−1 Dx U⊤
x Y.

Both operate on the singular values of the design matrix. But where principal component regression thresholds
the singular values of X, ridge regression shrinks them (depending on their size). Hence, one applies a discrete
map on the singular values while the other a continuous one.

1.4 Moments
The first two moments of the ridge regression estimator are derived. Next the performance of the ridge regression
estimator is studied in terms of the mean squared error, which combines the first two moments.

1.4.1 Expectation
The left panel of Figure 1.1 shows ridge estimates of the regression parameters converging to zero as the penalty
parameter tends to infinity. This behaviour of the ridge estimator does not depend on the specifics of the data set.
To see this study the expectation of the ridge estimator:
   
E β̂(λ) = E (X⊤ X + λIpp )−1 X⊤ Y
= (X⊤ X + λIpp )−1 X⊤ E(Y)
= (X⊤ X + λIpp )−1 (X⊤ X) β.
1.4 Moments 11

 
Clearly, E β̂(λ) 6= β for any λ > 0. Hence, the ridge estimator is biased.

Example 1.5 (Orthonormal design matrix)

Consider an orthonormal design matrix X, i.e.: X⊤ X = Ipp = (X⊤ X)−1 . An example of an orthonormal design
matrix would be:
 
−1 −1
1 −1 1 
.
X = 
2 1 −1 
1 1

This design matrix is orthonormal as X⊤ X = I22 , which is easily verified by working out the matrix multiplica-
tion. In case of an orthonormal design matrix the relation between the OLS and ridge estimator is:

β̂(λ) = (X⊤ X + λIpp )−1 X⊤ Y = (Ipp + λIpp )−1 X⊤ Y

= (1 + λ)−1 Ipp X⊤ Y = (1 + λ)−1 (X⊤ X)−1 X⊤ Y
= (1 + λ)−1 β̂.

Hence, the ridge estimator scales the OLS estimator by a factor. When taking the expectation on both sides, it is
evident that the ridge estimator is biased: E[β̂(λ)] = E[(1 + λ)−1 β̂] = (1 + λ)−1 E(β̂) = (1 + λ)−1 β 6= β. From
this it also evident that the estimator, and thus its expectation, vanish as λ → ∞. 

The bias of the ridge regression estimator may be decomposed into two parts (as pointed out by Shao and Deng,
2012), one attributable to the penalization and another to the high-dimensionality of the study design. To arrive
at this decomposition define the projection matrix, i.e. a matrix P such that P = P2 , that projects the parameter
space Rp onto the subspace R(X) ⊂ Rp spanned by the rows of the design matrix X, denoted Px , and given by:
Px = X⊤ (XX⊤ )− X, where (XX⊤ )− is the Moore-Penrose inverse of XX⊤ . The ridge regression estimator
lives in the subspace defined by the projection Px of Rp onto R(X). To verify this, consider the singular value
decomposition X = Ux Dx Vx⊤ (with matrices defined as before) and note that Px = Vx Vx⊤ . Then:

Px β̂(λ) = Vx Vx⊤ Vx (D2x + λIpp )−1 U⊤ 2

x Y = Vx (Dx + λIpp )
−1 ⊤
Ux Y = β̂(λ).

The ridge regression estimator is thus unaffected by the projection, as Px β̂(λ) = β̂(λ), and it must therefore
already be an element of the projected subspace R(X). The bias can now be decomposed as:

E[β̂(λ) − β] = E[β̂(λ) − Px β + Px β − β] = E[β̂(λ) − Px β] + (Px − Ipp )β.

The first summand on the right-hand side of the preceding display represents the bias of the ridge regression
estimator to the projection of the true parameter value, whereas the second summand is the bias introduced by
the high-dimensionality of the study design. Either if i) X is of full row rank (i.e. the study design in low-
dimensional and Px = Ipp ) or if ii) the true regression parameter β is an element the projected subspace (i.e.
β = Px β ∈ R(X)), the second summand of the bias will vanish.

1.4.2 Variance
As for the ML estimate of the regression parameter β of model (1.2), we derive the second moment of the ridge
estimator. Hereto define:

Wλ = (X⊤ X + λIpp )−1 X⊤ X.

Using Wλ the ridge estimator β̂(λ) can be expressed as Wλ β̂ for:

Wλ β̂ = Wλ (X⊤ X)−1 X⊤ Y
= [(X⊤ X)−1 (X⊤ X + λIpp )]−1 (X⊤ X)−1 X⊤ Y
= (X⊤ X + λIpp )−1 X⊤ X(X⊤ X)−1 X⊤ Y
= (X⊤ X + λIpp )−1 X⊤ Y
= β̂(λ).
12 Ridge regression

The linear operator Wλ thus transforms the ML estimator of the regression parameter into the ridge estimator.
It is now easily seen that:
Var[β̂(λ)] = Var[Wλ β̂] = Wλ Var[β̂]Wλ⊤
= σ 2 Wλ (X⊤ X)−1 Wλ⊤ = σ 2 (X⊤ X + λIpp )−1 X⊤ X[(X⊤ X + λIpp )−1 ]⊤ ,
in which we have used Var(AY) = AVar(Y)A⊤ for a non-random matrix A, the fact that Wλ is non-random,
and Var[β̂] = σ 2 (X⊤ X)−1 .
Like the expectation the variance of the ridge estimator vanishes as λ tends to infinity:
 
lim Var β̂(λ) = lim σ 2 Wλ (X⊤ X)−1 Wλ⊤ = 0pp .
λ→∞ λ→∞

Hence, the variance of the ridge regression coefficient estimates decreases towards zero as the penalty parameter
becomes large. This is illustrated in the right panel of Figure 1.1 for the data of Example 1.3.
With an explicit expression of the variance of the ridge estimator at hand, we can compare it to that of the OLS
estimator:
Var[β̂] − Var[β̂(λ)] = σ 2 [(X⊤ X)−1 − Wλ (X⊤ X)−1 Wλ⊤ ]
= σ 2 Wλ {[I + λ(X⊤ X)−1 ](X⊤ X)−1 [I + λ(X⊤ X)−1 ]⊤ − (X⊤ X)−1 }Wλ⊤
= σ 2 Wλ [2 λ (X⊤ X)−2 + λ2 (X⊤ X)−3 ]Wλ⊤
= σ 2 [X⊤ X + λIpp ]−1 [2 λ Ipp + λ2 (X⊤ X)−1 ]{[X⊤ X + λIpp ]−1 }⊤ .
The difference is non-negative definite as each component in the matrix product is non-negative definite. Hence,
the variance of the ML estimator exceeds (in the positive definite ordering) that of the ridge estimator:
Var[β̂]  Var[β̂(λ)], (1.6)
with the inequality being strict if λ > 0. In other words, the variance of the ML estimator is larger than that of
the ridge estimator (in the sense that their difference is non-negative definite). The variance inequality (1.6) can
be interpreted in terms of the stochastic behaviour of the estimate. This is illustrated by the next example.

Variance of the ML estimator Variance of the ridge estimator

50% 50%
75% 75%
95% 95%
1.0

1.0
0.5

0.5
beta_2

beta_2
0.0

0.0
−0.5

−0.5
−1.0

−1.0

−1.0 −0.5 0.0 0.5 1.0 −1.0 −0.5 0.0 0.5 1.0

beta_1 beta_1

Figure 1.2: Level sets of the distribution of the ML (left panel) and ridge (right panel) regression estimators.

Example 1.6 (Variance comparison)

Consider the design matrix:
 
−1 2
 0 1 
X =  
 2 −1  .
1 0
1.4 Moments 13

The variances of the ML and ridge (with λ = 1) estimates of the regression coefficients then are:
   
0.3 0.2 0.1524 0.0698
Var(β̂) = σ 2 and Var[β̂(λ)] = σ 2 .
0.2 0.3 0.0698 0.1524
These variances can be used to construct levels sets of the distribution of the estimates. The level sets that contain
50%, 75% and 95% of the distribution of the ML and ridge estimates are plotted in Figure 1.2. In line with
inequality (1.6) the level sets of the ridge estimate are smaller than that of the ML estimate, it thus varies less. 

Example 1.5 (Orthonormal design matrix, continued)

Assume the design matrix X is orthonormal. Then, Var[β̂] = σ 2 Ipp and

Var[β̂(λ)] = σ 2 Wλ (X⊤ X)−1 Wλ⊤ = σ 2 [Ipp + λIpp ]−1 Ipp {[Ipp + λIpp ]−1 }⊤ = σ 2 (1 + λ)−2 Ipp .

As the penalty parameter λ is non-negative the former exceeds the latter. In particular, this expression vanishes as
λ → ∞. 

The variance of the ridge regression estimator may be decomposed in the same way as its bias (cf. the end of
Section 1.4.1). There is, however, no contribution of the high-dimensionality of the study design as that is non-
random and, consequently, exhibits no variation. Hence, the variance only relates to the variation in the projected
subspace R(X) as is obvious from:

Var[β̂(λ)] = Var[Px β̂(λ)] = Px Var[β̂(λ)]P⊤

x = Var[β̂(λ)].

Perhaps this is seen more clearly when writing the variance of the ridge regression estimator in terms of the
matrices that constitute the singular value decomposition of X:

Var[β̂(λ)] = Vx (D2x + λIpp )−1 D2x (D2x + λIpp )−1 Vx⊤ .

High-dimensionally, (D2x )jj = 0 for j = n + 1, . . . , p. And if (D2x )jj = 0, so is [(D2x + λIpp )−1 D2x (D2x +
λIpp )−1 ]jj = 0. Hence, the variance is determined by the first n columns of Vx . When n < p, the variance is
then to interpreted as the spread of the ridge regression estimator (with the same choice of λ) when the study is
repeated with exactly the same design matrix such that the resulting estimator is confined to the same subspace
R(X). The following R-script illustrates this by an arbitrary data example (plot not shown):
Listing 1.2 R code
# set parameters
X <- matrix(rnorm(2), nrow=1)
betas <- matrix(c(2, -1), ncol=1)
lambda <- 1

# generate multiple ridge regression estimators with a fixed design matrixs

bHats <- numeric()
for (k in 1:1000){
Y <- matrix(X %*% betas + rnorm(1), ncol=1)
bHats <- rbind(bHats, t(solve(t(X) %*% X + lambda * diag(2)) %*% t(X) %*% Y))
}

# plot the ridge regression estimators

plot(bHats, xlab=expression(paste(hat(beta)[1], "(", lambda, ")", sep="")),
ylab=expression(paste(hat(beta)[2], "(", lambda, ")", sep="")), pch=20)

The full distribution of the ridge regression estimator is now known. The estimator, β̂(λ) = (X⊤ X+λIpp )−1 X⊤ Y
is a linear estimator, linear in Y. As Y is normally distributed, so is β̂(λ). Moreover, the normal distribution is
fully characterized by its first two moments, which are available. Hence:


β̂(λ) ∼ N (X⊤ X + λIpp )−1 X⊤ X β, σ 2 [X⊤ X + λIpp ]−1 X⊤ X{[X⊤ X + λIpp ]−1 }⊤ .

Given λ and X, the random behavior of the estimator is thus known. In particular, when n < p, the variance is
semi-positive definite and this p-variate normal distribution is degenerate, i.e. there is no probability mass outside
R(X) the subspace of Rp spanned by the rows of the X.
14 Ridge regression

1.4.3 Mean squared error

Previously, we motivated the ridge estimator as an ad hoc solution to collinearity. An alternative motivation comes
from studying the Mean Squared Error (MSE) of the ridge regression estimator: for a suitable choice of λ the
ridge regression estimator may outperform the ML regression estimator in terms of the MSE. Before we prove
this, we first derive the MSE of the ridge estimator and quote some auxiliary results.
Recall that (in general) for any estimator of a parameter θ:

MSE(θ̂) = E[(θ̂ − θ)2 ] = Var(θ̂) + [Bias(θ̂)]2 .

Hence, the MSE is a measure of the quality of the estimator.

The MSE of the ridge estimator is:

MSE[β̂(λ)] = E[(Wλ β̂ − β)⊤ (Wλ β̂ − β)]

= E(β̂ ⊤ Wλ⊤ Wλ β̂) − E(β ⊤ Wλ β̂) − E(β̂ ⊤ Wλ⊤ β) + E(β ⊤ β)
= E(β̂ ⊤ Wλ⊤ Wλ β̂) − E(β ⊤ Wλ⊤ Wλ β̂) − E(β̂ ⊤ Wλ⊤ Wλ β) + E(β ⊤ Wλ⊤ Wλ β)
−E(β ⊤ Wλ⊤ Wλ β) + E(β ⊤ Wλ⊤ Wλ β̂) + E(β̂ ⊤ Wλ⊤ Wλ β)
−E(β ⊤ Wλ β̂) − E(β̂ ⊤ Wλ⊤ β) + E(β ⊤ β)
= E[(β̂ − β)⊤ Wλ⊤ Wλ (β̂ − β)]
−β ⊤ Wλ⊤ Wλ β + β ⊤ Wλ⊤ Wλ β + β ⊤ Wλ⊤ Wλ β
−β ⊤ Wλ β − β ⊤ Wλ⊤ β + β ⊤ β

= E (β̂ − β)⊤ Wλ⊤ Wλ (β̂ − β) + β ⊤ (Wλ − Ipp )⊤ (Wλ − Ipp ) β

= σ 2 tr Wλ (X⊤ X)−1 Wλ⊤ + β ⊤ (Wλ − Ipp )⊤ (Wλ − Ipp ) β. (1.7)

In the last step we have used β̂ ∼ N (β, σ 2 [X⊤ X]−1 ) and the expectation of the quadratic form of a mul-
tivariate random variable ε ∼ N (µε , Σε ) for some nonrandom symmetric positive definite matrix Λ is (cf.
Mathai and Provost 1992):

E(ε⊤ Λ ε) = tr(Λ Σε ) + µ⊤
ε Λ µε ,

of course replacing ε by β̂ in this expectation. The first summand in the final derived expression for MSE[β̂(λ)]
is the sum of the variances of the ridge estimator, while the second summand can be thought of the “squared bias”
of the ridge estimator. In particular, limλ→∞ MSE[β̂(λ)] = β ⊤ β, which is the squared biased for an estimator
that equals zero (as does the ridge estimator in the limit).
Example 1.7 Orthonormal design matrix
Assume the design matrix X is orthonormal. Then, MSE[β̂] = p σ 2 and
p σ2 λ2
MSE[β̂(λ)] = 2
+ β ⊤ β.
(1 + λ) (1 + λ)2

The latter achieves its minimum at: λ = pσ 2 /β ⊤ β. 

The following theorem and proposition are required for the proof of the main result.
Theorem 1.1 (Theorem 1 of Theobald, 1974)
Let θ̂1 and θ̂2 be (different) estimators of θ with second order moments:

Mk = E[(θ̂k − θ)(θ̂k − θ)⊤ ] for k = 1, 2,

and

MSE(θ̂k ) = E[(θ̂k − θ)⊤ A(θ̂k − θ)] for k = 1, 2,

where A  0. Then, M1 − M2  0 if and only if MSE(θ̂1 ) − MSE(θ̂2 ) ≥ 0 for all A  0.

Proposition 1.1 (Farebrother, 1976)

Let A be a (p × p)-dimensional, positive definite matrix, b be a nonzero p dimensional vector, and c ∈ R+ . Then,
cA − bb⊤ ≻ 0 if and only if b⊤ A−1 b > c.
1.4 Moments 15

We are now ready to proof the main result, formalized as Theorem 1.2, that for some λ the ridge regression
estimator yields a lower MSE than the ML regression estimator.
Theorem 1.2 (Theorem 2 of Theobald, 1974)
There exists λ > 0 such that MSE[β̂(λ)] < MSE[β̂(0)] = MSE[β̂].

Proof. The second order moment matrix of the ridge estimator is:

M(λ) := E[(β̂(λ) − β)(β̂(λ) − β)⊤ ]

= E{β̂(λ)[β̂(λ)]⊤ } − E[β̂(λ)]{E[β̂(λ)]}⊤ + E[β̂(λ) − β)]{E[β̂(λ) − β)]}⊤
= Var[β̂(λ)] + E[β̂(λ) − β)]{E[β̂(λ) − β)]}⊤ .

Then:

M(0) − M(λ) = σ 2 (X⊤ X)−1 − σ 2 Wλ (X⊤ X)−1 Wλ⊤ ]

−(Wλ − Ipp )ββ ⊤ (Wλ − Ipp )⊤
= σ 2 Wλ [2 λ (X⊤ X)−2 + λ2 (X⊤ X)−3 ]Wλ⊤
−λ2 [X⊤ X + λIpp ]−1 ββ ⊤ {[X⊤ X + λIpp ]−1 }⊤
= σ 2 [X⊤ X + λIpp ]−1 [2 λ Ipp + λ2 (X⊤ X)−1 ]{[X⊤ X + λIpp ]−1 }⊤
−λ2 [X⊤ X + λIpp ]−1 ββ ⊤ {[X⊤ X + λIpp ]−1 }⊤
= λ[X⊤ X + λIpp ]−1 [2 σ 2 Ipp + λσ 2 (X⊤ X)−1 − λββ ⊤ ]{[X⊤ X + λIpp ]−1 }⊤ .

This is positive definite if and only if 2 σ 2 Ipp + λσ 2 (X⊤ X)−1 − λββ ⊤ ≻ 0. Hereto it suffices to show that
2 σ 2 Ipp − λββ ⊤ ≻ 0. By Proposition 1.1 this holds for λ such that 2σ 2 (β ⊤ β)−1 > λ. For these λ, we thus have
M(0) − M(λ). Application of Theorem 1.1 now concludes the proof. 

This result of Theobald (1974) is generalized by Farebrother (1976) to the class of design matrices X with
rank(X) < p.

Theorem 1.2 can be used to illustrate that the ridge regression estimator strikes a balance between the bias and
variance. This is illustrated in the left panel of Figure 1.3. For small λ, the variance of the ridge estimator dom-
inates the MSE. This may be understood when realizing that in this domain of λ the ridge estimator is close to
the unbiased ML regression estimator. For large λ, the variance vanishes and the bias dominates the MSE. For
small enough values of λ, the decrease in variance of the ridge regression estimator exceeds the increase in its
bias. As the MSE is the sum of these two, the MSE first decreases as λ moves away from zero. In particular, as
λ = 0 corresponds to the ML regression estimator, the ridge regression estimator yields a lower MSE for these
values of λ. In the right panel of Figure 1.3 MSE[β̂(λ)] < MSE[β̂(0)] for λ < 7 (roughly) and the ridge estimator
outperforms the ML estimator.

Besides another motivation behind the ridge regression estimator, the use of Theorem 1.2 is limited. The opti-
mal choice of λ depends on the quantities β and σ 2 . These are unknown in practice. Then, the penalty parameter
is chosen in a data-driven fashion (see e.g. Section 1.8.2) and various other places for aids in this challenge.

Theorem 1.2 may be of limited practical use, it does give insight in when the ridge regression estimator may
be preferred over its ML counterpart. Ideally, the range of penalty parameters for which the ridge regression
estimator outperforms – in the MSE sense – the ML regression estimator is as large as possible. The factors
that influence the size of this range may be deduced from the optimal penalty λopt = σ 2 (β ⊤ β/p)−1 found un-
der assumption of an orthonormal X (see Example 1.7). But also from the bound on the penalty parameter,
λmax = 2σ 2 (β ⊤ β)−1 such that M SE[β̂(λ)] < M SE[β̂(0)] for all λ ∈ (0, λmax ), derived in the proof of Theorem
1.2. Firstly, an increase of the error variance σ 2 yields a larger λopt and λmax . Put differently, more noisy data bene-
fits the ridge regression estimator. Secondly, λopt and λmax also become larger when their denominators decreases.
The denominator β ⊤ β/p may be viewed as an estimator of the ‘signal’ variance ‘σβ2 ’. A quick conclusion would
be that ridge regression profits from less signal. But more can be learned from the denominator. Contrast the two
regression parameters βunif = 1p and βsparse which comprises of only zeros except the first element Pp which equals p,
i.e. βsparse = (p, 0, . . . , 0)⊤ . Then, the βunif and βsparse have comparable signal in the sense that j=1 βj = p. The
denominator of λopt corresponding both parameters equals 1 and p, respectively. This suggests that ridge regres-
sion will perform better in the former case where the regression parameter is not dominated by a few elements
16 Ridge regression

MSE of the ridge estimator MSE, ridge vs. ML

MSE
Variance
Bias
4

3
3
MSE / bias / variance

2
MSE
2

1
1

ridge
ML
0

0
0 5 10 15 0 2 4 6 8 10

lambda lambda

Figure 1.3: Left panel: mean squared error, and its ‘bias’ and ‘variance’ parts, of the ridge regression estimator (for
artificial data). Right panel: mean squared error of the ridge and ML estimator of the regression coefficient vector
(for the same artificial data).

but rather all contribute comparably to the explanation of the variation in the response. Of course, more factors
contribute. For instance, collinearity among the columns of X, which give rise to ridge regression in the first
place.

Remark 1.1
Theorem 1.2 can also be used to conclude on the biasedness of the ridge regression estimator. The Gauss-Markov
theorem (Rao, 1973) states (under some assumptions) that the ML regression estimator is the best linear unbiased
estimator (BLUE) with the smallest MSE. As the ridge regression estimator is a linear estimator and outperforms
(in terms of MSE) this ML estimator, it must be biased (for it would otherwise refute the Gauss-Markov theorem).

1.5 Constrained estimation

The ad-hoc fix of Hoerl and Kennard (1970) to super-collinearity of the design matrix (and, consequently the sin-
gularity of the matrix X⊤ X) has been motivated post-hoc. The ridge estimator minimizes the ridge loss function,
which is defined as:
Xn Xp
Lridge (β; λ) = kY − X βk22 + λkβk22 = (Yi − Xi∗ β)2 + λ βj2 . (1.8)
i=1 j=1

This loss function is the traditional sum-of-squares augmented with a penalty. The particular form of the penalty,
λkβk22 is referred to as the ridge penalty and λ as the penalty parameter. For λ = 0, minimization of the ridge loss
function yields the ML estimator (if it exists). For any λ > 0, the ridge penalty contributes to the loss function,
affecting its minimum and its location. The minimum of the sum-of-squares is well-known. The minimum of the
ridge penalty is attained at β = 0p whenever λ > 0. The β that minimizes Lridge (β; λ) then balances the sum-
of-squares and the penalty. The effect of the penalty in this balancing act is to shrink the regression coefficients
towards zero, its minimum. In particular, the larger λ, the larger the contribution of the penalty to the loss function,
the stronger the tendency to shrink non-zero regression coefficients to zero (and decrease the contribution of the
penalty to the loss function). This motivates the name ‘penalty’ as non-zero elements of β increase (or penalize)
the loss function.
To verify that the ridge estimator indeed minimizes the ridge loss function, proceed as usual. Take the deriva-
tive with respect to β:
∂
L (β; λ) = −2 X⊤ (Y − Xβ) + 2 λ Ipp β = −2 X⊤ Y + 2 (X⊤ X + λ Ipp )β.
∂β ridge
1.5 Constrained estimation 17

Equate the derivative to zero and solve for β. This yields the ridge regression estimator.
The ridge estimator is thus a stationary point of the ridge loss function. A stationary point corresponds to a
minimum if the Hessian matrix with second order partial derivatives is positive definite. The Hessian of the ridge
loss function is
∂2
L (β; λ) = 2 (X⊤ X + λ Ipp ).
∂β ∂β ⊤ ridge

This Hessian is the sum of the (semi-)positive definite matrix X⊤ X and the positive definite matrix λ Ipp . Lemma
14.2.4 of Harville (2008) then states that the sum of these matrices is itself a positive definite matrix. Hence, the
Hessian is positive definite and the ridge loss function has a stationary point at the ridge estimator, which is a
minimum.
The ridge regression estimator minimizes the ridge loss function. It rests to verify that it is a global minimum.
To this end we introduce the concept of a convex function. As a prerequisite, a set S ⊂ Rp is called convex if for
all β1 , β2 ∈ S their weighted average βθ = (1 − θ)β1 + θβ2 for all θ ∈ [0, 1] is itself an element of S , thus
βθ ∈ S . If for all θ ∈ (0, 1), the weighted average βθ is inside S and not on its boundary, the set is called strictly
convex. Examples of (strict) convex and nonconvex sets are depicted in Figure 1.4. A function f (·) is (strict)
convex if the set {y : y ≥ f (β) for all β ∈ S for any convex S }, called the epigraph of f (·), is (strict) convex.
Examples of (strict) convex and nonconvex functions are depicted in Figure 1.4. The ridge loss function is the sum
of two parabola’s: one at least convex and the other a strictly convex function in β. The sum of convex and strictly
convex function is itself strictly convex (confer Lemma 9.4.2 of Fletcher 2008). The ridge loss function is thus
strictly convex. Theorem 9.4.1 of Fletcher 2008 then warrants, by the strict convexity of the ridge loss function,
that the ridge estimator is a global minimum.

From the ridge loss function the limiting behavior of the variance of the ridge regression estimator can be un-
derstood. The ridge penalty with its minimum β = 0p does not involve data and, consequently, the variance of its
minimum equals zero. With the ridge regression being a compromise between the ML estimator and the minimum
of the penalty, so is its variance a compromise of their variances. As λ tends to infinity, the ridge estimator and
its variance converge to the minimum and the variance of the minimum, respectively. Hence, in the limit (large λ)
the variance of the ridge regression estimator vanishes. Understandably, as the penalty now fully dominates the
loss function and, consequently, it does no longer involve data (i.e. randomness).

Above it has been shown that the ridge estimator can be defined as:

β̂(λ) = arg min kY − X βk22 + λkβk22 . (1.9)

β

This minimization problem can be reformulated into the following constrained optimization problem (illustrated
in Figure 1.4):

β̂(λ) = arg min

2
kY − X βk22 , (1.10)
kβk2 ≤c

for some suitable c > 0. The constrained optimization problem (1.10) can be solved by means of the Karush-
Kuhn-Tucker (KKT) multiplier method, which minimizes a function subject to inequality constraints. The KKT
multiplier method states that, under some regularity conditions (all met here), there exists a constant ν ≥ 0, called
the multiplier, such that the solution β̂(ν) of the constrained minimization problem (1.10) satisfies the so-called
KKT conditions. The first KKT condition (referred to as the stationarity condition) demands that the gradient
(with respect to β) of the Lagrangian associated with the minimization problem equals zero at the solution β̂(ν).
The Lagrangian for problem (1.10) is:

kY − X βk22 + ν(kβk22 − c).

The second KKT condition (the complementarity condition) requires that ν(kβ̂(ν)k22 − c) = 0. If ν = λ and
c = kβ̂(λ)k22 , the ridge estimator β(λ) satisfies both KKT conditions. Hence, both problems have the same solu-
tion when c = kβ̂(λ)k22 .

The relevance of viewing the ridge regression estimator as the solution to a constrained estimation problem be-
comes obvious when considering a typical threat to high-dimensional data analysis: overfitting. Overfitting refers
18 Ridge regression

4 Convex sets Nonconvex sets

4
3

3
I II
2

2
I II
1

1
y

y
0

0
III IV
−1

−1
III IV
−2

−2
−2 −1 0 1 2 3 4 −2 −1 0 1 2 3 4

x x

Convex functions Nonconvex functions

3
150

2
100

1
y

0
50

−1
−2
0

−4 −2 0 2 4 −4 −2 0 2 4

x x

Ridge as constrained estimation Overfitting

ML estimate model
8

ridge estimate fit

1.5
6

1.0
0.5
4
beta2

0.0
y
2

−0.5
−1.0
0

−1.5
−2

−2 0 2 4 6 8 −1.5 −1.0 −0.5 0.0 0.5 1.0 1.5

beta1 x1

Figure 1.4: Top panels show examples of convex (left) and nonconvex (right) sets. Middle panels show examples of
convex (left) and nonconvex (right) functions. The left bottom panel illustrates the ridge estimation as a constrained
estimation problem. The ellipses represent the contours of the ML loss function, with the blue dot at the center the
ML estimate. The circle is the ridge parameter constraint. The red dot is the ridge estimate. It is at the intersection
of the ridge constraint and the smallest contour with a non-empty intersection with the constraint. The right bottom
panel shows the data corresponding to Example 1.8. The grey line represents the ‘true’ relationship, while the black
line the fitted one.
1.6 Degrees of freedom 19

to the phenomenon of modelling the noise rather than the signal. In case the true model is parsimonious (few
covariates driving the response) and data on many covariates are available, it is likely that a linear combination of
all covariates yields a higher likelihood than a combination of the few that are actually related to the response. As
only the few covariates related to the response contain the signal, the model involving all covariates then cannot
but explain more than the signal alone: it also models the error. Hence, it overfits the data. In high-dimensional
settings overfitting is a real threat. The number of explanatory variables exceeds the number of observations. It
is thus possible to form a linear combination of the covariates that perfectly explains the response, including the
noise.
Large estimates of regression coefficients are often an indication of overfitting. Augmentation of the estimation
procedure with a constraint on the regression coefficients is a simple remedy to large parameter estimates. As a
consequence it decreases the probability of overfitting. Overfitting is illustrated in the next example.

Example 1.8 (Overfitting)

Consider an artificial data set comprising of ten observations on a response Yi and nine covariates Xi,j . All
covariate data are sampled from the standard normal distribution: Xi,j ∼ N (0, 1). The response is generated by
Yi = Xi,1 + εi with εi ∼ N (0, 1/4). Hence, only the first covariate contributes to the response.
P9
The regression model Yi = j=1 Xi,j βj + εi is fitted to the artificial data using R. This yields the regression
parameter estimates:

β̂ ⊤ = (0.048, −2.386, −5.528, 6.243, −4.819, 0.760, −3.345, −4.748, 2.136).

As β ⊤ = (1, 0, . . . , 0), many regression coefficient are clearly over-estimated.

The fitted values Ybi = Xi β̂ are plotted against the values of the first covariates in the right bottom panel of
Figure 1.4. As a reference the line x = y is added, which represents the ‘true’ model. The fitted model follows
the ‘true’ relationship. But it also captures the deviations from this line that represent the errors. 

1.6 Degrees of freedom

The degrees of freedom consumed by ridge regression is calculated. The degrees of freedom may be used in
combination with an information criterion to decide on the value of the penalty parameter. Recall from ordinary
regression that:
b
Y = X(X⊤ X)−1 X⊤ Y = HY,

where H is the hat matrix. The degrees of freedom used in the regression is then equal to tr(H), the trace of H.
In particular, if X is of full rank, i.e. rank(X) = p, then tr(H) = p.
By analogy, the ridge-version of the hat matrix is:

H(λ) = X(X⊤ X + λIpp )−1 X⊤ .

Continuing this analogy, the degrees of freedom of ridge regression is given by the trace of the ridge hat matrix
H(λ):

Xp d2jj
tr[H(λ)] = tr[X(X⊤ X + λIpp )−1 X⊤ ] = .
j=1 d2jj + λ

The degrees of freedom consumed by ridge regression is monotone decreasing in λ. In particular:

lim tr[H(λ)] = 0.
λ→∞

That is, in the limit no information from X is used. Indeed, β is forced to equal 0p which is not derived from data.

1.7 Efficient calculation

In the high-dimensional setting the number of covariates p is large compared to the number of samples n. In a
microarray experiment p = 40000 and n = 100 is not uncommon. To perform ridge regression in this context, the
following expression needs to be evaluated numerically: (X⊤ X + λIpp )−1 X⊤ Y. For p = 40000 this requires
20 Ridge regression

the inversion of a 40000 × 40000 dimensional matrix. This is not feasible on most desktop computers. However,
there is a workaround.
Revisit the singular value decomposition of X = Ux Dx Vx⊤ and write Rx = Ux Dx . As both Ux and Dx
are (n × n)-dimensional matrices, so is Rx . Consequently, X is now decomposed as X = Rx Vx⊤ . The ridge
estimator can be rewritten in terms of Rx and Vx :
β̂(λ) = (X⊤ X + λIpp )−1 X⊤ Y
= (Vx R⊤ ⊤
x Rx Vx + λIpp )
−1
Vx R⊤
xY
= (Vx Rx Rx Vx + λVx Vx ) Vx R⊤
⊤ ⊤ ⊤ −1
xY
= Vx (R⊤
x Rx + λInn )
−1 ⊤
Vx Vx R⊤
xY
⊤ −1 ⊤
= Vx (Rx Rx + λInn ) Rx Y.
Hence, the reformulated ridge estimator involves the inversion of an (n × n)-dimensional matrix. With n = 100
this is feasible on most standard computers.
Hastie and Tibshirani (2004) point out that the number of computation operations reduces from O (p3 ) to
O (pn2 ). In addition, they point out that this computational short-cut can be used in combination with other loss
functions, for instance that of standard generalized linear models (see Chapter 5).

Avoidance of the inversion of the (p × p)-dimensional matrix may be achieved in an other way. Hereto one needs
the Woodbury identity. Let A, U and V be (p × p)-, (p × n)- and (n × p)-dimensional matrices, respectively.
The (simplified form of the) Woodbury identity then is:
(A + UV)−1 = A−1 − A−1 U(Inn + VA−1 U)−1 VA−1 .
Application of the Woodbury identity to the matrix inverse in the ridge estimator of the regression parameter gives:
(λIpp + X⊤ X)−1 = λ−1 Ipp − λ−2 X⊤ (Inn + λ−1 XX⊤ )−1 X.
This gives:
(λIpp + X⊤ X)−1 X⊤ Y = λ−1 X⊤ Y − λ−2 X⊤ (Inn + λ−1 XX⊤ )−1 XX⊤ Y
 
= λ−1 X⊤ Y − λ−1 X⊤ (Inn + λ−1 XX⊤ )−1 XX⊤ Y .
The inversion of the (p × p)-dimensional matrix λIpp + X⊤ X is thus replaced by that of the (n × n)-dimensional
matrix Inn + λ−1 XX⊤ . In addition, this expression of the ridge regression estimator avoids the singular value
decomposition of X, which may in some cases introduce additional numerical errors (e.g. at the level of machine
precision).

1.8 Choice of the penalty parameter

Throughout the introduction of ridge regression and the subsequent discussion of its properties the penalty param-
eter is considered known or ‘given’. In practice, it is unknown and the user needs to make an informed decision
on its value. Several strategies to facilitate such a decision are presented.

1.8.1 Information criterion

A popular strategy is to choose a penalty parameter that yields a good but parsimonious model. Information
criteria measure the balance between model fit and model complexity. Here we present the Aikaike’s information
criterion (AIC), but many other criteria have been presented in the literature (e.g. Akaike, 1974, Schwarz, 1978).
The AIC measures model fit by the log-likelihood and model complexity as measured by the number of parameters
used by the model. The number of model parameters in regular regression simply corresponds to the number of
covariates in the model. Or, by the degrees of freedom consumed by the model, which is equivalent to the trace of
the hat matrix. For ridge regression it thus seems natural to define model complexity analogously by the trace of
the ridge hat matrix. This yields the AIC for the linear regression model with ridge estimates:
AIC(λ) = 2 p − 2 log(L̂)
= 2 tr[H(λ)] − 2 log{L[β̂(λ), σ̂ 2 (λ)]}
Xp d2jj √ 1 Xn
= 2 + 2n log[ 2 π σ̂(λ)] + 2 [yi − Xi,∗ β̂(λ)]2 .
j=1 d2 + λ σ̂ (λ) i=1
jj
1.8 Choice of the penalty parameter 21

The value of λ which minimizes AIC(λ) corresponds to the ‘optimal’ balance of model complexity and overfitting.
Information criteria guide the decision process when having to decide among various different models. Dif-
ferent models use different sets of explanatory variables to explain the behaviour of the response variable. In
that sense, the use of information criteria for the deciding on the ridge penalty parameter may be considered in-
appropriate: ridge regression uses the same set of explanatory variables irrespective of the value of the penalty
parameter. Moreover, often ridge regression is employed to predict a response and not to provide an insightful
explanatory model. The latter need not yield the best predictions. Finally, empirically we observe that the AIC
often does not show an optimum inside the domain of the ridge penalty parameter. Henceforth, we refrain from
the use of the AIC (or any of its relatives) in determining the optimal ridge penalty parameter.

1.8.2 Cross-validation
Instead of choosing the penalty parameter to balance model fit with model complexity, cross-validation requires
it (i.e. the penalty parameter) to yield a model with good prediction performance. Commonly, this performance
is evaluated on novel data. Novel data need not be easy to come by and one has to make do with the data at
hand. The setting of ‘original’ and novel data is then mimicked by sample splitting: the data set is divided into
two (groups of samples). One of these two data sets, called the training set, plays the role of ‘original’ data on
which the model is built. The second of these data sets, called the test set, plays the role of the ‘novel’ data and
is used to evaluate the prediction performance (often operationalized as the log-likelihood or the prediction error)
of the model built on the training data set. This procedure (model building and prediction evaluation on training
and test set, respectively) is done for a collection of possible penalty parameter choices. The penalty parameter
that yields the model with the best prediction performance is to be preferred. The thus obtained performance
evaluation depends on the actual split of the data set. To remove this dependence the data set is split many times
into a training and test set. For each split the model parameters are estimated for all choices of λ using the training
data and estimated parameters are evaluated on the corresponding test set. The penalty parameter that on average
over the test sets performs best (in some sense) is then selected.
When the repetitive splitting of the data set is done randomly, samples may accidently end up in a fast majority
of the splits in either training or test set. Such samples may have an unbalanced influence on either model building
or prediction evaluation. To avoid this k-fold cross-validation structures the data splitting. The samples are divided
into k more or less equally sized exhaustive and mutually exclusive subsets. In turn (at each split) one of these
subsets plays the role of the test set while the union of the remaining subsets constitutes the training set. Such
a splitting warrants a balanced representation of each sample in both training and test set over the splits. Still
the division into the k subsets involves a degree of randomness. This may be fully excluded when choosing
k = n. This particular case is referred to as leave-one-out cross-validation (LOOCV). For illustration purposes
the LOOCV procedure is detailed fully below:
0) Define a range of interest for the penalty parameter.
1) Divide the data set into training and test set comprising samples {1, . . . , n} \ i and {i}, respectively.
2) Fit the linear regression model by means of ridge estimation for each λ in the grid using the training set.
This yields:

β̂−i (λ) = (X⊤

−i,∗ X−i,∗ + λIpp )
−1 ⊤
X−i,∗ Y−i
2
and the corresponding estimate of the error variance σ̂−i (λ).
2
3) Evaluate the prediction performance of these models on the test set by log{L[Yi , Xi,∗ ; β̂−i (λ), σ̂−i (λ)]}.
Or, by the prediction error |Yi − Xi,∗ β̂−i (λ)|, possibly squared.
4) Repeat steps 1) to 3) such that each sample plays the role of the test set once.
5) Average the prediction performances of the test sets at each grid point of the penalty parameter:
1 Xn 2
log{L[Yi , Xi,∗ ; β̂−i (λ), σ̂−i (λ)]}.
n i=1

The quantity above is called the cross-validated log-likelihood. It is an estimate of the prediction perfor-
mance of the model corresponding to this value of the penalty parameter on novel data.
6) The value of the penalty parameter that maximizes the cross-validated log-likelihood is the value of choice.
The procedure is straightforwardly adopted to k-fold cross-validation, a different criterion, and different estima-
tors.
In the LOOCV procedure above resampling can be avoided when the prediction performance is measured by
Allen’s PRESS (Predicted Residual Error Sum of Squares) statistic (Allen, 1974). For then, the LOOCV prediction
22 Ridge regression

performance can be expressed analytically in terms of the known quantities derived from the design matrix and
response (as pointed out but not detailed in Golub et al. 1979). Define the optimal penalty parameter to minimize
Allen’s PRESS statistic:
1 Xn
λopt = arg min [Yi − Xi,∗ β̂−i (λ)]2 .
λ n i=1

To derive an analytic expression for the right-hand side first rewrite (X⊤
−i,∗ X−i,∗ + λIpp )
−1
by means of the
Woodbury identity as:

(X⊤
−i,∗ X−i,∗ + λIpp )
−1
= (X⊤ X + λIpp − X⊤
i,∗ Xi,∗ )
−1

= (X⊤ X + λIpp )−1 + (X⊤ X + λIpp )−1 X⊤ ⊤

i,∗ [1 − Xi,∗ (X X + λIpp )
−1 ⊤ −1
Xi,∗ ]
Xi,∗ (X⊤ X + λIpp )−1
= (X⊤ X + λIpp )−1 + (X⊤ X + λIpp )−1 X⊤
i,∗ [1 − Hii (λ)]
−1
Xi,∗ (X⊤ X + λIpp )−1

with Hii (λ) = Xi,∗ (X⊤ X + λIpp )−1 X⊤ ⊤ ⊤ ⊤

i,∗ . Furthermore, X−i Y−i = X Y − Xi,∗ Yi . Substitute both in the
leave-one-out ridge regression estimator and manipulate:

β̂−i (λ) = (X⊤

−i,∗ X−i,∗ + λIpp )
−1 ⊤
X−i,∗ Y−i
= {(X⊤ X + λIpp )−1 + (X⊤ X + λIpp )−1 X⊤
i,∗ [1 − Hii (λ)]
−1
Xi,∗ (X⊤ X + λIpp )−1 }
×(X⊤ Y − X⊤
i,∗ Yi )

= (X⊤ X + λIpp )−1 X⊤ Y − (X⊤ X + λIpp )−1 X⊤

i,∗ Yi

+(X⊤ X + λIpp )−1 X⊤

i,∗ [1 − Hii (λ)]
−1
Xi,∗ (X⊤ X + λIpp )−1 X⊤ Y
−(X⊤ X + λIpp )−1 X⊤
i,∗ [1 − Hii (λ)]
−1
Xi,∗ (X⊤ X + λIpp )−1 X⊤
i,∗ Yi

= β̂(λ) − (X⊤ X + λIpp )−1 X⊤

i,∗ [1 − Hii (λ)]
−1
[1 − Hii (λ)]Yi
+(X⊤ X + λIpp )−1 X⊤
i,∗ [1 − Hii (λ)]
−1
Xi,∗ β̂(λ)
−(X⊤ X + λIpp )−1 X⊤
i,∗ [1 − Hii (λ)]
−1
Hii (λ)Yi
= β̂(λ) − (X⊤ X + λIpp )−1 X⊤
i,∗ [1 − Hii (λ)]
−1
{[1 − Hii (λ)]Yi − Xi,∗ β̂(λ) + Hii (λ)Yi }
= β̂(λ) − (X⊤ X + λIpp )−1 X⊤
i,∗ [1 − Hii (λ)]
−1
[Yi − Xi,∗ β̂(λ)].

The latter enables the reformulation of the prediction error as:

Yi − Xi,∗ β̂−i (λ) = Yi − Xi,∗ {β̂(λ) − (X⊤ X + λIpp )−1 X⊤

i,∗ [1 − Hii (λ)]
−1
[Yi − Xi,∗ β̂(λ)]}
= Yi − Xi,∗ β̂(λ) + Xi,∗ (X⊤ X + λIpp )−1 X⊤
i,∗ [1 − Hii (λ)]
−1
[Yi − Xi,∗ β̂(λ)]
= Yi − Xi,∗ β̂(λ) + Hii (λ)[1 − Hii (λ)]−1 [Yi − Xi,∗ β̂(λ)]
= [1 − Hii (λ)]−1 [Yi − X⊤
i,∗ β̂(λ)],

which in turn results in the re-expression of Allen’s PRESS statistic:

1 Xn
λopt = arg min [Yi − Xi,∗ β̂−i (λ)]2 = arg min n1 kB(λ)[Inn − H(λ)]Yk2F ,
λ n i=1 λ

where B(λ) is diagonal with [B(λ)]ii = [1 − Hii (λ)]−1 . Hence, the prediction performance for a given λ can be
assessed directly from the ridge hat matrix and the response vector without the recalculation of the n leave-one-out
ridge estimators. Computationally, this is a considerable gain.

1.8.3 Generalized cross-validation

Generalized cross-validation is another methode to guide the choice of the penalty parameter. It is like cross-
validation but with a different criterion to evaluate the performance of the ridge regression estimator on novel data.
This criterion, denoted GCV(λ) (where GCV is an acronym of Generalized Cross-Validation), is an approximation
to Allen’s PRESS statistic. In the previous subsection this statistic was reformulated as:
Xn Xn
1
n [Yi − Xi,∗ β̂−i (λ)]2 = n1 [1 − Hii (λ)]−2 [Yi − X⊤ 2
i,∗ β̂(λ)] .
i=1 i=1
1.9 Simulations 23

Pn
The identity tr[H(λ)] = i=1 [H(λ)]ii suggests [H(λ)]ii ≈ n1 tr[H(λ)]. The approximation thus proposed by
Golub et al. (1979), which they endow with a ‘weighted version of Allen’s PRESS statistic’-interpretation, is:
Xn
GCV(λ) = n1 {1 − n1 tr[H(λ)]}−2 [Yi − X⊤ 2
i,∗ β̂(λ)] .
i=1

The need for this approximation is pointed out by Golub et al. (1979) by example through an ‘extreme’ case where
the minimization of Allen’s PRESS statistic fails to produce a well-defined choice of the penalty parameter λ. This
‘extreme’ case requires a (unit) diagonal design matrix X. Straightforward (linear) algebraic manipulations then
yield:
Xn Xn
1
n [1 − Hii (λ)]−2 [Yi − X⊤
i,∗ β̂(λ)]
2
= 1
n Yi2 ,
i=1 i=1

which indeed has no unique minimizer in λ. Additionally, the GCV(λ) criterion may in some cases be preferred
computationally when it is easier to evaluate tr[H(λ) (e.g. from the singular values) than the individual diagonal
elements of H(λ). Finally, Li (1986) showed that the λ that minimizes GCV(λ) is optimal asymptotically (i.e. for
ever larger sample sizes).

1.9 Simulations
Simulations are presented that illustrate properties of the ridge estimator not discussed explicitly in the previous
sections of this chapter.

1.9.1 Role of the variance of the covariates

In many applications of high-dimensional data the covariates are standardized prior to the execution of the ridge
regression. Before we discuss whether this is appropriate, we first illustrate the effect of ridge penalization on
covariates with distinct variances using simulated data.
The simulation involves one response to be (ridge) regressed on fifty covariates. Data (with n = 1000) for the
covariates, denoted X, are drawn from a multivariate normal distribution: X ∼ N (050 , Σ) with Σ diagonal and
(Σ)jj = j/10. From this the response is generated through Y = Xβ + ε with β = 150 and ε ∼ N (050 , I50×50 ).
With the simulated data at hand the ridge regression estimates of β are evaluated for a large grid of the penalty
parameter λ. The resulting ridge regularization paths of the regression coefficients are plotted (Figure 1.5). All
paths start (λ = 0) close to one and vanish as λ → ∞. However, ridge regularization paths of regression
coefficients corresponding to covariates with a large variance dominate those with a low variance.
Ridge regression’s preference of covariates with a large variance can intuitively be understood as follows. First
note that the ridge regression estimator now can be written as:

β(λ) = [Var(X) + λI50×50 ]−1 Cov(X, Y)

= (Σ + λI50×50 )−1 Σ[Var(X)]−1 Cov(X, Y)
= (Σ + λI50×50 )−1 Σβ.

Plug in the employed parametrization of Σ, which gives: [β(λ)]j = j(j + 50λ)−1 (β)j . Hence, the larger the
covariate’s variance (corresponding to the larger j), the larger its ridge regression coefficient estimate. Ridge
regression thus prefers (among a set of covariates with comparable effect sizes) those with larger variances.
The reformulation of ridge penalized estimation as a constrained estimation problem offers a geometrical
interpretation of this phenomenon. Let p = 2 and the design matrix X be orthogonal, while both covariates
contribute equally to the response. Contrast the cases with Var(X1 ) ≈ Var(X2 ) and Var(X1 ) ≫ Var(X2 ). The
level sets of the least squares loss function associated with the former case are circular, while that of the latter
are strongly ellipsoidal (see Figure 1.5). The diameters along the principal axes (that – due to the orthogonality
of X – are parallel to that of the β1 - and β2 -axes) of both circle and ellipsoid are reciprocals of the variance of
the covariates. When the variances of both covariates are equal, the level sets of the loss function expand equally
fast along both axis. With the two covariates having the same regression coefficient, the point of these level sets
closest to the parameter constraint is to be found on the line β1 = β2 (Figure 1.5, left panel). Consequently, the
ridge regression estimate satisfies β̂1 (λ) ≈ β̂2 (λ). With unequal variances between the covariates, the ellipsoidal
level sets of the loss function have diameters of rather different sizes. In particular, along the β1 -axis it is narrow
(as Var(X1 ) is large), and – vice versa – wide along the β2 -axis. Consequently, the point of these level sets closest
24 Ridge regression

Solution paths of covariates with distinct variance

1.0
σ2 in (0,1]
σ2 in (1,2]
σ2 in (2,3]
σ2 in (3,4]
σ2 in (4,5]

0.8
0.6
Ridge estimate

0.4
0.2
0.0

5 6 7 8 9 10 11

log(lambda)

Ridge estimates with equal covariate variances Ridge estimates with unequal covariate variances

loss level sets

5

5
constraint
4

∝ 1/Var(X1) ∝ 1/Var(X1)
3

3
∝ 1/Var(X2)

∝ 1/Var(X2)
2

2
β2

β2

^
β2(λ)
1

^
β2(λ)
0

0
−1

−1

loss level sets

^ ^
β1(λ) constraint β1(λ)

−1 0 1 2 3 4 5 −1 0 1 2 3 4 5

β1 β1

Figure 1.5: Top panel: Ridge regularization paths for coefficients of the 50 uncorrelated covariates with distinct
variances. Color and line type indicated the grouping of the covariates by their variance. Bottom panels: Graphical
illustration of the effect of a covariate’s variance on the ridge estimator. The grey circle depicts the ridge parameter
constraint. The dashed black ellipsoids are the level sets of the least squares loss function. The red dot is the ridge
regression estimate. Left and right panels represent the cases with equal and unequal, respectively, variances of
the covariates.

to the circular parameter constraint will be closer to the β1 - than to the β2 -axis (Figure 1.5, left panel). For the
ridge estimates of the regression parameter this implies 0 ≪ β̂1 (λ) < 1 and 0 < β̂2 (λ) ≪ 1. Hence, the covariate
with a larger variance yields the larger ridge regression estimate.
Should one thus standardize the covariates prior to ridge regression analysis? When dealing with gene expres-
sion data from microarrays, the data have been subjected to a series of pre-processing steps (e.g. quality control,
background correction, within- and between-normalization). The purpose of these steps is to make the expression
levels of genes comparable both within and between hybridizations. The preprocessing should thus be considered
an inherent part of the measurement. As such it is to be done independently of whatever down-stream analysis is
to follow and further tinkering with the data is preferably to be avoided (as it may mess up the ‘comparable-ness’
of the expression levels as achieved by the preprocessing). For other data types different considerations may apply.
1.9 Simulations 25

Among the considerations to decide on standardization of the covariates, one should also include the fact
that ridge estimates prior and posterior to scaling do not simply differ by a factor. To see this assume that the
covariates have been centered. Scaling of the covariates amounts to post-multiplication of the design matrix by
a (p × p)-dimensional diagonal matrix A with the reciprocals of the covariates’ scale estimates on its diagonal
(Sardy, 2008). Hence, the ridge estimator (for the rescaled data) is then given by:
min kY − XAβk22 + λkβk22 .
β

Apply the change-of-variable γ = Aβ and obtain:

Xp
min kY − Xγk22 + λkA−1 γk22 = min kY − Xγk22 + λ[(A)jj ]−2 γj2 .
γ β j=1

Effectively, the scaling is equivalent to covariate-wise penalization (see Chapter 3 for more on this). The ‘scaled’
ridge estimator may then be derived along the same lines as before in Section 1.5:
β̂ (scaled) (λ) = A−1 γ̂(λ) = A−1 (X⊤ X + λA−2 )−1 X⊤ Y.
In general, this is unequal to the ridge estimator without the rescaling of the columns of the design matrix. More-
over, it should be clear that β̂ (scaled) (λ) 6= Aβ̂(λ).

1.9.2 Ridge regression and collinearity

Initially, ridge regression was motivated as an ad-hoc fix of (super)-collinear covariates in order to obtain a well-
defined estimator. We now study the effect of this ad-hoc fix on the regression coefficient estimates of collinear
covariates. In particular, their ridge regularization paths are contrasted to those of ‘non-collinear’ covariates.
To this end, we consider a simulation in which one response is regressed on 50 covariates. The data of these
covariates, stored in a design matrix denoted X, are sampled from a multivariate normal distribution, with mean
zero and a 5 × 5 blocked covariance matrix:
 
Σ11 010×10 010×10 010×10 010×10
 010×10 Σ22 010×10 010×10 010×10 
 

Σ =  010×10 010×10 Σ33 010×10 010×10  
 010×10 010×10 010×10 Σ44 010×10 
010×10 010×10 010×10 010×10 Σ55
with
k−1 6−k
Σkk = 110×10 + I10×10 .
5 5
The data of the response variable Y are then obtained through: Y = Xβ + ε, with ε ∼ N (0n , Inn ) and β = 150 .
Hence, all covariates contribute equally to the response. Would the columns of X be orthogonal, little difference
in the ridge estimates of the regression coefficients is expected.
The results of this simulation study with sample size n = 1000 are presented in Figure 1.6. All 50 regular-
ization paths start close to one as λ is small and converge to zero as λ → ∞. But the paths of covariates of the
same block of the covariance matrix Σ quickly group, with those corresponding to a block with larger off-diagonal
elements above those with smaller ones. Thus, ridge regression prefers (i.e. shrinks less) coefficient estimates of
strongly positively correlated covariates.
Intuitive understanding of the observed behaviour may be obtained from the p = 2 case. Let U , V and ε be
independent random variables with zero mean. Define X1 = U + V , X2 = U − V , and Y = β1 X1 + β2 X2 + ε
with β1 and β2 constants. Hence, E(Y ) = 0. Then:
Y = (β1 + β2 )U + (β1 − β2 )V + ε
= γu U + γv V + ε
and Cor(X1 , X2 ) = [Var(U ) − Var(V )]/[Var(U ) + Var(V )]. The random variables X1 and X2 are strongly
positively correlated if Var(U ) ≫ Var(V ).
The ridge regression estimator associated with regression of Y on U and V is:
 −1  
Var(U ) + λ 0 Cov(U, Y )
γ(λ) = .
0 Var(V ) + λ Cov(V, Y )
26 Ridge regression

Solution paths of correlated covariates Ridge estimates with correlated covariates

r=0.0 loss level sets

5
r=0.3 constraint, correlated X
1.0

r=0.4 constraint, uncorrelated X

r=0.6

4
r=0.8
0.8

∝ 1/Var(X1)

∝ 1/Var(X2)
Ridge estimate

0.6

2
β2
^
β2(λ)
0.4

1
0
0.2

−1
^
β1(λ)
0.0

5 6 7 8 9 10 11 −1 0 1 2 3 4 5

log(lambda) β1

Figure 1.6: Left panel: Ridge regularization paths for coefficients of the 50 covariates, with various degree of
collinearity but equal variance. Color and line type correspond to the five blocks of the covariate matrix Σ. Right
panel: Graphical illustration of the effect of the collinearity among covariates on the ridge estimator. The solid
and dotted grey circles depict the ridge parameter constraint for the collinear and orthogonal cases, respectively.
The dashed black ellipsoids are the level sets of the sum-of-squares squares loss function. The red dot and violet
diamond are the ridge regression for the positive collinear and orthogonal case, respectively.

For large enough λ

  
1 Var(U ) 0 β1 + β2
γ(λ) ≈ .
λ 0 Var(V ) β1 − β2
When Var(U ) ≫ Var(V ) and β1 ≈ β2 , the ridge estimate of γv vanishes for large λ. Hence, ridge regression
prefers positively covariates with similar effect sizes.
This phenomenon too can be explained geometrically. For the illustration consider ridge estimation with λ = 1
of the linear model Y = Xβ + ε with β = (3, 3)⊤ , ε ∼ N (02 , I22 ) and the columns of X strongly and positively
collinear. The level sets of the sum-of-squares loss, kY −Xβk22 , are plotted in the right panel of Figure 1.6. Recall
that the ridge estimate is found by looking for the smallest loss level set that hits the ridge contraint. The sought-
for estimate is then the point of intersection between this level set and the constraint, and – for the case at hand
– is on the x = y-line. This is no different from the case with orthogonal X columns. Yet their estimates differ,
even though the same λ is applied. The difference is to due to fact that the radius of the ridge constraint depends
on λ, X and Y. This is immediate from the fact that the radius of the constraint equals kβ̂(λ)k22 (see Section 1.5).
To study the effect of X on the radius, we remove its dependence on Y by considering its expectation, which is:
E[kβ̂(λ)k22 ] = E{[(X⊤ X + λIpp )−1 (X⊤ X) β̂]⊤ (X⊤ X + λIpp )−1 (X⊤ X) β̂}
= E[Y⊤ X(X⊤ X + λIpp )−2 X⊤ Y]

= σ 2 tr X(X⊤ X + λIpp )−2 X⊤ + β ⊤ X⊤ X(X⊤ X + λIpp )−2 X⊤ Xβ.
In the last step we have used Y ∼ N (Xβ, σ 2 Ipp ) and the expectation of the quadratic form of a multivariate
random variable ε ∼ N (µε , Σε ) is E(ε⊤ Λ ε) = tr(Λ Σε ) + µ⊤ ε Λ µε (cf. Mathai and Provost, 1992). The
expression for the expectation of the radius of the ridge constraint can now be evaluated for the orthogonal X and
the strongly, positively collinear X. It turns out that the latter is larger than the former. This results in a larger ridge
constraint. For the larger ridge constraint there is a smaller level set that hits it first. The point of intersection, still
on the x = y-line, is now thus closer to β and further from the origin (cf. right panel of Figure 1.6). The resulting
estimate is thus larger than that from the orthogonal case.
The above needs some attenuation. Among others it depends on: i) the number of covariates in each block, ii)
the size of the effects, i.e. regression coefficients of each covariate, and iii) the degree of collinearity. Possibly,
there are more factors influencing the behaviour of the ridge estimator presented in this subsection.
1.9 Simulations 27

This behaviour of ridge regression is to be understood when using (say) gene expression data to predict a
certain clinical outcome. Genes work in concert to fulfil a certain function in the cell. Consequently, one expects
their expression levels to be correlated. Indeed, gene expression studies exhibit many co-expressed genes, that is,
genes with correlating transcript levels.

1.9.3 Variance inflation factor

The ridge regression estimator was introduced to resolve the undefinedness of its maximum likelihood counterpart
in the face of (super)collinearity amoung the explanatory variables. The effect of collinearity on the uncertainty of
estimates is often quantified by the Variance Inflation Factor (VIF). The VIF measures the change in the variance
of the estimate due to the collinearity. Here we investigate how penalization affects the VIF. This requires a
definition of the VIF of the ridge regression estimator.
The VIF of the maximum likelihood estimator of the j-th element of the regression parameter is defined as a
factor in the following factorization of the variance of β̂j :

Var(β̂j ) = n−1 σ 2 [(X⊤ X)−1 ]jj = n−1 σ 2 [Var(Xi,j | Xi,1 , . . . , Xi,j−1 , Xi,j+1 , . . . , Xi,p )]−1
n−1 σ 2 Var(Xi,j )
= ·
Var(Xi,j ) Var(Xi,j | Xi,1 , . . . , Xi,j−1 , Xi,j+1 , . . . , Xi,p )
:= n−1 σ 2 [Var(Xi,j )]−1 VIF(β̂j ),

in which it assumed that the Xi,j ’s are random and – using the column-wise zero ‘centered-ness’of X – that
n−1 X⊤ X is estimator of their covariance matrix. Moreover, the identity used to arrive at the second line of
the display, [(X⊤ X)−1 ]jj = [Var(Xi,j | Xi,1 , . . . , Xi,j−1 , Xi,j+1 , . . . , Xi,p )]−1 , originates from Corollary 5.8.1
of Whittaker (1990). Thus, Var(β̂j ) factorizes into σ 2 [Var(Xi,j )]−1 and the variance inflation factor VIF(β̂j ).
When the j-th covariate is orthogonal to the other, i.e. there is no collinearity, then the VIF’s denominator,
Var(Xi,j | Xi,1 , . . . , Xi,j−1 , Xi,j+1 , . . . , Xi,p ), equals Var(Xi,j ). Consequently, VIF(β̂j ) = 1. When there is
collinearity among the covariates Var(Xi,j | Xi,1 , . . . , Xi,j−1 , Xi,j+1 , . . . , Xi,p ) < Var(Xi,j ) and VIF(β̂j ) > 1.
The VIF then inflates the variance of the estimator of βj under orthogonality – hence, the name – by a factor
attributable to the collinearity.
The definition of the VIF needs modification to apply to the ridge regression estimator. In Marquardt (1970)
the ‘ridge VIF’ is defined analogously to the above definition of the VIF of the maximum likelihood regression
estimator as:

Var[β̂j (λ)] = σ 2 [(X⊤ X + λIpp )−1 X⊤ X(X⊤ X + λIpp )−1 ]jj

n−1 σ 2
= · nVar(Xi,j )[(X⊤ X + λIpp )−1 X⊤ X(X⊤ X + λIpp )−1 ]jj
Var(Xi,j )
:= n−1 σ 2 [Var(Xi,j )]−1 VIF[β̂j (λ)],

where the factorization is forced in line with that of the ‘maximum likelihood VIF’ but lacks a similar interpre-
tation. When X is orthogonal, VIF[β̂j (λ)] = [Var(Xi,j )]2 [Var(Xi,j ) + λ]−2 < 1 for λ > 0. Penalization then
deflates the variance.
An alternative definition of the ‘ridge VIF’ presented by Garcı́a et al. (2015) for the ‘p = 2’-case, which they
motivate from counterintuitive behaviour observed in the ‘ridge VIF’ defined by Marquardt (1970), adopts the
‘maximum likelihood VIF’ definition but derives the ridge regression estimator from augmented data to comply
with the maximum likelihood approach. This requires to augment √ the⊤response vector with p zeros, i.e. Yaug =
(Y⊤ , 0⊤p )⊤
and the design matrix with p rows as Xaug = (X⊤
, λIpp ) . The ridge regression estimator can then
⊤ −1 ⊤
be written as β̂(λ) = (Xaug Xaug ) Xaug Yaug (see Exercise 1.3). This reformulation of the ridge regression estimator
in the form of its maximum likelihood counterpart suggests the adoption of latter’s VIF definition for the former.
However, in the ‘maximum likelihood VIF’ the design matrix is assumed to be zero centered column-wise. Within
the augmented data formulation this may be achieved by the inclusion of a column of ones in Xaug representing
the intercept. The inclusion of an intercept, however, requires a modification of the estimators of Var(Xi,j ) and
Var(Xi,j | Xi,1 , . . . , Xi,j−1 , Xi,j+1 , . . . , Xi,p ). The former is readily obtained, while the latter is given by the
reciprocals of the 2nd to the (p + 1)-th diagonal elements of the inverse of:
 ⊤    √ ⊤ 
1n √X 1n √X n+p
√ λ1p
= ⊤ .
1p λIpp 1p λIpp λ1p X X + λIpp
28 Ridge regression

The lower right block of this inverse is obtained using well-known linear algebra results i) the analytic expression
of the inverse of a 2 × 2-partitioned matrix and i) the inverse of the sum of an invertible and a rank one matrix
(given by the Sherman-Morrison formula, see Corollary 18.2.10, Harville, 2008). It equals:

(X⊤ X + λIpp )−1 − (1 + c)−1 (n + p)−1 λ(X⊤ X + λIpp )−1 1p 1⊤ ⊤

p (X X + λIpp )
−1
,
Pp
where c = (n + p)−1 λ 1⊤ ⊤
p (X X + λIpp )
−1
1p = (n + p)−1 λ j,j ′ =1 [(X⊤ X + λIpp )−1 ]j,j ′ . Substitution of
these expressions in the ratio of Var(Xi,j ) and Var(Xi,j | Xi,1 , . . . , Xi,j−1 , Xi,j+1 , . . . , Xi,p ) in the above yields
the alternative VIF of Garcı́a et al. (2015).
The effect of collinearity on the variance of the ridge regression estimator and the influence of penalization
⊤
on this effect is studied in two small simulation studies. In the first study the rows of the design matrix Xi,∗
are sampled from N (0p , Σ) with Σ = (1 − ρ)Ipp + ρ1pp fixing the dimension at p = 50 and the sample size

’ridge VIF’ (Marquardt), n=100, p=50 ’ridge VIF’ (Garcia), n=100, p=50
1.0

1.0
4
50 35 30 25 22 19 16
40 40 12
25 19 14
14 10
22 16
12 10
0.8

0.8
9 9
8 8
7 7

6 6
0.6

0.6
5 5

4 4
ρ

ρ
0.4

0.4

3
3
0.2

0.2

2
0.0

0.0

1.5 2

0 1 2 3 4 0 1 2 3 4

λ λ

‘ridge VIF’ (Marquardt), ρ=0, p=50 ‘ridge VIF’ (Garcia), ρ=0, p=50
100

100
1.
5
80

80

2
2.5
3

4
4
60

60
n

10
7

5
25

15

5
40

40

3
2

1.5
1
0.8
0.6
0.4
20

20

0.2

3 2.5 2

0 1 2 3 4 0 1 2 3 4

λ λ

Figure 1.7: Contour plots of ‘Marquardt VIFs’ and ‘Garcia VIFs’, left and right columns, respectively. The top
panels show these VIFs against the degree of penalization (x-axis) and collinearity (y-axis) for a fixed sample size
(n = 100) and dimension (p = 50). The bottom panels show these VIFs against the degree of penalization (x-axis)
and the sample size (y-axis) for a fixed dimension (p = 50).
1.10 Illustration 29

at n = 100. The correlation coefficient ρ is varied over the unit interval [0, 1), representing various levels of
collinearity. The columns of the thus drawn X are zero centered. The response is then formed in accordance
with the linear regression model Y = Xβ + ε with β = 1p and the error drawn from N (0n , 14 Inn ). The
effect of penalization is studied by varying λ. For each (ρ, λ)-combination data, X and Y, are sampled thousand
times and both ‘ridge VIFs’, for discriminative purposes referred as the Marquardt and Garcia VIFs (after the first
author of the proposing papers), are calculated and averaged. Figure 1.7 shows the contour plots of the averaged
Marquardt and Garcia VIF against ρ and λ. At (ρ, λ) ≈ (0, 0) both VIFs are close to two, which – although the
set-up is not high-dimensional in the strict ‘p > n’-sense – is due to the streneous p/n-ratio. Nonetheless, as
expected an increase in collinearity results in an increase in the VIF (irrespective of the type). Moreover, indeed
some counterintuitive behaviour is observed in the Marquardt VIF: at (say) a value of λ = 3 the VIF reaches a
maximum for ρ ≈ 0.95 and declines for larger degrees of collinearity. This is left without further interpretation
as interest is not in deciding on the most appropriate operationalization among both VIFs of the ridge regression
estimator, but is primarily in the effect of penalization on the VIF. In this respect both VIFs exhibit the same
behaviour: a monotone decrease of both VIFs in λ.
In the second simulation the effect of ‘spurious collinearity’ introduced by the varying the sample size on the
ridge estimator is studied. The settings are identical to that of the first simulation but with ρ = 0 and a sample size
n that varies from ten to hundred. With p = 50 in particular the lower sample sizes will exhibit high degrees of
collinearity as the sample correlation coefficient has been seen to inflate then (as is pointed out by ? and illustrated
in Section ??). The resulting contour plots (Figure 1.7) now present the VIFs against n and λ. Although some
counterintuitive behaviour can be seen around n = p and small λ, the point to be noted and relevant here – as
interest is in the VIF’s behaviour for data sets with a fixed sample size and covariates drawn without collinearity
– is the monotone decrease of both VIFs in λ at any sample size.
In summary, the penalization does not remove collinearity but, irrespective of the choice of VIF, it reduces the
effect of collinearity on the variance of the ridge estimator (as measured by the VIFs above). This led Garcı́a et al.
(2015) – although admittingly their focus appears to be low-dimensionally – to suggest that the VIFs may guide
the choice the penalty parameter: choose λ such that the variance of the estimator is increased at most by a
user-specified factor.

1.10 Illustration
The application of ridge regression to actual data aims to illustrate its use in practice.

1.10.1 MCM7 expression regulation by microRNAs

Recently, a new class of RNA was discovered, referred to as microRNA. MicroRNAs are non-coding, single
stranded RNAs of approximately 22 nucleotides. Like mRNAs, microRNAs are encoded in and transcribed from
the DNA. MicroRNAs play an important role in the regulatory mechanism of the cell. MicroRNAs down-regulate
gene expression by either of two post-transcriptional mechanisms: mRNA cleavage or transcriptional repression.
This depends on the degree of complementarity between the microRNA and the target. Perfect or nearly perfect
complementarity of the mRNA to the microRNA will lead to cleavage and degradation of the target mRNA. Imper-
fect complementarity will repress the productive translation and reduction in protein levels without affecting the
mRNA levels. A single microRNA can bind to and regulate many different mRNA targets. Conversely, several mi-
croRNAs can bind to and cooperatively control a single mRNA target (Bartel, 2004; Esquela-Kerscher and Slack,
2006; Kim and Nam, 2006).
In this illustration we wish to confirm the regulation of mRNA expression by microRNAs in an independent
data set. We cherry pick an arbitrary finding from literature reported in Ambs et al. (2008), which focusses on
the microRNA regulation of the MCM7 gene in prostate cancer. The MCM7 gene is involved in DNA replication
(Tye, 1999), a cellular process often derailed in cancer. Furthermore, MCM7 interacts with the tumor-suppressor
gene RB1 (Sterner et al., 1998). Several studies indeed confirm the involvement of MCM7 in prostate cancer
(Padmanabhan et al., 2004). And recently, it has been reported that in prostate cancer MCM7 may be regulated
by microRNAs (Ambs et al., 2008).
We here assess whether the MCM7 down-regulation by microRNAs can be observed in a data set other than
the one upon which the microRNA-regulation of MCM7 claim has been based. To this end we download from
the Gene Expression Omnibus (GEO) a prostate cancer data set (presented by Wang et al., 2009). This data set
(with GEO identifier: GSE20161) has both mRNA and microRNA profiles for all samples available. The prepro-
cessed (as detailed in Wang et al., 2009) data are downloaded and require only minor further manipulations to suit
30 Ridge regression

our purpose. These manipulations comprise i) averaging of duplicated profiles of several samples, ii) gene- and
mir-wise zero-centering of the expression data, iii) averaging the expression levels of the probes that interrogate
MCM7. Eventually, this leaves 90 profiles each comprising of 735 microRNA expression measurements.

Listing 1.3 R code

# load libraries
library(GEOquery)
library(RmiR.hsa)
library(penalized)

# extract data
slh <- getGEO("GSE20161", GSEMatrix=TRUE)
GEdata <- slh[1][[1]]
MIRdata <- slh[2][[1]]

# average duplicate profiles

Yge <- numeric()
Xmir <- numeric()
for (sName in 1:90){
Yge <- cbind(Yge, apply(exprs(GEdata)[,sName,drop=FALSE], 1, mean))
Xmir <- cbind(Xmir, apply(exprs(MIRdata)[,sName,drop=FALSE], 1, mean))
}
colnames(Yge) <- paste("S", 1:90, sep="")
colnames(Xmir) <- paste("S", 1:90, sep="")

# extact mRNA expression of the MCM7N tumor suppressor gene

entrezID <- c("4176")
geneName <- "MCM7"
Y <- Yge[which(levels(fData(GEdata)[,6])[fData(GEdata)[,6]] == geneName),]

# average gene expression levels over probes

Y <- apply(Y, 2, mean)

# mir-wise centering mir expression data

X <- t(sweep(Xmir, 1, rowMeans(Xmir)))

# generate cross-validated likelihood profile

profL2(Y, penalized=X, minlambda2=1, maxlambda2=20000, plot=TRUE)

# decide on the optimal penalty value directly

optLambda <- optL2(Y, penalized=X)$lambda

# obtain the ridge regression estimages

ridgeFit <- penalized(Y, penalized=X, lambda2=optLambda)

# plot them as histogram

hist(coef(ridgeFit, "penalized"), n=50, col="blue", border="lightblue",
xlab="ridge regression estimates with optimal lambda",
main="Histogram of ridge estimates")

# linear prediction from ridge

Yhat <- predict(ridgeFit, X)[,1]
plot(Y ˜ Yhat, pch=20, xlab="pred. MCM7 expression",
ylab="obs. MCM7 expression")

With this prostate data set at hand we now investigate whether MCM7 is regulated by microRNAs. Hereto
we fit a linear regression model regressing the expression levels of MCM7 onto those of the microRNAs. As
the number of microRNAs exceeds the number of samples, ordinary least squares fails and we resort to the ridge
estimator of the regression coefficients. First, an informed choice of the penalty parameter is made through
maximization of the LOOCV log-likelihood, resulting in λopt = 1812.826. Having decided on the value of the to-
be-employed penalty parameter, the ridge regression estimator can now readily be evaluated. The thus fitted model
1.10 Illustration 31

allows for the evaluation of microRNA-regulation of MCM7. E.g., by the proportion of variation of the MCM7
expression levels by the microRNAs as expressed in coefficient of determination: R2 = 0.4492. Alternatively, but
closely related, observed expression levels may be related to the linear predictor of the MCM7 expression levels:
Ŷ(λopt ) = Xβ̂(λopt ). The Spearman correlation of response and predictor equals 0.6295. A visual inspection is
provided by the left panel of Figure 1.8. Note the difference in scale of the x- and y-axes. This is due to the
fact that the regression coefficients have been estimated in penalized fashion, consequently shrinking estimates of
the regression coefficients towards zero leading to small estimates and in turn compressing the range of the linear
prediction. The above suggests there is indeed association between the microRNA expression levels and those of
MCM7.

Fit of ridge analysis Histogram of ridge regression estimates

200
9.2

150
9.1
obs. MCM7 expression level

Frequency
9.0

100
8.9

50
8.8
8.7

8.94 8.96 8.98 9.00 9.02 9.04 −0.002 −0.001 0.000 0.001

pred. MCM7 expression level ridge estimates with optimal λ

Figure 1.8: Left panel: Observed vs. (ridge) fitted MCM7 expression values. Right panel: Histogram of the ridge
regression coefficient estimates.

The overall aim of this illustration was to assess whether microRNA-regulation of MCM7 could also be ob-
served in this prostate cancer data set. In this endeavour the dogma (stating this regulation should be negative)
has nowhere been used. A first simple assessment of the validity of this dogma studies the signs of the estimated
regression coefficients. The ridge regression estimate has 394 out of the 735 microRNA probes with a negative
coefficient. Hence, a small majority has a sign in line with the ‘microRNA ↓ mRNA’ dogma. When, in addi-
tion, taking the size of these coefficients into account (Figure 1.8, right panel), the negative regression coefficient
estimates do not substantially differ from their positive counterparts (as can be witnessed from their almost sym-
metrical distribution around zero). Hence, the value of the ‘microRNA ↓ mRNA’ dogma is not confirmed by this
ridge regression analysis of the MCM7-regulation by microRNAs. Nor is it refuted.
The implementation of ridge regression in the penalized-package offers the possibility to fully obey the
dogma on negative regulation of mRNA expression by microRNAs. This requires all regression coefficients to be
negative. Incorporation of the requirement into the ridge estimation augments the constrained estimation problem
with an additional constraint:

β̂(λ) = arg min kY − X βk22 .

kβk22 ≤c(λ)
βj ≤0 for all j

With the additional non-positivity constraint on the parameters, there is no explicit solution for the estimator.
The ridge estimate of the regression parameters is then found by numerical optimization using e.g. the Newton-
Raphson algorithm or a gradient descent approach. The next listing gives the R-code for ridge estimation with the
non-positivity constraint of the linear regression model.

Listing 1.4 R code

# decide on the optimal penalty value with sign constraint on paramers
32 Ridge regression

optLambda <- optL2(Y, penalized=-X, positive=rep(TRUE, ncol(X)))$lambda

# obtain the ridge regression estimages

ridgeFit <- penalized(Y, penalized=-X, lambda2=optLambda,
positive=rep(TRUE, ncol(X)))

# linear prediction from ridge

Yhat <- predict(ridgeFit, -X)[,1]
plot(Y ˜ Yhat, pch=20, xlab="predicted MCM7 expression level",
ylab="observed MCM7 expression level")
cor(Y, Yhat, m="s")
summary(lm(Y ˜ Yhat))[8]

The linear regression model linking MCM7 expression to that of the microRNAs is fitted by ridge regression
while simultaneously obeying the ‘negative regulation of mRNA by microRNA’-dogma to the prostate cancer
data. In the resulting model 401 out of 735 microRNA probes have a nonzero (and negative) coefficient. There is
a large overlap in microRNAs with a negative coefficient between those from this and the previous fit. The models
are also compared in terms of their fit to the data. The Spearman rank correlation coefficient between response and
predictor for the model without positive regression coefficients equals 0.679 and its coefficient of determination
0.524 (confer the left panel of 1.9 for a visualization). This is a slight improvement upon the unconstrained ridge
estimated model. The improvement may be small but it should be kept in mind that the number of parameters used
by both models is 401 (for the model without positive regression coefficients) vs. 735. Hence, with close to half
the number of parameters the dogma-obeying model gives a somewhat better description of the data. This may
suggest that there is some value in the dogma as inclusion of this prior information leads to a more parsimonious
model without any loss in fit.

Fit of ridge analysis with constraints Histogram of ridge regression estimates with constraints
400
9.2

300
9.1
obs. MCM7 expression level

Frequency
9.0

200
8.9

100
8.8
8.7

8.94 8.96 8.98 9.00 9.02 9.04 9.06 −0.005 −0.004 −0.003 −0.002 −0.001 0.000

pred. MCM7 expression level ridge estimates with optimal λ

Figure 1.9: Left panel: Observed vs. (ridge) fitted MCM7 expression values (with the non-positive constraint on the
parameters in place). Right panel: Histogram of the ridge regression coefficient estimates (from the non-positivity
constrained analysis).

The dogma-obeying model selects 401 microRNAs that aid in the explanation of the variation in the gene
expression levels of MCM7. There is an active field of research, called target prediction, trying to identify which
microRNAs target the mRNA of which genes. Within R there is a collection of packages that provide the target
prediction of known microRNAs. The packages differ on the method (e.g. experimental or sequence comparison)
that has been used to arrive at the prediction. These target predictions may be used to evaluate the value of the
found 401 microRNAs. Ideally, there would be a substantial amount of overlap. The R-script that loads the target
predictions and does the comparison is below.
1.11 Conclusion 33

Listing 1.5 R code

# extract mir names and their (hypothesized) mrna target
mir2target <- numeric()
mirPredProgram <- c("targetscan", "miranda", "mirbase", "pictar", "mirtarget2")
for (program in mirPredProgram){
slh <- dbReadTable(RmiR.hsa_dbconn(), program)
slh <- cbind(program, slh[,1:2])
colnames(slh) <- c("method", "mir", "target")
mir2target <- rbind(mir2target, slh)
}
mir2target <- unique(mir2target)
mir2target <- mir2target[which(mir2target[,3] == entrezID),]
uniqMirs <- tolower(unique(mir2target[,2]))

# extract names of mir-probe on array

arrayMirs <- tolower(levels(fData(MIRdata)[,3])[fData(MIRdata)[,3]])

# which mir-probes are predicted to down-regulate MCM7

selMirs <- intersect(arrayMirs, uniqMirs)
ids <- which(arrayMirs %in% selMirs)

# which ridge estimates are non-zero

nonzeroBetas <- (coef(ridgeFit, "penalized") != 0)

# which mirs are predicted to

nonzeroPred <- 0 * betas
nonzeroPred[ids] <- 1

# contingency table and chi-square test

table(nonzeroBetas, nonzeroPred)
chisq.test(table(nonzeroBetas, nonzeroPred))

β̂j = 0 β̂j < 0

microRNA not target 323 390

microRNA target 11 11

Table 1.1: Cross-tabulation of the microRNAs being a potential target of MCM7 vs. the value of its regression
coefficient in the dogma-obeying model.

With knowledge available on each microRNA whether it is predicted (by at least one target prediction pack-
age) to be a potential target of MCM7, it may be cross-tabulated against its corresponding regression coefficient
estimate in the dogma-obeying model being equal to zero or not. Table 1.1 contains the result. Somewhat super-
fluous considering the data, we may test whether the targets of MCM7 are overrepresented in the group of strictly
negatively estimated regression coefficients. The corresponding chi-squared test (with Yates’ continuity correc-
tion) yields the test statistic χ2 = 0.0478 with a p-value equal to 0.827. Hence, there is no enrichment among
the 401 microRNAS of those that have been predicted to target MCM7. This may seem worrisome. However, the
microRNAs have been selected for their predictive power of the expression levels of MCM7. Variable selection
has not been a criterion (although the sign constraint implies selection). Moreover, criticism on the value of the
microRNA target prediction has been accumulating in recent years (REF).

1.11 Conclusion
We discussed ridge regression as a modification of linear regression to overcome the empirical non-identifiability
of the latter when confronted with high-dimensional data. The means to this end was the addition of a (ridge)
penalty to the sum-of-squares loss function of the linear regression model, which turned out to be equivalent to
constraining the parameter domain. This warranted the identification of the regression coefficients, but came at
34 Ridge regression

the cost of introducing bias in the estimates. Several properties of ridge regression like moments, MSE, and its
Bayesian interpretation have been reviewed. Finally, its behaviour and use have been illustrated in simulation and
omics data.

1.12 Exercises
Question 1.1 †
Find the ridge regression solution for the data below for a general value of λ and for the straight line model
Y = β0 + β1 X + ε (only apply the ridge penalty to the slope parameter, not to the intercept). Show that
when λ is chosen as 4, the ridge solution fit is Ŷ (λ) = 40 + 1.75X. Data: X⊤ = (X1 , X2 , . . . , X8 )⊤ =
(−2, −1, −1, −1, 0, 1, 2, 2)⊤, and Y⊤ = (Y1 , Y2 , . . . , Y8 )⊤ = (35, 40, 36, 38, 40, 43, 45, 43)⊤.
Question 1.2
Consider the standard linear regression model Yi = Xi,∗ β + εi for i = 1, . . . , n and with εi ∼i.i.d. N (0, σ 2 ).
The model comprises a single covariate and an intercept. Response and covariate data are: {(yi , xi,1 )}4i=1 =
{(1.4, 0.0), (1.4, −2.0), (0.8, 0.0), (0.4, 2.0)}. Find the value of λ that yields the ridge regression estimate (with
an unpenalized intercept) equal to (1, − 81 )⊤ .
Question 1.3 ‡
Show that the ridge regression estimator can be obtained by ordinary
√ least squares regression on an augmented
data set. Hereto augment the matrix X with p additional row λIpp , and augment the response vector Y with p
zeros.
Question 1.4
The coefficients β of a linear regression model, Y = Xβ + ε, are estimated by β̂ = (X⊤ X)−1 X⊤ Y. The
associated fitted values then given by Y b = X β̂ = X(X⊤ X)−1 X⊤ Y = HY, where H = X(X⊤ X)−1 X⊤
referred to as the hat matrix. The hat matrix H is a projection matrix as it satisfies H = H2 . Hence, linear
regression projects the response Y onto the vector space spanned by the columns of Y. Consequently, the residuals
ε̂ and Ŷ are orthogonal. Now consider the ridge estimator of the regression coefficients: β̂(λ) = (X⊤ X +
λIpp )−1 X⊤ Y. Let Ŷ(λ) = Xβ̂(λ) be the vector of associated fitted values.
a) Show that the ridge hat matrix H(λ) = X(X⊤ X + λIpp )−1 X⊤ , associated with ridge regression, is not a
projection matrix (for any λ > 0), i.e. H(λ) 6= [H(λ)]2 .
b
b) Show that the ‘ridge fit’ Y(λ) is not orthogonal to the associated ‘ridge residuals’ ε̂(λ) (for any λ > 0).
Question 1.5
Consider the standard linear regression model Yi = Xi,∗ β + εi for i = 1, . . . , n and with the εi ∼i.i.d N (0, σ 2 ).
Suppose estimates of the regression parameters β of this model are obtained through the minimization of the
sum-of-squares augmented with a ridge penalty, kY − Xβk22 + λkβk22 , in which λ > 0 is the penalty parameter.
The minimizer is called the ridge estimator and is denoted by β̂(λ).
a) The vector of ‘ridge residuals’, defined as ε(λ) = Y − Xβ̂(λ), are normally distributed. Why?
b) Show that E[ε(λ)] = [Inn − X(X⊤ X + λIpp )−1 X⊤ ]Xβ.
c) Show that Var[ε(λ)] = σ 2 [Inn − X(X⊤ X + λIpp )−1 X⊤ ]2 .
d) Could the normal probability plot, i.e. a qq-plot with the quantiles of standard normal distribution plotted
against those of the ridge residuals, be used to assess the normality of the latter? Motivate.
Question 1.6
Recall that there exists λ > 0 such that M SE(β̂) > M SE[β̂(λ)]. Verify that this carries over to the linear
b = M SE(Xβ̂) > M SE[Xβ̂(λ)].
predictor. That is, then there exists a λ > 0 such thatM SE(Y)
Question 1.7
Consider the standard linear regression model Yi = Xi,∗ β + εi for i = 1, . . . , n and with εi ∼i.i.d. N (0, σ 2 )
Consider the following two ridge regression estimators of the regression parameter of this model, defined as:
Xn Xn
arg min (Yi − Xi,∗ β)2 + λkβk22 and arg min (Yi − Xi,∗ β)2 + nλkβk22 .
β i=1 β i=1

Which do you prefer? Motivate.

† This exercise is freely rendered from Draper and Smith (1998)

‡ This exercise is freely rendered from Hastie et al. (2009), but can be found in many other places. The original source is unknown to the
author.
1.12 Exercises 35

Question 1.8
Consider the standard linear regression model Yi = Xi,∗ β + εi for i = 1, . . . , n and with the εi i.i.d. normally
distributed with zero mean and a common variance. The rows of the design matrix X are of length 2, neither
column represents the intercept, but X∗,1 = X∗,2 .
a) Suppose an estimate of the regression parameter β of this model is obtained through the minimization of
the sum-of-squares augmented with a ridge penalty, kY − Xβk22 + λkβk22 , in which λ > 0 is the penalty
parameter. The minimizer is called the ridge estimator and is denoted by β̂(λ). Show that [β̂(λ)]1 = [β̂(λ)]2
for all λ > 0.
b) The covariates are now related as X∗,1 = −2X∗,2 . Data on the response and the covariates are:

{(yi , xi,1 , xi,2 )}6i=1 = {(1.5, 1.0, −0.5), (1.9, −2.0, 1.0), (−1.6, 1.0, −0.5),
(0.8, 4.0, −2.0), (0.9, 2.0, −1.0), (−0.5, 4.0, −2.0)}.

Evaluate the ridge regression estimator for these data with λ = 1.

c) The data are as in part b). Show β̂(λ + δ) = (52.5 + λ)(52.5 + λ + δ)−1 β̂(λ) for a fixed λ and any δ > 0.
√ the singular value decomposition of the design matrix X and the fact that its largest singular value
Hint: Use
equals 52.5.
d) The data are as in part b). Consider the model Yi = Xi,1 γ + εi . The parameter γ is estimated through
P6
minimization of i=1 (Yi − Xi,1 γ)2 + λγ γ 2 . For which value of λγ does the resulting linear predictor
Xi,1 γ̂(λγ ) coincide with that obtained from the estimate evaluated in part b) of this exercise, i.e. Xβ̂(λ)?

Question 1.9 (foreshadowing Chapter 3)

Consider a pathway comprising of three genes called A, B, and C. Let random variables Yi,a , Yi,b , and Yi,c be
the random variable representing the expression of levels of genes A, B, and C in sample i. Hundred realizations,
i.e. i = 1, . . . , n, of Yi,a , Yi,b , and Yi,c are available from an observational study. In order to assess how the
expression levels of gene A are affect by that of genes B and C a medical researcher fits the

Yi,a = βb Yi,b + βc Yi,c + εi ,

with εi ∼ N (0, σ 2 ). This model fitted by means of ridge regression, but with a separate penalty parameter, λb
and λc , for the two regression coefficient, βb and βc , respectively.
a) Write down the ridge penalized loss function employed by the researcher.
b) Does a different choice of penalty parameter for the second regression coefficient affect the estimation of
the first regression coefficient? Motivate your answer.
c) The researcher decides that the second covariate Yi,c is irrelevant. Instead of removing the covariate from
model, the researcher decides to set λc = ∞. Show that this results in the same ridge estimate for βb as
when fitting (again by means of ridge regression) the model without the second covariate.
2 Bayesian regression

The ridge regression estimator is equivalent to a Bayesian regression estimator. On one hand this equivalence
provides another interpretation of the ridge regression estimator. But it also shows that within the Bayesian
framework the high-dimensionality of the data need not frustrate the numerical evaluation of the estimator. In
addition, the framework provides ways to quantify the consequences of high-dimensionality on the uncertainty of
the estimator. Within this chapter focus is on the equivalence of Bayesian and ridge regression. In this particular
case, the connection is immediate from the analytic formulation of the Bayesian regression estimator. After this
has been presented, it is shown how this estimator may also be obtained by means of sampling. The relevance of
the sampling for the evaluation of the estimator and its uncertainty becomes apparent in subsequent chapters when
discussing other penalized estimators for which the connection cannot be captured in analytic form.

2.1 A minimum of prior knowledge on Bayesian statistics

The schism between Bayesian and frequentist statistics centers on the interpretation of the concept of probability.
A frequentist views the probability of an event as the limiting frequency of observing the event among a large
number of trials. In contrast, a Bayesian considers it to be a measure of believe (in the occurence) of the event.
The difference between the two interpretations becomes clear when considering events that can occur only once
(or a small number of times). A Bayesian would happily discuss the probability of this (poosibly hypothetical)
event happening, which would be meaningless to a frequentist.
What are the consequences of this schism for the current purpose of estimating a regression model? Expo-
nents from both paradigms assume a statistical model, e.g. here the linear regression model, to describe the data
generating mechanism. But a frequentist treats the parameters as platonic quantities for which a true value exists
that is to be estimated from the data. A Bayesian, however, first formalizes his/her current believe/knowledge
on the parameters in the form of probability distributions. This is referred to as the prior – to the experiment –
distribution. The parameters are thus random variables and their distributions are to be interpreted as reflecting
the (relative) likelihood of the parameters’ values. From the Bayesian point it then makes sense to talk about the
random behaviour of the parameter, e.g., what is probability of that the parameter is larger than a particular value.
In the frequentist context one may ask this of the estimator, but not of the parameter. The parameter either is or
is not larger than this value as a platonic quantity is not governed by a chance process. Then, having specified
his/her believe on the parameters, a Bayesian uses the data to update this believe of the parameters of the statistical
model, which again is a distribution and called the posterior – to the experiment – distribution.
To illustrate this process of updating assume that the data Y1 , . . . , Yn ∼ {0, 1} are assumed to be independently
and identically drawn from a Bernouilli distribution with parameter θ = P (Yi = 1). The likelihood of these data
for a given choice of theQ
Q parameter θ then is: L(Y = y; θ) = P (Y = y | θ) = P (Y1 = y1 , . . . , Yn = yn | θ) =
n n yi 1−yi
i=1 P (Yi = y i | θ) = i=1 θ (1 − θ) . A Bayesian now needs to specificy the prior distribution, denoted
πθ (·), on the parameter θ. A common choice in this case would be a beta-distribution: θ ∼ B (α, β). The posterior
distribution is now arrived at by the use of Bayes’ rule:

P (Y = y | θ) π(θ) P (Y = y | θ) π(θ)
π(θ | Y = y) = = R .
P (Y = y) 0,1
P (Y = y | θ) π(θ) dθ

The posterior distribution thus contains all knowledge on the parameter. As the denomenator – referred to as the
distribution’s normalizing constant – in the expression of the posterior distribution does not involve the parameter
θ, one often writes π(θ | Y = y) ∝ P (Y = y | θ) π(θ), thus specifying the (relative) density of the posterior
distribution of θ as ‘likelihood × prior’.
While the posterior distribution is all one wishes to know, often a point estimate is required. A point estimate
of θ can be obtained from the posterior by taking the mean or the mode. Formally, the Bayesian point estimator of
2.2 Relation to ridge regression 37

a parameter θ is defined as the estimator

R that minimizes the Bayes risk over a prior distribution of the parameter
θ. The Bayes risk is defined as θ E[(θ̂ − θ)2 ]πθ (θ; α)dθ, where πθ (θ; α) is the prior distribution of θ with
hyperparameter α. It is thus a weighted average of the Mean Squared Error, with weights specified through the
prior. The Bayes risk is minimized by the posterior mean:
R
θ P (Y = y | θ) π(θ) dθ
Eθ (θ | data) = Rθ .
θ
P (Y = y | θ) π(θ) dθ

(cf., e.g., Bijma et al., 2017). The Bayesian point estimator of θ yields the smallest possible expected MSE, under
the assumption of the employed prior. This estimator thus depends on the likelihood and the prior, and a different
prior yields a different estimator.
A point estimator is preferably accompanied by a quantification of its uncertainty. Within the Bayesian context
this is done by so-called credible intervals or regions, the Bayesian equivalent of confidence intervals or regions.
A Bayesian credible interval encompass a certain percentage of the probability R mass of the posterior. For instance,
a subset of the parameter space C forms an 100(1 − α)% credible interval if C π(θ | data) dθ = 1 − α.
In the example above it is important to note the role of the prior in the updating of the knowledge on θ. First,
when the prior distribution is uniform on the unit interval, the mode of the posterior coincides with the maximum
likelihood estimator. Furthermore, when n is large the influence of the prior in the posterior is negligible. It is
therefore that for large sample sizes frequentist and Bayesian analyses tend to produce similar results. However,
when n is small, the prior’s contribution to the posterior distribution cannot be neglected. The choice of the prior
is then crucial as it determines the shape of the posterior distribution and, consequently, the posterior estimates.
It is this strong dependence of the posterior on the arbitrary (?) choice of the prior that causes unease with a
frequentist (leading some to accuse Bayesians of subjectivity). In the high-dimensional setting the sample size
is usually small, especially in relation to the parameter dimension, and the choice of the prior distribution then
matters. Interest here is not in resolving the frequentist’s unease but in identifying or illustrating the effect of the
choose of the prior distribution on the parameter estimates.

2.2 Relation to ridge regression

Ridge regression has a close connection to Bayesian linear regression. Bayesian linear regression assumes the
parameters β and σ 2 to be the random variables, while at the same time considering X and Y as fixed. Within
the regression context, the commonly chosen priors of β and σ 2 are β | σ 2 ∼ N (0p , σ 2 λ−1 Ipp ) and σ 2 ∼
IG (α0 , β0 ), where IG denotes the inverse Gamma distribution with shape parameter α0 and scale parameter β0 .
The penalty parameter can be interpreted as the (scaled) precision of the prior of β, determining how informative
the prior should be. A smaller penalty (i.e. precision) corresponds to a wider prior, and a larger penalty to a more
informative, concentrated prior (Figure 2.1).
The joint posterior distribution of β and σ 2 is, under the assumptions of the (likelihood of) the linear regression
model and the priors above:

fβ,σ2 (β, σ 2 | Y, X) ∝ fY (Y | X, β, σ 2 ) fβ (β|σ 2 ) fσ (σ 2 )

∝ σ −n exp[− 21 σ −2 (Y − Xβ)⊤ (Y − Xβ)]
× σ −p exp[− 21 σ −2 λβ ⊤ β] × (σ 2 )−α0 −1 exp(− 12 σ −2 β0 ).

The posterior distribution can be expressed as a multivariate normal distribution. Hereto group the terms from the
exponential functions that involve β and manipulate as follows:

(Y − Xβ)⊤ (Y − Xβ) + λβ ⊤ β
= Y⊤ Y − β ⊤ X⊤ Y − Y⊤ Xβ + β ⊤ X⊤ Xβ + λβ ⊤ β
= Y⊤ Y − β ⊤ (X⊤ X + λIpp )(X⊤ X + λIpp )−1 X⊤ Y
− Y⊤ X(X⊤ X + λIpp )−1 (X⊤ X + λIpp )β + β ⊤ (X⊤ X + λIpp )β
= Y⊤ Y − β ⊤ (X⊤ X + λIpp )β̂(λ)
− [β̂(λ)]⊤ (X⊤ X + λIpp )β + β ⊤ (X⊤ X + λIpp )β
= Y⊤ Y − Y⊤ X(X⊤ X + λIpp )−1 X⊤ Y
+ [β − β̂(λ)]⊤ (X⊤ X + λIpp )[β − β̂(λ)].
38 Bayesian regression

Prior of beta

lambda=1

1.2
lambda=2
lambda=5
lambda=10

1.0
0.8
density

0.6
0.4
0.2
0.0

−3 −2 −1 0 1 2 3

beta

Figure 2.1: Conjugate prior of the regression parameter β for various choices of λ, the penalty parameters c.q.
precision.

Using this result, the posterior distribution can be rewritten to:

fβ,σ2 (β, σ 2 | Y, X) ∝ gβ (β | σ 2 , Y, X) gσ2 (σ 2 | Y, X)

with
  ⊤  
gβ (β | σ 2 , Y, X) ∝ exp − 12 σ −2 β − β̂(λ) (X⊤ X + λIpp ) β − β̂(λ) .

Clearly, the conditional posterior mean of β is E(β | σ 2 , Y, X) = β̂(λ). Hence, the ridge regression estimator
can be viewed as the Bayesian posterior mean estimator of β when imposing a Gaussian prior on the regression
parameter.
The conditional posterior distribution of β, gβ (β | σ 2 , Y, X), related to a high-dimensional situation (n = 1,
p = 2) is depicted in Figure 2.2 for two choices of the penalty parameter λ. Put differently, for two different priors.
In one, the left panel, λ is arbitrarily set equal to one. The choice of the employed λ, i.e. λ = 1, is irrelevant,
the resulting posterior distribution only serves as a reference. This choice results in a posterior distribution that is
concentrated around the Bayesian point estimate, which coincides with the ridge regression estimate. The almost
spherical level sets around the point estimate may be interpreted as credible intervals for β. The grey dashed
line, spanned by the row of the design matrix, represents the support of the degenerated normal distribution of the
frequentist’s ridge regression estimate (cf. end of Section 1.4.2). The contrast between the degenerated frequentist
and well-defined Bayesian normal distribution illustrates that – for a suitable choice of the prior – within the
Bayesian context high-dimensionality need not be an issue with respect to the evaluation of the posterior. In the
right panel of Figure 2.2 the penalty parameter λ is set equal to a very small value, i.e. 0 < λ ≪ 1. This
represents a very imprecise or uninformative prior. It results in a posterior distribution with level sets that are far
from spherical and are very streched in the direction orthogonal to the subspace spanned by the row of the design
matrix and indicates in which direction there is most uncertainty with respect to β. In particular, when λ ↓ 0,
the level sets loose their ellipsoid form and the posterior collapses to the degenerated normal distribution of the
frequentist’s ridge regression estimate. Finally, in combination with the left-hand plot this illustrates the large
effect of the prior in the high-dimensional context.
With little extra work we may also obtain the conditional posterior of σ 2 from the joint posterior distribution:

fσ2 (σ 2 | β, Y, X) ∝ (σ 2 )−[(n+p)/2+α0 +1] exp[− 21 σ −2 (kY − Xβk22 + λkβk22 + β0 )],

in which one can recognize the shape of an inverse gamma distribution. The relevance of this conditional distri-
bution will be made clear in Section 2.3.
2.2 Relation to ridge regression 39

conditional posterior density, unit penalty conditional posterior density, small penalty
6

04

5
003

004
025
015
1e−

0.0
0.0
0.00
0.00
55

04
04
00

04
0.0

4e−
3e−

5e−
4

4
4
−0
6e

5
2

5e−0

4
0.01

2e−0
0.02
β2

β2
3 0.0
0.0 3 5
45 0.0
0.0 5
0

0
0.055

0.04

4
4e−0
0.025

4
3e−0
0.015
−2

−2

4
2e−0

4
04

1e−0
0.005

5e−

5
5e−0
045

025
0.00

015
035
0.00

0.00
0.00
−4

−4
−4 −2 0 2 4 6 −4 −2 0 2 4 6

β1 β1

Figure 2.2: Level sets of the (unnormalized) conditional posterior of the regression parameter β. The grey dashed
line depicts the support of the degenerated normal distribution of the frequentist’s ridge regression estimate.

The Bayesian point estimator minimizes the Bayes risk, over a prior distribution. The risk cannot be used to
choose the prior c.q. the penalty parameter λ. This can be seen from the risk of the Bayesian regression estimator.
The Bayes risk of the Bayesian regression estimator over the normal prior β ∼ N (0p , σ 2 λ−1 Ipp ) is:

Eβ {MSE[β̂(λ)] | σ 2 , Y, X} = σ 2 tr Wλ (X⊤ X)−1 Wλ⊤ + Eβ [β ⊤ (Wλ − Ipp )⊤ (Wλ − Ipp ) β]
  
= σ 2 tr Wλ (X⊤ X)−1 Wλ⊤ + λ−1 tr[(Wλ − Ipp )⊤ (Wλ − Ipp )]
Xp
= σ2 (d2jj + λ)−1 ,
j=1

in which Wλ = (X⊤ X+λIpp )−1 X⊤ X and we have used i) the previously derived explicit expression (1.7) of the
ridge estimator’s MSE, ii) the expectation of the quadratic form of a multivariate random variable (Mathai and Provost,
1992), iii) the singular value decomposition of X with singular values djj , and iv) the fact that the trace of a square
matrix equals the sum of its eigenvalues. As the ridge estimator coincides with the posterior mean, this is the min-
imal achievable MSE under a zero-centered normal prior with an uncorrelated and equivariant covariance matrix.
One may now be tempted to choose the λ that minimizes the Bayes risk as optimal and use it in the evaluation
of the ridge regression estimator. However, above the Bayes risk of the ridge estimator factorizes with respect to
σ 2 and λ. Hence, the larger the hyperparameter λ the lower the Bayes risk of the ridge estimator. In particular, its
Bayes risk converges to zero as λ → ∞. This can be understood as follows. The limit corresponds to an infinite
precision of the prior, thus reducing the contribution of the MSE’s variance term to zero. Moreover, as the ridge
estimator shrinks towards zero and the prior distribution of β has a zero mean, the bias too vanishes as λ → ∞. In
particular, the λ that minimizes the Bayes risk is thus a useless suggestion for the ridge regression estimator. The
failure to produce a useful choice of the penalty (or hyper-) paramer is due to the fact that the Bayes estimator is
defined with respect to a specific prior, i.e. corresponding to a specific value of λ, and not a class of priors relating
to all λ ∈ R>0 .
The calculation of the Bayes risk above relates the Bayesian and frequentist statements on the MSE of the
ridge estimator. For the latter revisit Theorem 1.2 of Section 1.4.3, which warrants the existence of a λ such that
the resulting ridge estimator has a superior MSE over that of the ML estimator. This result made no assumption on
(the distribution of) β. In fact, it can be viewed as a statement of the MSE conditional on β. The Bayesian result
integrates out the uncertainty – specified by the prior – in β from the (frequentist’s) conditional MSE to arrive at
the unconditional MSE.

In general, any penalized estimator has a Bayesian equivalent. That is generally not the posterior mean as for
40 Bayesian regression

the ridge regression estimator, which is more a coincide due to the normal form of its likelihood and conjugate
prior. A penalized estimator always coincides with the Bayesian MAP (Mode A Posteriori) estimator. Then, the
MAP estimates estimates a parameter θ by the mode, i.e. the maximum, of the posterior density. To see the
equivalence of both estimators we derive the MAP estimator. The latter is defined as:

P (Y = y | θ) π(θ)
θ̂map = arg max π(θ | Y = y) = arg max R .
θ θ P (Y = y | θ) π(θ) dθ

To find the maximum of the posterior density take the logarithm (which does not change the location of the
maximum) and drop terms that do not involve θ. The MAP estimator then is:

θ̂map = arg max log[P (Y = y | θ)] + log[π(θ)].

θ

The first summand on the right-hand side is the loglikelihood, while the second is the logarithm of the prior density.
The latter, in case of a normal prior, is proportional to σ −2 λkβk22 . This is – up to some factors – exactly the loss
function of the ridge regression estimator. If the quadratic ridge penalty is replaced by another, it is easy to see
what form the prior density should have in order for both estimators – the penalized and MAP – to coincide.

2.3 Markov chain Monte Carlo

The ridge regression estimator was shown to coincide with the posterior mean of the regression parameter when it
is endowed with a normal prior. This particular choice of the prior yielded a closed form expression of the poste-
rior, and its mean. Prior distributions that result in well-characterized posterior ones are referred to as conjugate.
E.g., for the standard linear regression model a normal prior is conjugate. Conjugate priors, however, are the ex-
ception rather than the rule. In general, an arbitrary prior distribution will not result in a posterior distribution that
is familiar (amongst others due to the fact that its normalizing constant is not analytically evaluable). For instance,
would a wildly different prior for the regression parameter be chosen, its posterior is unlikely to be analytically
known. Then, although analytically unknown, such posteriors can be investigated in silico by means of the Markov
chain Monte Carlo (MCMC) method. In this subsection the MCMC method is explained and illustrated – despite
its conjugancy – on the linear regression model with a normal prior.
Markov chain Monte Carlo is a general purpose technique for sampling from complex probabilistic models/dis-
tributions. It draws a sample from a Markov chain that has been constructed such that its stationary distribution
equals the desired distribution (read: the analytically untractable posterior distribution). The chain is, after an
initial number of iterations (called the burn-in period), believed to have converged and reached stationarity. A
sample from the stationary chain is then representative of the desired distribution. Statistics derived from this
sample can be used to characterize the desired distribution. Hence, estimation is reduced to setting up and running
a Markov process on a computer. R
Recall Monte Carlo integration. Assume the analytical evaluation of E[h(Y)] = h(y)π(y)dy is impossible.
This quantity can nonetheless be estimated when samples from π(·) can be drawn. For, if Y(1) , . . . , Y(T ) ∼ π(y),
b PT
the integral may be estimated by: E[h(Y)] = T1 t=1 h(Y(t) ). By the law of large numbers this is a consistent
estimator, i.e. if T → ∞ the estimator converges (in probability) to its true value. Thus, irrespective of the
specifics of the posterior distribution π(·), if one is able to sample from it, its moments (or other quantities) can
be estimated. Or, by the same principle it may be used in the Bayesian regression framework of Section 2.2 to
sample from the marginal posterior of β,
Z ∞ Z ∞
fβ (β | Y, X) = fβ,σ2 (β, σ 2 | Y, X) dσ 2 = gβ (β | σ 2 , Y, X)gσ2 (σ 2 | Y, X) dσ 2 ,
0 0

given that it of σ 2 is known. By drawing a sample σ 2,(1) , . . . , σ 2,(T ) of gσ2 (σ 2 | Y, X) and, subsequently, a sample
{β (t) }Tt=1 from gβ (β | σ 2,(t) , Y, X) for t = 1, . . . , T , the parameter σ 2 has effectively been integrated out and
the resulting sample of β (1) , β (2) , . . . , β (T ) is from fβ (β | Y, X).
It is clear from the above that the ability to sample from the posterior distribution is key to the estimation
of the parameters. But this sampling is hampered by knowledge of the normalizing constant of the posterior.
This is overcome by the acceptance-rejection sampler. This sampler generates independent draws from a target
density π(y) = f (y)/K, where f (y) is an unnormalized density and K its (unknown) normalizing constant.
The sampler relies on the existence of a density h(y) that dominates f (y), i.e., f (y) ≤ c h(y) for some known
c ∈ R>0 , from which it is possible to simulate. Then, in order to draw a Y from the posterior π(·) run Algorithm 1:
2.3 Markov chain Monte Carlo 41

input : densities f (·) and h(·);

constant c > 0;
output: a draw from π(·).
1 Generate Y from h(·).
2 Generate U from the uniform distribution U [0, 1].
3 if U ≤ f (Y) / [c × h(Y)] then
4 Return Y.
5 else
6 Go back to line 1.
7 end
Algorithm 1: Acceptance-rejection sampling.

A proof that this indeed yields a random sample from π(·) is given in Flury (1990). For this method to be com-
putationally efficient, c is best set equal to supy {f (y)/h(y)}. The R-script below illustrates this sampler for the
unnormalized density f (y) = cos2 (2πy) on the unit interval. As maxy∈[0,1] cos2 (2πy) = 1, the density f (y) is
dominated by the density function of the uniform distribution U [0, 1] and, hence, the script uses h(y) = 1 for all
y ∈ [0, 1].

Listing 2.1 R code

# define unnormalized target density
cos2density <- function(x){ (cos(2*pi*x))ˆ2 }

# define acceptance-rejection sampler

acSampler <- function(n){
draw <- numeric()
for(i in 1:n){
accept <- FALSE
while (!accept){
Y <- runif(1)
if (runif(1) <= cos2density(Y)){
accept <- TRUE
draw <- c(draw, Y)
}
}
}
return(draw)
}

# verify by eye-balling
hist(acSampler(100000), n=100)

In practice, it may not be possible to find a density h(x) that dominates the unnormalized target density f (y) over
the whole domain. Or, the constant c is too large, yielding a rather small acceptance probability, which would
make the acceptance-rejection sampler impractically slow. A different sampler is then required.
The Metropolis-Hastings sampler overcomes the problems of the acceptance-rejection sampler and generates
a sample from a target distribution that is known up to its normalizing constant. Hereto it constructs a Markov
chain that converges to the target distribution. A Markov chain is a sequence of random variables {Yt }∞ t=1 with
Yt ∈ Rp for all t that exihibit a simple dependence relationship among subsequent random variables in the
sequence. Here that simple relationship refers to the fact/assumption that the distribution of Yt+1 only depends
on Yt and not on the part of the sequence preceeding it. The Markov chain’s random walk is usually initiated by a
single draw from some distribution, resulting in Y1 . From then on the evolution of the Markov chain is described
by the transition kernel. The transition kernel is a the conditional density gYt+1 | Yt (Yt+1 = ya | Yt = yb ) that
specifies the distribution of the random variable at the next instance given the realization of the current one. Under
some conditions (akin to aperiodicity and irreducibility for Markov chains in discrete time and with a discrete
state space), the influence of the initiation washes out and the random walk converges. Not to a specific value, but
to a distribution. This is called the stationary distribution, denoted by ϕ(y), and Yt ∼ ϕ(y) for large enough t.
42 Bayesian regression

The stationary distribution satisfies:

Z
ϕ(ya ) = gYt+1 | Yt (Yt+1 = ya | Yt = yb ) ϕ(yb ) dyb . (2.1)
Rp

That is, the distribution of Yt+1 , obtained by marginalization over Yt , coincides with that of Yt . Put differently,
the mixing by the transition kernel does not affect the distribution of individual random variables of the chain.
To verify that a particular distribution ϕ(y) is the stationary one it is sufficient to verify it satisfies the detailed
balance equations:

gYt+1 | Yt (yb | ya ) ϕ(ya ) = gYt+1 | Yt (ya | yb ) ϕ(yb ),

for all choices of ya , yb ∈ Rp . If a Markov chain satisfies this detailed balance equations, it is said to be reversible.
Reversibility means so much as that, from the realizations, the direction of the chain cannot be discerned as:
fYt ,Yt+1 (ya , yb ) = fYt ,Yt+1 (yb , ya ), that is, the probability of starting in state ya and finishing in state yb
equals that of starting in yb and finishing in ya . The sufficiency of this condition is evident after its integration on
both sides with respect to yb , from which condition (2.1) follows.
MCMC assumes the stationary distribution of the Markov chain to be known up to a scalar – this is the target
density from which is to be sampled – but the transition kernel is unknown. This poses a problem as the transition
kernel is required to produce a sample from the target density. An arbitrary kernel is unlikely to satisfy the detailed
balance equations with the desired distribution as its stationary one. If indeed it does not, then:

gYt+1 | Yt (yb | ya ) ϕ(ya ) > gYt+1 | Yt (ya | yb ) ϕ(yb ),

for some ya and yb . This may (loosely) be interpreted as that the process moves from ya to yb too often and from
yb to ya too rarely. To correct this the probability of moving from yb to yb is introduced to reduce the number of
moves from ya to yb . As a consequence not always a new value is generated, the algorithm may decide to stay in
ya (as opposed to acceptance-rejection sampling). To this end a kernel is constructed and comprises compound
transitions that propose a possible next state which is simultaneously judged to be acceptable or not. Hereto take
an arbitrary candidate-generating density function gYt+1 | Yt (yt+1 | yt ). Given the current state Yt = yt , this
kernel produces a suggestion yt+1 for the next point in the Markov chain. This suggestion may take the random
walk too far afield from the desired and known stationary distribution. If so, the point is to be rejected in favour of
the current state, until a new suggestion is produced that is satisfactory close to or representative of the stationary
distribution. Let the probability of an acceptable suggestion yt+1 , given the current state Yt = yt , be denoted by
A(yt+1 | yt ). The thus constructed transition kernel then formalizes to:

hYt+1 | Yt (ya | yb ) = gYt+1 | Yt (ya | yb ) A(ya | yb ) + r(ya ) δyb (ya ),

where A(ya | yb ) is the acceptance probability of the suggestion ya given the current state yb and is defined as:
n ϕ(y ) g o
a Yt+1 | Yt (yb | ya )
A = min 1, .
ϕ(yb ) gYt+1 | Yt (ya | yb )
R
Furthermore, δyb (·) is the Dirac delta function and r(ya ) = 1 − Rp gYt+1 | Yt (ya | yb )A(ya | yb ) dya , which is
associated with the rejection. The transition kernel hYt+1 | Yt (· | ·) equipped with the above specified acceptance
probability is referred to as the Metropolis-Hastings kernel. Note that, although the normalizing constant of the
stationary distribution may be unknown, the acceptance probability can be evaluated as this constant cancels out
in the ϕ(ya ) [ϕ(yb )]−1 term.
It rests now to verify that ϕ(·) is the stationary distribution of the thus defined Markov process. Hereto first
the reversibility of the proposed kernel is assessed. The contribution of the second summand of the kernel to the
detailed balance equations, r(ya ) δyb (ya )ϕ(yb ), exists only if ya = yb . Thus, if it contributes to the detailed
balance equations, it does so equally on both sides of the equation. It is now left to assess whether:

gYt+1 | Yt (ya | yb ) A(ya | yb )ϕ(yb ) = gYt+1 | Yt (yb | ya ) A(yb | ya )ϕ(ya ).

To verify this equality use the definition of the acceptance probability from which we note that if A(ya | yb ) ≤ 1
(and thus A(ya | yb ) = [ϕ(ya )gYt+1 | Yt (yb | ya )][ϕ(yb )gYt+1 | Yt (ya | yb )]−1 ), then A(yb | ya ) = 1 (and vice
versa). In either case, the equality in the preceeding display holds, and thereby, together with the observation
regarding the second summand, so do the detailed balance equations for Metropolis-Hastings kernel. Then, ϕ(·)
2.3 Markov chain Monte Carlo 43

is indeed the stationary distribution of the constructed transition kernel hYt+1 | Yt (ya | yb ) as can be verified from
Condition (2.1):
Z Z
hYt+1 | Yt (ya | yb ) ϕ(yb ) dyb = hYt+1 | Yt (yb | ya ) ϕ(ya ) dyb
Rp Rp
Z Z
= gYt+1 | Yt (yb | ya ) A(yb | ya ) ϕ(ya ) dyb + r(yb )δya (yb ) ϕ(ya ) dyb
Rp Rp
Z Z
= ϕ(ya ) gYt+1 | Yt (yb | ya ) A(yb | ya ) dyb + ϕ(ya ) r(yb )δya (yb ) dyb
Rp Rp
= ϕ(ya )[1 − r(ya )] + r(ya ) ϕ(ya ) = ϕ(ya ),
in which the reversibility of hYt+1 | Yt (·, ·), the definition of r(·), and the properties of the Dirac delta function
have been used.

The Metropolis-Hastings algorithm is now described by:

input : densities f (·) and h(·);

constant c > 0;
output: A draw from π(·).
1 Choose starting value x(0) ..
2 Generate y from q(x(j) , ·) and U from U [0, 1].
3 if U ≤ α(X (j) , y) then
4 set x(j+1) = y.
5 else
6 set x(j+1) = x(j) .
7 end
8 Return the values {x(1) , x(2) , x(3) , . . . , }
Algorithm 2: Metropolis-Hastings algorithm.

The convergence rate of this sequence is subject of on-going research.

The following R-script shows how the Metropolis-Hastings sampler can be used to from a mixture of two nor-
mals f (y) = θφµ=2,σ2 =0.5 (y) + (1 − θ)φµ=−2,σ2 =2 (y) with θ = 14. The sampler assumes this distribution is
known up to its normalizing constant and uses its unnormalized density exp[−(y − 2)2 ] + 3 exp[−(y + 2)2 /4].
The sampler employs the Cauchy distribution centered at the current state as transition kernel from a candidate for
the next state is drawn. The chain is initiated arbitrarily with Y (1) = 1.
Listing 2.2 R code
# define unnormalized mixture of two normals
mixDensity <- function(x){
# unnormalized mixture of two normals
exp(-(x-2)ˆ2) + 3*exp(-(x+2)ˆ2/4)
}

# define the MCMC sampler

mcmcSampler <- function(n, initDraw){
draw <- initDraw
for (i in 1:(n-1)){
# sample a candidate
candidate <- rcauchy(1, draw[i])

# calculate acceptance probability:

alpha <- min(1, mixDensity(candidate) / mixDensity(draw[i]) *
dcauchy(draw[i], candidate) / dcauchy(candidate, draw[i]))

# accept/reject candidate
if (runif(1) < alpha){
44 Bayesian regression

draw <- c(draw, candidate)

} else {
draw <- c(draw, draw[i])
}
}
return(draw)
}

# verify by eye-balling
Y <- mcmcSampler(100000, 1)
hist(Y[-c(1:1000)], n=100)

The histogram (not shown) shows that the sampler, although using a unimodal kernel, yields a sample from the
bimodal mixture distribution.

The Gibbs sampler is a particular version of the MCMC algorithm. The Gibbs sampler enhances convergence
to the stationary distribution (i.e. the posterior distribution) of the Markov chain. It requires, however, the full
conditionals of all random variables (here: model parameters), i.e. the conditional distributions of one random
variable given all others, to be known analytically. Let the random vector Y for simplicity – more refined par-
titions possible – be partioned as (Ya , Yb ) with subscripts a and b now refering to index sets that partition the
random vector Y (instead of the previously employed meaning of referring to two – possibly different – elements
from the state space). The Gibbs sampler thus requires that both fYa | Yb (ya , yb ) and fYb | Ya (ya , yb ) are known.
Being a specific form of the MCMC algorithm the Gibbs sampler seeks to draw Yt+1 = (Ya,t+1 , Yb,t+1 ) given
the current state Yt = (Ya,t , Yb,t ). It draws, however, only a new instance for a single element of the partition
(e.g. Ya,t+1 ) keeping the remainder of the partition (e.g. Yb,t ) temporarily fixed. Hereto define the transition
kernel:


fYa,t+1 | Yb,t+1 (ya,t+1 , yb,t+1 ) if yb,t+1 = yb,t ,
gYt+1 | Yt (Yt+1 = yt+1 | Yt = yt+1 ) =
0 otherwise.

Using the definition of the conditional density the acceptance probability for the t + 1-th proposal of the subvector
Ya then is:

n ϕ(y ) g o
t+1 Yt+1 | Yt (yt , yt+1 )
A(yt+1 | yt ) = min 1,
ϕ(yt ) gYt+1 | Yt (yt+1 , yt )
n ϕ(y ) f o
t+1 Ya,t+1 | Yb,t+1 (ya,t , yb,t )
= min 1,
ϕ(yt ) fYa,t+1 | Yb,t+1 (ya,t+1 , yb,t+1 )
n ϕ(y ) fYa,t+1 ,Yb,t+1 (ya,t , yb,t )/fYb,t+1 (yb,t ) o
t+1
= min 1,
ϕ(yt ) fYa,t+1 ,Yb,t+1 (ya,t+1 , ya,t+1 )/fYb,t+1 (yb,t+1 )
n f (yb,t+1 ) o
Y
= min 1, b,t+1 = 1.
fYb,t+1 (yb,t )

The acceptance probability of each proposal is thus one (which contributes to the enhanced convergence of the
Gibbs sampler to the joint posterior). Having drawn an acceptable proposal for this element of the partition, the
Gibbs sampler then draws a new instance for the next element of the partition, i.e. now Yb , keeping Ya fixed.
This process of subsequently sampling each partition element is repeated until enough samples have been drawn.
To illustrate the Gibbs sampler revisit Bayesian regression. In Section 2.2 the full conditional distributions of
β and σ 2 were derived. The Gibbs sampler now draws in alternating fashion from these conditional distributions
(see Algorithm 3 for its pseudo-code).
2.4 Empirical Bayes 45

input : sample size T

length of burn in period Tburn-in
thinning factor fthinning
data {xi , yi }ni=1 ;
conditional distributions fσ2 | β (σ 2 , β; {xi , yi }ni=1 ) and fβ | σ2 (β, σ 2 ; {xi , yi }ni=1 ).
output: draws from the joint posterior π(β, σ 2 | {xi , yi }ni=1 ).
1 initialize (β0 , σ02 ).
2 for t = 1 to Tburn-in + T fthinning do
2
3 draw βt from conditional distribution fβ | σ2 (β, σt−1 ; {xi , yi }ni=1 ),
4 draw σt from conditional distribution fσ2 | β (σ , βt ; {xi , yi }ni=1 ).
2 2

5 end
6 Remove the first Tburn-in draws (representing the burn-in phase).
7 Select every fthinning-th sample (thinning).
Algorithm 3: Pseudocode of the Gibbs sampler of the joint posterior of the Bayesian regression param-
eters.

2.4 Empirical Bayes

Empirical Bayes (EB) is a branch of Bayesian statistics that meets the subjectivity criterion of frequentists. Instead
of fully specifying the prior distribution empirical Bayesians identify only its form. The hyper parameters of this
prior distribution are left unspecified and are to be found empirically. In practice, these hyper-parameters are
estimated from the data at hand. However, the thus estimated hyper parameters are used to obtain the Bayes
estimator of the model parameters. As such the data are then used multiple times. This is usually considered an
inappropriate practice but is deemed acceptable when the number of model parameters is large in comparison to
the number of hyper parameters. Then, the data are not used twice but ‘1 + ε’-times (i.e. once-and-a-little-bit)
and only little information from the data is spent on the estimation of the hyper parameters. Having obtained an
estimate of the hyper parameters, the prior is fully known, and the posterior distribution (and summary statistics
thereof) are readily obtained by Bayes’ formula.
The most commonly used procedure for the estimation of the hyper parameters is marginal likelihood maxi-
mization, which is a maximum likelihood-type procedure. But the likelihood cannot directly be maximized with
respect to the hyper parameters as it contains the model parameters that are assumed to be random within the
Bayesian framework. This may be circumvented by choosing a specific value for the model parameter but would
render the resulting hyper parameter estimates dependent on this choice. Instead of maximization with the model
parameter set to a particular value one would preferably maximize over all possible realizations. The latter is
achieved by marginalization with respect to the random model parameter, in which the (prior) distribution of the
model parameterRis taken into account. This amounts to integrating out the model parameter from the posterior
distribution, i.e. P (Y = y | θ) π(θ) dθ, resulting in the so-called marginal posterior. After marginalization the
specifics of the model parameter have been discarded and the marginal posterior is a function of the observed data
and the hyper parameters. The estimator of the hyper parameter is now defined as the maximizer of this marginal
posterior.
To illustrate the estimation of hyper parameters of the Bayesian linear regression model through marginal
likelihood maximization assume the regression parameter β and and the error variance σ 2 to be endowed with
conjugate priors: β | σ 2 ∼ N (0p , σ 2 λ−1 Ipp ) and σ 2 ∼ IG (α0 , β0 ). Three hyper parameters are thus to be esti-
mated: the shape and scale parameters, α0 and β0 , of the inverse gamma distribution and the λ parameter related
to the variance of the regression coefficients. Straightforward application of the outlined marginal likelihood prin-
ciple does, however, not work here. The joint prior, π(β | σ 2 )π(σ 2 ), is too flexible and does not yield sensible
estimates of the hyper parameters. As interest is primarily in λ, this is resolved by setting the hyper parameters
of π(σ 2 ) such that the resulting prior is uninformative, i.e. as objectively as possible. This is operationalized as a
very flat distribution. Then, with the particular choices of α0 and β0 that produce an uninformative prior for σ 2 ,
46 Bayesian regression

the empirical Bayes estimate of λ is:

Z ∞Z
λ̂eb = arg max fβ,σ2 (β, σ 2 | Y, X) dβ dσ 2
λ p
Z0 ∞ ZR
= arg max σ −n exp[− 21 σ −2 (Y − Xβ)⊤ (Y − Xβ)]
λ 0 Rp
× σ −p exp(− 12 σ −2 λβ ⊤ β) × (σ 2 )−α0 −1 exp(−β0 σ −2 ) dβ dσ 2
Z ∞ Z
= arg max σ −n exp{− 21 σ −2 [Y⊤ Y − Y⊤ X(X⊤ X + λIpp )−1 X⊤ Y}
λ 0 Rp
× σ −p exp{− 21 σ −2 [β − β̂(λ)]⊤ (X⊤ X + λIpp )[β − β̂(λ)]}
× (σ 2 )−α0 −1 exp(−β0 σ −2 ) dβ dσ 2
Z ∞
= arg max σ −n exp{− 21 σ −2 [Y⊤ Y − Y⊤ X(X⊤ X + λIpp )−1 X⊤ Y}
λ 0
× |X⊤ X + λIpp |−1/2 (σ 2 )−α0 −1 exp(−β0 σ −2 ) dσ 2
Z ∞
⊤ −1/2


= arg max |X X + λIpp | exp − σ −2 {β0 + 12 [Y⊤ Y − Y⊤ X(X⊤ X + λIpp )−1 X⊤ Y]}
λ 0
× (σ 2 )−α0 −n/2−1 dσ 2
−a0 −n/2
= arg max |X⊤ X + λIpp |−1/2 b1 ,
λ

where the factors not involving λ have been dropped throughout and b1 = β0 + 21 [Y⊤ Y − Y⊤ X(X⊤ X +
λIpp )−1 X⊤ Y]. Prior to the maximization of the marginal likelihood the logarithm is taken. That changes the
maximum, but not its location, and yields an expression that is simpler to maximize. With the empirical Bayes
estimate λ̂eb at hand, the Bayesian estimate of the regression parameter β is β̂eb = (X⊤ X + λ̂eb Ipp )−1 X⊤ Y.
Finally, the particular choice of the hyper parameters of the prior on σ 2 is not too relevant. Most values of α0 and
β0 that correspond to a rather flat inverse gamma distribution yield resulting point estimates β̂eb that do not differ
too much numerically.

2.5 Conclusion
Bayesian regression was introduced and shown to be closely connected to ridge regression. Under a conjugate
Gaussian prior on the regression parameter the Bayesian regression estimator coincides with the ridge regression
estimator, which endows the ridge penalty with the interpretation of this prior. While an analytic expression of
these estimators is available, a substantial part of this chapter was dedicated to evaluation of the estimator through
resampling. The use of this resampling will be evident when other penalties and non-conjugate priors will be
studied (cf. Excercise ?? and Sections 5.4 and 6.6). Finally, another informative procedure, empirical Bayes, to
choose the penalty parameter was presented.

2.6 Exercises
Question 2.1
Consider the linear regression model Yi = Xi β + εi with the εi i.i.d. following a standard normal law N (0, 1).
Data on the response and covariate are available: {(yi , xi )}8i=1 = {(−5, −2), (0, −1),
(−4, −1), (−2, −1), (0, 0), (3, 1), (5, 2), (3, 2)}.
a) Assume a zero-centered normal prior on β. What variance, i.e. which σβ2 ∈ R>0 , of this prior yields a mean
posterior E(β | {(yi , xi )}8i=1 , σβ2 ) equal to 1.4?
b) Assume a non-zero centered normal prior. What (mean, variance)-combinations for the prior will yield a
mean posterior estimate β̂ = 2?
Question 2.2
Revisit the microRNA data example of Section 1.10. Use the empirical Bayes procedure outlined in Section 2.4
to estimate the penalty parameter. Compare this to the one obtained via cross-validation. In particular, compare
the resulting point estimates of the regression parameter.
3 Generalizing ridge regression

The exposé on ridge regression may be generalized in many ways. Among others different generalized linear
models may be considered (confer Section 5.2). In this section we stick to the linear regression model Y = Xβ+ε
with the usual assumptions, but fit it in weighted fashion and generalize the common, spherical penalty. The loss
function corresponding to this scenario is:
(Y − Xβ)⊤ W(Y − Xβ) + (β − β0 )⊤ ∆(β − β0 ), (3.1)
which comprises a weighted least squares criterion and a generalized ridge penalty. In this W is a (n × n)-
dimensional, diagonal matrix with (W)ii ∈ [0, 1] representing the weight of the i-th observation. The penalty is
now a quadratic form with penalty parameter ∆, a (p×p)-dimensional, positive definite, symmetric matrix. When
∆ = λIpp , one regains the spherical penalty of ‘regular ridge regression’. This penalty shrinks each element of
the regression parameter β equally along the unit vectors ej . Generalizing ∆ to the class of symmetric, positive
definite matrices S++ allows for i) different penalization per regression parameter, and ii) joint (or correlated)
shrinkage among the elements of β. The penalty parameter ∆ determines the speed and direction of shrinkage.
The p-dimensional column vector β0 is a user-specified, non-random target towards which β is shrunken as the
penalty parameter increases. When recasting generalized ridge estimation as a constrained estimation problem,
the implications of the penalty may be visualized (Figure 3.1, left panel). The generalized ridge penalty is a
quadratic form centered around β0 . In Figure 3.1 the parameter constraint clearly is ellipsoidal (and not spherical).
Moreover, the center of this ellipsoid is not at zero.

Generalized ridge penalty Generalized ridge regularization paths

β1(λ)
3.0

0.015
β2(λ)
β3(λ)
6

0.025 β4(λ)
2.5

0.035

0.045

0.055
4

2.0

0.06
βj(λ)

1.5
2
β2

0.05

0.04

0.03
1.0
0

0.02

0.01
0.5

0.005
−2

loss
0.0

generalized ridge constraint

−2 0 2 4 6 0 2 4 6 8 10 12

β1 log(λ)

Figure 3.1: Left panel: the contours of the likelihood (grey solid ellipsoids) and the parameter constraint implied
by the generalized penalty (black dashed ellipsoid. Right panel: generalized (fat coloured lines) and ‘regular’ (thin
coloured lines) regularization paths of four regression coefficients. The dotted grey (straight) lines indicated the
targets towards the generalized ridge penalty shrinks regression coefficient estimates.

The addition of the generalized ridge penalty to the sum-of-squares ensures the existence of a unique regression
estimator in the face of super-collinearity. The generalized penalty is a non-degenerated quadratic form in β due
to the positive definiteness of the matrix ∆. As it is non-degenerate, it is strictly convex. Consequently, the
generalized ridge regression loss function (3.1), being the sum of a convex and strictly convex function, is also
strictly convex. This warrants the existence of a unique global minimum and, thereby, a unique estimator.
48 Generalizing ridge regression

Like for the ‘regular’ ridge loss function (1.8), there is an explicit expression for the optimum of the generalized
ridge loss function (3.1). To see this, obtain the estimating equation of β through equating its derivative with
respect to β to zero:
2X⊤ WY − 2X⊤ WXβ − 2∆β + 2∆β0 = 0p .
This is solved by:
β̂(∆) = (X⊤ WX + ∆)−1 (X⊤ WY + ∆β0 ). (3.2)
Clearly, this reduces to the ‘regular’ ridge estimator by setting W = Inn , β0 = 0p , and ∆ = λIpp . The effects of
the generalized ridge penalty on the estimates can be seen in the regularization paths of the estimates. Figure 3.1
(right panel) contains an example of the regularization paths for coefficients of a linear regression model with four
explanatory variables. Most striking is the limiting behaviour of the estimates of β3 and β4 for large values of the
penalty parameter λ: they convergence to a non-zero value (as was specified by a nonzero β0 ). More subtle is the
(temporary) convergence of the regularization paths of the estimates of β2 and β3 . That of β2 is pulled away from
zero (its true value and approximately its unpenalized estimate) towards the estimate of β3 . In the regularization
path of β3 this can be observed in a delayed convergence to its nonzero target value (for comparison consider that
of β4 ). For reference the corresponding regularization paths of the ‘regular’ ridge estimates (as thinner lines of the
same colour) are included in Figure 3.1.
Example 3.1 Fused ridge estimation
An example of a generalized ridge penalty is the fused ridge penalty (as introduced by Goeman, 2008). Consider
the standard linear model Y = Xβ + ε. The fused ridge estimator of β then minimizes:
p
X
kY − Xβk22 + λ kβj − βj−1 k22 . (3.3)
j=2

The penalty in the loss function above can be written as a generalized ridge penalty:
 
λ −λ 0 ... ... 0
..
 −λ 2λ −λ . . . . 
 . . . 
Xp  .. .. .. 
 0 −λ 2λ 
λ kβj − βj−1 k22 = β ⊤  .. . . .. .. ..  β.
 . . . . . 0 
j=2  
 ... ..
.
..
.
..
. −λ 
0 ... ... 0 −λ λ
The matrix ∆ employed above is semi-positive definite and therefore the loss function (3.3) need not be not strictly
convex. Hence, often a regular ridge penalty kβk22 is added (with its own penalty parameter).
To illustrate the effect of the fused ridge penalty on the estimation of the linear regression model Y = Xβ + ε,
6
let βj = φ0,1 (zj ) with zj = −30 + 50 j for j = 1, . . . , 500. Sample the elements of the design matrix X and those
of the error vector ε from the standard normal distribution, then form the response Y from the linear model. The
regression parameter is estimated through fused ridge loss minimization with λ = 1000. The estimate is shown in
Figure 3.2 (red line). For reference the figure includes the true β (black line) and the ‘regular ridge’ estimate with
λ = 1 (blue line). Clearly, the fused ridge estimate yields a nice smooth vector of β estimates 

3.1 Moments
The expectation and variance of β̂(∆) are obtained through application of the same matrix algebra and expectation
and covariance rules used in the derivation of their counterparts of the ‘regular’ ridge regression estimator. This
leads to:
E[β̂(∆)] = (X⊤ WX + ∆)−1 (X⊤ WXβ + ∆β0 ),
Var[β̂(∆)] = σ 2 (X⊤ WX + ∆)−1 X⊤ W2 X(X⊤ WX + ∆)−1 .
From these expressions similar limiting behaviour as for the ‘regular’ ridge regression case can be deduced. To
this end let Vδ Dδ Vδ⊤ be the eigendecomposition of ∆ and dδ,j = (Dδ )jj . Furthermore, define (with some abuse
of notation) lim∆→∞ as the limit of all dδ,j simultaneously tending to infinity. Then, lim∆→∞ E[β̂(∆)] = β0
and lim∆→∞ Var[β̂(∆)] = 0pp .
3.2 The Bayesian connection 49

0.4

betas ridge
ridge (λ=1) fused ridge
gen. ridge (λ=1000)
0.3

copy number effect

0.2
betas

0.1
0.0
−0.1

0 100 200 300 400 500 0 200 400 600 800

Index chromosomal location

Figure 3.2: Left panel: illustration of the fused ridge estimator (in simulation). The true parameter β and its ridge
and fused ridge estimates against their spatial order. Right panel: Ridge vs. fused ridge estimates of the DNA copy
effect on KRAS expression levels. The dashed, grey vertical bar indicates the location of the KRAS gene.

Example 3.2
Let X be an n × p-dimensional, orthonormal design matrix with p ≥ 2. Contrast the regular and generalized
ridge regression estimator, the latter with W = Ipp , β0 = 0p and ∆ = λR where R = (1 − ρ)Ipp + ρ1pp for
ρ ∈ (−(p − 1)−1 , 1). For ρ = 0 the two estimators coincide. The variance of the generalized ridge regression
estimator then is Var[β̂(∆)] = (Ipp +∆)−2 . The efficiency of this estimator, measured by its generalized variance,
is:

det{Var[β̂(∆)]} = {[1 + λ + (p − 1)ρ](1 + λ − ρ)p−1 }−2 .

This efficiency attains its minimum at ρ = 0. In the present case, the regular ridge regression estimator is thus
more efficient than its generalized counterpart. 

Example 3.3 (MSE with perfect target)

Set β0 = β, i.e. the target is equal to the true value of the regression parameter. Then:

E[β̂(∆)] = (X⊤ WX + ∆)−1 (X⊤ WXβ + ∆β) = β.

Hence, irrespective of the choice of ∆, the generalized ridge is then unbiased. Thus:

MSE[β̂(∆)] = tr{Var[β̂(∆)]}
= tr[σ 2 (X⊤ WX + ∆)−1 X⊤ W2 X(X⊤ WX + ∆)−1 ]
= σ 2 tr[X⊤ W2 X(X⊤ WX + ∆)−2 ].

When ∆ = λIpp , this MSE is smaller than that of the ML regression estimator, irrespective of the choice of λ. 

3.2 The Bayesian connection

This generalized ridge estimator can, like the regular ridge estimator, be viewed as a Bayesian estimator. It requires
to replace the conjugate prior on β by a more general normal law, β ∼ N (β0 , σ 2 ∆−1 ), but retains the inverse
gamma prior on σ 2 . The joint posterior distribution of β and σ 2 is then obtained analogously to the derivation of
posterior with a standard normal prior on β as presented in Chapter 2 (the details are left as Exercise 3.2):

fβ,σ2 (β, σ 2 | Y, X) = fY (Y | X, β, σ 2 ) fβ (β|σ 2 ) fσ (σ 2 )

∝ gβ (β | σ 2 , Y, X) gσ2 (σ 2 | Y, X)
50 Generalizing ridge regression

with
 ⊤  
gβ (β | σ 2 , Y, X) ∝ exp{− 21 σ −2 β − β̂(∆) (X⊤ X + ∆) β − β̂(∆) }.

This implies E(β | σ 2 , Y, X) = β̂(∆). Hence, the generalized ridge regression estimator too can be viewed as the
Bayesian posterior mean estimator of β when imposing a multivariate Gaussian prior on the regression parameter.

3.3 Application
An illustration involving omics data can be found in the explanation of a gene’s expression levels in terms of
its DNA copy number. The latter is simply the number of gene copies encoded in the DNA. For instance, for
most genes on the autosomal chromosomes the DNA copy number is two, as there is a single gene copy on
each chromosome and autosomal chromosomes come in pairs. Alternatively, in males the copy number is one
for genes that map to the X or Y chromosome, while in females it is zero for genes on the Y chromosome. In
cancer the DNA replication process has often been compromised leading to a (partially) reshuffled and aberrated
DNA. Consequently, the cancer cell may exhibit gene copy numbers well over a hundred for classic oncogenes.
A faulted replication process does – of course – not nicely follow the boundaries of gene encoding regions. This
causes contiguous genes to commonly share aberrated copy numbers. With genes being transcribed from the DNA
and a higher DNA copy number implying an enlarged availability of the gene’s template, the latter is expected
to lead to elevated expression levels. Intuitively, one expects this effect to be localized (a so-called cis-effect),
but some suggest that aberrations elsewhere in the DNA may directly affect the expression levels of distant genes
(referred to as a trans-effect).
The cis- and trans-effects of DNA copy aberrations on the expression levels of the KRAS oncogene in colorec-
tal cancer are investigated. Data of both molecular levels from the TCGA (The Cancer Genome Atlas) repository
are downloaded (Cancer Genome Atlas Network, 2012). The gene expression data are limited to that of KRAS,
while for the DNA copy number data only that of chromosome 12, which harbors KRAS, is retained. This leaves
genomic profiles of 195 samples comprising 927 aberrations. Both molecular data types are zero centered feature-
wise. Moreover, the data are limited to ten – conveniently chosen? – samples. The KRAS expression levels are
explained by the DNA copy number aberrations through the linear regression model. The model is fitted by means
of ridge regression, with λ∆ and ∆ = Ipp and a single-banded ∆ with unit diagonal and the elements of the first
off-diagonal equal to the arbitrary value of −0.4. The latter choice appeals to the spatial structure of the genome
and encourages similar regression estimates for contiguous DNA copy numbers. The penalty parameter is chosen
by means of leave-one-out cross-validation using the squared error loss.
Listing 3.1 R code
# load libraries
library(cgdsr)
library(biomaRt)
library(Matrix)

# get list of human genes

ensembl <- useMart("ensembl", dataset="hsapiens_gene_ensembl")
geneList <- getBM(attributes=c("ensembl_gene_id", "external_gene_name",
"entrezgene_trans_name", "chromosome_name",
"start_position", "end_position"), mart=ensembl)

# remove all gene without entrezID

geneList <- geneList[!is.na(geneList[,3]),]

# remove all genes not mapping to chr 12

geneList <- geneList[which(geneList[,4] %in% c(12)),]
geneList <- geneList[,-1]
geneList <- unique(geneList)
geneList <- geneList[order(geneList[,3], geneList[,4], geneList[,5]),]

# create CGDS object

mycgds <- CGDS("http://www.cbioportal.org/public-portal/")

# get available case lists (collection of samples) for a given cancer study
3.3 Application 51

mycancerstudy <- getCancerStudies(mycgds)[37,1]

mycaselist <- getCaseLists(mycgds,mycancerstudy)[1,1]

# get available genetic profiles

mrnaProf <- getGeneticProfiles(mycgds,mycancerstudy)[c(4),1]
cnProf <- getGeneticProfiles(mycgds,mycancerstudy)[c(6),1]

# get data slices for a specified list of genes, genetic profile and case list
cnData <- numeric()
geData <- numeric()
geneInfo <- numeric()
for (j in 1:nrow(geneList)){
geneName <- as.character(geneList[j,1])
geneData <- getProfileData(mycgds, geneName, c(cnProf, mrnaProf), mycaselist)
if (dim(geneData)[2] == 2 & dim(geneData)[1] > 0){
cnData <- cbind(cnData, geneData[,1])
geData <- cbind(geData, geneData[,2])
geneInfo <- rbind(geneInfo, geneList[j,])
}
}
colnames(cnData) <- rownames(geneData)
colnames(geData) <- rownames(geneData)

# preprocess data
Y <- geData[, match("KRAS", geneInfo[,1]), drop=FALSE]
Y <- Y - mean(Y)
X <- sweep(cnData, 2, apply(cnData, 2, mean))

# subset data
idSample <- c(50, 58, 61, 75, 66, 22, 67, 69, 44, 20)
Y <- Y[idSample]
X <- X[idSample,]

# generate banded penalty matrix

diags <- list(rep(1, ncol(X)), rep(-0.4, ncol(X)-1))
Delta <- as.matrix(bandSparse(ncol(X), k=-c(0:1), diag=c(diags), symm=TRUE))

# define loss function

CVloss <- function(lambda, X, Y, Delta){
loss <- 0
for (i in 1:nrow(X)){
betasLoo <- solve(crossprod(X[-i,]) + lambda * Delta) %*%
crossprod(X[-i,], Y[-i])
loss <- loss + as.numeric((Y[i] - X[i,,drop=FALSE] %*% betasLoo)ˆ2)
}
return(loss)
}

# optimize penalty parameter

limitsL <- c(10ˆ(-10), 10ˆ(10))
optLr <- optimize(CVloss, limitsL, X=X, Y=Y, Delta=diag(ncol(X)))$minimum
optLgr <- optimize(CVloss, limitsL, X=X, Y=Y, Delta=Delta)$minimum

# evaluate (generalized) ridge estimators

betasGr <- solve(crossprod(X) + optLgr * Delta) %*% crossprod(X, Y)
betasR <- solve(crossprod(X) + optLr * diag(ncol(X))) %*% crossprod(X, Y)

# plot estimates vs. location

ylims <- c(min(betasR, betasGr), max(betasR, betasGr))
plot(betasR, type="l", ylim=ylims, ylab="copy number effect",
lty=2, yaxt="n", xlab="chromosomal location")
52 Generalizing ridge regression

lines(betasGr, lty=1, col="red")

lines(seq(ylims[1], ylims[2], length.out=50) ˜
rep(match("KRAS", geneInfo[,1]), 50), col="grey", lwd=2, lty=3)
legend("topright", c("ridge", "fused ridge"), lwd=2,
col=c("black", "red"), lty=c(2, 1))

The right panel of Figure 3.2 shows the ridge regression estimate with both choices of ∆ and optimal penalty
parameters plotted against the chromosomal order. The location of KRAS is indicated by a vertical dashed bar.
The ordinary ridge regression estimates show a minor peak at the location of KRAS but is otherwise more or
less flat. In the generalized ridge estimates the peak at KRAS is emphasized. Moreover, the region close to
KRAS exhibits clearly elevated estimates, suggesting co-abberated DNA. For the remainder the generalized ridge
estimates portray a flat surface, with the exception of a single downward spike away from KRAS. Such negative
effects are biologically nonsensible (more gene templates leading to reduced expression levels?). On the whole the
generalized ridge estimates point towards the cis-effect as the dominant genomic regulation mechanism of KRAS
expression. The isolated spike may suggest the presence of a trans-effect, but its sign is biological nonsensible
and the spike is fully absent in the ordinary ridge estimates. This leads us to ignore the possibility of a genomic
trans-effect on KRAS expression levels in colorectal cancer.
The sample selection demands justification. It yields a clear illustrate-able difference between the ordinary
and ridge estimates. When all samples are left in, the cis-effect is clearly present, discernable from both estimates
that yield a virtually similar profile.

3.4 Generalized ridge regression

What is generally referred to as ‘generalized ridge regression’ (cf. Hoerl and Kennard, 1970; Hemmerle, 1975) is
the particular case of loss function (3.1) in which W = Inn , β0 = 0p , and ∆ = Vx ΛVx⊤ , where Vx is obtained
from the singular value decomposition of X (i.e., X = Ux Dx Vx⊤ with its constituents endowed with the usual
interpretation) and Λ a positive definite diagonal matrix. This gives the estimator:

β̂(Λ) = (X⊤ X + ∆)−1 X⊤ Y

= (Vx Dx U⊤ ⊤ ⊤ −1
x Ux Dx Vx + Vx ΛVx ) Vx Dx Ux Y
2 −1
= Vx (Dx + Λ) Dx Ux Y.

From this last expression it becomes clear how this estimator generalizes the ‘regular ridge estimator’. The latter
shrinks all eigenvalues, irrespectively of their size, in the same manner through a common penalty parameter. The
‘generalized ridge estimator’, through differing penalty parameters (i.e. the diagonal elements of Λ), shrinks them
individually.
The generalized ridge estimator coincides with the Bayesian linear regression estimator with the normal prior
N [0p , (Vx ΛVx⊤ )−1 ] on the regression parameter β (and preserving the inverse gamma prior on the error vari-
ance). Assume X to be of full column rank and choose Λ = g −1 D2x with g a positive scalar. The prior on β then
– assuming (X⊤ X)−1 exits – reduces to Zellner’s g-prior: β ∼ N [0p , g(X⊤ X)−1 ] (Zellner, 1986). The corre-
sponding estimator of the regression coefficient is: β̂(g) = g(1 + g)−1 (X⊤ X)−1 X⊤ Y, which is proportional to
the unpenalized ordinary least squares estimator of β.
For convenience of notation in the analysis of the generalized ridge estimator the linear regression model is
usually rewritten as:

Y = Xβ + ε = XVx Vx⊤ β + ε = X̃α + ε,

with X̃ = XVx = Ux Dx (and thus X̃⊤ X̃ = D2x ) and α = Vx⊤ β with loss function (Y − X̃α)⊤ (Y − X̃α) +
α⊤ Λα. In the notation above the generalized ridge estimator is then:

α̂(Λ) = (X̃⊤ X̃ + Λ)−1 X̃⊤ Y = (D2x + Λ)−1 X̃⊤ Y,

from which one obtains β̂(Λ) = Vx α̂(Λ). Using E[α̂(Λ)] = (D2x + Λ)−1 D2x α and Var[α̂(Λ)] = σ 2 (D2x +
Λ)−1 D2x (D2x + Λ)−1 , the MSE for the generalized ridge estimator can be written as:
p
X
MSE[α̂(Λ)] = (σ 2 d2x,j + α2j λ2j )(d2x,j + λj )−2 ,
j=1
3.5 Conclusion 53

where dx,j = (Dx )jj and λj = (Λ)jj . Having α and σ 2 available, it is easily seen (equate the derivative w.r.t.
λj to zero and solve) that the MSE of α̂(Λ) is minimized by λj = σ 2 /α2j for all j. With α and σ 2 unknown,
Hoerl and Kennard (1970) suggest an iterative procedure to estimate the λj ’s. Initiate the procedure with the OLS
estimates of α and σ 2 , followed by sequentially updating the λj ’s and the estimates of α and σ 2 . An analytic
expression of the limit of this procedure exists (Hemmerle, 1975). This limit, however, still depends on the
observed Y and as such it does not necessarily yield the minimal attainable value of the MSE. This limit may
nonetheless still yield a potential gain in MSE. This is investigated in Lawless (1981). Under a variety of cases it
seems to indeed outperform the OLS estimator, but there are exceptions.
A variation on this theme is presented by Guilkey and Murphy (1975) and dubbed “directed” ridge regression.
Directed ridge regression only applies the above ‘generalized shrinkage’ in those eigenvector directions that have
a corresponding small(er) – than some user-defined cut-off – eigenvalue. This intends to keep the bias low while
yield good (or supposedly better) performance.

3.5 Conclusion
To conclude: a note of caution. The generalized ridge penalty is extremely flexible. It can incorporate any
prior knowledge on the parameter values (through specification of β0 ) and the relations among these parameters
(via ∆). While a pilot study or literature may provide a suggestion for β0 , it is less obvious how to choose an
informative ∆ (although a spatial structure is a nice exception). In general, exact knowledge on the parameters
should not be incorporated implicitly via the penalty (read: prior) but preferably be used explicitly in the model –
the likelihood – itself. Though this may be the viewpoint of a prudent frequentist and a subjective Bayesian might
disagree.

3.6 Exercises
Question 3.1
Consider the linear regression model Yi = β1 Xi,1 + β2 Xi,2 + εi for i = 1, . . . , n. Suppose estimates of the regres-
sion parameters (β1 , β2 ) of this model are obtained through the minimization of the sum-of-squares augmented
with a ridge-type penalty:
Xn
(Yi − β1 Xi,1 − β2 Xi,2 )2 + λ(β12 + β22 + 2νβ1 β2 ),
i=1

with penalty parameters λ ∈ R>0 and ν ∈ (−1, 1).

a) Recall the equivalence between constrained and penalized estimation (cf. Section 1.5). Sketch (for both
ν = 0 and ν = 0.9) the shape of the parameter constraint induced by the penalty above and describe in
words the qualitative difference between both shapes.
b) When ν = −1 and λ → ∞ the estimates of β1 and β2 (resulting from minimization of the penalized loss
function above) converge towards each other: limλ→∞ β̂1 (λ, −1) = limλ→∞ β̂2 (λ, −1). Motivated by this
observation a data scientists incorporates the equality constraint β1 = β = β2 explicitly into the model, and
s/he estimates the ‘joint regression parameter’ β through the minimization (with respect to β) of:
Xn
(Yi − βXi,1 − βXi,2 )2 + δβ 2 ,
i=1

with penalty parameter δ ∈ R>0 . The data scientist is surprised to find that resulting estimate β̂(δ) does
not have the same limiting (in the penalty parameter) behavior as the β̂1 (λ, −1), i.e. limδ→∞ β̂(δ) 6=
limλ→∞ β̂1 (λ, −1). Explain the misconception of the data scientist.
c) Assume that i) n ≫ 2, ii) the unpenalized estimates (β̂1 (0, 0), β̂2 (0, 0))⊤ equal (−2, 2), and iii) that the
two covariates X1 and X2 are zero-centered, have equal variance, and are strongly negatively correlated.
Consider (β̂1 (λ, ν), β̂2 (λ, ν))⊤ for both ν = −0.9 and ν = 0.9. For which value of ν do you expect the
sum of the absolute value of the estimates to be largest? Hint: Distinguish between small and large values
of λ and think geometrically!
Question 3.2
Consider the linear regression model Y = Xβ + ε with ε ∼ N (0p , σ 2 Ipp ). Assume β ∼ N (β0 , σ 2 ∆−1 ) with
β0 ∈ Rp and ∆ ≻ 0 and a gamma prior on the error variance. Verify (i.e., work out the details of the derivation)
that the posterior mean coincides with the generalized ridge estimator defined as:
β̂ = (X⊤ X + ∆)−1 (X⊤ Y + ∆β0 ).
54 Generalizing ridge regression

Question 3.3
The ridge penalty may be interpreted as a multivariate normal prior on the regression coefficients: β ∼ N (0, λ−1 Ipp ).
Different priors may be considered. In case the covariates are spatially related in some sense (e.g. genomically), it
may of interest to assume a first-order autoregressive prior: β ∼ N (0, λ−1 Σa ), in which Σa is a p× p-correlation
matrix with (Σa )j1 ,j2 = ρ|j1 −j2 | for some correlation coefficient ρ ∈ [0, 1). Hence,
 
1 ρ . . . ρp−1
 ρ 1 . . . ρp−2 
 
Σa =  . .. .. ..  .
 .. . . . 
p−1 p−2
ρ ρ ... 1

a) The penalized loss function associated with this AR(1) prior is:

L(β; λ, Σa ) = kY − Xβk22 + λβ ⊤ Σ−1

a β.

Find the minimizer of this loss function.

b) What is the effect of ρ on the ridge estimates? Contrast this to the effect of λ. Illustrate this on (simulated)
data.
c) Instead of an AR(1) prior assume a prior with a uniform correlation between the elements of β. That is,
replace Σa by Σu , given by Σu = (1 − ρ)Ipp + ρ1pp . Investigate (again on data) the effect of changing
from the AR(1) to the uniform prior on the ridge regression estimates.

Question 3.4
Consider the standard linear regression model Yi = Xi,∗ β + εi for i = 1, . . . , n. Suppose estimates of the
regression parameters β of this model are obtained through the minimization of the sum-of-squares augmented
with a ridge-type penalty:
 
kY − Xβk22 + λ (1 − α)kβ − βt,a k22 + αkβ − βt,b k22 ,

for known α ∈ [0, 1], nonrandom p-dimensional target vectors βt,a and βt,b with βt,a 6= βt,b , and penalty
parameter λ > 0. Here Y = (Y1 , . . . , Yn )⊤ and X is n × p matrix with the n row-vectors Xi,∗ stacked.
a) When p > n the sum-of-squares part does not have a unique minimum. Does the above employed penalty
warrant a unique minimum for the loss function above (i.e., sum-of-squares plus penalty)? Motivate your
answer.
b) Could it be that for intermediate values of α, i.e. 0 < α < 1, the loss function assumes smaller values than
for the boundary values α = 0 and α = 1? Motivate your answer.
c) Draw the parameter constraint induced by this penalty for α = 0, 0.5 and 1 when p = 2
d) Derive the estimator of β, defined as the minimum of the loss function, explicitly.
e) Discuss the behaviour of the estimator α = 0, 0.5 and 1 for λ → ∞.

Question 3.5
Revisit Exercise 1.2. There the standard linear regression model Yi = Xi,∗ β + εi for i = 1, . . . , n and with
εi ∼i.i.d. N (0, σ 2 ) is considered. The model comprises a single covariate and an intercept. Response and
covariate data are: {(yi , xi,1 )}4i=1 = {(1.4, 0.0), (1.4, −2.0), (0.8, 0.0), (0.4, 2.0)}.
a) Evaluate the generalized ridge regression estimator of β with target β0 = 02 and penalty matrix ∆ given
by (∆)11 = λ = (∆)22 and (∆)12 = 12 λ = (∆)21 in which λ = 8.
b) A data scientist wishes to leave the intercept unpenalized. Hereto s/he sets in part a) (∆)11 = 0. Why does
the resulting estimate not coincide with the answer to Exercise 1.2? Motivate.
4 Mixed model

Here the mixed model introduced by Henderson (1953), which generalizes the linear regression model, is studied
and estimated in unpenalized (!) fashion. Nonetheless, it will turn out to have an interesting connection to ridge
regression. This connection may be exploited to arrive at an informed choice of the ridge penalty parameter.
The linear regression model, Y = Xβ + ε, assumes the effect of each covariate to be fixed. In certain
situations it may be desirable to relax this assumption. For instance, a study may be replicated. Conditions
need not be exactly constant across replications. Among others this may be due to batch effects. These may be
accounted for and are then incorporated in the linear regression model. But it is not the effects of these particular
batches included in the study that are of interest. Would the study have been carried out at a later date, other
batches may have been involved. Hence, the included batches are thus a random draw from the population of all
batches. With each batch possibly having a different effect, these effects may also be viewed as random draws
from some hypothetical ‘effect’-distribution. From this point of view the effects estimated by the linear regression
model are realizations from the ‘effect’-distribution. But interest is not in the particular but the general. Hence, a
model that enables a generalization to the distribution of batch effects would be more suited here.
Like the linear regression model the mixed model, also called mixed effects model or random effects model,
explains the variation in the response by a linear combination of the covariates. The key difference lies in the fact
that the latter model distinguishes two sets of covariates, one with fixed effects and the other with random effects.
In matrix notation mirroring that of the linear regression model, the mixed model can be written as:

Y = Xβ + Zγ + ε,

where Y is the response vector of length n, X the (n × p)-dimensional design matrix with the fixed vector β with
p fixed effects, Z the (n × q)- dimensional design matrix with an associated q × 1 dimensional vector γ of random
effects, and distributional assumptions ε ∼ N (0n , σε2 Inn ), γ ∼ N (0q , Rθ ) and ε and γ independent. In this Rθ
is symmetric, positive definite and parametrized by a low-dimensional parameter θ.
The distribution of Y is fully defined by the mixed model and its accompanying assumptions. As Y is a linear
combination of normally distributed random variables, it is itself normally distributed. Its mean is:

E(Y) = E(Xβ + Zγ + ε) = E(Xβ) + E(Zγ) + E(ε) = Xβ + ZE(γ) = Xβ,

while its variance is:

Var(Y) = Var(Xβ) + Var(Zγ) + Var(ε) = ZVar(γ)Z⊤ + σε2 Inn = ZRθ Z⊤ + σε2 Inn

in which the independence between ε and γ and the standard algebra rules for the Var(·) and Cov(·) operators
have been used. Put together, this yields: Y ∼ N (Xβ, ZRθ Z⊤ + σε2 Inn ). Hence, the random effects term Zγ
of the mixed model does not contribute to the explanation of the mean of Y, but aids in the decomposition of its
variance around the mean. From this formulation of the model it is obvious that the random part of two distinct
observations of the response are – in general – not independent: their covariance is given by the corresponding
element of ZRθ Z⊤ . Put differently, due to the independence assumption on the error two observations can only
be (marginally) dependent through the random effect which is attenuated by the associated design matrix Z. To
illustrate this, temporarily set Rθ = σγ2 Iqq . Then, Var(Y) = σγ2 ZZ⊤ + σε2 Inn . From this it is obvious that
two variates of Y are now independent if and only if the corresponding rows of Z are orthogonal. Moreover,
two pairs of variates have the same covariance if they have the same covariate information in Z. Two distinct
observations of the same individual have the same covariance as one of these observations with that of another
individual with identical covariate information as the left-out observation on the former individual. In particular,
their ‘between-covariance’ equals their individual ‘within-covariance’.
The mixed model and the linear regression model are clearly closely related: they share a common mean, a
normally distributed error, and both explain the response by a linear combination of the explanatory variables.
56 Mixed model

Moreover, when γ is known, the mixed model reduces to a linear regression model. This is seen from the condi-
tional distribution of Y: Y | γ ∼ N (Xβ + Zγ, σε2 Inn ). Conditioning on the random effect γ thus pulls in the
term Zγ to the systematic, non-random explanatory part of the model. In principle, the conditioned mixed model
could now be rewritten as a linear regression model by forming a new design matrix and parameter from X and Z
and β and γ, respectively.
Example 4.1 (Mixed model for a longitudinal study)
A longitudinal study looks into the growth rate of cells. At the beginning of the study cells are placed in n petri
dishes, with the same growth medium but at different concentrations. The initial number of cells in each petri dish
is counted as is done at several subsequent time points. The change in cell count is believed to be – at the log-scale
– a linear function of the concentration of the growth medium. The linear regression model may suffice. However,
variation is omnipresent in biology. That is, apart from variation in the initial cell count, each cell – even if they
are from common decent – will react (slightly?) differently to the stimulus of the growth medium. This intrinsic
cell-to-cell variation in growth response may be accommodated for in the linear mixed model by the introduction
of a random cell effect, both in off-set and slope. The (log) cell count of petri dish i at time point t, denoted Yit ,
is thus described by:

Yit = β0 + Xi β1 + Zi γ + εit ,

with intercept β0 , growth medium concentration Xi in petri dish i, and fixed growth medium effect β1 , and
Zi = (1, Xi ), γ the 2 dimensional random effect parameter bivariate normally distributed with zero mean and
diagonal covariance matrix, and finally εit ∼ N (0, σε2 ) the error in the cell count of petri dish i at time t. In
matrix notation the matrix Z would comprise of 2n columns: two columns for each cell, ei and Xi ei (with ei
the n-dimensional unit vector with a one at the i-th location and zeros elsewhere), corresponding to the random
intercept and slope effect, respectively. The fact that the number columns of Z, i.e. the explanatory random effects,
20
15
10
5
log(cell count)

0
−5
−10
−15

0 1 2 3 4 5

concentration

Figure 4.1: Linear regession (thick black solid line) vs. mixed model fit (thin colored and patterned lines).

equals 2n does not pose identifiability problems as per column only a single parameter is estimated. Finally, to
illustrate the difference between the linear regression and the linear mixed model their fits on artifical data are
plotted (top left panel, Figure 4.1). Where the linear regression fit shows the ‘grand mean relationship’ between
cell count and growth medium, the linear mixed model fit depicts the petri dish specific fits. 

The mixed model was motivated by its ability to generalize to instances not included in the study. From the
examples above another advantage can be deduced. E.g., the cells’ effects are modelled by a single parameter
(rather than one per cell). More degrees of freedom are thus left to estimate the noise level. In particular, a test for
the presence of a cell effect will have more power.

The parameters of the mixed model are estimated either by means of likelihood maximization or a related proce-
dure known as restricted maximum likelihood. Both are presented, with the exposé loosely based on Bates and DebRoy
 57

(2004). First the maximum likelihood procedure is introduced, which requires the derivation of the likelihood.
Hereto the assumption on the random effects is usually transformed. Let R̃θ = σε−2 Rθ , which is the covariance
of the random effects parameter relevative to the error variance, and R̃θ = Lθ L⊤ θ its Cholesky decomposition.
Next define the change-of-variables γ = Lθ γ̃. This transforms the model to: Y = Xβ + ZLθ γ̃ + ε but now with
the assumption γ̃ ∼ N (0q , σε2 Iqq ). Under this assumption the conditional likelihood, conditional on the random
effects, is:

L(Y | γ̃ = g) = (2πσε2 )−n/2 exp(− 21 σε−2 kY − Xβ − ZLθ gk22 ).

From this the unconditional likelihood is obtained through:

Z
L(Y) = L(Y | γ̃ = g) fγ̃ (g) dg
Rq
Z
= (2πσε2 )−(n+q)/2 exp[− 12 σε−2 (kY − Xβ − ZLθ gk22 + kgk22 )] dg.
Rq

To evaluate the integral, the exponent needs rewriting. Hereto first note that:

kY − Xβ − ZLθ gk22 + kgk22 = (Y − Xβ − ZLθ g)⊤ (Y − Xβ − ZLθ g) + g⊤ g.

Now expand the right-hand side as follows:

(Y − Xβ − ZLθ g)⊤ (Y − Xβ − ZLθ g) + g⊤ g

= Y⊤ Y + g⊤ (L⊤ ⊤ ⊤ ⊤ ⊤ ⊤ ⊤
θ Z ZLθ + Iqq )g + β X Xβ − Y Xβ − β X Y
−(Y⊤ ZLθ − β ⊤ X⊤ ZLθ )g − g⊤ (L⊤ ⊤ ⊤ ⊤
θ Z Y − Lθ Z Xβ)
= (g − µγ̃ |Y )⊤ (L⊤ ⊤
θ Z ZLθ + Iqq )(g − µγ̃ | Y )

+ (Y − Xβ)⊤ [Inn − ZLθ (L⊤ ⊤

θ Z ZLθ + Iqq )
−1 ⊤ ⊤
Lθ Z ](Y − Xβ)
⊤ ⊤ ⊤
= (g − µγ̃ |Y ) (Lθ Z ZLθ + Iqq )(g − µγ̃ | Y )
+ (Y − Xβ)⊤ (Inn + ZR̃θ Z⊤ )−1 (Y − Xβ),

where µγ̃ |Y = (L⊤ ⊤

θ Z ZLθ + Iqq )
−1 ⊤ ⊤
Lθ Z (Y − Xβ) and the Woodbury identity has been used in the last
step. As the notation suggests µγ̃ |Y is the conditional expectation of the random effect conditional on the data:
E(γ̃ | Y). This may be verified from the conditional distribution γ̃ | Y when exploiting the equality derived in
the preceeding display. Substitute the latter in the integral of the likelihood and use the change-of-variables:
h = (L⊤ ⊤
θ Z ZLθ + Iqq )
1/2
(g − µγ̃ | Y ) with Jacobian |(L⊤ ⊤
θ Z ZLθ + Iqq )
1/2
|:
Z
L(Y) = (2πσε2 )−(n+q)/2 |L⊤ ⊤
θ Z ZLθ + Iqq |
−1/2
exp(− 21 σε−2 h⊤ h)
Rq
exp[− 21 σε−2 (Y − Xβ)⊤ (Inn + ZR̃θ Z⊤ )−1 (Y − Xβ)] dg
= (2πσε2 )−n/2 |Inn + ZR̃θ Z⊤ |−1/2
exp[− 21 σε−2 (Y − Xβ)⊤ (Inn + ZR̃θ Z⊤ )−1 (Y − Xβ)], (4.1)

where in the last step Sylvester’s determinant identity has been used.
The maximum likelihood estimators of the mixed model parameters β, σε2 and R̃θ are found through the
maximization of the logarithm of the likelihood (4.1). Find the roots of the partial derivatives of this log-likelihood
with respect to the mixed model parameters. For β and σε2 this yields:

β̂ = [X⊤ (Inn + ZR̃θ Z⊤ )−1 X]−1 X⊤ (Inn + ZR̃θ Z⊤ )−1 Y,

σ̂ε2 = 1 ⊤
n (Y − Xβ) (Inn + ZR̃θ Z )
⊤ −1
(Y − Xβ).

The former estimate can be substituted into the latter to remove its dependency on β. However, both estimators
still depend on θ. An estimator of θ may be found by substitution of β̂ and σ̂ε2 into the log-likelihood followed by
its maximization. For general parametrizations of R̃θ by θ there are no explicit solutions. Then, resort to standard
nonlinear solvers such as the Newton-Raphson algorithm and the like. With a maximum likelihood estimate of
θ at hand, those of the other two mixed model parameters are readily obtained from the formula’s above. As θ
is unknown at the onset, it needs to be initiated followed by sequential updating of the parameter estimates until
convergence.
58 Mixed model

Restricted maximum likelihood (REML) considers the fixed effect parameter β as a ‘nuisance’ parameter
and concentrates
R on the estimation of the variance components. The nuisance parameter is integrated out of the
likelihood, Rp L(Y)dβ, which is referred to as the restricted likelihood. Those values of θ (and thereby R̃θ ) and
σε2 that maximize the restricted likelihood are the REML estimators. The restricted likelihood, by an argument
similar to that used in the derivation of the likelihood, simplifies to:
Z
L(Y)dβ = (2πσε2 )−n/2 |Q̃|−1/2 exp{− 21 σε−2 Y⊤ [Q̃−1 −1 ⊤ −1
θ − Q̃θ X(X Q̃θ X)
−1 ⊤ −1
X Q̃θ ]Y}
R p
Z
exp{− 21 σε−2 [β − (X⊤ Q̃−1θ X)
−1 ⊤ −1
X Q̃θ Y]⊤ X⊤ Q̃−1
θ X
Rp
[β − (X⊤ Q̃−1
θ X)
−1 ⊤ −1
X Q̃θ Y]}dβ
= (2πσε2 )−(n−p)/2 |Q̃θ |−1/2 |X⊤ Q̃−1
θ X|
−1/2

exp{− 21 σε−2 Y⊤ [Q̃−1 −1 ⊤ −1

θ − Q̃θ X(X Q̃θ X)
−1 ⊤ −1
X Q̃θ ]Y},
where Q̃θ = Inn + ZR̃θ Z⊤ is the relative covariance (relative to the error variance) of Y. The REML estimators
are now found by equating the partial derivatives of this restricted loglikelihood to zero and solving for σε2 and θ.
The former, given the latter, is:
−1
σ̂ε2 = 1 ⊤
n−p Y [Q̃θ − Q̃−1 ⊤ −1
θ X(X Q̃θ X)
−1 ⊤ −1
X Q̃θ ]Y
⊤ −1/2 −1/2 −1/2 −1/2 −1/2 −1/2
= 1
n−p Y Q̃θ [Inn − Q̃θ X(X⊤ Q̃θ Q̃θ X)−1 X⊤ Q̃θ ]Q̃θ Y,
where the rewritten form reveals a projection matrix and, consequently, a residual sum of squares. Like the
maximum likelihood estimator of θ, its REML counterpart is generally unknown analytically and to be found
numerically. Iterating between the estimation of both parameters until convergence yields the REML estimators.
Obviously, REML estimation of the mixed model parameters does not produce an estimate of the fixed parameter
β (as it has been integrated out). Should however a point estimate be desired, then in practice the ML estimate of
β with the REML estimates of the other parameters is used.

An alternative way to proceed (and insightful for the present purpose) follows the original approach of Henderson,
who aimed to construct a linear predictor for Y.
Definition 4.1
A predictand is the function of the parameters that is to be predicted. A predictor is a function of the data that
predicts the predictand. When this latter function is linear in the observation it is said to be a linear predictor.
In case of the mixed model the predictand is Xnew β + Znew γ for (nnew × p)- and (nnew × q)-dimensional design
matrices Xnew and Znew , respectively. Similarly, the predictor is some function of the data Y. When it can be
expressed as AY for some matrix A it is a linear predictor.
The construction of the aforementioned linear predictor requires estimates of β and γ. To obtain these esti-
mates first derive the joint density of (γ, Y):
     
γ 0q Rθ Rθ Z⊤
∼ N ,
Y Xβ ZRθ σε2 Inn + ZRθ Z⊤
From this the likelihood is obtained and after some manipulations the loglikelihood can be shown to be propor-
tional to:
σε−2 kY − Xβ − Zγk22 + γ ⊤ R−1
θ γ, (4.2)
in which – following Henderson – Rθ and σε2
are assumed known (for instance by virtue of maximum likelihood
or REML estimation). The estimators of β and γ are now the minimizers of loss criterion (4.2). Effectively, the
random effect parameter γ is now temporarily assumed to be ‘fixed’. That is, it is temporarily treated as fixed in
the derivations below that lead to the construction of the linear predictor. However, γ is a random variable and
one therefore speaks of a linear predictor rather than linear estimator.
To find the estimators of β and γ, defined as the minimizer of loss function, equate the partial derivatives of
mixed model loss function (4.2) with respect to β and γ to zero. This yields the estimating equations (also referred
to as Henderson’s mixed model equations):
X⊤ Y − X⊤ Xβ − X⊤ Zγ = 0p ,
σε−2 Z⊤ Y − σε−2 Z⊤ Zγ − σε−2 Z⊤ Xβ − R−1
θ γ = 0q .
 59

Solve each estimating equation for the parameters individually and find:

β̂ = (X⊤ X)−1 X⊤ (Y − Zγ), (4.3)

γ̂ = (Z⊤ Z + σε2 R−1
θ )
−1 ⊤
Z (Y − Xβ). (4.4)

Note, using the Cholesky decomposition of R̃θ and applying the Woodbury identity twice (in both directions),
that:

γ̂ = (ZT Z + R̃θ−1 )−1 Z⊤ (Y − Xβ)

= [R̃θ − R̃θ Z⊤ (Inn + ZR̃θ Z⊤ )−1 ZR̃θ ]Z⊤ (Y − Xβ)
= Lθ [Iqq − L⊤ ⊤ ⊤ ⊤ −1
θ Z (Inn + ZLθ Lθ Z ) ZLθ ]L⊤ ⊤
θ Z (Y − Xβ)
⊤ ⊤ −1 ⊤ ⊤
= Lθ (Lθ Z ZLθ + Iqq ) Lθ Z (Y − Xβ)
= Lθ µγ̃ |Y .

It thus coincides with the conditional estimate of the γ found in the derivation of the maximum likelihood estimator
of the mixed model. This expression could also have been found by conditioning with the multivariate normal
above which would have given E(γ | Y).
The estimator of both β and γ can be expressed fully and explicitly in terms of X, Y, Z and Rθ . To obtain
that of β substitute the estimator of γ of equation (4.4) into that of β given by equation 4.3):

β = (X⊤ X)−1 X⊤ [Y − Z(Z⊤ Z + σε2 R−1

θ )
−1 ⊤
Z (Y − Xβ)]
= (X⊤ X)−1 X⊤ {Y − [Inn − (σε−2 ZRθ Z⊤ + Inn )−1 ](Y − Xβ)},

in which the Woodbury identity has been used. Now group terms and solve for β:

β̂ = [X⊤ (ZRθ Z⊤ + σε2 Inn )−1 X]−1 X⊤ (ZRθ Z⊤ + σε2 Inn )−1 Y. (4.5)

This coincides with the maximum likelihood estimator of β presented above (for known Rθ and σε2 ). Moreover, in
the preceeding display one recognizes a generalized least squares (GLS) estimator. The GLS regression estimator
is BLUE (Best Linear Unbiased Estimator) when Rθ and σε are known. To find an explicit expression for γ use
Qθ as previously defined and substitute the explicit expression (4.5) for the estimator of β in the estimator of γ,
shown in display (4.4) above. This gives:

γ̂ = (Z⊤ Z + σε2 Rθ−1 )−1 Z⊤ [Inn − X(XQ−1 ⊤ −1 ⊤ −1

θ X ) X Qθ ]Y,

an explicit expression for the estimator of γ.

The linear predictor constructed from these estimator can be shown (cf. Theorem 4.1) to be optimal, in the
BLUP sense.
Definition 4.2
A Best Linear Unbiased Predictor (BLUP) i) is linear in the observations, ii) is unbiased, and iii) has a minimum
(variance of its) predictor error, i.e. the difference among the predictor and predictand, among all unbiased linear
predictors.

Theorem 4.1
The predictor Xβ̂ + Zγ̂ is the BLUP of Ỹ = Xβ + Zγ.

Proof. The predictor of Xβ̂ + Zγ̂ is:

Xβ̂ + Zγ̂ = [Inn − σε2 Q−1 −1 −1 ⊤ −1 ⊤ −1

θ + Qθ X(XQθ X ) X Qθ ]Y := BY.

Clearly, this is a linear function in Y.

The expectation of the linear predictor is

E(Xβ̂ + Zγ̂) = E[Xβ̂ + Z(Z⊤ Z + σε2 Rθ )−1 Z⊤ (Y − Xβ̂)]

= XE(β̂) + (Inn − σε2 Q−1
θ )[E(Y) − E(Xβ̂)] = Xβ.

This is also the expectation of the predictand Xβ + Zγ. Hence, the predictor is unbiased.
60 Mixed model

To show the predictor BY has minimum prediction error variance within the class of unbiased linear predic-
tors, assume the existence of another unbiased linear predictor AY of Xβ + Zγ. The predictor error variance of
the latter predictor is:

Var(Xβ + Zγ − AY) = Var(Xβ + Zγ − BY − AY + BY)

= Var[(A − B)Y] + Var(Xβ + Zγ − BY)
−2 Cov[Xβ + Zγ − BY, (A − B)Y].

The last term vanishes as:

Cov[Xβ + Zγ − BY, (A − B)Y]

= [ZCov(γ, Y) − BVar(Y)](A − B)⊤
= {ZRθ Z⊤ − [Inn − σε2 Q−1 −1 −1 ⊤ −1 ⊤ −1
θ + Qθ X(XQθ X ) X Qθ ]Qθ }(A − B)⊤
= Q−1 −1 ⊤ −1 ⊤
θ X(XQθ X ) X (A − B)⊤
= Q−1 −1 ⊤ −1
θ X(XQθ X ) [(A − B)X]⊤ = 0nn ,

where the last step uses AX = BX, which follows from the fact that

AXβ = E(AY) = E(BY) = BXβ,

for all β ∈ Rp . Hence,

Var(Xβ + Zγ − AY) = Var[(A − B)Y] + Var(Xβ + Zγ − BY),

from which the minimum variance follows as the first summand on the right-hand side is nonnegative and zero if
and only if A = B. 

4.1 Link to ridge regression

The link with ridge regression, implicit in the exposé on the mixed model, is now explicated. Recall that ridge
regression fits the linear regression model Y = Xβ + ε by means of a penalized maximum likelihood procedure,
which defines – for given penalty parameter λ – the estimator as:

β̂(λ) = arg minp kY − Xβk22 + λβ ⊤ β.

β∈R

Constrast this to a mixed model void of covariates with fixed effects and comprising only covariates with a random
effects: Y = Zγ + ε with distributional assumptions γ ∼ N (0q , σγ2 Iqq ) and ε ∼ N (0n , σε2 Inn ). This model,
when temporarily considering γ as fixed, is fitted by the minimization of loss function (4.2). The corresponding
estimator of γ is then defined, with the current mixed model assumptions in place, as:

γ̂ = arg minp kY − Zγk22 + σγ−2 γ ⊤ γ.

γ∈R

The estimators are – up to a reparamatrization of the penalty parameter – defined identically. This should not
come as a surprise after the discussion of Bayesian regression (cf. Chapter 2) and the alert reader would already
have recognized a generalized ridge loss function in Equation (4.2). The fact that we discarded the fixed effect
part of the mixed model is irrelevant for the analogy as those would correspond to unpenalized covariates in the
ridge regression problem.
The link with ridge regression is also immenent from the linear predictor of the random effect. Recall: γ̂ =
(Z⊤ Z + R−1 θ ) Z (Y − Xβ). When we ignore R−1
−1 ⊤
θ , the predictor reduces to a least squares estimator. But
with a symmetric and positive definite matrix Rθ−1 , the predictor is actually of the shrinkage type as is the ridge
regression estimator. This shrinkage estimator also reveals, through the term (Z⊤ Z + R−1 θ )
−1
, that a q larger than
n does not cause identifiability problems as long as Rθ is parametrized low-dimensionally enough.
The following mixed model result provide an alternative approach to choice of the penalty parameter in ridge
regression. It assumes a mixed model comprising of the random effects part only. Or, put differently, it assume
the linear regression model Y = Xβ + ε with β ∼ N (0p , σβ2 Ipp ) and ε ∼ N (0n , σε2 Inn ).
Theorem 4.2 (Theorem 2, Golub et al)
The expected generalized cross-validation error Eβ {Eε [GCV (λ)]} is minimized for λ = σε2 /σβ2 .
4.2 REML consistency, high-dimensionally 61

Proof. The proof first finds an analytic expression of the expected GCV (λ), then its minimum. Its expectation
can be re-expressed as follows:
 2

Eβ {Eε [GCV (λ)]} = Eβ Eε n1 {tr[Inn − H(λ)]/n}−2 k[Inn − H(λ)]Y 2


= n{tr[Inn − H(λ)]}−2 Eβ Eε {Y⊤ [Inn − H(λ)]2 Y}


= n{tr[Inn − H(λ)]}−2 Eβ Eε tr{(Xβ + ε)⊤ [Inn − H(λ)]2 (Xβ + ε)}
= n{tr[Inn − H(λ)]}−2 tr{[Inn − H(λ)]2 XX⊤ Eβ [Eε (ββ ⊤ )]}


+ tr{[Inn − H(λ)]2 Eβ [Eε (εε⊤ )]}


= n σβ2 tr{[Inn − H(λ)]2 XX⊤ } + σε2 tr{[Inn − H(λ)]2 } {tr[Inn − H(λ)]}−2 .

To get a handle on this expression, use (X⊤ X + λIpp )−1 X⊤ X

P= Ipp − λ(X⊤ X + λIpp )−1P= X⊤ X(X⊤ X +
p p
λIpp ) , the cyclic property of the trace, and define A(λ) = j=1 (d2x,j + λ)−1 , B(λ) = j=1 (d2x,j + λ)−2 ,
−1
Pp 2 −3
and C(λ) = j=1 (dx,j + λ) . The traces in the expectation of GCV (λ) can now be written as:

tr[Inn − H(λ)] = λ tr[(X⊤ X + λIpp )−1 ] = λA(λ),

2
tr{[Inn − H(λ)] } = λ tr[(X X + λIpp ) ] = λ2 B(λ),
2 ⊤ −2

tr{[Inn − H(λ)]2 XX⊤ } = λ2 tr[(X⊤ X + λIpp )−1 ] − λ3 tr[(X⊤ X + λIpp )−2 ]

= λ2 A(λ) − λ3 B(λ).

The expectation of GCV (λ) can then be reformulated as:

Eβ {Eε [GCV (λ)]} = n{σβ2 [A(λ) − λB(λ)] + σε2 B(λ)}[A(λ)]−2 .

Equate the derivative of this expectation w.r.t. λ to zero, which can be seen to be proportional to:

2(λσβ2 − σε2 )[B(λ)]2 + 2(λσβ2 − σε2 )A(λ)C(λ) = 0.

Indeed, λ = σε2 /σβ2 is the root of this equation. 

Theorem 4.2 can be extended to include unpenalized covariates. This leaves the result unaltered: the optimal (in
the expected GCV sense) ridge penalty is the same signal-to-noise ratio.
We have encountered the result of Theorem 4.2 before. Revisit Example 1.7 which derived the mean squared
error (MSE) of the ridge regression estimator when X is orthonormal. It was pointed out that this MSE is minized
for λ = pσε /β ⊤ β. As β ⊤ β/p is an estimator for σβ2 , this implies the same optimal choice of the penalty
parameter.
To point out the relevance of Theorem 4.2 for the choice of the ridge penalty parameter still assume the
regression parameter random. The theorem then says that the optimal penalty parameter (in the GCV sense)
equals the ratio of the error variance and that of the regression parameter. Both variances can be estimated by
means of the mixed model machinery (provided for instance by the lme4 package in R). These estimates may
be plugged in the ratio to arrive at a choice of ridge penalty parameter (see Section 4.3 for an illustration of this
usage).

4.2 REML consistency, high-dimensionally

Here a result on the asymptotic quality of the REML estimators of the random effect and error variance parameters
is presented and discussed. It is the ratio of these parameters that forms the optimal choice (in the expected GCV
sense) of the penalty parameter of the ridge regression estimator. As in practice the parameters are replaced by
estimates to arrive at a choice for the penalty parameter, the quality of these estimators propogates to the chosen
penalty parameter.
Consider the standard linear mixed model Y = Xβ + Zγ + ε, now with equivariant and uncorrelated random
effects: γ ∼ N (0q , σγ2 Iqq ). Write θ = σγ2 /σε2 . The REML estimators of θ and σε2 are to be found from the
estimating equations:

tr(Pθ ZZ⊤ ) = σε−2 tr(Y⊤ Pθ ZZ⊤ Pθ Y),

σε2 = (n − p)−1 Y⊤ Pθ Y,
62 Mixed model

where Pθ = Q̃−1 −1 ⊤ −1
θ − Q̃θ X(X Q̃θ X)
−1 ⊤ −1
X Q̃θ and Q̃θ = Inn + θZZ⊤ . To arrive at the REML estimators
choose initial values for the parameters. Choose one of the estimating equations substitute the initial value of the
one of the parameters and solve for the other. The found root is then substituted into the other estimating equation,
which is subsequently solved for the remaining parameter. Iterate between these two steps until convergence. The
discussion of the practical evaluation of a root for θ from these estimating equations in a high-dimensional context
is postponed to the next section.
The employed linear mixed model assumes that each of the q covariates included as a column in Z contributes
to the variation of the response. However, it may be that only a fraction of these covariates exerts any influence on
the response. That is, the random effect parameter γ is sparse, which could be operationalized as γ having q0 zero
elements while the remaining qc = q − q0 elements are non-zero. Only for the latter qc elements of γ the normal
assumption makes sense, but is invalid for the q0 zeros in γ. The posed mixed model is then misspecified.
The next theorem states that the REML estimators of θ = σγ2 /σε2 and σε2 are consistent (possibly after adjust-
ment, see the theorem), even under the above mentioned misspecification.

Theorem 4.3 (Theorem 3.1, Jiang et al. (2016))

Let Z be standardized column-wise and with its unstandardized entries i.i.d. from a sub-Gaussian distribution.
Furthermore, assume that n, q, qc → ∞ such that
n qc
→τ and → ω,
q q

where τ, ω ∈ (0, 1]. Finally, suppose that σε2 and σγ2 are positive. Then:
i) The ‘adjusted’ REML estimator of the variance ratio σγ2 /σε2 is consistent:
q \ P
(σ 2 /σ 2 ) −→ σγ2 /σε2 .
qc γ ε
P
ii) The REML estimator of the error variance is consistent: σ̂ε2 −→ σε2 .

Proof. Confer Jiang et al. (2016). 

Before the interpretation and implication of Theorem 4.3 are discussed, its conditions for the consistency result
are reviewed:
◦ The standardization and distribution assumption on the design matrix of the random effects has no direct
practical interpretation. These conditions warrant the applicability of certain results from random matrix
theory upon which the proof of the theorem hinges.
◦ The positive variance assumption σε2 , σγ2 > 0, in particular that of the random effect parameter, effectively
states that some – possibly misspecified – form of the mixed model applies.
◦ Practically most relevant are the conditions on the sample size, random effect dimension, and sparsity.
The τ and ω in Theorem 4.3 are the limiting ratio’s of the sample size n and non-zero random effects qc ,
respectively, to the total number of random effects q. The number of random effects thus exceeds the sample
size, as long as the latter grows (in the limit) at some fixed rate with the former. Independently, the model
may be misspecified. The sparsity condition only requires that (in the limit) a fraction of the random effects
is nonzero.
Now discuss the interpretation and relevance of the theorem:
◦ Theorem 4.3 complements the classical low-dimensional consistency results on the REML estimator.
◦ Theorem 4.3 shows that not all (i.e. consistency) is lost when the model is misspecified.
◦ The practical relevance of the part i) of Theorem 4.3 is limited as the number of nonzero random effects qc ,
or ω for that matter, is usually unknown. Consequently, the REML estimator of the variance ratio σγ2 /σε2
cannot be adjusted correctly to achieve asymptotically unbiasedness and – thereby – consistency
◦ Part ii) in its own right may not seem very useful. But it is surprising that high-dimensionally (i.e. when
the dimension of the random effect parameter exceeds the sample size) the standard (that is, derived for
low-dimensional data) REML estimator of σε2 is consistent. Beyond this surprise, a good estimator of σε2
indicates how much of the variation in the response cannot be attributed to the covariates represented by
the columns Z. A good indication of the noise level in the data finds use at many place. In particular, it is
helpful in deciding on the order of the penalty parameter.
◦ Theorem 4.2 suggests to choose the ridge penalty parameter equal to the ratio of the error variance and that
of the random effects. Confronted with data the reciprocal of the REML estimator of θ = σγ2 /σε2 may be
4.3 Illustration: P-splines 63

used as value for the penalty parameter. Without the adjustment for the fraction of nonzero random effects,
this value is off. But in the worst case this value is an over-estimation of the optimal (in the GCV sense)
ridge penalty parameter. Consequently, too much penalization is applied and the ridge regression estimate
of the regression parameter is conservative as it shrinks the elements too much to zero.

4.3 Illustration: P-splines

An organism’s internal circadian clock enables it to synchronize its activities to the earth’s day-and-night cycle.
The circadian clock maintains, due to environmental feedback, oscillations of approximately 24 hours. Molec-
ularly, these oscillations reveal themselves in the fluctuation of the transcription levels of genes. The molecular
core of the circadian clock is made up of ±10 genes. Their behaviour (in terms of their expression patterns) is
described by a dynamical system with feedback mechanisms. Linked to this core are genes that tap into the clock’s
rythm and use it to regulate the molecular processes. As such many genes are expected to exhibit circadian rythms.
This is investigated in a mouse experiment in which the expression levels of several transcipts have been measured
during two days with a resolution of one hour, resulting in a time-series of 48 time points publicly available from
the R-package MetaCycle. Circadian rythms may be identified simply by eye-balling the data. But to facilitate
this identification the data are smoothed to emphasize the pattern present in these data.
1.0

0.8
0.8

0.6
0.6
B(X)

B(X)

0.4
0.4

0.2
0.2
0.0

0.0

0 1 2 3 4 5 0 1 2 3 4 5

x x

Fkbp5; # segments: 50 Clock; # segments: 50

600
300
250

500
RNA concentration

RNA concentration
200

400
150

300
100

200
50

0 10 20 30 40 0 10 20 30 40

time time

Figure 4.2: Top left and right panels: B-spline basis functions of degree 1 and 2, respectively. Bottom left and right
panel: P-spline fit to transcript levels of circadian clock experiment in mice.
64 Mixed model

Smooothing refers to nonparametric – in the sense that parameters have no tangible interpretation – description
of a curve. For instance, one may wish to learn some general functional relationship between two variable, X and
Y , from data. Statistically, the model Y = f (X) + ε, for unknown and general function f (·), is to be fitted to
paired observations {(yi , xi )}ni=1 . Here we use P-splines, penalized B-splines with B for Basis (Eilers and Marx,
1996).
A B-spline is formed through a linear combination of (pieces of) polynomial basis functions of degree r.
For their construction specify the interval [xstart , xend ] on which the function is to be learned/approximated. Let
m+2r
{tj }j=0 be a grid, overlapping the interval, of equidistantly placed points called knots given by tj = xstart + (j −
1
r)h for all j = 0, . . . , m + 2r with h = m (xend − xstart ). The B-spline base functions are then defined as:

Bj (x; r) = (−1)r+1 (hr r!)−1 ∆r+1 [(x − tj )r 1{x≥tj } ]

where ∆r [fj (·)] is the r-th difference operator applied to fj (·). For r = 1: ∆[fj (·)] = fj (·) − fj−1 (·),
while r = 2: ∆2 [fj (·)] = ∆{∆[fj (·)]} = ∆[fj (·) − fj−1 (·)] = fj (·) − 2fj−1 (·) + fj−2 (·), et cetera.
The top right and bottom left P panels of Figure 4.2 show a 1st and 2nd degree B-spline basis functions. A P-
m+2r
spline is a curve of the form j=0 αj Bj (x; r) fitted to the data by means of penalized least squares mini-
mization. The least squares are kY − Bαk22 where B is a n × (m + 2r)-dimensional matrix with the j-th
column equalling (Bj (xi ; r), Bj (x2 ; r), . . . , Bj (xn ; r))⊤ . The employed penalty is of the ridge type: the sum
of the squared difference among contiguous αj . Let D be the first order differencing matrix. The penalty
Pm+2r
can then be written as kDαk22 = 2
j=2 (αj − αj−1 ) . A second order difference matrix would amount to
P m+2r
kDαk22 = j=3 (αj − 2αj−1 + αj−2 )2 . Eilers (1999) points out how P-splines may be interpret as a mixed
model. Hereto choose X̃ such that its columns span the null space of D⊤ D, which comprises a single column
representing the intercept when D is a first order differencing matrix, and Z̃ = D⊤ (DD⊤ )−1 . Then, for any α:

Bα = B(X̃β + Z̃γ) := Xβ + Zγ.

This parametrization simplifies the employed penalty to:

kDαk22 = kD(X̃β + Z̃γ)k22 = kDD⊤ (DD⊤ )−1 γk22 = kγk22 ,

where DX̃β has vanished by the construction of X̃. Hence, the penalty only affects the random effect parameter,
leaving the fixed effect parameter unshrunken. The resulting loss function, kY − Xβ − Zγk22 + λkγk22 , coincides
for suitably chosen λ to that of the mixed model (as will become apparent later). The bottom panels of Figure 4.2
shows the flexibility of this approach.
The following R-script fits a P-spline to a gene’s transcript levels of the circadian clock study in mice. It uses
a basis of m = 50 truncated polynomial functions of degree r = 3 (cubic), which is generated first alongside
several auxillary matrices. This basis forms, after post-multiplication with a projection matrix onto the space
spanned by the columns of the difference matrix D, the design matrix for the random coefficient of the mixed
model Y = Xβ + Zγ + ε with γ ∼ N (0q , σγ2 Iqq ) and ε ∼ N (0n , σε2 Inn ). The variance parameters of this
model are then estimated by means of restricted maximum likelihood (REML). The final P-spline fit is obtained
from the linear predictor using, in line with Theorem 4.2, λ = σε2 /σγ2 in which the REML estimates of these
variance parameters are substituted. The resulting P-spline fit of two transcripts is shown in the bottom panels of
Figure 4.2.

Listing 4.1 R code

# load libraries
library(gridExtra)
library(MetaCycle)
library(MASS)

#------------------------------------------------------------------------------
# intermezzo: declaration of functions used analysis
#------------------------------------------------------------------------------

tpower <- function(x, knots, p) {

# function for evaluation of truncated p-th
# power functions positions x, given knots
return((x - knots)ˆp * (x > knots))
4.3 Illustration: P-splines 65

bbase <- function(x, m, r) {

# function for B-spline basis generation
# evaluated at the extremes of x
# with m segments and spline degree r
h <- (max(x) - min(x))/m
knots <- min(x) + (c(0:(m+2*r)) - r) * h
P <- outer(x, knots, tpower, r)
D <- diff(diag(m+2*r+1), diff=r+1) / (gamma(r+1) * hˆr)
return((-1)ˆ(r+1) * P %*% t(D))
}

thetaEstEqREML <- function(theta, Z, Y, X, sigma2e){

# function for REML estimation:
# estimating equation of theta
QthetaInv <- solve(diag(length(Y)) + theta * Z %*% t(Z))
Ptheta <- QthetaInv -
QthetaInv %*% X %*%
solve(t(X) %*% QthetaInv %*% X) %*% t(X) %*% QthetaInv
return(sum(diag(Ptheta %*% Z %*% t(Z))) -
as.numeric(t(Y) %*% Ptheta %*% Z %*% t(Z) %*% Ptheta %*% Y) / sigma2e)
}

#------------------------------------------------------------------------------

# load data
data(cycMouseLiverRNA)
id <- 14
Y <- as.numeric(cycMouseLiverRNA[id,-1])
X <- 1:length(Y)

# set P-spline parameters

m <- 50
r <- 3
B <- bbase(X, m=m, r=r)

# prepare some matrices

D <- diff(diag(m+r), diff = 2)
Z <- B %*% t(D) %*% solve(D %*% t(D))
X <- B %*% Null(t(D) %*% D)

# initiate
theta <- 1
for (k in 1:100){
# for-loop, alternating between theta and error variance estimation
thetaPrev <- theta
QthetaInv <- solve(diag(length(Y)) + theta * Z %*% t(Z))
Ptheta <- QthetaInv -
QthetaInv %*% X %*%
solve(t(X) %*% QthetaInv %*% X) %*% t(X) %*% QthetaInv
sigma2e <- t(Y) %*% Ptheta %*% Y / (length(Y)-2)
theta <- uniroot(thetaEstEqREML, c(0, 100000),
Z=Z, Y=Y, X=X, sigma2e=sigma2e)$root
if (abs(theta - thetaPrev) < 10ˆ(-5)){ break }
}

# P-spline fit
bgHat <- solve(t(cbind(X, Z)) %*% cbind(X, Z) +
diag(c(rep(0, ncol(X)), rep(1/theta, ncol(Z))))) %*%
t(cbind(X, Z)) %*% Y
66 Mixed model

# plot fit
plot(Y, pch=20, xlab="time", ylab="RNA concentration",
main=paste(strsplit(cycMouseLiverRNA[id,1], "_")[[1]][1],
"; # segments: ", m, sep=""))
lines(cbind(X, Z) %*% bgHat, col="blue", lwd=2)
The fitted splines displayed Figure 4.2 nicely match the data. From the circadian clock perspective it is especially
the fit in the right-hand side bottom panel that displays the archetypical sinusoidal behaviour associated by the
layman with the sought-for rythm. Close inspection of the fits reveals some minor discontinuities in the derivative
of the spline fit. These minor discontinuities are indicative of a little overfitting, due to too large an estimate of σγ2 .
This appears to be due to numerical instability of the solution of the estimating equations of the REML estimators
of the mixed model’s variance parameter estimators when m is large compared to the sample size n.
5 Ridge logistic regression

Ridge penalized estimation is not limited to the standard linear regression model, but may be used to estimate
(virtually) any model. Here we illustrate how it may be used to fit the logistic regression model. To this end
we first recap this model and the (unpenalized) maximum likelihood estimation of its parameters. After which
the model is estimated by means of ridge penalized maximum likelihood, which will turn out to be a relatively
straightforward modification of unpenalized estimation.

5.1 Logistic regression

The logistic regression model explains a binary response variable (through some transformation) by a linear com-
bination of a set of covariates (as in the linear regression model). Denote this response of the i-th sample by Yi
with Yi ∈ {0, 1} for i = 1, . . . , n. The n-dimensional column vector Y stacks these n responses. For each sample
information on the p explanatory variables Xi,1 , . . . , Xi,p is available. In row vector form this information is de-
noted Xi,∗ = (Xi,1 , . . . , Xi,p ). Or, in short, Xi when the context tolerates no confusion. The (n × p)-dimensional
matrix X aggregates these vectors, such that Xi is the i-th row vector.
The binary response cannot be modelled as in the linear model like Yi = Xi β + εi . With each element
of Xi and β assuming a value in R, the linear predictor is not restricted to the domain of the response. This
is resolved by modeling pi = P (Yi = 1) instead. Still the linear predictor may exceed the domain of the
response (pi ∈ [0, 1]). Hence, a transformation is applied to map pi to R, the range of the linear predictor. The
transformation associated with the logistic regression model is the logarithm of the odds, with the odds defined as:
odds = P (succes)/P (failure) = pi /(1 − pi ). The logistic model is then written as log[pi /(1 − pi )] = Xi β for
all i. Or, expressed in terms of the response:

pi = P (Yi = 1) = g −1 (Xi ; β) = exp(Xi β)[1 + exp(Xi β)]−1 .

The function g(·; ·) is called the link function. It links the response to the explanatory variables. The one above
is called the logistic link function. Or short, logit. The regression parameters have tangible interpretations. When
the first covariate represents the intercept, i.e. Xi,j = 1 for all i, then β1 determines where the link function equals
a half when all other covariates fail to contribute to the linear predictor (i.e. where P (Yi = 1 | Xi ) = 0.5 when
Xi β = β1 ). This is illustrated in the top-left panel of Figure 5.1 for various choices of the intercept. On the other
hand, the regression parameters are directly related to the odds ratio: odds ratio = odds(Xi,j + 1)/odds(Xi,j ) =
exp(βj ). Hence, the effect of a unit change in the j-th covariate on the odds ratio is exp(βj ) (see Figure 5.1,
top-right panel). Other link functions (depicted in Figure 5.1, bottom-left panel) are common, e.g. the probit:
pi = Φ0,1 (Xi β); the cloglog: pi = π1 arctan(Xi β) + 12 ; the Cauchit: pi = exp[− exp(Xi β)]. All these
link function are invertible. Irrespective of the choice of the link function, the binary data are thus modelled
as Yi ∼ B [g −1 (Xi ; β), 1]. That is, as a single draw from the Binomial distribution with success probability
g −1 (Xi ; β).
Let us now estimate the parameter of the logistic regression model by means of the maximum likelihood
method. The likelihood of the experiment is then:
n
Y   Yi  1−Yi
L(Y | X; β) = P (Yi = 1 | Xi ) P (Yi = 0 | Xi ) .
i=1

After taking the logarithm and some ready algebra, the log-likelihood is found to be:
Xn 
L(Y | X; β) = Yi Xi β − log[1 + exp(Xi β)] .
i=1
68 Ridge logistic regression

effect of β0 (with β1=1) effect of β1 (with β0=0)

β0=−2
1.0

1.0
β0=−1
β0= 0
β0= 1
β0= 2
0.8

0.8
β1=−2
β1=−1
β1= 0
β1= 1
0.6

0.6
β1= 2
P(Y=1 | X)

P(Y=1 | X)
0.4

0.4
0.2

0.2
0.0

0.0
−4 −2 0 2 4 −4 −2 0 2 4

X X

Various link functions

1.0

logit 1.0
probit
cauchit
cloglog
0.8

0.8
0.6

0.6
P(Y=1 | X)

Y
0.4

0.4
0.2

0.2

obs.
0.0

0.0

pred.

−4 −2 0 2 4 −4 −2 0 2 4

X X

Figure 5.1: Top row, left panel: the response curve for various choices of the intercept β0 . Top row, right panel: the
response curve for various choices of the regression coefficent β1 . Bottom row, left panel: the responce curve for
various choices of the link function. Bottom panel, right panel: observations, fits and their deviations.

Differentiate the log-likelihood with respect to β, equate it zero, and obtain the estimating equation for β:

n h
∂L X exp(Xi β) i ⊤
= Yi − X = 0p . (5.1)
∂β i=1
1 + exp(Xi β) i

The ML estimate of β strikes a (weighted by the Xi ) balance between observation and model. Put differently (and
illustrated in the bottom-right panel of Figure 5.1), a curve is fit through data by minimizing the distance between
them: at the ML estimate of β a weighted average of their deviations is zero.
The maximum likelihood estimate of β is evaluated by solving Equation (5.1) with respect to β by means of
the Newton-Raphson algorithm. The Newton-Raphson algorithm iteratively finds the zeros of a smooth enough
function f (·). Let x0 denote an initial guess of the zero. Then, approximate f (·) around x0 by means of a
first order Taylor series: f (x) ≈ f (x0 ) + (x − x0 ) (df /dx)|x=x0 . Solve this for x and obtain: x = x0 −
[(df /dx)|x=x0 ]−1 f (x0 ). Let x1 be the solution for x, use this as the new guess and repeat the above until con-
vergence. When the function f (·) has multiple arguments, is vector-valued and denoted by ~f , and the Taylor
5.2 Ridge estimation 69


approximation becomes: ~f (x) ≈ f (x0 ) + J~f x=x0 (x − x0 ) with
 ∂f1 ∂f1 ∂f1 
∂x1 ∂x2 . . . ∂x p
 ∂f1 ∂f2 ∂f2
. . . ∂x 
 ∂x1 ∂x2 
~
Jf = 
p
,
 .. .. . . .. 
 . . . . 
∂fq ∂fq ∂f
∂x1 ∂x2 . . . ∂xqp

the Jacobi matrix. An update of x0 is now readily constructed by solving (the approximation for) ~f (x) = 0 for x.
When applied here to the maximum likelihood estimation of the regression parameter β of the logistic regres-
sion model, the Newton-Raphson update is:
 ∂ 2 L −1  ∂ L 

β̂ new = β̂ old −  
∂β∂β ⊤ β=β̂ old ∂β β=β̂ old

where the Hessian of the log-likelihood equals:

n
X
∂2L exp(Xi β)
= − X⊤ Xi .
∂β∂β ⊤ i=1
[1 + exp(Xi β)]2 i

Iterative application of this updating formula converges to the ML estimate of β.

The Newton-Raphson algorithm is often reformulated as an iteratively re-weighted least squares algorithm.
Hereto, first write the gradient and Hessian in matrix notation:

∂L ∂2L
= X⊤ [Y − ~g−1 (X; β)] and = −X⊤ WX,
∂β ∂β∂β ⊤

where ~g−1 (X; β) = [g −1 (X1,∗ ; β), . . . , g −1 (Xn,∗ ; β)]⊤ with g −1 (·; ·) = exp(·; ·)/[1 + exp(·; ·)] and W di-
agonal with (W)ii = exp(Xi β̂ old )[1 + exp(Xi β̂ old )]−2 . The notation W was already used in Chapter 3 and,
generally, refers to a (diagonal) weight matrix with the choice of the weights depending on the context. The
updating formula of the estimate then becomes:

β̂ new = β̂ old + (X⊤ WX)−1 X⊤ [Y − ~g−1 (X; β old )]

= (X⊤ WX)−1 X⊤ W{Xβ̂ old + W−1 [Y − ~g−1 (X; β old )]}
= (X⊤ WX)−1 X⊤ WZ,

where Z = {Xβ̂ old +W−1 [Y−~g−1 (X; β old )]}. The Newton-Raphson update is thus the solution to the following
weighted least squares problem:

β̂ new = arg min (Z − Xβ)⊤ W(Z − Xβ).

β

Effectively, at each iteration the adjusted response Z is regressed on the covariates that comprise X. For more on
logistic regression confer the monograph of Hosmer Jr et al. (2013).

5.2 Ridge estimation

High-dimensionally, the linear predictor Xβ may be uniquely defined, but the maximum likelihood estimate of the
logistic regression parameter is not. Assume p > n and an estimate β̂ available. Due to the high-dimensionality,
the null space of X is non-trivial. Hence, let γ ∈ null(span(X)). Then: Xβ̂ = Xβ̂ + Xγ = X(β̂ + γ). As
the null space is a p − n-dimensional subspace, γ need not equal zero. Hence, an infinite number of estimates of
the logistic regression parameter exists that yield the same log-likelihood. Augmentation of the loss function with
a ridge penalty resolves the matter, as their sum is strictly concave in β (not convex as a maximum rather than a
minimum is sought here) and thereby has a unique maximum.
The binary nature of the response may bring about another problem, called separable data, that frustates the
estimation of the logistic regression estimator. High-dimensionally, this problem is virtually always encountered.
Separable data refer to the situation where the covariate space can be separated by a hyperplane such that the
samples with indices in the set {i : Yi = 0} fall on side of this hyperplane while those with an index in the set
70 Ridge logistic regression

{i : Yi = 1} on the other. High-dimensionally, such a hyperplane always be found (unless there is at least one pair
of samples with a common variate vector, i.e. Xi,∗ = Xi′ ,∗ , with different responses Yi 6= Yi′ ). The existence of
a separating hyperplane implies that the optimal fit is perfect and all samples have – according to the fitted logistic
regression model – a probability of one of being assigned to the correct outcome, i.e. P (Yi = 1 | Xi ) equals either
zero or one. Consequently, the loglikelihood vanishes, cf.:
Xn 
L(Y | X; β) = Yi log[P (Yi = 1 | Xi )] + (1 − Yi ) log[P (Yi = 0 | Xi ) = 0,
i=1

and does no longer involve the logistic regression parameter. The logistic regression parameter is then to be chosen
such that P (Yi = 1 | Xi ) = exp(Xi β)[1 + exp(Xi β)]−1 ∈ {0, 1} (depending on whether Yi is indeed of the
‘1’ class). This only occurs when (some) elements of β equal (minus) infinity. Hence, the logistic regression
parameter cannot be learned from separable data (which high-dimensional data generally are).

4
20
0

30

−110
−170

−14
−160

−1
−15

−1
4

2
−100
2

penalized estimate

0
β2

0
−2

−2
−4

0
−10

−4

−4 −2 0 2 4 −2 −1 0 1 2 3 4

β1 log(lambda)
1.0

λ=0
2.0

λ=1
λ=2.5
λ=5
λ=10
0.8

λ=100
1.5
variance of penalized estimate

0.6
1.0

y^

0.4
0.5

0.2
0.0

0.0

−2 −1 0 1 2 3 4 −2 −1 0 1 2

log(lambda) linear predictor

Figure 5.2: Top row, left panel: contour plot of the penalized log-likelihood of a logistic regression model with
the ridge constraint (red line). Top row, right panel: the regularization paths of the ridge estimator of the logistic
regression parameter. Bottom row, left panel: variance of the ridge estimator of the logistic regression parameter
against the logarithm of the penalty parameter. Bottom panel, right panel: the predicted success probability versus
the linear predictor for various choices of the penalty parameter.

Ridge maximum likelihood estimates of the logistic model parameters are found by the maximization of the
5.3 Moments 71

ridge penalized loglikelihood (cf. Schaefer et al. 1984; Le Cessie and Van Houwelingen 1992):

Lpen (Y, X; β, λ) = L(Y, X; β) − 21 λkβk22

Xn 
= Yi Xi β − log[1 + exp(Xi β)] − 12 λβ ⊤ β,
i=1

where the second summand is the ridge penalty (the sum of the square of the elements of β) with λ the penalty
parameter. Note that as in Section 1.5 maximization of this penalized loss function can be reformulated as a
constrained estimation problem. This is illustrated by the top left panel of Figure 5.2, which depicts the contours
(black lines) of the log-likelihood and the spherical domain of the parameter (red line). The optimization of the
above loss function proceeds, due to the differentiability of the penalty, fully analogous to the unpenalized case
and uses the Newton-Raphson algorithm for solving the (penalized) estimating equation. Hence, the unpenalized
ML estimation procedure is modified straightforwardly by replacing gradient and Hessian by their ‘penalized’
counterparts:

∂ Lpen ∂L ∂ 2 Lpen ∂2L

= − λβ and ⊤
= − λIpp .
∂β ∂β ∂β∂β ∂β∂β ⊤

With these at hand, the Newton-Raphson algorithm is (again) reformulated as an iteratively re-weighted least
squares algorithm with the updating step changing accordingly to:

β̂ new = β̂ old + V−1 {X⊤ [Y − ~g−1 (X; β old )] − λβ old }

= V−1 Vβ̂ old − λV−1 β̂ old + V−1 X⊤ WW−1 [Y − ~g−1 (X; β old )]
= V−1 X⊤ W{Xβ̂ old + W−1 [Y − ~g−1 (X; β old )]}
= [X⊤ WX + λIpp ]−1 X⊤ WZ,

where V = X⊤ WX+λIpp and W and Z as before. Hence, use this to update the estimate of β until convergence,
which yields the desired ridge ML estimate.
Obviously, the ridge estimate of the logistic regression parameter tends to zero as λ → ∞. Now consider a
linear predictor with an intercept that is left unpenalized. When λ tends to infinity, all regression coefficients but
the intercept
Pn vanish. PnThe intercept is left to model the success probability. Hence, in this case limλ→∞ β̂0 (λ) =
log[ n1 i=1 Yi / n1 i=1 (1 − Yi )].
The effect of the ridge penalty on parameter estimates propagates to the predictor p̂i . The linear predictor of the
linear regression model involving the ridge estimator Xi β̂(λ) shrinks towards a common value for each i, leading
to a scale difference between observation and predictor (as seen before in Section 1.10). This behaviour transfers
to the ridge logistic regression predictor, as is illustrated on simulated data. The dimension and sample size of
these data are p = 2 and n = 200, respectively. The covariate data are drawn from the standard normal, while
that of the response is sampled from a Bernoulli distribution with success probability P (Yi = 1) = exp(2Xi,1 −
2Xi,2 )/[1 + exp(2Xi,1 − 2Xi,2 )]. The logistic regression model is estimated from these data by means of ridge
penalized likelihood maximization with various choices of the penalty parameter. The bottom right plot in Figure
5.2 shows the predicted success probability versus the linear predictor for various choices of the penalty parameter.
Larger values of the penalty parameter λ flatten the slope of this curve. Consequently, for larger λ more excessive
values of the covariates are needed to achieve the same predicted success probability as those obtained with smaller
λ at more moderate covariate values. The implications for the resulting classification may become clearer when
studying the effect of the penalty parameter on the ‘failure’ and ‘success regions’ respectively defined by:
{(x1 , x2 ) : P (Y = 0 | X1 = x1 , X2 = x2 , β̂(λ)) > 0.75},
{(x1 , x2 ) : P (Y = 1 | X1 = x1 , X2 = x2 , β̂(λ)) > 0.75}.
This separates the design space in a light red (‘failure’) and light green (‘success’) domain. The white bar between
them is the domain where samples cannot be classified with high enough certainty. As λ grows, so does the white
area that separates the failure and success regions. Hence, as stronger penalization shrinks the logistic regression
parameter estimate towards zero, it produces a predictor that is less outspoken in its class assignments.

5.3 Moments
The 1st and 2nd order moment of the ridge ML parameter of the logistic model may be approximated by the final
update of the Newton-Raphson estimate. Assume the one-to-last update β̂ old to be non-random and proceed as for
72 Ridge logistic regression

2
1

1
0

0
x2

x2
−1

−1
−2

−2
−3

−3
−2 −1 0 1 2 −2 −1 0 1 2

x1 x1
2

2
1

1
0

0
x2

x2
−1

−1
−2

−2
−3

−3

−2 −1 0 1 2 −2 −1 0 1 2

x1 x1

Figure 5.3: The realized design as scatter plot (X1 vs X2 overlayed by the success (RED) and failure regions
(GREEN) for various choices of the penalty parameter: λ = 0 (top row, left panel), λ = 10 (top row, right panel)
λ = 40 (bottom row, left panel), λ = 100 (bottom row, right panel).

the ridge estimator of the linear regression model parameter to arrive at:


E β̂ new = (X⊤ WX + λIpp )−1 X⊤ WE(Z),

 
Var β̂ new
= (X⊤ WX + λIpp )−1 X⊤ W Var(Z) WX(X⊤ WX + λIpp )−1 ,

with

E(Z) = {Xβ̂ old + W−1 [E(Y) − ~g−1 (X; β old )]},

Var(Z) = W−1 Var(Y)W−1 = W−1 ,

where the identity Var(Y) = W follows from the variance of a Binomial distributed random variable. From these
expressions similar properties as for the ridge ML estimate of the regression parameter of the linear model may be
deduced. For instance, the ridge ML estimate of the logistic regression parameter converges to zero as the penalty
parameter tends to infinity (confer the top right panel of Figure 5.2). Similarly, their variances vanish as λ → ∞
(illustrated in the bottom left panel of Figure 5.2).
5.4 The Bayesian connection 73

5.4 The Bayesian connection

All penalized estimators can be formulated as Bayesian estimators, including the ridge logistic estimator. In
particular, ridge estimators correspond to Bayesian estimators with a multivariate normal prior on the regression
coefficients. Thus, assume β ∼ N (0p , ∆−1 ). The posterior distribution of β then is:

nY
n
  Yi  1−Yi o
fβ (β | Y, X) ∝ P (Yi = 1 | Xi ) P (Yi = 0 | Xi ) exp(− 21 β ⊤ ∆β).
i=1

This does not coincide with any standard distribution. But, under appropriate conditions, the posterior distribution
is asymptotically normal. This invites a (multivariate) normal approximation to the posterior distribution above.
The Laplace’s method provides (cf. Bishop, 2006).

posterior
Laplace approx.
0.005
0.004
0.003
posterior

0.002
0.001
0.000

−2 0 2 4 6 8 10

Figure 5.4: Laplace approximation to the posterior density of the Bayesian logistic regression parameter.

Laplace’s method i) centers the normal approximation at the mode of the posterior, and ii) chooses the co-
variance to match the curvature of the posterior at the mode. The posterior mode is the location of the maximum
of the posterior distribution. The location of this maximum coincides with that of the logarithm of the posterior.
The latter is the log-likelihood augmented with a ridge penalty. Hence, the posterior mode, which is taken as
the mean of the approximating Gaussian, coincides with the ridge logistic estimator. For the covariance of the
approximating Gaussian, the logarithm of the posterior is approximated by a second order Taylor series around
the posterior mode and limited to second order terms:

log[fβ (β | Y, X)] ∝ log[fβ (β | Y, X)]β=β̂MAP

∂2 
+ 12 (β − β̂MAP ) ⊤
⊤
log[fβ (β | Y, X)] (β − β̂MAP )⊤ ,
∂β∂β β=β̂MAP

in which the first order term cancels as the derivative of fβ (β | Y, X) with respect to β vanishes at the posterior
mode – its maximum. Take the exponential of this approximation and match its arguments to that of a multivariate
Gaussian exp[− 12 (β − µβ )⊤ Σ−1β (β − µβ )]. The covariance of the sought Gaussian approximation is thus the
inverse of the Hessian of the negative penalized log-likelihood. Put together the posterior is approximated by:

β | Y, X ∼ N [β̂MAP , (∆ + X⊤ WX)−1 ].

The Gaussian approximation is convenient but need not be good. Fortunately, the Bernstein-Von Mises Theorem
(Van der Vaart, 2000) tells it is very accurate when the model is regular, the prior smooth, and the sample size
sufficiently large. The quality of the approximation for an artificial example data set is shown in Figure 5.4.
74 Ridge logistic regression

5.5 Penalty parameter selection

As before the penalty parameter may be chosen through K-fold cross-validation. For the K = n case Meijer and Goeman
(2013) describe a computationally efficient approximation of the leave-one-out cross-validated loglikelihood. It
is based on the exact evaluation of the LOOCV loss, discussed in Section 1.8.2, that avoided resampling. The
approach of Meijer and Goeman (2013) hinges upon the first-order Taylor expansion of the left-out penalized
loglikelihood of the left-out estimate β̂−i (λ) around β̂(λ), which yields an approximation of the former:
 !−1 
∂ 2 Lpen
−i 
 ∂ Lpen
−i 

β̂−i (λ) ≈ β̂(λ) − 
⊤
∂β∂β β=β̂(λ) ∂β β=β̂(λ)
= β̂(λ) + (X⊤
−i,∗ W−i,−i X−i,∗ + λIpp )
−1
{X⊤ g−1 (X−i,∗ ; β̂(λ))] − λβ̂(λ)}.
−i,∗ [Y−i − ~

This approximation involves the inverse of a p × p dimensional matrix, which amounts to the evaluation of n such
inverses for the LOOCV loss. As in Section 1.8.2 this may be avoided. Rewrite both the gradient and the Hessian
of the left-out loglikelihood in the approximation of the preceding display:

X⊤ g−1 (X−i,∗ ; β̂(λ)]} − λβ̂(λ)

−i,∗ {Y−i − ~ = X⊤ {Y − ~g−1 [X; β̂(λ)]} − λβ̂(λ) − X⊤
i,∗ {Yi − g
−1
[Xi,∗ ; β̂(λ)]}
= −X⊤
i,∗ {Yi − g
−1
[Xi,∗ ; β̂(λ)]}

and

(X⊤
−i,∗ W−i,−i X−i,∗ + λIpp )
−1
= (X⊤ WX + λIpp )−1 + Wii (X⊤ WX + λIpp )−1 X⊤
i,∗

[1 − Hii (λ)]−1 Xi,∗ (X⊤ WX + λIpp )−1 ,

where the Woodbury identity has been used and now Hii (λ) = Wii Xi,∗ (X⊤ WX + λIpp )−1 X⊤ i,∗ . Substitute
both in the approximation of the left-out ridge logistic regression estimator and manipulate as in Section 1.8.2 to
obtain:

β̂−i (λ) ≈ β̂(λ) − (X⊤ WX + λIpp )−1 X⊤

i,∗ [1 − Hii (λ)]
−1
[Yi − g −1 (Xi,∗ ; β̂(λ))].
Pn
Hence, the leave-one-out cross-validated loglikelihood i=1 L[Yi | Xi,∗ , β̂−i (λ)] can now be evaluated by means
of a single inverse of a p × p dimensional matrix and some matrix multiplications. For the performance of this
approximation in terms of accuracy and speed confer Meijer and Goeman (2013).

5.6 Application
The ridge logistic regression is used here to explain the status (dead or alive) of ovarian cancer samples at the close
of the study from gene expression data at baseline. Data stem from the TCGA study (Cancer Genome Atlas Network,
2011), which measured gene expression by means of sequencing technology. Available are 295 samples with both
status and transcriptomic profiles. These profiles are composed of 19990 transcript reads. The sequencing data,
being representative of the mRNA transcript count, is heavily skewed. Zwiener et al. (2014) show that a simple
transformation of the data prior to model building generally yields a better model than tailor-made approaches.
Motivated by this observation the data were – to accommodate the zero counts – asinh-transformed. The logistic
regression model is then fitted in ridge penalized fashion, leaving the intercept unpenalized. The ridge penalty
parameter is chosen through 10-fold cross-validation minimizing the cross-validated error. R-code, and that for
the sequel of this example, is to be found below.
Listing 5.1 R code
# load libraries
library(glmnet)
library(TCGA2STAT)

# load data
OVdata <- getTCGA(disease="OV", data.type="RNASeq", type="RPKM", clinical=TRUE)
Y <- as.numeric(OVdata[[3]][,2])
X <- asinh(data.matrix(OVdata[[3]][,-c(1:3)]))
5.6 Application 75

# start fit
# optimize penalty parameter
cv.fit <- cv.glmnet(X, Y, alpha=0, family=c("binomial"),
nfolds=10, standardize=FALSE)
optL2 <- cv.fit$lambda.min

# estimate model
glmFit <- glmnet(X, Y, alpha=0, family=c("binomial"),
lambda=optL2, standardize=FALSE)

# construct linear predictor and predicted probabilities

linPred <- as.numeric(glmFit$a0 + X %*% glmFit$beta)
predProb <- exp(linPred) / (1+exp(linPred))

# visualize fit
boxplot(linPred ˜ Y, pch=20, border="lightblue", col="blue",
ylab="linear predictor", xlab="response",
main="fit")

# evaluate predictive performance

# generate k-folds balanced w.r.t. status
fold <- 10
folds1 <- rep(1:fold, ceiling(sum(Y)/fold))[1:sum(Y)]
folds0 <- rep(1:fold, ceiling((length(Y)-length(folds1))
/fold))[1:(length(Y)-length(folds1))]
shuffle1 <- sample(1:length(folds1), length(folds1))
shuffle0 <- sample(1:length(folds0), length(folds0))
folds1 <- split(shuffle1, as.factor(folds1))
folds0 <- split(shuffle0, as.factor(folds0))
folds <- list()
for (f in 1:fold){
folds[[f]] <- c(which(Y==1)[folds1[[f]]], which(Y==0)[folds0[[f]]])
}
for (f in 1:fold){
print(sum(Y[folds[[f]]]))
}

# build model
pred2obsL2 <- matrix(nrow=0, ncol=4)
colnames(pred2obsL2) <- c("optLambda", "linPred", "predProb", "obs")
for (f in 1:length(folds)){
print(f)
cv.fit <- cv.glmnet(X[-folds[[f]],], Y[-folds[[f]]], alpha=0,
family=c("binomial"), nfolds=10, standardize=FALSE)
optL2 <- cv.fit$lambda.min
glmFit <- glmnet(X[-folds[[f]],], Y[-folds[[f]]], alpha=0,
family=c("binomial"), lambda=optL2, standardize=FALSE)
linPred <- glmFit$a0 + X[folds[[f]],,drop=FALSE] %*% glmFit$beta
predProb <- exp(linPred) / (1+exp(linPred))
pred2obsL2 <- rbind(pred2obsL2, cbind(optL2, linPred, predProb, Y[folds[[f]]]))
}

# visualize fit
boxplot(pred2obsL2[,3] ˜ pred2obsL2[,4], pch=20, border="lightblue", col="blue",
ylab="linear predictor", xlab="response",
main="prediction")

The fit of the resulting model is studied. Hereto the fitted linear predictor Xβ̂(λopt ) is plotted against the
status (Figure 5.5, left panel). The plot shows some overlap between the boxes, but also a clear separation. The
latter suggests gene expression at baseline thus enables us to distinguish surviving from the to-be-diseased ovarian
cancer patients. Ideally, a decision rule based on the linear predictor can be formulated to predict an individual’s
76 Ridge logistic regression

outcome.

fit prediction
0.8

0.70
0.6

0.65
linear predictor

linear predictor
0.4

0.60
0.55
0.2

0.50
0.0

0 1 0 1

response response

Figure 5.5: Left panel: Box plot of the status vs. the fitted linear predictor using the full data set. Right panel: Box
plot of the status vs. the linear prediction in the left-out samples of the 10 folds.

The fit, however, is evaluated on the samples that have been used to build the model. This gives no insight on
the model’s predictive performance on novel samples. A replication of the study is generally costly and comparable
data sets need not be at hand. A common workaround is to evaluate the predictive performance on the same data
(Subramanian and Simon, 2010). This requires to put several samples aside for performance evaluation while
the remainder is used for model building. The left-out sample may accidently be chosen to yield an exaggerated
(either dramatically poor or overly optimistic) performance. This is avoided through the repetition of this exercise,
leaving (groups of) samples out one at the time. The left-out performance evaluations are then averaged and
believed to be representative of the predictive performance of the model on novel samples. Note that, effectively,
as the model building involves cross-validation and so does the performance evaluation, a double cross-validation
loop is applied. This procedure is applied with a ten-fold split in both loops. Denote the outer folds by f =
1, . . . , 10. Then, Xf and X−f represent the design matrix of the samples comprising fold f and that of the
remaining samples, respectively. Define Yf and Y−f similarly. The linear prediction for the left-out fold f is
then Xf β̂−f (λopt, -f ). For reference to the fit, this is compared to Yf visually by means of a boxplot as used above
(see Figure 5.5, right panel). The boxes overlap almost perfectly. Hence, little to nothing remains of the predictive
power suggested by the boxplot of the fit. The fit may thus give a reasonable description of the data at hand, but it
extrapolates poorly to new samples.

5.7 Conclusion
To deal with response variables other than continuous ones, ridge logistic regression was discussed. High-
dimensionally, the empirical identifiability problem then persists. Again, penalization came to the rescue: the
ridge penalty may be combined with other link functions than the identity. Properties of ridge regression were
shown to carry over to its logistic equivalent.

5.8 Exercises
Question 5.1
Consider an experiment involving n cancer samples. For each sample i the transcriptome of its tumor has been
profiled and is denoted Xi = (Xi1 , . . . , Xip )⊤ where Xij represents the gene j = 1, . . . , p in sample i. Addi-
tionally, the overall survival data, (Yi , ci ) for i = 1, . . . , n of these samples is available. In this Yi denotes the
survival time of sample i and ci the event indicator with ci = 0 and ci = 1 representing non- and censoredness,
respectively. You may ignore the possibility of ties in the remainder.
5.8 Exercises 77

a) Write down the Cox proportional regression model that links overall survival times (as the response variable)
to the expression levels.
b) Specify its loss function for penalized maximum partial (!) likelihood estimation of the parameters. Penal-
ization is via the ridge penalty.
c) From this loss function, derive the estimation equation for the Cox regression coefficients.
d) Describe (in words) how you would find the ‘ridge ML estimate’.

Question 5.2
Download the multtest package from BioConductor:
> source("http://www.bioconductor.org/biocLite.R")
> biocLite("multtest")
Activate the library and load leukemia data from the package:
> library(multtest)
> data(golub)
The objects golub and golub.cl are now available. The matrix-object golub contains the expression profiles
of 38 leukemia patients. Each profile comprises expression levels of 3051 genes. The numeric-object golub.cl
is an indicator variable for the leukemia type (AML or ALL) of the patient.
a) Relate the leukemia subtype and the gene expression levels by a logistic regression model. Fit this model by
means of penalized maximum likelihood, employing the ridge penalty with penalty parameter λ = 1. This
is implemented in the penalized-packages available from CRAN. Note: center (gene-wise) the expression
levels around zero.
b) Obtain the fits from the regression model. The fit is almost perfect. Could this be due to overfitting the data?
Alternatively, could it be that the biological information in the gene expression levels indeed determines the
leukemia subtype almost perfectly?
c) To discern between the two explanations for the almost perfect fit, randomly shuffle the subtypes. Refit the
logistic regression model and obtain the fits. On the basis of this and the previous fit, which explanation is
more plausible?
d) Compare the fit of the logistic model with different penalty parameters, say λ = 1 and λ = 1000. How does
λ influence the possibility of overfitting the data?
e) Describe what you would do to prevent overfitting.

Question 5.3
Download the breastCancerNKI package from BioConductor:
> source("http://www.bioconductor.org/biocLite.R")
> biocLite("breastCancerNKI")
Activate the library and load leukemia data from the package:
> library(breastCancerNKI)
> data(nki)
The eset-object nki is now available. It contains the expression profiles of 337 breast cancer patients. Each
profile comprises expression levels of 24481 genes. Extract the expression data from the object, remove all genes
with missing values, center the gene expression gene-wise around zero, and limit the data set to the first thousand
genes. The reduction of the gene dimensionality is only for computational speed.
X <- exprs(nki)
X <- X[-which(rowSums(is.na(X)) > 0),]
X <- apply(X[1:1000,], 1, function(X) X - mean(X) ) .
Furthermore, extract the estrogen receptor status (short: ER status), an important prognostic indicator for breast
cancer.
Y <- pData(nki)[,8]
a) Relate the ER status and the gene expression levels by a logistic regression model, which is fitted by means
of ridge penalized maximum likelihood. First, find the optimal value of the penalty parameter of λ by means
of cross-validation. This is implemented in optL2-function of the penalized-package available from
CRAN.
b) Evaluate whether the cross-validated likelihood indeed attains a maximum at the optimal value of λ. This
can be done with the profL2-function of the penalized-package available from CRAN.
c) Investigate the sensitivity of the penalty parameter selection with respect to the choice of the cross-validation
fold.
d) Does the optimal lambda produce a reasonable fit?
78 Ridge logistic regression

Question 5.4
The iteratively reweighted least squares (IRLS) algorithm for the numerical evaluation of the ridge logistic regres-
sion estimator requires the inversion of a p × p-dimensional matrix at each iteration. In Section 1.7 the singular
value decomposition (SVD) of the design matrix is exploited to avoid the inversion of such a matrix in the numer-
ical evaluation of the ridge regression estimator. Use this trick to show that the computational burden of the IRLS
algorithm may be reduced to one SVD prior to the iterations and the inversion of an n × n dimensional matrix at
each iteration (as is done in Eilers et al., 2001).

Question 5.5
The ridge estimator of parameter β of the logistic regression model is the maximizer of the ridge penalized
loglikelihood:
Xn 
Lpen (Y, X; β, λ) = Yi Xi β − log[1 + exp(Xi β)] − 12 λkβk22 .
i=1

The maximizer is found numerically by the iteratively reweighted least squares (IRLS) algorithm which is outlined
in Section 5.2. Modify the algorithm to find the generalized ridge estimator of β defined as:
Xn 
Lpen (Y, X; β, λ) = Yi Xi β − log[1 + exp(Xi β)] − 21 (β − β0 )⊤ ∆(β − β0 ),
i=1

where β0 and ∆ are as in Chapter 3.

6 Lasso regression

In this chapter we return to the linear regression model, which is still fitted in penalized fashion but this time with
a so-called lasso penalty. Yet another penalty? Yes, but it will turn out to have interesting consequences. The
outline of this chapter loosely follows that of its counterpart on ridge regression (Chapter 1). The chapter can – at
least partially – be seen as an elaborated version of the original work on lasso regression, i.e. Tibshirani (1996),
with most topics covered and visualized more extensively and incorporating results and examples published since.
Recall that ridge regression finds an estimator of the parameter of the linear regression model through the
minimization of:

kY − Xβk22 + fpen (β, λ), (6.1)

with fpen (β, λ) = λkβk22 . The particular choice of the penalty function originated in a post-hoc motivation of the
ad-hoc fix to the singularity of the matrix X⊤ X, stemming from the design matrix X not being of full rank (i.e.
rank(X) < p). The ad-hoc nature of the fix suggests that the choice for the squared Euclidean norm of β as a
penalty is arbitrary and other choices may be considered, some of which were already encountered in Chapter 3.
One such choice is the so-called lasso penalty giving rise to lasso regression, as introduced by Tibshirani
(1996). Like ridge regression, lasso regression fits the linear regression model Y = Xβ + ε with the standard
assumption on the error ε. Like ridge regression, it does so by minimizing the sum of squares augmented with
a penalty. Hence, lasso regression too minimizes loss function (6.1). The difference with ridge regression is in
the penalty function. Instead of the squared Euclidean norm, lasso regression uses the ℓ1 -norm: fpen (β, λ1 ) =
λ1 kβk1 , the sum of the absolute values of the regression parameters multiplied by the lasso penalty parameter λ1 .
To distinguish the ridge and lasso penalty parameters they are henceforth denoted λ2 and λ1 , respectively, with
the subscript referring to the norm used in the penalty. The lasso regression loss function is thus:
Xn Xp
Llasso (β; λ) = kY − X βk22 + λ1 kβk1 = (Yi − Xi∗ β)2 + λ1 |βj |. (6.2)
i=1 j=1

The lasso regression estimator is then defined as the minimizer of this loss function. As with the ridge regression
loss function, the maximum likelihood estimate of β minimizes the first part, while the second part is minimized
by setting β equal to the p dimensional zero vector. For λ1 close to zero, the lasso estimate is close to the
maximum likelihood estimate. Whereas for large λ1 , the penalty term overshadows the sum-of-squares, and
the lasso estimate is small (in some sense). Intermediate choices of λ1 mold a compromise between those two
extremes, with the penalty parameter determining the contribution of each part to this compromise. The lasso
regression estimator thus is not one but a whole sequence of estimators of β, one for every λ1 ∈ R>0 . This
sequence is the lasso regularization path, defined as {β̂(λ1 ) : λ1 ∈ R>0 }. To arrive at a final lasso estimator of
β, like its ridge counterpart, the lasso penalty parameter λ1 needs to be chosen (see Section ??).
The ℓ1 penalty of lasso regression is equally arbitrary as the ℓ2 -penalty of ridge regression. The latter ensured
the existence of a well-defined estimator of the regression parameter β in the presence of super-collinearity in the
design matrix X, in particular when the dimension p exceeds the sample size n. The augmentation of the sum-
of-squares with the lasso penalty achieves the same. This is illustrated in Figure 6.1. For the high-dimensional
setting with p = 2 and n = 1 and arbitrary data the level sets of the sum-of-squares kY − X βk22 and the lasso
regression loss kY − X βk22 + λ1 kβk1 are plotted (left and right panel, respectively). In both panels the minimum
is indicated in red. For the sum-of-squares the minimum is a line. As pointed out before in Section 1.2 of Chapter
1 on ridge regression, this minimum is determined up to an element of the null set of the design matrix X, which
in this case is non-trivial. In contrast, the lasso regression loss exhibits a unique well-defined minimum. Hence,
the augmentation of the sum-of-squares with the lasso penalty yields a well-defined estimator of the regression
parameter. (This needs some attenuation: in general the minimum of the lasso regression loss need not be unique,
confer Section 6.1).
80 Lasso regression

sum−of−squares loss lasso regression loss

2

10
7.5
5
5
2
0.1
1
1

1
1
1
0.5

0.5

3.5
β2

β2
0

3.5
0.25

0.5
0.1
−1

−1
0.25

2
2

5
−2

−2
−2 −1 0 1 2 −2 −1 0 1 2

β1 β1

Figure 6.1: Contour plots of the sum-of-squares and the lasso regression loss (left and right panel, respectively).
The dotted grey line represent level sets. The red line and dot represent the location of minimum in both panels.

The mathematics involved in the derivation in this chapter tends to be more intricate than for ridge regression.
This is due to the non-differentiability of the lasso penalty at zero. This has consequences on all aspects of the
lasso regression estimator as is already obvious in the right-hand panel of Figure 6.1: confer the non-differentiable
points of the lasso regression loss level sets.

6.1 Uniqueness
The lasso regression loss function is the sum of the sum-of-squares criterion and a sum of absolute value functions.
Both are convex in β: the former is not strict convex due to the high-dimensionality and the absolute value function
is convex due to its piece-wise linearity. Thereby the lasso loss function too is convex but not strict. Consequently,
its minimum need not be uniquely defined. But, the set of solutions of a convex minimization problem is convex
(Theorem 9.4.1, Fletcher, 1987). Hence, would there exist multiple minimizers of the lasso loss function, they
can be used to construct a convex set of minimizers. Thus, if β̂a (λ1 ) and β̂b (λ1 ) are lasso estimators, then so are
(1 − θ)β̂a (λ1 ) + θβ̂b (λ1 ) for θ ∈ (0, 1). This is illustrated in Example 6.1.

Example 6.1 (Perfectly super-collinear covariates)

Consider the standard linear regression model Yi = Xi,∗ β + εi for i = 1, . . . , n and with the εi i.i.d. normally
distributed with zero mean and a common variance. The rows of the design matrix X are of length two, neither
column represents the intercept, but X∗,1 = X∗,2 . Suppose an estimate of the regression parameter β of this model
is obtained through the minimization of the sum-of-squares augmented with a lasso penalty, kY−Xβk22 +λ1 kβk1
with penalty parameter λ1 > 0. To find the minimizer define u = β1 + β2 and v = β1 − β2 and rewrite the lasso
loss criterion to:

kY − Xβk22 + λ1 kβk1 = kY − X∗,1 uk22 + 21 λ1 (|u + v| + |u − v|).

The function |u + v| + |u − v| is minimized with respect to v for any v such that |v| < |u| and the corresponding
minimum equals 2|u|. The estimator of u thus minimizes:

kY − X∗,1 uk22 + λ1 |u|.

For sufficiently small values of λ1 the estimate of u will be unequal to zero. Then, any v such that |v| < |u| will
yield the same minimum of the lasso loss function. Consequently, β̂(λ1 ) is not uniquely defined as β̂1 (λ1 ) =
1 1
2 [û(λ1 ) + v̂(λ1 )] need not equal β̂2 (λ1 ) = 2 [û(λ1 ) − v̂(λ1 )] for any v̂(λ1 ) such that 0 < |v̂(λ1 )| < |û(λ1 )|. 
6.1 Uniqueness 81

The lasso regression estimator β̂(λ1 ) need not be unique, but its linear predictor Xβ̂(λ1 ) is. This can be
proven by contradiction (Tibshirani, 2013). Suppose there exists two lasso regression estimators of β, denoted
β̂a (λ1 ) and β̂b (λ1 ), such that Xβ̂a (λ1 ) 6= Xβ̂b (λ1 ). Define c to be the minimum of the lasso loss function. Then,
by definition of the lasso estimators β̂a (λ1 ) and β̂b (λ1 ) satisfy:

kY − Xβ̂a (λ1 )k22 + λ1 kβ̂a (λ1 )k1 = c = kY − Xβ̂b (λ1 )k22 + λ1 kβ̂b (λ1 )k1 .

For θ ∈ (0, 1) we then have:

kY − X[(1 − θ)β̂a (λ1 ) + θβ̂b (λ1 )]k22 + λ1 k(1 − θ)β̂a (λ1 ) + θβ̂b (λ1 )k1
= k(1 − θ)[Y − Xβ̂a (λ1 )] + θ[Y − Xβ̂b (λ1 )]k22 + λ1 k(1 − θ)β̂a (λ1 ) + θβ̂b (λ1 )k1
< (1 − θ)kY − Xβ̂a (λ1 )k22 + θkY − Xβ̂b (λ1 )k22 + (1 − θ)λ1 kβ̂a (λ1 )k1 + θλ1 kβ̂b (λ1 )k1
= (1 − θ)c + θc = c,

by the strict convexity of kY − Xβk22 in Xβ and the convexity of kβk1 on θ ∈ (0, 1). This implies that (1 −
θ)β̂a (λ1 )+θβ̂b (λ1 ) yields a lower minimum of the lasso loss function and contradicts our assumption that β̂a (λ1 )
and β̂b (λ1 ) are lasso regression estimators.

Example 6.2 (Perfectly super-collinear covariates, revisited)

Revisit the setting of Example 6.1, where a linear regression model without intercept and only two but perfectly
correlated covariates is fitted to data. The example revealed that the lasso estimator need not be unique. The lasso
predictor, however, is
b 1 ) = Xβ̂(λ1 ) = X∗,1 β̂1 (λ1 ) + X∗,2 β̂2 (λ1 )
Y(λ = X∗,1 [β̂1 (λ1 ) + β̂2 (λ1 )] = X∗,1 û(λ1 ),

with u defined and (uniquely) estimated as in Example 6.1 and v dropping from the predictor. 

Example 6.3
The issues, non- and uniqueness of the lasso-estimator and predictor, respectively, raised above are illustrated in a
numerical setting. Hereto data are generated in accordance with the linear regression model Y = Xβ + ε where
the n = 5 rows of X are sampled from N [0p , (1 − ρ)Ipp + ρ1pp ] with p = 10, ρ = 0.99, β = (1⊤ ⊤
3 , 0p−3 )
⊤
1
and ε ∼ N (0p , 10 Inn ). With these data the lasso estimator of the regression parameter β for λ1 = 1 is evaluated
using two different algorithms (see Section 6.4). Employed implementations of the algorithms are those available
through the R-packages penalized and glmnet. Both estimates, denoted β̂p (λ1 ) and β̂g (λ1 ) (the subscript
refers to the first letter of the package), are given in Table 6.3. The table reveals that the estimates differ, in par-

β1 β2 β3 β4 β5 β6 β7 β8 β9 β10
penalized β̂p (λ1 ) 0.267 0.000 1.649 0.093 0.000 0.000 0.000 0.571 0.000 0.269
glmnet β̂g (λ1 ) 0.269 0.000 1.776 0.282 0.195 0.000 0.000 0.325 0.000 0.000

Table 6.1: Lasso estimates of the linear regression β for both algorithms.

ticular in their support (i.e. the set of nonzero values of the estimate of β). This is troublesome when it comes
to communication of the optimal model. From a different perspective the realized loss kY − Xβk22 + λ1 kβk1
for each estimate is approximately equal to 2.99, with the difference possibly due to convergence criteria of the
algorithms. On another note, their corresponding predictors, Xβ̂p (λ1 ) and Xβ̂g (λ1 ), correlate almost perfectly:
cor[Xβ̂p (λ1 ), Xβ̂g (λ1 )] = 0.999. These results thus corroborate the non-uniqueness of the estimator and the
uniqueness of the predictor.

The R-script provides the code to reproduce the analysis.

Listing 6.1 R code

# set the random seed
set.seed(4)
82 Lasso regression

# load libraries
library(penalized)
library(glmnet)
library(mvtnorm)

# set sample size

p <- 10

# create covariance matrix

Sigma <- matrix(0.99, p, p)
diag(Sigma) <- 1

# sample the design matrix

n <- 5
X <- rmvnorm(10, sigma=Sigma)

# create a sparse beta vector

betas <- c(rep(1, 3), rep(0, p-3))

# sample response
Y <- X %*% betas + rnorm(n, sd=0.1)

# evaluate lasso estimator with two methods

Bhat1 <- matrix(as.numeric(coef(penalized(Y, X, lambda1=1, unpenalized=˜0),
"all")), ncol=1)
Bhat2 <- matrix(as.numeric(coef(glmnet(X, Y, lambda=1/(2*n), standardize=FALSE,
intercept=FALSE)))[-1], ncol=1)

# compare estimates
cbind(Bhat1, Bhat2)

# compare the loss

sum((Y - X %*% Bhat1)ˆ2) + sum(abs(Bhat1))
sum((Y - X %*% Bhat2)ˆ2) + sum(abs(Bhat2))

# compare predictor
cor(X %*% Bhat1, X %*% Bhat2)
Note that in the code above the evaluation of the lasso estimator appears to employ a different lasso penalty
parameter λ1 . This is due to the fact that internally (after removal of standardization of X and Y) the loss
1
functions optimized are kY − Xβk22 + λ1 kβk1 vs. 2n kY − Xβk22 + λ1 kβk1 . Rescaling of λ1 resolves this
issue. 

6.2 Analytic solutions

In general, no explicit expression for the lasso regression estimator exists. There are exceptions, as illustrated in
Examples 6.4 and 6.6. Nonetheless, it is possible to show properties of the lasso estimator, amongst others of the
smoothness of its regularization path (Theorem 6.1) and the limiting behaviour as λ1 → ∞ (see the end of this
section).
Theorem 6.1 (Theorem 2, Rosset and Zhu, 2007)
The lasso regression loss function (6.2) yields a piecewise linear (in λ1 ) regularization path {β̂(λ1 ) : R>0 }.

Proof. Confer Rosset and Zhu (2007). 

This piecewise linear nature of the lasso solution path is illustrated in the left-hand panel of Figure 6.2 of an arbi-
trary data set. At each vertical dotted line a discontinuity in the derivative with respect to λ1 of the regularization
path of a lasso estimate of an element of β may occur. The plot also foreshadows the λ1 → ∞ limiting behaviour
of the lasso regression estimator: the estimator tends to zero. This is no surprise knowing that the ridge regression
estimator exhibits the same behaviour and the lasso regression loss function is of similar form as that of ridge
regression: a sum-of-squares plus a penalty term (which is linear in the penalty parameter).
6.2 Analytic solutions 83

Lasso regularization path The soft−threshold function

0.15

3
0.10

2
0.05

1
β(lamdba1)
0.00
β(λ1)

0
^

^
−0.05

−1
−0.10

−2
−0.15

soft−threshold

−3
hard−threshold

0 5 10 15 20 25 30 −3 −2 −1 0 1 2 3
^
λ1 β

Figure 6.2: The left panel shows the regularization path of the lasso regression estimator for simulated data. The
vertical grey dotted lines indicate the values of λ1 at which there is a discontinuity in the derivative (with respect to
λ1 ) of the lasso regularization path of one the regression estimates. The right panel displays the soft (solid, red)
and hard (grey, dotted) threshold functions.

For particular cases, an orthormal design (Example 6.4) and p = 2 (Example 6.6), an analytic expression for
the lasso regression estimator exists. While the latter is of limited use, the former is exemplary and will come of
use later in the numerical evaluation of the lasso regression estimator in the general case (see Section 6.4).
Example 6.4 Orthonormal design matrix
Consider an orthonormal design matrix X, i.e. X⊤ X = Ipp = (X⊤ X)−1 . The lasso estimator then is:

β̂j (λ1 ) = sign(β̂j )(|β̂j | − 12 λ1 )+ ,

where β̂ = (X⊤ X)−1 X⊤ Y = X⊤ Y is the maximum likelihood estimator of β and β̂j its j-th element and
f (x) = (x)+ = max{x, 0}. This expression for the lasso regression estimator can be obtained as follows.
Rewrite the lasso regression loss criterion:
Xp
min kY − X βk22 + λ1 kβk1 = min Y⊤ Y − Y⊤ X β − β ⊤ X⊤ Y + β ⊤ X⊤ X β + λ1 |βj |
β β j=1
Xp
∝ min −β̂ ⊤ β − β ⊤ β̂ + β ⊤ β + λ1 |βj |
β j=1
Xp

= min − 2β̂jOLS βj + βj2 + λ1 |βj |
β1 ,...,βp j=1
Xp
= min −2β̂j βj + βj2 + λ1 |βj |).
j=1 βj

The minimization problem can thus be solved per regression coefficient. This gives:
(
2 minβj −2β̂j βj + βj2 + λ1 βj if βj > 0,
min −2β̂j βj + βj + λ1 |βj | =
βj minβj −2β̂j βj + βj2 − λ1 βj if βj < 0.

The minimization within the sum over the covariates is with respect to each element of the regression parameter
separately. Optimization with respect to the j-th one gives:

 β̂j − 21 λ1 if β̂j (λ1 ) > 0
β̂j (λ1 ) = β̂ + 1 λ if β̂j (λ1 ) < 0
 j 2 1
0 otherwise
84 Lasso regression

Put these two equations together to arrive at the form of the lasso regression estimator above.
The analytic expression for the lasso regression estimator above provides insight in how it relates to the maxi-
mum likelihood estimator of β. The right-hand side panel of Figure 6.2 depicts this relationship. Effectively, the
lasso regression estimator thresholds (after a translation) its maximum likelihood counterpart. The function is also
referred to as the soft-threshold function (for contrast the hard-threshold function is also plotted – dotted line – in
Figure 6.2). 
Example 6.5 (Orthogonal design matrix)
The analytic solution of the lasso regression estimator for experiments with an orthonormal design matrix applies
to those with an orthogonal design matrix. This is illustrated by a numerical example. Use the lasso estimator
with λ1 = 10 to fit the linear regression model to the response data and the design matrix:


Y⊤ = −4.9 −0.8 −8.9 4.9 1.1 −2.0 ,
 
⊤ 1 −1 3 −3 1 1
X = .
−3 −3 −1 0 3 0
Note that the design matrix is orthogonal, i.e. its columns are orthogonal (but not normalized to one). The
orthogonality of X yields a diagonal X⊤ X, and so it its inverse (X⊤ X)−1 . Here diag(X⊤ X) = (22, 28).
Rescale X to an orthonormal design matrix, denoted X̃, and rewrite the lasso regression loss function to:
 √ −1  √ 
2
2 22 √ 0 22 √ 0
kY − Xβk2 + λ1 kβk1 = Y − X β + λ1 kβk1
0 28 0 28
2
2
√ √
= kY − X̃γk2 + (λ1 / 22)|γ1 | + (λ1 / 28)|γ2 |,
√ √ ⊤
where γ = ( 22β1 , 28β2 ) . By the same argument this loss can be minimized with respect to each element of
γ separately. In particular, the soft-threshold function provides an analytic expression for the estimates of γ:
√ √ √
γ̂1 (λ1 / 22) = sign(γ̂1 )[|γ̂1 | − 21 (λ1 / 22)]+ = −[9.892513 − 12 (10/ 22)]+ = −8.826509,
√ √ √
γ̂2 (λ1 / 28) = sign(γ̂2 )[|γ̂2 | − 21 (λ1 / 28)]+ = [5.537180 − 12 (10/ 28)]+ = 4.592269,
where γ̂1 and γ̂2 are the ordinary least square estimates of γ1 and γ2 obtained from regressing Y on the correspond-
ing column of X̃. Rescale back and obtain the lasso regression estimate: β̂(10) = (−1.881818, 0.8678572)⊤. 
Example 6.6 (p = 2 with equivariant covariates, Leng et al., 2006)
Let p = 2 and suppose the design matrix X has equivariant covariates. Without loss of generality they are assumed
to have unit variance. We may thus write
 
⊤ 1 ρ
X X = ,
ρ 1
for some ρ ∈ (−1, 1). The lasso regression estimator is then of similar form as in the orthonormal case: β̂j (λ1 ) =
sign(β̂j )(|β̂j | − γ)+ , with soft-threshold parameter γ that now depends on λ1 , ρ and the maximum likelihood
estimate β̂ (see Exercise 6.6). 
Apart from the specific cases outlined in the two examples above no other explicit solutions for the minimizer
of the lasso regression loss function appears to be known. Locally though, for large enough values of λ1 , an
analytic expression for solution can also be derived. Hereto we point out that (details to be included later) the
lasso regression estimator satisfies the following estimating equation:
X⊤ Xβ̂(λ1 ) = X⊤ Y − 12 λ1 ẑ
for some ẑ ∈ Rp with (ẑ)j = sign{[β̂(λ1 )]j } whenever [β̂j (λ1 )]j 6= 0 and (ẑ)j ∈ [−1, 1] if [β̂j (λ1 )]j = 0. Then:
Xp
0 ≤ [β̂(λ1 )]⊤ X⊤ Xβ̂(λ1 ) = [β̂(λ1 )]⊤ (X⊤ Y − 21 λ1 ẑ) = [β̂(λ1 )]j (X⊤ Y − 21 λ1 ẑ)j .
j=1

For λ1 > 2kX⊤ Yk∞ the summands on the right-hand side satisfy:
[β̂(λ1 )]j (X⊤ Y − 12 λ1 ẑ)j < 0 if [β̂(λ1 )]j > 0,
[β̂(λ1 )]j (X⊤ Y − 21 λ1 ẑ)j = 0 if [β̂(λ1 )]j = 0,
[β̂(λ1 )]j (X⊤ Y − 21 λ1 ẑ)j < 0 if [β̂(λ1 )]j < 0.
This implies that β̂(λ1 ) = 0p if λ1 > 2kX⊤ Yk∞ , where kak∞ is the supremum norm of vector a defined as
kak∞ = max{|a1 |, |a2 |, . . . , |ap |}.
6.3 Sparsity 85

6.3 Sparsity
The change from the ℓ2 -norm to the ℓ1 -norm in the penalty may seem only a detail. Indeed, both ridge and
lasso regression fit the same linear regression model. But the attractiveness of the lasso lies not in what it fits,
but in a consequence of how it fits the linear regression model. The lasso estimator of the vector of regression
parameters may contain some or many zero’s. In contrast, ridge regression yields an estimator of β with elements
(possibly) close to zero, but unlikely equal to zero. Hence, lasso penalization results in β̂j (λ1 ) = 0 for some j (in
particular for large values of λ1 , see Section 6.1), while ridge penalization yields an estimate of the j-th element
of the regression parameter β̂j (λ2 ) 6= 0. A zero estimate of a regression coefficient means that the corresponding
covariate has no effect on the response and can be excluded from the model. Effectively, this amounts to variable
selection. Where traditionally the linear regression model is fitted by means of maximum likelihood followed by
testing step to weed out these covariates with effects indistinguishable from zero, lasso regression is a one-step-go
procedure that simulatenously estimates and selects.
The in-built variable selection of the lasso regression estimator is a geometric accident. To understand how
it comes about the lasso regression loss optimization problem (6.2) is reformulated as a constrained estimation
problem (using the same argumentation as previously employed for ridge regression, see Section 1.5):

min kY − Xβk22 .
kβk1 ≤c(λ1 )

where c(λ1 ) = kβ̂(λ1 )k1 . Again, this is the standard least squares problem, with the only difference that the
sum of the (absolute) regression parameters β1 , β2 , . . . , βp is required to be smaller than c(λ1 ). The effect of this
requirement is that the lasso estimates of the regression parameters can no longer assume any value (from −∞ to
∞, as is the case in standard linear regression), but are limited to a certain range of values. With the lasso and
ridge regression estimators minimizing the same sum-of-squares, the key difference with the constrained estima-
tion formulation of ridge regression is not in the explicit form of c(λ1 ) (and is set to some arbitrary convenient
value in the remainder of this section) but in what is bounded by c(λ1 ) and the domain of acceptable values for β
that it implies. For the lasso regression estimator the domain is specified by a bound on the ℓ1 -norm of the regres-
sion parameter while for its ridge counterpart the bound is applied to the squared ℓ2 -norm of β. The parameter
constraints implied by the lasso and ridge norms result in balls in different norms:

{β ∈ Rp : |β1 | + |β2 | + . . . + |βp | ≤ c1 (λ1 )},

{β ∈ Rp : β12 + β22 + . . . + βp2 ≤ c2 (λ2 )},

respectively, and where c(·) is now equipped with a subscript referring to the norm to stress that it is different
for lasso and ridge. The left-hand panel of Figure 6.3 visualizes these parameter constraints for p = 2 and
c1 (λ1 ) = 2 = c2 (λ2 ). In the Euclidean space ridge yields a spherical constraint for β, while a diamond-like shape
for the lasso. The lasso regression estimate is then that β inside this diamond domain which yields the smallest
sum-of-squares (as is visualized by right-hand panel of Figure 6.3).
The selection property of the lasso is due to the fact that the diamond-shaped parameter constraint has its
corners falling on the axes. For a point to lie on an axis, one coordinate needs to equal zero. The lasso regression
estimator coincides with the point inside the diamond closest to the maximum likelihood estimate. This point
may correspond to a corner of the diamond, in which case one of the coordinates (regression parameters) equals
zero and, consequently, the lasso regression estimator does not select this element of β. Figure 6.4 illustrates the
selection property for the case with p = 2 and an orthonormal design matrix. An orthornormal design matrix
yields level sets (orange dotted circles in Figure 6.4) of the sum-of-squares that are spherical and centered around
the maximum likelihood estimate (red dot in Figure 6.4). For maximum likelihood estimates inside the grey
areas the closest point in the diamond-shaped parameter domain will be on one of its corners. Hence, for these
maximum likelihood estimates the corresponding lasso regression estimate will include on a single covariate in
the model. The geometrical explanation of the selection property of the lasso regression estimator also applies to
non-orthonormal design matrices and in dimensions larger than two. In particular, high-dimensionally, the sum-
of-squares may be a degenerated ellipsoid, that can and will still hit a corner of the diamond-shaped parameter
domain. Finally, note that a zero value of lasso regression estimate does imply neither that the parameter is indeed
zero nor that it will be statistically indistinguishable from zero.
Larger values of the lasso penalty parameter λ1 induce smaller parameter constraints. Consequently, the num-
ber of zero elements in the lasso regression estimator of β increases as λ1 increases. However, where kβ̂(λ1 )k1
decreases monotonically as λ1 increases (left panel of Figure 6.5 for an example and Exercise 6.7), the number of
non-zero coefficients does not. Locally, at some finite λ1 , the number of non-zero elements in β̂(λ1 ) may increase
86 Lasso regression

Lasso and ridge penalty Lasso as constrained estimation

ML estimate

8
lasso estimate
2

6
1

4
0
beta2

beta2

2
−1

0
−2

lasso penalty
−3

−2
ridge penalty

−3 −2 −1 0 1 2 −2 0 2 4 6 8

beta1 beta1

Figure 6.3: Left panel: The lasso parameter constraint (|β1 | + |β2 | ≤ 2) and its ridge counterpart (β12 + β22 ≤ 2).
Solution path of the ridge estimator and its variance. Right panel: the lasso regression estimator as a constrained
least squares estimtor.

Figure 6.4: Shrinkage with the lasso. The range of possible lasso estimates is demarcated by the diamond around
the origin. The grey areas contain all points that are closest to one of the diamond’s corners than to any other
point inside the diamond. If the OLS estimate falls inside any of these grey areas, the lasso shrinks it to the closest
diamond tip (which corresponds to a sparse solution). For example, let the red dot in the fourth quadrant be an
OLS estimate. It is in a grey area. Hence, its lasso estimate is the red dot at the lowest tip of the diamond.

with λ1 , to only go down again as λ1 is sufficiently increased (as in the λ1 → ∞ limit the number of non-zero
elements is zero, see the argumentation at the end of Section 6.2). The right panel of Figure 6.5 illustrates this
6.3 Sparsity 87

behavior for an arbitrary data set.

L1−norm vs. penalty parameter Number of nonzero vs. penalty parameter

50
3.5
3.0

45
2.5

40
#[β(λ1) != 0]
||β(λ1) ||

2.0
^

35
1.5
1.0

30
0.5

25
0.0

0 10 20 30 40 50 0 2 4 6 8 10

λ1 λ1

Figure 6.5: Contour plots of the sum-of-squares and the lasso regression loss (left and right panel, respectively).
The dotted grey line represent level sets. The red line and dot represent the the location of minimum in both panels.

The attractiveness of the lasso regression estimator is in its simultaneous estimation and selection of parame-
ters. For large enough values of the penalty parameter λ1 the estimated regression model comprises only a subset
of the supplied covariates. In high-dimensions (demanding a large penalty parameter) the number of selected
parameters by the lasso regression estimator is usually small (relative to the total number of parameters), thus
producing a so-called sparse model. Would one adhere to the parsimony principle, such a sparse and thus simpler
model is preferable over a full model. Simpler may be better, but too simple is worse. The phenomenon or system
that is to be described by the model need not be sparse. For instance, in molecular biology the regulatory network
of the cell is no longer believed to be sparse (Boyle et al., 2017). Similarly, when analyzing brain image data, the
connectivity of the brain is not believed to be sparse.

6.3.1 Maximum number of selected covariates

The number of parameter/covariates selected by the lasso regression estimator is bounded non-trivially. The
cardinality (i.e. the number of included covariates) of every lasso estimated linear regression model is smaller than
or equal to min{n, p} (Bühlmann and Van De Geer, 2011). According to Bühlmann and Van De Geer (2011) this
is obvious from the analysis of the LARS algorithm of Efron et al. (2004) (which is to be discussed in Section
??). For now we just provide an R-script that generates the regularization paths using the lars-package for
the diabetes data included in the package for a random number of samples n not exceeding the number of
covariates p.

Listing 6.2 R code

# activate library
library(lars)

# load data
data(diabetes)
X <- diabetes$x
Y <- diabetes$y

# set sample size

n <- sample(1:ncol(X), 1)
id <- sample(1:length(Y), n)
88 Lasso regression

# plot regularization paths

plot(lars(X[id,], Y[id], intercept=FALSE))
Irrespective of the drawn sample size n the plotted regularization paths all terminate before the n + 1-th variate
enters the model. This could of course be circumstantial evidence at best, or even be labelled a bug in the software.
But even without the LARS algorithm the nontrivial part of the inequality, that the number of selected variates
p does not exceed the sample size n, can be proven (Osborne et al., 2000).
Theorem 6.2 (Theorem 6, Osborne et al., 2000)
If p > n and β̂(λ1 ) is a minimizer of the lasso regresssion loss function (6.2), then β̂(λ1 ) has at most n non-zero
entries.

Proof. Confer Osborne et al. (2000). 

In the high-dimensional setting, when p is large compared to n small, this implies a considerable dimension
reduction. It is, however, somewhat unsatisfactory that it is the study design, i.e. the inclusion of the number of
samples, that determines the upperbound of model size.

6.4 Estimation
In the absence of an analytic expression for the optimum of the lasso loss function (6.2), much attention is devoted
to numerical procedures to find it.

6.4.1 Quadratic programming

In the original lasso paper Tibshirani (1996) reformulates the lasso optimization problem to a quadratic program.
A quadratic problem optimizes a quadratic form subject to linear constraints. This is a well-studied optimiza-
tion problem for which many readily available implementations exist (e.g., the quadprog-package in R). The
quadratic program that is equivalent to the lasso regression problem (which minimizes the least squares criterion,
kY − Xβk22 subject to kβk1 < c(λ1 )) is:

min 1 (Y − Xβ)⊤ (Y − Xβ), (6.3)

Rβ≥0 2

where R is a q × p dimensional linear constraint matrix that specifies the linear constraints on the parameter β.
For p = 2 the domain implied by lasso parameter constraint {β ∈ R2 : kβk1 < c(λ1 )} is equal to:

{β ∈ R2 : β1 + β2 ≤ c(λ1 )} ∩ {β ∈ R2 : β1 − β2 ≥ −c(λ1 )} ∩ {β ∈ R2 : β1 − β2 ≤ c(λ1 )}

∩ {β ∈ R2 : β1 + β2 ≥ −c(λ1 )}.

This collection of linear parameter constraints can be aggregated, when using:

 
1 1
 −1 −1 
R =   1 −1  ,


−1 1

into {β ∈ R2 : Rβ ≥ −c(λ1 )}.

To solve the quadratic program (6.3) it is usually reformulated in terms of its dual. Hereto we introduce the
Lagrangian:

L(β, ν) = 1
2 (Y − Xβ)⊤ (Y − Xβ) + ν ⊤ Rβ, (6.4)

where ν = (ν1 , . . . , νq )⊤ is the vector of non-negative multipliers. The dual function is now defined as inf β L(β, ν).
This infimum is attained at:

β̃ = (X⊤ X)−1 X⊤ Y + (X⊤ X)−1 R⊤ ν, (6.5)

which can be verified by equating the first order partial derivative with respect to β of the Lagrangian to zero and
solving for β. Substitution of β = β ∗ into the dual function gives, after changing the minus sign:
1 ⊤ ⊤ −1 ⊤
2 ν R(X X) R ν + ν ⊤ R(X⊤ X)−1 X⊤ Y + 21 Y⊤ X(X⊤ X)−1 X⊤ Y.
6.4 Estimation 89

The dual problem minimizes this expression (from which the last term is dropped as is does not involve ν) with
respect to ν, subject to ν ≥ 0. Although also a quadratic programming problem, the dual problem a) has simpler
constraints and b) is defined on a lower dimensional space (if the number of columns of R exceeds its number
of rows) than the primal problem. If ν̃ is the solution of the dual problem, the solution of the primal problem is
obtained from Equation (6.5). Note that in the first term on the right hand side of Equation (6.5) we recognize the
unconstrained least squares estimator of β. Refer to, e.g., Bertsekas (2014) for more on quadratic programming.
Example 6.5 (Orthogonal design matrix, continued)
The evaluation of the lasso regression estimator by means of quadratic programming is illustrated using the data
from the numerical Example 6.5. The R-script below solves, the implementation of the quadprog-package, the
quadratic program associated with the lasso regression problem of the aforementioned example.
Listing 6.3 R code
# load library
library(quadprog)

# data
Y <- matrix(c(-4.9, -0.8, -8.9, 4.9, 1.1, -2.0), ncol=1)
X <- t(matrix(c(1, -1, 3, -3, 1, 1, -3, -3, -1, 0, 3, 0), nrow=2, byrow=TRUE))

# constraint radius
L1norm <- 1.881818 + 0.8678572

# solve the quadratic program

solve.QP(t(X) %*% X, t(X) %*% Y,
t(matrix(c(1, 1, -1, -1, 1, -1, -1, 1), ncol=2, byrow=TRUE)),
L1norm*c(-1, -1, -1, -1))$solution
The resulting estimates coincide with those found earlier. 

For relatively small p quadratic programming is a viable option to find the lasso regression estimator. For large p
it is practically not feasible. Above the linear constraint matrix R is 4 × 2 dimensional for p = 2. When p = 3, it
requires a linear constraint matrix R with eight rows. In general, 2p linear constraints are required to fully specify
the lasso parameter constraint on the regression parameter. Already when p = 100, the specification of only the
linear constraint matrix R will take endlessly, leave alone solving the corresponding quadratic program.

6.4.2 Iterative ridge

Why develop something new, when one can also make do with existing tools? The loss function of the lasso
regression estimator can be optimized by iterative application of ridge regression (as pointed out in Fan and Li,
2001). It requires an approximation of the lasso penalty, or the absolute value function. Set p = 1 and let β0 be
an initial parameter value for β around which the absolute value function |β| is to be approximated. Its quadratic
approximation then is:

|β| ≈ |β0 | + 21 |β0 |−2 (β 2 − β02 ).

An illustration of this approximation is provided in the left panel of Figure 6.6.

The lasso regression estimator is evaluated through iterative application of the ridge regression estimator. This
iterative procedure needs initiation by some guess β (0) for β. For example, the ridge estimator itself may serve
as such. Then, at the k + 1-th iteration an update β (k+1) of the lasso regression estimator of β is to be found.
Application of the quadratic approximation to the absolute value functions of the elements of β (around the k-th
update β (k) ) in the lasso penalty yields an approximation to the lasso regression loss function:

kY − X β (k+1) k22 + λ1 kβ (k+1) k1 ≈ kY − X β (k+1) k22 + λ1 kβ (k) k1

Xp (k) (k+1) 2
Xp (k) (k)
+ 21 λ1 |βj |−1 [βj ] − 12 λ1 |βj |−1 [βj ]2
j=1 j=1
Xp (k) (k+1) 2
∝ kY − X β (k+1) k22 + 21 λ1 |βj |−1 [βj ] .
j=1

The loss function now contains a weighted ridge penalty. In this one recognizes a generalized ridge regression loss
function (see Chapter 3). As its minimizer is known, the approximated lasso regression loss function is optimized
90 Lasso regression

Approximation to lasso penalty

5

10
7.5
5
4

1
3

1
| beta |

0.5

3.5
β2

3.5
2

−1
1

lasso penalty
approximation
0

5
−2
−4 −2 0 2 4
−2 −1 0 1 2
beta
β1

Figure 6.6: Left panel: quadratic approximation (i.e. the ridge penalty) to the absolute value function (i.e. the lasso
penalty). Right panel: Illustration of the coordinate descent algorithm. The dashed grey lines are the level sets
of the lasso regression loss function. The red arrows depict the parameter updates. These arrows are parallel to
either the β1 or the β2 parameter axis, thus indicating that the regression parameter β is updated coordinate-wise.

by:

β (k+1) (λ1 ) = {X⊤ X + λ1 Ψ[β (k) (λ1 )]}−1 X⊤ Y

where
(k) (k)
diag{Ψ[β (k) (λ1 )]} = (1/|β1 |, 1/|β2 |, . . . , 1/|βp(k) |).

The thus generated sequence of updates {β (k) (λ1 )}∞

k=0 converges (under ‘nice’ conditions) to the lasso regression
estimator β̂(λ1 ).
A note of caution. The in-built variable selection property of the lasso regression estimator may – for large
enough choices of the penalty parameter λ1 – cause elements of β (k) (λ1 ) to become arbitrary close to zero (or,
in R exceed machine precision and thereby being effectively zero) after enough updates. Consequently, the ridge
penalty parameter for the j-th element of regression parameter may approach infinity, as the j-th element of
(k)
Ψ[β (k) (λ1 ) equals |βj |−1 . To accommodate this, the iterative ridge regression algorithm for the evaluation of
the lasso regression estimator requires a modification. Effectively, that amounts to the removal of j-th covariate
from the model all together (for its estimated regression coefficient is indistinguishable from zero). After its
removal, it does not return to the set of covariates. This may be problematic if two covariates are (close to)
super-collinear.

6.4.3 Gradient ascent

Another method of finding the lasso regression estimator and implemented in penalized-package (Goeman,
2010) makes use of gradient ascent. Gradient ascent/descent is an maximization/minization method that finds the
optimum of a smooth function by iteratively updating a first-order local approximation to this function. Gradient
ascents runs through the following sequence of steps repetitively until convergence:
◦ Choose a starting value.
◦ Calculate the derivative of the function, and determine the direction in which the function increases most.
This direction is the path of steepest ascent.
◦ Proceed in this direction, until the function no longer increases.
◦ Recalculate at this point the gradient to determine a new path of steepest ascent.
◦ Repeat the above until the (region around the) optimum is found.
6.4 Estimation 91

The procedure above is illustrated in Figure 6.7. The top panel shows the choice of the initial value. From this
point the path of the steepest ascent is followed until the function no longer increases (right panel of Figure 6.7).
Here the path of steepest ascent is updated along which the search for the optimum is proceeded (bottom panel of
Figure 6.7).
function
loss

β1
β2

optimum in chosen
initial direction
value
β1

β2

path of
global optimum steepest ascent
initial value
β1

β2

new path of
steepest ascent

Figure 6.7: Illustration of the gradient ascent procedure.

The use of gradient ascent to find the lasso regression estimator is frustrated by the non-differentiability (with
respect to any of the regression parameters) of the lasso penalty function at zero. In Goeman (2010) this is
overcome by the use of a generalized derivative. Define the directional or Gâteaux derivative of the function
f : Rp → R at x ∈ Rp in the direction of v ∈ Rp as:
 
f ′ (x) = lim τ −1 f (x + τ v) − f (x) ,
τ ↓0

assuming this limit exists. The Gâteaux derivative thus gives the infinitesimal change in f at x in the direction of
v. As such f ′ (x) is a scalar (as is immediate from the definition when noting that f (·) ∈ R) and should not be
confused with the gradient (the vector of partial derivatives). Furthermore, at each point x there are infinitely many
Gâteaux differentials (as there are infinitely many choices for v ∈ Rp ). In the particular case when v = ej , ej
the unit vector along the axis of the j-th coordinate, the directional derivative coincides with the partial derivative
of f in the direction of xj . Relevant for the case at hand is the absolute value function f (x) = |x| with x ∈ R.
Evaluation of the limits in its Gâteaux derivative yields:
 x
′ v |x| if x 6= 0,
f (x) =
v if x = 0,

for any v ∈ R \ {0}. Hence, the Gâteaux derivative of |x| does exits at x = 0. In general, the Gâteaux differential
may be uniquely defined by limiting the directional vectors v to i) those with unit length (i.e. kvk = 1) and ii) the
direction of steepest ascent. Using the Gâteaux derivative a gradient of f (·) at x ∈ Rp may then be defined as:
 ′
f (x) · vopt if f ′ (x) ≥ 0,
∇f (x) = (6.6)
0p if f ′ (x) < 0,
92 Lasso regression

in which vopt = arg max{v : kvk=1} f ′ (x). This is the direction of steepest ascent, vopt , scaled by Gâteaux deriva-
tive, f ′ (x), in the direction of vopt .
Goeman (2010) applies the definition of the Gâteaux gradient to the lasso penalized likelihood (6.2) using the
direction of steepest ascent as vopt . The resulting partial Gâteaux derivative with respect to the j-th element of the
regression parameter β is:

∂
∂  ∂βj L(Y, X; β) − λ1 sign(β

 j∂
)

if βj 6= 0
∂
Llasso (Y, X; β) = ∂β L (Y, X; β) − λ1 sign ∂βj L (Y, X; β) if βj = 0 and |∂ L/∂βj | > λ1
∂βj 
 0 j otherwise ,
Pp
where ∂ L/∂βj = j ′ =1 (X⊤ X)j ′ ,j βj − (X⊤ Y)j . This can be understood through a case-by-case study. The
partial derivative above is assumed to be clear for the βj 6= 0 and the ‘otherwise’ cases. That leaves the clarification
of the middle case. When βj = 0, the direction of steepest ascent of the penalized loglikelihood points either into
{β ∈ Rp : βj > 0}, or {β ∈ Rp : βj < 0}, or stays in {β ∈ Rp : βj = 0}. When the direction of steepest
ascent points into the positive or negative half-hyperplanes, the contribution of λ1 |βj | to the partial Gâteaux
derivative is simply λ1 or −λ1 , respectively. Then, only when the partial derivative of the log-likelihood together
with this contribution is larger then zero, the penalized loglikelihood improves and the direction is of steepest
ascent. Similarly, the direction of steepest ascent may be restricted to {β ∈ Rp | βj = 0} and the contribution
of λ1 |βj | to the partial Gâteaux derivative vanishes. Then, only if the partial derivative of the loglikelihood is
positive, this direction is to be pursued for the improvement of the penalized loglikelihood.
Convergence of gradient ascent can be slow close to the optimum. This is due to its linear approximation
of the function. Close to the optimum the linear term of the Taylor expansion vanishes and is dominated by the
second-order quadratic term. To speed-up convergence close to the optimum the gradient ascent implementation
offered by the penalized-package switches to a Newton-Raphson procedure.

6.4.4 Coordinate descent

Coordinate descent is another optimization algorithm that may be used to evaluate the lasso regression estimator
numerically, as is done by the implemention offered via the glmnet-package. Coordinate descent, instead of
following the gradient of steepest descent (as in Section 6.4.3), minimizes the loss function along the coordinates
one-at-the-time. For the j-th regression parameter this amounts to finding:
arg min kY − Xβk22 + λ1 kβk1 = arg min kY − X∗,\j β\j − X∗,j βj k22 + λ1 |βj |1
βj βj

= arg min kỸ − X∗,j βj k22 + λ1 |βj |1 ,

βj

where Ỹ = Y − X∗,\j β\j . After a simple rescaling of both X∗,j and βj , the minimization of the lasso regression
loss function with respect to βj is equivalent to one with an orthonormal design matrix. From Example 6.4 it is
known that the minimizer is obtained by application of the soft-threshold function to the corresponding maximum
likelihood estimator (now derived from Ỹ and Xj ). The coordinate descent algorithm iteratively runs over the
p elements until convergence. The right panel of Figure 6.6 provides an illustration of the coordinate descent
algorithm.
Convergence of the coordinate descent algorithm to the minimum of the lasso regression loss function (6.2) is
warranted by the convexity of this function. At each minization step the coordinate descent algorithm yields an
update of the parameter estimate that corresponds to an equal or smaller value of the loss function. It, together with
the compactness of diamond-shaped parameter domain and the boundedness (from below) of the lasso regression
loss function, implies that the coordinate descent algorithm converges to the minimum of this lasso regression loss
function. Although convergence is assured, it may take many steps for it to be reached. In particular, when i) two
covariates are strongly collinear, ii) one of the two covariate contributes only slightly more to the response, and
iii) the algorithm is initiated with the weaker explanatory covariate. The coordinate descent algorithm will then
take may iterations to replace the latter covariate by the preferred one. In such cases simultaneous updating, as is
done by the gradient ascent algorithm (Section 6.4.3), may be preferable.

6.5 Moments
In general the moments of the lasso regression estimator appear to be unknown. In certain cases an approximation
may be given. This is pointed out here. Use the quadratic approximation to the absolute value function of Section
6.6 The Bayesian connection 93

6.4.2 and approximate the lasso regression loss function around the lasso regression estimate:
Xp 1
kY − Xβk22 + λ1 kβk1 ≈ kY − Xβk22 + 21 λ1 βj2 .
j=1 |β̂(λ1 )|

Optimization of the right-hand side of the preceeding display with respect to β gives a ‘ridge approximation’ to
the lasso estimate:

β̂(λ1 ) ≈ {X⊤ X + λ1 Ψ[β̂(λ1 )]}−1 X⊤ Y,

with (Ψ[β̂(λ1 )])jj = |β̂j (λ1 )|−1 if β̂j (λ1 ) 6= 0. Now use this ‘ridge approximation’ to obtain the approximation
to the moments of the lasso regression estimator:


E[β̂(λ1 )] ≈ E {X⊤ X + λ1 Ψ[β̂(λ1 )]}−1 X⊤ Y
= {X⊤ X + λ1 Ψ[β̂(λ1 )]}−1 X⊤ X E[(X⊤ X)−1 X⊤ Y]
= {X⊤ X + λ1 Ψ[β̂(λ1 )]}−1 X⊤ Xβ

and


Var[β̂(λ1 )] ≈ Var {X⊤ X + λ1 Ψ[β̂(λ1 )]}−1 X⊤ Y
= {X⊤ X + λ1 Ψ[β̂(λ1 )]}−1 X⊤ X Var[(X⊤ X)−1 X⊤ Y]X⊤ X{X⊤ X + λ1 Ψ[β̂(λ1 )]}−1
= σ 2 {X⊤ X + λ1 Ψ[β̂(λ1 )]}−1 X⊤ X{X⊤ X + λ1 Ψ[β̂(λ1 )]}−1 .

These approximations can only be used when the lasso regression estimate is not sparse, which is at odds with
its attractiveness. A better approximation of the variance of the lasso regression estimator can be found in
Osborne et al. (2000), but even this becomes poor when many elements of β are estimated as zero.
Although the above approximations are only crude, they indicate that the moments of the lasso regression
estimator exhibit similar behaviour as those of its ridge counterpart. The (approximation of the) mean E[β̂(λ1 )]
tends to zero as λ1 → ∞. This was intuitively already expected from the form of the lasso regression loss
function (6.2), in which the penalty term dominates for large λ1 and is minimized for β̂(λ1 ) = 0p . This may
also be understood geometrically when appealing to the equivalent constrained estimation formation of the lasso
regression estimator. The parameter constraint shrinks to zero with increasing λ1 . Hence, so must the estimator.
Similarly, the (approximation of the) variance of the lasso regression estimator vanishes as the penalty parameter
λ1 grows. Again, its loss function (6.2) provides the intuition: for large λ1 the penalty term, which does not
depend on data, dominates. Or, from the perspective of the constrained estimation formulation, the parameter
constraint shrinks to zero as λ1 → ∞. Hence, so must the variance of the estimator, as less and less room is left
for it to fluctuate.
The behaviour of the mean squared error, bias squared plus variance, of the lasso regression estimator in
terms of λ1 is hard to characterize exactly without knowledge of the quality of the approximations. In particular,
does a λ1 exists such that the MSE of the lasso regression estimator outperforms that of its maximum likelihood
counterpart. Nonetheless, a first observation may be obtained from reasoning in extremis. Suppose β = 0p ,
which corresponds to an empty or maximally sparse model. A large value of λ1 then yields a zero estimate of
the regression parameter: β̂(λ1 ) = 0p . The bias squared is thus minimized: kβ̂(λ1 ) − βk22 = 0. With the
bias vanished and the (approximation of the) variance decreasing in λ1 , so must the MSE decrease for λ1 larger
than some value. So, for an empty model the lasso regression estimator with a sufficiently large penalty parameter
yields a better MSE than the maximum likelihood estimator. For very sparse models this property may be expected
to uphold, but for non-sparse models the bias squared will have a substantial contribution to the MSE, and it is thus
not obvious whether a λ1 exists that yields a favourable MSE for the lasso regression estimator. This is investigated
in silico in Hansen (2015). The simulations presented there indicate that the MSE of the lasso regression estimator
is particularly sensitive to the actual β. Moreover, for a large part of the parameter space β ∈ Rp the MSE of
β̂(λ1 ) is behind that of the maximum likelihood estimator.

6.6 The Bayesian connection

The lasso regression estimator, being a penalized estimator, knows a Bayesian formulation, much like the (gener-
alized) ridge regression estimator could be viewed as a Bayesian estimator when imposing a Gaussian prior (cf.
94 Lasso regression

Chapter 2 and Section 3.2). Instead of normal prior, the lasso regression estimator requires (as suggested by the
form of the lasso penalty) a zero-centered Laplacian (or double exponential) prior for it to be viewed as a Bayesian
estimator. A zero-centered Laplace distributed random variable X has density fX (x) = 21 b−1 exp(−|x|/b) with
scale parameter b > 0. The top panel of Figure 6.8 shows the Laplace prior, and for contrast the normal prior of
the ridge regression estimator. This figure reveals that the ‘lasso prior’ puts more mass close to zero and in the tails
than the Gaussian ‘ridge prior’. This corroborates with the tendency of the lasso regression estimator to produce
either zero or large (compared to ridge) estimates.

Laplace prior

0.5
0.4
0.3
density

0.2
0.1
0.0

−4 −2 0 2 4

β
0.0025

0.00

λ1 = 0.01
λ1 = 0.50
λ1 = 1.00
λ1 = 1.50
0.0020

λ1 = 2.00
−0.05

λ1 = 4.00
0.0015
posterior distribution

−0.10
Posterior mode
0.0010

−0.15
0.0005

−0.20
0.0000

−1.5 −1.0 −0.5 0.0 0.5 1.0 1.5 0 1 2 3 4 5

β λ1

Figure 6.8: Solution path of the ridge estimator and its variance. The left panel shows the solution path of the ridge
estimator for the data of Example 1.3. In the right panel the corresponding variance of the ridge estimator is plotted
against the (logarithm of the) penalty parameter.

The lasso regression estimator corresponds to the maximum a posteriori (MAP) estimator of β, when the prior
is a Laplace distribution. The posterior distribution is then proportional to:
n
Y p
Y
2 −1/2 2 −1 2
(2πσ ) exp[−(2σ ) (Yi Xi,∗ β) ] × (2b)−1 exp(−|βj |/b).
i=1 j=1

The posterior is not a well-known and characterized distribution. This is not necessary as interest concentrates here
on its maximum. The location of the posterior mode coincides with the location of the maximum of logarithm
of the posterior. The log-posterior is proportional to: −(2σ 2 )−1 kY − Xβk22 − b−1 kβk1, with its maximizer
minimizing kY − Xβk22 + (2σ 2 /b)kβk1 . In this one recognizes the form of the lasso regression loss function
6.7 Comparison to ridge 95

(6.2). It is thus clear that the scale parameter of the Laplace distribution reciprocally relates to lasso penalty
parameter λ1 , similar to the relation of the ridge penalty parameter λ2 and the variance of the Gaussian prior of
the ridge regression estimator.
The posterior may not be a standard distribution, in the univariate case (p = 1) it is can visualized. Specifically,
the behaviour of the MAP can then be illustrated, which – as the MAP estimator corresponds to the lasso regression
estimator – should also exhibit the selection property. The bottom left panel of Figure 6.8 shows the posterior
distribution for various choices of the Laplace scale parameter (i.e. lasso penalty parameter). Clearly, the mode
shifts towards zero as the scale parameter decreases / lasso penalty parameter increases. In particular, the posterior
obtained from the Laplace prior with the smallest scale parameter (i.e. largest penalty parameter λ1 ), although
skewed to the left, has a mode placed exactly at zero. The Laplace prior may thus produce MAP estimators that
select. However, for smaller values of the lasso penalty parameter the Laplace prior is not concentrated enough
around zero and the contribution of the likelihood in the posterior outweighs that of the prior. The mode is then
not located at zero and the parameter is ‘selected’ by the MAP estimator. The bottom right panel of Figure 6.8
plots the mode of the normal-Laplace posterior vs. the Laplace scale parameter. In line with Theorem 6.1 it is
piece-wise linear.
Park and Casella (2008) go beyond the elementary correspondence of the frequentist lasso estimator and the
Bayesian posterior mode and formulate the Bayesian lasso regression model. To this end they exploit the fact that
the Laplace distribution can be written as a scale mixture of normal distributions with an exponentional mixing
density. This allows the construction of a Gibbs sampler for the Bayesian lasso estimator. Finally, they suggest to
impose a gamma-type hyperprior on the (square of the) lasso penalty parameter. Such a full Bayesian formulation
of the lasso problem enables the construction of credible sets (i.e. the Bayesian counterpart of confidence intervals)
to express the uncertainty of the maximum a posterior estimator. However, the lasso regression estimator may be
seen as a Bayesian estimator, in the sense that it coincides with the posterior mode, the ‘lasso’ posterior distribution
cannot be blindly used for uncertainty quantification. In high-dimensional sparse settings the ‘lasso’ posterior
distribution of β need not concentrate around the true parameter, even though its mode is a good estimator of the
regression parameter (cf. Section 3 and Theorem 7 of Castillo et al., 2015).

6.7 Comparison to ridge

Here an inventory of the similarities and differences between the lasso and ridge regression estimators is presented.
To recap what we have seen so far: both estimators optimize a loss function of the form (6.1) and can be viewed
as Bayesian estimators. But in various respects the lasso regression estimator exhibited differences from its ridge
counterpart: i) the former need not be uniquely defined (for a given value of the penalty parameter) whereas the
latter is, ii) an analytic form of the lasso regression estimator does in general not exists, but iii) it is sparse (for
large enough values of the lasso penalty parameter). The remainder of this section expands this inventory.

6.7.1 Linearity
The ridge regression estimator is a linear (in the observations) estimator, while the lasso regression estimator
is not. This is immediate from the analytic expression of the ridge regression estimator, β̂(λ2 ) = (X⊤ X +
λ2 Ipp )−1 X⊤ Y, which is a linear combination of the observations Y. To show the non-linearity of the lasso
regression estimator available, it suffices to study the analytic expression of j-th element of β̂(λ1 ) in the orthonor-
mal case: β̂j (λ1 ) = sign(β̂j )(|β̂j | − 12 λ1 )+ = sign(X⊤ ⊤ 1
∗,j Y)(|X∗,j Y| − 2 λ1 )+ . This clearly is not linear in Y.
Consequently, the response Y may be scaled by some constant c, denoted Ỹ = cY, and the corresponding ridge
regression estimators are one-to-one related by this same factor β̂(λ2 ) = cβ̃(λ2 ). The lasso regression estimator
based on the unscaled data is not so easily recovered from its counterpart obtained from the scaled data.

6.7.2 Shrinkage
Both lasso and ridge regression estimation minimize the sum-of-squares plus a penalty. The latter encourages
the estimator to be small, in particular closer to zero. This behavior is called shrinkage. The particular form of
the penalty yields different types of this shrinkage behavior. This is best grasped in the case of an orthonormal
design matrix. The j-the element of the ridge regression estimator then is: β̂j (λ2 ) = (1 + λ2 )β̂j , while that of
the lasso regression estimator is: β̂j (λ1 ) = sign(β̂j )(|β̂j | − 12 λ1 )+ . In Figure 6.9 these two estimators β̂j (λ2 )
and β̂j (λ1 ) are plotted as a function of the maximum likelihood estimator β̂j . Figure 6.9 shows that lasso and
ridge regression estimator translate and scale, respectively, the maximum likelihood estimator, which could also
96 Lasso regression

have been concluded from the analytic expression of both estimators. The scaling of the ridge regression estimator
amounts to substantial and little shrinkage (in an absolute sense) for elements of the regression parameter β with
a large and small maximum likelihood estimate, respectively. In contrast, the lasso regression estimator applies an
equal amount of shrinkage to each element of β, irrespective of the coefficients’ sizes.

Lasso shrinkage Ridge shrinkage

lasso estimate ridge estimate

5

5
ML estimate ML estimate
4

4
3

3
β(λ1)

β(λ2)
^

^
2

2
1

1
0

0
0 1 2 3 4 5 0 1 2 3 4 5
^ ^
β β

Figure 6.9: Solution path of the ridge estimator and its variance. The left panel shows the solution path of the ridge
estimator for the data of Example 1.3. In the right panel the corresponding variance of the ridge estimator is plotted
against the (logarithm of the) penalty parameter.

6.7.3 Simulation I: Covariate selection

Here it is investigated whether lasso regression exhibits the same behaviour as ridge regression in the presence of
covariates with differing variances. Recall: the simulation of Section 1.9.1 showed that ridge regression shrinks
the estimates of covariates with a large spread less than those with a small spread. That simulation has been
repeated, with the exact same parameter choices and sample size, but now with the ridge regression estimator
replaced by the lasso regression estimator. To refresh the memory: in the simulation of Section 1.9.1 the linear
regression model is fitted, now with the lasso regression estimator. The (n = 1000) × (p = 50) dimensional
design matrix X is sampled from a multivariate normal distribution: X⊤ i,∗ ∼ N (050 , Σ) with Σ diagonal and
(Σ)jj = j/10 for j = 1, . . . , p. The response Y is generated through Y = Xβ + ε with β a vector of all ones
and ε sampled from the multivariate standard normal distribution. Hence, all covariates contribute equally to the
response.
The results of the simulation are displayed in Figure 6.10, which shows the regularization paths of the p = 50
covariates. The regularization paths are demarcated by color and style to indicate the size of the spread of the
corresponding covariate. These regularization paths show that the lasso regression estimator shrinks – like the
ridge regression estimator – the covariates with the smallest spread most. For the lasso regression this translates
(for sufficiently large values of the penalty parameter) into a preference for the selection of covariates with largest
variance.
Intuition for this behavior of the lasso regression estimator may be obtained through geometrical arguments
analogous to that provided for the similar behaviour of the ridge regression estimator in Section 1.9.1. Alge-
braically it is easily seen when assuming an orthonormal design with Var(X1 ) ≫ Var(X2 ). The lasso regression
loss function can then be rewritten, as in Example 6.5, to:

kY − Xβk22 + λ1 kβk1 = kY − X̃γk22 + λ1 [Var(X1 )]−1/2 |γ1 | + λ1 [Var(X2 )]−1/2 |γ2 |,

where γ1 = [Var(X1 )]1/2 β1 and γ2 = [Var(X2 )]1/2 β2 . The rescaled design matrix X̃ is now orthonormal and
analytic expressions of estimators of γ1 and γ2 are available. The former parameter is penalized substantially less
6.8 Pandora’s box 97

Solution paths of covariates with distinct variance Solution paths of correlated covariates

σ2 in [0,1]

1.2
1.0

σ2 in [1,2]
σ2 in [2,3]
σ2 in [3,4]
σ2 in [4,5]

1.0
0.8

0.8
0.6

βj(λ1)
β(λ1)

0.6
^

^
0.4

0.4
0.2

0.2
r=0.0
r=0.3
r=0.4
r=0.6
0.0

0.0
r=0.8

3 4 5 6 7 8 9 3 4 5 6 7 8 9

log(λ1) log(λ)

Figure 6.10: Solution path of the ridge estimator and its variance. The left panel shows the solution path of the
ridge estimator for the data of Example 1.3. In the right panel the corresponding variance of the ridge estimator is
plotted against the (logarithm of the) penalty parameter.

than the latter as λ1 [Var(X1 )]−1/2 ≪ λ1 [Var(X2 )]−1/2 . As a result, if for large enough values of λ1 one variable
is selected, it is more likely to be γ1 .

6.7.4 Simulation II: correlated covariates

The behaviour of the lasso regression estimator is now studied in the presence of collinearity among the covariates.
Previously, in simulation, Section 1.9.2, the ridge regression estimator was shown to exhibit the joint shrinkage
of strongly collinear covariates. This simulation is repeated for the lasso regression estimator. The details of
the simulation are recapped. The linear regression model is fitted by means of the lasso regression estimator.
The (n = 1000) × (p = 50) dimensional design matrix X is samples from a multivariate normal distribution:
X⊤ i,∗ ∼ N (050 , Σ) with a block-diagonal Σ. The k-the, k = 1, . . . , 5, diagonal block, denoted Σkk comprises
ten covariates and equals k−1 6−k
5 110×10 + 5 I10×10 for k = 1, . . . , 5. The response vector Y is then generated
by Y = Xβ + ε, with ε sampled from the multivariate standard normal distribution and β containing only ones.
Again, all covariates contribute equally to the response.
The results of the above simulation results are captured in Figure 6.10. It shows the lasso regularization paths
for all elements of the regression parameter β. The regularization paths of covariates corresponding to the same
block of Σ (indicative of the degree of collinearity) are now marcated by different colors and styles. Whereas the
ridge regularization paths nicely grouped per block, the lasso counterparts do not. The selection property spoils the
party. Instead of shrinking the regression parameter estimates of collinear covariates together, the lasso regression
estimator (for sufficiently large values of its penalty parameter λ1 ) tends to pick one covariates to enters the model
while forcing the others out (by setting their estimates to zero).

6.8 Pandora’s box

Many variants of penalized regression, in particular of lasso regression, have been presented in the literature. Here
we give an overview of some of the more current ones. Not a full account is given, but rather a brief introduction
with emphasis on their motivation and use.

6.8.1 Elastic net

The elastic net regression estimator is a modication of the lasso regression estimator that preserves its strength
and harnesses its weaknesses. The biggest appeal of the lasso regression estimator is clearly its ability to perform
98 Lasso regression

selection. Less pleasing are i) the non-uniquess of the lasso regression estimator due to the non-strict convexity of
its loss function, ii) the bound on the number of selected variables, i.e. maximally min{n, p} can be selected, and
iii) the observation that strongly (positively) collinear covariates are not shrunken together: the lasso regression
estimator selects among them while it is hard to distinguish their contributions to the variation of the response.
While it does not select, the ridge regression estimator does not exhibit these less pleasing features. These consid-
erations led Zou and Hastie (2005) to combine the strengths of the lasso and ridge regression estimators and form
a ‘best-of-both-worlds’ estimator, called the elastic net regression estimator, defined as:
β̂(λ1 , λ2 ) = arg minp kY − Xβk22 + λ1 kβk1 + 12 λ2 kβk22 .
β∈R

The elastic net penalty – defined implicitly in the preceeding display – is thus simply a linear combination of
the lasso and ridge penalties. Consequently, the elastic net regression estimator encompasses its lasso and ridge
counterparts. Hereto just set λ2 = 0 or λ1 = 0, respectively. A novel estimator is defined when both penalties act
simultaneously, i.e. when their corresponding penalty parameters are both nonzero.
Does this novel elastic net estimator indeed inherit the strengths of the lasso and ridge regression estimators?
Let us turn to the aforementioned motivation behind the elastic net estimator. Starting with the uniqueness, the
strict convexity of the ridge penalty renders the elastic net loss function strict convex as it is a combination of the
ridge penalty and the lasso function – notably non-strict convex when the dimension p exceeds the sample size n.
This warrants the existence of a unique minimizer of the elastic net loss function. To assess the preservation of the
selection property, now without the bound on the maximum number of selectable variables, exploit the equivalent
constraint estimation formulation of the elastic net estimator. Figure 6.11 shows the parameter constraint of the
elastic net estimator for the ‘p = 2’-case, which is defined by the set:
{(β1 , β2 ) ∈ R2 : λ1 (|β1 | + |β2 |) + 21 λ2 (β12 + β22 ) ≤ c(λ1 , λ2 )}.
Visually, the ‘elastic net parameter constraint’ is a comprise between the circle and the diamond shaped constraints
of the ridge and lasso regression estimators. This compromise inherits exactly the right geometrical features: the
strict convexity of the ‘ridge circle’ and the ‘corners’ (referring to points at which the constraint’s boundary
is non-smootness/non-differentiability) falling at the axes of the ‘lasso constraint’. The latter feature, by the
same argumentation as presented in Section 6.3, endows the elastic net estimator with the selection property.
Moreover, it can – in principle – select p features as the point in the parameter space where the smallest level
set of the unpenalized loss hits the elastic net parameter constraint need not fall on any axis. For example, in
the ‘p = 2, n = 1’-case the level sets of the sum-of-squares loss are straight lines that, when almost parallel to
the edges of the ‘lasso diamond’, are unlikely to first hit the elastic net parameter constraint at one of its corners.
Finally, the largest penalty parameter relates (reciprocally) to the volume of the elastic net parameter constraint,
while the ratio between λ1 and λ2 determines whether it is closer to the ‘ridge circle’ or to the ‘lasso diamond’.

lasso
ridge
elastic net
1.0
0.5
β2

0.0
−0.5
−1.0

−1.0 −0.5 0.0 0.5 1.0

β1

Figure 6.11: The left panel depicts the parameter constraint induced by the elastic net penalty and, for reference,
those of the lasso and ridge are added. The right panel shows the contour plot of the cross-validated loglikelihood
vs. the two penalty parameters of the elastic net estimator.

Whether the elastic net regression estimator also delivers on the joint shrinkage property is assessed by simu-
lation (not shown). The impression given by these simulations is that the elastic net has joint shrinkage potential.
6.8 Pandora’s box 99

This, however, usually requires a large ridge penalty.

The elastic net regression estimator can be found with procedures similar to those that evaluate the lasso
regression estimator (see Section 6.4) as the elastic net loss can be reformulated as a lasso loss. Hereto the ridge
part of the elastic net penalty is absorbed into the sum of squares using the data augmentation trick of Exercise ??
which showed that the ridge regression estimator is the ML regression estimator of the related regression model
with p zeros and rows added to the response and design matrix, respectively. That is, write Ỹ = (Y⊤ , 0⊤ ⊤
p ) and
⊤
√ ⊤
X̃ = (X , λ2 Ipp ) . Then:

kỸ − X̃βk22 = kY − Xβk22 + λ2 kβk22 .

Hence, the elastic net loss function can be rewritten to kỸ − X̃βk22 + λ1 kβk1 . This is familiar territory and the
lasso algorithms of Section 6.4 can be used. Zou and Hastie (2005) present a different algorithm for the evaluation
of the elastic net estimator that is faster and numerically more stable (see also Exercise 6.12). Irrespectively, the
reformulation of the elastic net loss in terms of augmented data also reveals that the elastic net regression estimator
can select p variables, even for p > n, which is immediate from the observation that rank(X̃) = p.

The penalty parameters need tuning, e.g. by cross-validation. They are subject to empirically indeterminancy.
That is, often a large range of (λ1 , λ2 )-combinations will yield a similar cross-validated performance as can be
witnessed from Figure 6.11. It shows the contourplot of the penalty parameters vs. this performance. There is a
yellow ‘banana-shaped’ area that corresponds to the same and optimal performance. Hence, no single (λ1 , λ2 )-
combination can be distinguished as all yield the best performance. This behaviour may be understood intuitively.
Reasoning loosely, while the lasso penalty λ1 kβk1 ensures the selection property and the ridge penalty 12 λ2 kβk22
warrants the uniqueness and joint shrinkage of coefficients of collinear covariates, they have a similar effect on
the size of the estimator. Both shrink, although in different norms. But a reduction in the size of β̂(λ1 , λ2 ) in one
norm implies a reduction in another. An increase in either the lasso and ridge penalty parameter will have a similar
effect on the elastic net estimator: it shrinks. The selection and ‘joint shrinkage’ properties are only consequences
of the employed penalty and are not criteria in the optimization of the elastic net loss function. There, only size
matters. The size of β refers to λ1 kβk1 + 21 λ2 kβk22 . As in the size the lasso and ridge penalties appear as a
linear combination in the elastic net loss function and having a similar effect on the elastic net estimator, there
are many positive (λ1 , λ2 )-combinations that constrain the size of the elastic net estimator equally. In contrast,
for both the lasso and ridge regression estimators different penalty parameters yield estimators of different sizes
(defined accordingly). Moreover, it is mainly the size that determines the cross-validated performance as the size
determines the shrinkage of the estimator and, consequently, the size of the errors. But only a fixed size leaves
enough freedom to distribute this size over the p elements of the regression parameter estimator β̂(λ1 , λ2 ) and, due
to the collinearity, among them many that yield a comparable performance. Hence, if a particularly sized elastic
net estimator β̂(λ1 , λ2 ) optimizes the cross-validated performance, then high-dimensionally there are likely many
others with a different (λ1 , λ2 )-combination but of equal size and similar performance.
The empirical indeterminancy of penalty parameters touches upon another issues. In principle, the elastic net
regression estimator can decide whether a sparse or non-sparse solution is most appropriate. The indeterminancy
indicates that for any sparse elastic net regression estimator a less sparse one can be found with comparable
performance, and vice versa. Care should be exercised when concluding on the sparsity of the linear relation
under study from the chosen elastic net regression estimator.
A solution to the indeterminancy of the optimal penalty parameter combination is to fix their ratio. For inter-
pretation purposes this is done through the introduction of a ‘mixing parameter’ α ∈ [0, 1]. The elastic net penalty
is then written as λ[αkβk1 + 12 (1 − α)kβk22 ]. The mixing parameter is set by the user while λ > 0 is typically
found through cross-validation (cf. the implementation in the glmnet-package) (Friedman et al., 2009). Gener-
ally, no guidance on the choice of mixing parameter α can be given. In fact, it is a tuning parameter and as such
needs tuning rather then setting out of the blue.

6.8.2 Fused lasso

The fused lasso regression estimator proposed by Tibshirani et al. (2005) is the counterpart of the fused ridge
regression estimator encountered in Example 3.1. It is a generalization of the lasso regression estimator for
situations where the order of index j, j = 1, . . . , p, of the covariates has a certain meaning such as a spatial
or temporal one. The fused lasso regression estimator minimizes the sum-of-squares augmented with the lasso
penalty, the sum of the absolute values of the elements of the regression parameter, and the ℓ1 -fusion (or simply
fusion if clear from the context) penalty, the sum of the first order differences of the regression parameter. Formally,
100 Lasso regression

the fused lasso estimator is defined as:

Xp
β̂(λ1 , λ1,f ) = arg minp kY − Xβk22 + λ1 kβk1 + λ1,f |βj − βj−1 |,
β∈R j=2

which involves two penalty parameters λ1 and λ1,f for the lasso and fusion penalties, respectively. As a result of
adding the fussion penalty the fused lasso regression estimator not only shrinks elements of β towards zero but
also the difference of neighboring elements of β. In particular, for large enough values of the penalty parameters
the estimator selects elements of and differences of neighboring elements of β. This corresponds to a sparse
estimate of β while the vector of its first order differences too is dominated by zeros. That is many elements of
β̂(λ1 , λ1,f ) equal zero with few changes in β̂(λ1 , λ1,f ) when running over j. Hence, the fused lasso regression
penalty encourages large sets of neighboring elements of j to have a common (or at least a comparable) regression
parameter estimate. This is visualized – using simulated data from a simple toy model with details considered
irrelevant for the illustration – in Figure 6.12 where the elements of the fused lasso regression estimate β̂(λ1 , λ1,f )
are plotted against the index of the covariates. For reference the true β and the lasso regression estimate with the
same λ1 are added to the plot. Ideally, for a large enough fusion penalty parameter, the elements of β̂(λ1 , λ1,f )
would form a step-wise function in the index j, with many equalling zero and exhibiting few changes, as the
elements of β do. While this is not the case, it is close, especially in comparison to the elements of its lasso cousin
β̂(λ1 ), thus showing the effect of the inclusion of the fusion penalty.

(Fused) lasso regression estimate 1.0

true λ1=1, λ1=5.0

lasso λ1=1, λ1=1
fused lasso λ1=1, λ1=1/5
λ1=1/2, λ1=1/2
2

0.5
1
βj and βj
^

β2

0.0
0

−0.5
−1

0 20 40 60 80 100 −0.5 0.0 0.5

covariate index β1

Figure 6.12: The left panel shows the lasso (red, diamonds) and fused lasso (black circles) regression parameter
estimates and the true parameter values (grey circles) plotted against their index j. The (β1 , β2 )-parameter con-
straint induced by the fused lasso penalty for various combinations of the lasso and fusion penalty parameters λ1
and λ1,f , respectively. The grey dotted lines corresponds to the ‘β1 = 0’-, ‘β2 = 0’- and ‘β1 = β2 ’-lines where
selection takes place.

It is insightful to view the fused lasso regression problem as a constrained P estimation problem. The fused
lasso penalty induces a parameter constraint: {β ∈ Rp : λ1 kβk1 + λ1,f pj=2 |βj − βj−1 | ≤ c(λ1 , λ1,f )}.
This constraint is plotted for p = 2 in the right panel of Figure 6.12 (clearly, it is not the intersection of the
constraints induced by the lasso and fusion penalty separately as one might accidently conclude from Figure 2
in Tibshirani et al., 2005). The constraint is convex, although not strict, which is convenient for optimization
purposes. Morever, the geometry of this fused lasso constraint reveals why the fused lasso regression estimator
selects the elements of β as well as its first order difference. Its boundary, while continuous and generally smooth,
has six points at which it is non-differentiable. These all fall on the grey dotted lines in the right panel of Figure
6.12 that correspond to the axes and the diagonal, put differently, on either the ‘β1 = 0’, ‘β2 = 0’ , or ‘β1 = β2 ’-
lines. The fused lasso regression estimate is the point where the smallest level set of the sum-of-squares criterion
kY − Xβk22 , be it an ellipsoid or hyper-plane, hits the fused lasso constraint. For an element or the first order
difference to be zero it must fall on one of the dotted greys lines of the right panel of Figure 6.12. Exactly this
happens on one of the aforementioned six point of the constraint. Finally, the fused lasso regression estimator
has, when – for reasonably comparable penalty parameters λ1 and λ1,f – it shrinks the first order difference to
6.8 Pandora’s box 101

zero, a tendency to also estimate the corresponding individual elements as zero. In part, this is due to the fact that
|β1 | = 0 = |β2 | implies that |β1 − β2 | = 0, while the reverse does not necessary hold. Moreover, if |β1 | = 0, then
|β1 − β2 | = |β2 |. The fusion penalty thus converts to a lasso penalty of the remaining nonzero element of this first
order difference, i.e. (λ1 + λ1,f )|β2 |, thus furthering the shrinkage of this element to zero.
The evaluation of the fused lasso regression estimator is more complicated than that of the ‘ordinary’ lasso
regression estimator. For ‘moderately sized’ problems Tibshirani et al. (2005) suggest to use a variant of the
quadratic programming method (see also Section 6.4.1) that is computationally efficient when many linear con-
straints are active, i.e. when many elements of and first order difference of β are zero. Chaturvedi et al. (2014)
extend the gradient ascent approach discussed in Section 6.4.3 to solve the minimization of the fused lasso loss
function. For the limiting ‘λ1 = 0’-case the fused lasso loss function can be reformulated as a lasso loss function
(see Exercise 6.8). Then, the algorithms of Section 6.4 may be applied to find the estimate β̂(0, λ1,f ).

6.8.3 The (sparse) group lasso

The lasso regression estimator selects covariates, irrespectively of the relation among them. However, groups of
covariates may be discerned. For instance, a group of covariates may be dummy variables representing levels of
a categorical factor. Or, within the context of gene expression studies such groups may be formed by so-called
pathways, i.e. sets of genes that work in concert to fulfill a certain function in the cell. In such cases a group-
structure can be overlayed on the covariates and it may be desirable to select the whole group, i.e. all covariates
together, rather than an individual covariate of the group. To achieve this Yuan and Lin (2006) proposed the group
lasso regression estimator. It minimizes the sum-of-squares now augmented with the group lasso penalty, i.e.:
XG q XG q rX
λ1,G |Jg | kβg k2 = λ1,G |J g | βj2 ,
g=1 g=1 j∈Jg

where λ1,G is the group lasso penalty parameter (with subscript G for Group), G is the total number of groups,
Jg ⊂ {1, . . . , p} is covariate index set of the g-th group such that the Jg are mutually exclusive and exhaustive,
i.e. Jg1 ∩ Jg2 = ∅ for all g1 6= g2 and ∪G g=1 Jg = {1, . . . , p}, and |Jg | denotes the cardinality (the number of
elements) of Jg .
The group lasso estimator performs covariate selection at the group level but does not result in a sparse
within-group estimate. This may be achieved through employment of the sparse group lasso regression estimator
(Simon et al., 2013):
XG q
β̂(λ1 , λ1,G ) = arg minp kY − Xβk22 + λ1 kβk1 + λ1,G |Jg | kβg k2 ,
β∈R g=1

which combines the lasso with the group lasso penalty. The inclusion of the former encourages within-group
sparsity, while the latter performs selection at the group level. The sparse group lasso penalty resembles the
elastic net penalty with the kβk2 -term replacing the kβk22 -term of the latter.
The (sparse) group lasso regression estimation problems can be reformulated as constrained estimation prob-
lems. Their parameter constraints are depicted in Figure 6.13. By now the reader will be familiar with the
charactistic feature, i.e. the non-differentiability of the boundary at the axes, of the constraint that endows the es-
timator with the potential to select. This feature is clearly present for the sparse group lasso regression estimator,
covariate-wise. Although both the group lasso and the sparse group lasso regression estimator select group-wise,
illustration of the associated geometrical feature requires plotting in dimensions larger than two and is not at-
tempted. However, when all groups are singletons, the (sparse) group lasso penalties are equivalent to the regular
lasso penalty.
The sparse group lasso regression estimator is found through exploitation of the convexity of the loss function
(Simon et al., 2013). It alternates between group-wise and within-group optimization. The resemblance of the
sparse group lasso and elastic net penalties propagates to the optimality conditions of both estimators. In fact, the
within-group optimization amounts to the evaluation of an elastic net regression estimator (Simon et al., 2013).
When within each group the design matrix is orthonormal and λ1,G = 0, the group lasso regression estimator can
be found by a group-wise coordinate descent procedure for the evaluation of the estimator (cf. Exercise ??).
Both the sparse group lasso and the elastic net regression estimators have two penalty parameters that need
tuning. In both cases the corresponding penalties have a similar effect: shrinkage towards zero. If the g-th group’s
contribution to the group lasso penalty has vanished, then so has the contribution of all covariates to the regular
lasso penalty. And vice versa. This complicates the tuning of the penalty parameters as it is hard to distinguish
which shrinkage effect is most beneficial for the estimator. Simon et al. (2013) resolve this by setting the ratio of
the two penalty parameters λ1 and λ1,G to some arbitrary but fixed value, thereby simplifying the tuning.
102 Lasso regression

The adaptive threshold function

lasso

3
group lasso
sparse group lasso
1.0

2
0.5

1
β(λ1)
β2

0
0.0

−1
−0.5

−2
adaptive threshold
−1.0

soft threshold

−3
hard threshold

−1.0 −0.5 0.0 0.5 1.0 −3 −2 −1 0 1 2 3

^ (ols)
β1 β

1.0
true curve
lasso fit
gauss lasso fit
6

0.5
5
4

0.0
β2
Y

−0.5
2
1

−1.0

0 5 10 15 20 −1.0 −0.5 0.0 0.5 1.0

X β1

Figure 6.13: Top left panel: The (β1 , β2 )-parameter constraint induced by the lasso, group lasso and sparse
group lasso penalty. Top right panel: the adaptive threshold function associated with the adaptive lasso regression
estimator for orthonormal design matrices. Bottom left panel: illustration of the lasso and adaptive lasso fit and the
true curve. Bottom right panel: the parameter constraint induced by the ℓ0 -penalty.

6.8.4 Adaptive lasso

The lasso regression estimator does not exhibit some key and desirable asymptotic properties. Zou (2006) pro-
posed the adaptive lasso regression estimator to achieve these properties. The adaptive lasso regression estimator
is a two-step estimation procedure. First, an initial estimator of the regression parameter β, denoted β̂ init, is to be
obtained. The adaptive lasso regression estimator is then defined as:
Xp
β̂ adapt (λ1 ) = arg minp kY − Xβk22 + λ1 |β̂jinit |−1 |βj |.
β∈R j=1

Hence, it is a generalization of the lasso penalty with covariate-specific weighing. The weight of the j-th covariate
is reciprocal to the j-th element of the initial regression parameter estimate β̂ init. If the initial estimate of βj is
large or small, the corresponding element in the adaptive lasso estimator will be penalized less or more and thereby
determine the amount of shrinkage, which may now vary between the estimates of the elements of β. In particular,
if β̂jinit = 0, the adaptive lasso penalty parameter corresponding to the j-th element is infinite and yields β̂ adapt = 0.
The adaptive lasso regression estimator, given an initial regression estimate β̂ init , can be found numerically by
minor changes of the algorithms presented in Section 6.4. In case of an orthonormal design an analytic expression
6.9 Exercises 103

of the adaptive lasso estimator exists (see Exercise 6.13):

β̂jadapt (λ1 ) = sign(β̂jols )(|β̂jols | − 21 λ1 /|β̂jols |)+ .

This adaptive lasso estimator can be viewed as a compromise between the soft thresholding function, associated
with the lasso regression estimator for orthonormal design matrices (Section 6.2), and the hard thresholding func-
tion, associated with truncation of the ML regression estimator (see the top right panel of Figure 6.13 for an
illustration of these thresholding functions).
How is the initial regression parameter estimate β̂ init to be chosen? Low-dimensionally the maximum likelihood
regression estimator one may used. The resulting adaptive lasso regression estimator is sometimes referred to as
the Gauss-Lasso regression estimator. High-dimensionally, the lasso or ridge regression estimators will do. Any
other estimator may in principle be used. But not all yield the desirable asymptotic properties.
A different motivation for the adaptive lasso is found in its ability to undo some or all of the shrinkage of the
lasso regression estimator due to penalization. This is illustrated in the left bottom panel of Figure 6.13. It shows
the lasso and adaptive lasso regression fits. The latter clearly undoes some of the bias of the former.

6.8.5 The ℓ0 penalty

An alternative estimators, considered to be superior to both the lasso and ridge regression estimators, is the ℓ0 -
penalized regression estimator. It too minimizes Ppthe sum-of-squares now with the ℓ0 -penalty. The ℓ0 -penalty,
denoted λ0 kβk0 , is defined as λ0 kβk0 = λ0 j=1 I{βj 6=0} with penalty parameter λ0 and I{·} the indicator
function. The parameter constraint associated with this penalty is shown in the right panel of Figure 6.13. From
the form of the penalty it is clear that the ℓ0 -penalty penalizes only for the presence of a covariate in the model.
As such it is concerned with the number of covariates in the model, and not the size of their regression coefficients
(or a derived quantity thereof). The latter is considered only a surrogate of the number of covariates in the model.
As such the lasso and ridge estimators are proxies to the ℓ0 -penalized regression estimator.
The ℓ0 -penalized regression estimator is not used for large dimensional problems as its evaluation is computa-
tionally too demanding. It requires a search over all possible subsets of the p covariates to find the optimal model.
As each covariate can either be in or out of the model, in total 2p models need to be considered. This is not feasible
with present-day computers.
The adaptive lasso regression estimator may be viewed as an approximation of the ℓ0 -penalized regression
estimator. When the covariate-wise weighing employed in the penalization of the adaptive lasso regression esti-
mation is equal to λ1,j = λ/|βj | with βj known true value of the j-th regression coefficient, the j-th covariate’s
estimated regression coefficient contributes only to the penalty if it is nonzero. In practice, this weighing involves
an initial estimate of β and is therefore an approximation at best, which the quality of the approximation hinging
upon that of the weighing.

6.9 Exercises
Question 6.1
Find the lasso regression solution for the data below for a general value of λ and for the straight line model Y =
β0 +β1 X+ε (only apply the lasso penalty to the slope parameter, not to the intercept). Show that when λ1 is chosen
as 7, the lasso solution fit is Ŷ = 40 + 1.75X. Data: X⊤ = (X1 , X2 , . . . , X8 )⊤ = (−2, −1, −1, −1, 0, 1, 2, 2)T ,
and Y⊤ = (Y1 , Y2 , . . . , Y8 )⊤ = (35, 40, 36, 38, 40, 43, 45, 43)⊤.

Question 6.2
Consider the standard linear regression model Yi = Xi,∗ β + εi for i = 1, . . . , n and with εi ∼i.i.d. N (0, σ 2 ). The
model comprises a single covariate and, depending on the subquestion, an intercept. Data on the response and the
covariate are: {(yi , xi,1 )}4i=1 = {(1.4, 0.0), (1.4, −2.0), (0.8, 0.0),
(0.4, 2.0)}.
a) Evaluate the lasso regression estimator of the model without intercept for the data at hand with λ1 = 0.2.
b) Evaluate the lasso regression estimator of the model with intercept for the data at hand with λ1 = 0.2 that
does not apply to the intercept (which is left unpenalized).

Question 6.3
Consider the standard linear regression model Yi = Xi,1 β1 + Xi,2 β2 + εi for i = 1, . . . , n and with the εi
i.i.d. normally distributed with zero mean and some known common variance. In the estimation of the regression
parameter (β1 , β2 )⊤ a lasso penalty is used: λ1,1 |β1 | + λ1,2 |β2 | with penalty parameters λ1,1 , λ1,2 > 0.
104 Lasso regression

a) Let λ1,1 = λ1,2 and assume the covariates are orthogonal with the spread of the first covariate being much
larger than that of the second. Draw a plot with β1 and β2 on the x- and y-axis, repectively. Sketch the
parameter constraint as implied by the lasso penalty. Add the levels sets of the sum-of-squares, kY −Xβk22 ,
loss criterion. Use the plot to explain why the lasso tends to select covariates with larger spread.
b) Assume the covariates to be orthonormal. Let λ1,2 ≫ λ1,1 . Redraw the plot of part a of this exercise. Use
the plot to explain the effect of differening λ1,1 and λ1,2 on the resulting lasso estimate.
c) Show that the two cases (i.e. the assumptions on the covariates and penalty parameters) of part a and b of
this exercise are equivalent, in the sense that their loss functions can be rewritten in terms of the other.
Question 6.4
Investigate the effect of the variance of the covariates on variable selection by the lasso. Hereto consider the toy
model: Yi = X1i + X2i + εi , where ǫi ∼ N (0, 1), X1i ∼ N (0, 1), and X2i = a X1i with a ∈ [0, 2]. Draw a
hundred samples for both X1i and εi and construct both X2i and Yi for a grid of a’s. Fit the model by means of
the lasso regression estimator with λ1 = 1 for each choice of a. Plot e.g. in one figure a) the variance of Xi1 , b)
the variance of X2i , and c) the indicator of the selection of X2i . Which covariate is selected for which values of
scale parameter a?
Question 6.5
Show the non-uniqueness of the lasso regression estimator for p > 2 when the design matrix X contains linearly
dependent columns.
Question 6.6
Consider the linear regression model Y = Xβ + ε with β ∈ R>0 × R>0 , ε ∼ N (0, 1) and an n × 2-dimensional
design matrix with zero-centered and standardized but positively collinear columns, i.e.:
 
1 ρ
X⊤ X =
ρ 1

where ρ > 0. Show that the lasso regression estimator is β̂(λ1 ) = β̂ (ml) − 12 λ1 (1 + ρ)−1 12 with β̂ (ml) =
(X⊤ X)−1 X⊤ Y, the ML regression estimator.
Question 6.7
Show kβ̂(λ1 )k1 is monotone increasing in λ1 . In this assume orthonormality of the design matrix X.
Question 6.8
Augment the lasso penalty with the sum of the absolute differences all pairs of successive regression coefficients:
Xp Xp
λ1 |βj | + λF |βj − βj−1 |.
j=1 j=2

This augmented lasso penalty is referred to as the fused lasso penalty.Pp

a) Consider the standard multiple linear regression model: Yi = j=1 Xij βj + εi . Estimation of the regres-
sion parameters takes place via minimization of penalized sum of squares, in which the fused lasso penalty
is used with λ1 = 0. Rewrite the corresponding loss function to the standard lasso problem by application
of the following change-of-variables: γ1 = β1 and γj = βj − βj−1 .
b) Investigate on simulated data the effect of the second summand of the fused lasso penalty on the parameter
estimates. In this, temporarily set λ1 = 0.
c) Let λ1 equal zero still. Compare the regression estimates of Question 4b to the ridge estimates with a first-
order autoregressive prior. What is qualitatively the difference in the behavior of the two estimates? Hint:
plot the full solution path for the penalized estimates of both estimation procedures.
d) How do the estimates of part b) of this question change if we allow λ1 > 0?
Question 6.9
A researcher has measured gene expression measurements for 1000 genes in 40 subjects, half of them cases and
the other half controls.
a) Describe and explain what would happen if the researcher would fit an ordinary logistic regression to these
data, using case/control status as the response variable.
b) Instead, the researcher chooses to fit a lasso regression, choosing the tuning parameter lambda by cross-
validation. Out of 1000 genes, 37 get a non-zero regression coefficient in the lasso fit. In the ensuing
publication, the researcher writes that the 963 genes with zero regression coefficients were found to be
“irrelevant”. What is your opinion about this statement?
6.9 Exercises 105

Question 6.10
Consider the standard linear regression model Yi = Xi,∗ β + εi for i = 1, . . . , n and with the εi i.i.d. normally
distributed with zero mean and a common variance. Let the first covariate correspond to the intercept. The
model is fitted to data by means of the minimization
Pp of the sum-of-squares augmented with a lasso penalty in
which the intercept is left unpenalized: λ1 j=2 |βj | with penalty parameter λ1 > 0. The penalty parameter is
chosen through leave-one-out cross-validation (LOOCV). The predictive performance of the model is evaluated,
again by means of LOOCV. Thus, creating a double cross-validation loop. At each inner loop the optimal λ1
yields an empty intercept-only model, from which a prediction for the left-out sample is obtained. The vector of
these prediction is compared to the corresponding observation vector through their Spearman correlation (which
measures the monotonicity of a relatonship and – as a correlation measure – assumed values on the [−1, 1] interval
with an analogous interpretation to the ‘ordinary’ correlation). The latter equals −1. Why?
Question 6.11
Download the breastCancerNKI package from BioConductor:
> source("http://www.bioconductor.org/biocLite.R")
> biocLite("breastCancerNKI")
Activate the library and load leukemia data from the package:
> library(breastCancerNKI)
> data(nki)
The eset-object nki is now available. It contains the expression profiles of 337 breast cancer patients. Each
profile comprises expression levels of 24481 genes. Extract the expression data from the object, remove all genes
with missing values, center the gene expression gene-wise around zero, and limit the data set to the first thousand
genes. The reduction of the gene dimensionality is only for computational speed.
X <- exprs(nki)
X <- X[-which(rowSums(is.na(X)) > 0),]
X <- apply(X[1:1000,], 1, function(X) X - mean(X) ) .
Furthermore, extract the estrogen receptor status (short: ER status), an important prognostic indicator for breast
cancer.
Y <- pData(nki)[,8]
a) Relate the ER status and the gene expression levels by a logistic regression model, which is fitted by means
of the lasso penalized maximum likelihood method. First, find the optimal value of the penalty parameter
of λ1 by means of cross-validation. This is implemented in optL1-function of the penalized-package
available from CRAN.
b) Evaluate whether the cross-validated likelihood indeed attains a maximum at the optimal value of λ1 . This
can be done with the profL1-function of the penalized-package available from CRAN.
c) Investigate the sensitivity of the penalty parameter selection with respect to the choice of the cross-validation
fold.
d) Does the optimal lambda produce a reasonable fit? And how does it compare to the ‘ridge fit’?
Question 6.12
Consider fitting the linear regression model by means of the elastic net regression estimator.
a) Recall the data augmentation trick of Question 1.3 of the ridge regression exercises. Use the same trick to
show that the elastic net least squares loss function can be reformulated to the form of the traditional lasso
function. Hint: absorb the ridge part of the elastic net penalty into the sum of squares.
b) The elastic net regression estimator can be evaluated by a coordinate descent procedure outlined in Section
6.4.4. Show that in such a procedure at each step the j-th element of the elastic net regression estimate is
updated according to:
 ⊤ 
β̂j (λ1 , λ2 ) = (kX∗,j k22 + λ2 )−1 sign(X⊤ 1
∗,j Ỹ) |X∗,j Ỹ| − 2 λ1 + .

with Ỹ = Y − X∗,\j β\j .

Question 6.13 ∗
Consider the linear regression model Y = Xβ + ε. It is fitted to data from a study with an orthonormal design
matrix by means of the adaptive lasso regression estimator initiated by the OLS/ML regression estimator. Show
that the j-th element of the resulting adaptive lasso regression estimator equals:
β̂jadapt (λ1 ) = sign(β̂jols )(|β̂jols | − 12 λ1 /|β̂jols |)+ .

∗ This question is freely copied from Bühlmann and Van De Geer (2011): Problem 2.5a, page 43.
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