Principal Component Analysis - Wikipedia
Principal Component Analysis - Wikipedia
PCA is mostly used as a tool in exploratory data analysis and for making predictive models. It is
often used to visualize genetic distance and relatedness between populations. PCA can be done by
eigenvalue decomposition of a data covariance (or correlation) matrix or singular value
decomposition of a data matrix, usually after a normalization step of the initial data. The
normalization of each attribute consists of mean centering – subtracting each data value from its
variable's measured mean so that its empirical mean (average) is zero – and, possibly, normalizing
each variable's variance to make it equal to 1; see Z-scores.[4] The results of a PCA are usually
discussed in terms of component scores, sometimes called factor scores (the transformed variable
values corresponding to a particular data point), and loadings (the weight by which each
standardized original variable should be multiplied to get the component score).[5] If component
scores are standardized to unit variance, loadings must contain the data variance in them (and that
is the magnitude of eigenvalues). If component scores are not standardized (therefore they contain
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the data variance) then loadings must be unit-scaled, ("normalized") and these weights are called
eigenvectors; they are the cosines of orthogonal rotation of variables into principal components or
back.
PCA is the simplest of the true eigenvector-based multivariate analyses. Often, its operation can be
thought of as revealing the internal structure of the data in a way that best explains the variance in
the data. If a multivariate dataset is visualised as a set of coordinates in a high-dimensional data
space (1 axis per variable), PCA can supply the user with a lower-dimensional picture, a projection
of this object when viewed from its most informative viewpoint. This is done by using only the first
few principal components so that the dimensionality of the transformed data is reduced.
PCA is closely related to factor analysis. Factor analysis typically incorporates more domain
specific assumptions about the underlying structure and solves eigenvectors of a slightly different
matrix.
PCA is also related to canonical correlation analysis (CCA). CCA defines coordinate systems that
optimally describe the cross-covariance between two datasets while PCA defines a new orthogonal
coordinate system that optimally describes variance in a single dataset.[6][7]
Contents
Intuition
Details
First component
Further components
Covariances
Dimensionality reduction
Singular value decomposition
Further considerations
Table of symbols and abbreviations
Properties and limitations of PCA
Properties
Limitations
PCA and information theory
Computing PCA using the covariance method
Organize the data set
Calculate the empirical mean
Calculate the deviations from the mean
Find the covariance matrix
Find the eigenvectors and eigenvalues of the covariance matrix
Rearrange the eigenvectors and eigenvalues
Compute the cumulative energy content for each eigenvector
Select a subset of the eigenvectors as basis vectors
Project the z-scores of the data onto the new basis
Derivation of PCA using the covariance method
Covariance-free computation
Iterative computation
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Intuition
PCA can be thought of as fitting a p-dimensional ellipsoid to the data, where each axis of the
ellipsoid represents a principal component. If some axis of the ellipsoid is small, then the variance
along that axis is also small, and by omitting that axis and its corresponding principal component
from our representation of the dataset, we lose only an equally small amount of information.
To find the axes of the ellipsoid, we must first subtract the mean of each variable from the dataset
to center the data around the origin. Then, we compute the covariance matrix of the data and
calculate the eigenvalues and corresponding eigenvectors of this covariance matrix. Then we must
normalize each of the orthogonal eigenvectors to become unit vectors. Once this is done, each of
the mutually orthogonal, unit eigenvectors can be interpreted as an axis of the ellipsoid fitted to
the data. This choice of basis will transform our covariance matrix into a diagonalised form with
the diagonal elements representing the variance of each axis. The proportion of the variance that
each eigenvector represents can be calculated by dividing the eigenvalue corresponding to that
eigenvector by the sum of all eigenvalues.
This procedure is sensitive to the scaling of the data, and there is no consensus as to how to best
scale the data to obtain optimal results.
Details
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PCA is mathematically defined as an orthogonal linear transformation that transforms the data to
a new coordinate system such that the greatest variance by some scalar projection of the data
comes to lie on the first coordinate (called the first principal component), the second greatest
variance on the second coordinate, and so on.[3]
Consider a data matrix, X, with column-wise zero empirical mean (the sample mean of each
column has been shifted to zero), where each of the n rows represents a different repetition of the
experiment, and each of the p columns gives a particular kind of feature (say, the results from a
particular sensor).
in such a way that the individual variables of t considered over the data set successively
inherit the maximum possible variance from X, with each coefficient vector w constrained to be a
unit vector (where is usually selected to be less than to reduce dimensionality).
First component
In order to maximize variance, the first weight vector w(1) thus has to satisfy
Since w(1) has been defined to be a unit vector, it equivalently also satisfies
The quantity to be maximised can be recognised as a Rayleigh quotient. A standard result for a
positive semidefinite matrix such as XTX is that the quotient's maximum possible value is the
largest eigenvalue of the matrix, which occurs when w is the corresponding eigenvector.
With w(1) found, the first principal component of a data vector x(i) can then be given as a score t1(i)
= x(i) ⋅ w(1) in the transformed co-ordinates, or as the corresponding vector in the original
variables, {x(i) ⋅ w(1)} w(1).
Further components
The kth component can be found by subtracting the first k − 1 principal components from X:
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and then finding the weight vector which extracts the maximum variance from this new data
matrix
It turns out that this gives the remaining eigenvectors of XTX, with the maximum values for the
quantity in brackets given by their corresponding eigenvalues. Thus the weight vectors are
eigenvectors of XTX.
The kth principal component of a data vector x(i) can therefore be given as a score tk(i) = x(i) ⋅ w(k)
in the transformed co-ordinates, or as the corresponding vector in the space of the original
variables, {x(i) ⋅ w(k)} w(k), where w(k) is the kth eigenvector of XTX.
where W is a p-by-p matrix of weights whose columns are the eigenvectors of XTX. The transpose
of W is sometimes called the whitening or sphering transformation. Columns of W multiplied by
the square root of corresponding eigenvalues, i.e. eigenvectors scaled up by the variances, are
called loadings in PCA or in Factor analysis.
Covariances
XTX itself can be recognised as proportional to the empirical sample covariance matrix of the
dataset XT.
The sample covariance Q between two of the different principal components over the dataset is
given by:
where the eigenvalue property of w(k) has been used to move from line 2 to line 3. However
eigenvectors w(j) and w(k) corresponding to eigenvalues of a symmetric matrix are orthogonal (if
the eigenvalues are different), or can be orthogonalised (if the vectors happen to share an equal
repeated value). The product in the final line is therefore zero; there is no sample covariance
between different principal components over the dataset.
In matrix form, the empirical covariance matrix for the original variables can be written
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where Λ is the diagonal matrix of eigenvalues λ(k) of XTX. λ(k) is equal to the sum of the squares
over the dataset associated with each component k, i.e. λ(k) = Σi tk2(i) = Σi (x(i) ⋅ w(k))2.
Dimensionality reduction
The transformation T = X W maps a data vector x(i) from an original space of p variables to a new
space of p variables which are uncorrelated over the dataset. However, not all the principal
components need to be kept. Keeping only the first L principal components, produced by using
only the first L eigenvectors, gives the truncated transformation
where the matrix TL now has n rows but only L columns. In other words, PCA learns a linear
transformation where the columns of p × L matrix W form an
orthogonal basis for the L features (the components of representation t) that are decorrelated.[8]
By construction, of all the transformed data matrices with only L columns, this score matrix
maximises the variance in the original data that has been preserved, while minimising the total
squared reconstruction error or .
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Dimensionality reduction may also be appropriate when the variables in a dataset are noisy. If
each column of the dataset contains independent identically distributed Gaussian noise, then the
columns of T will also contain similarly identically distributed Gaussian noise (such a distribution
is invariant under the effects of the matrix W, which can be thought of as a high-dimensional
rotation of the co-ordinate axes). However, with more of the total variance concentrated in the first
few principal components compared to the same noise variance, the proportionate effect of the
noise is less—the first few components achieve a higher signal-to-noise ratio. PCA thus can have
the effect of concentrating much of the signal into the first few principal components, which can
usefully be captured by dimensionality reduction; while the later principal components may be
dominated by noise, and so disposed of without great loss.
Here Σ is an n-by-p rectangular diagonal matrix of positive numbers σ(k), called the singular
values of X; U is an n-by-n matrix, the columns of which are orthogonal unit vectors of length n
called the left singular vectors of X; and W is a p-by-p whose columns are orthogonal unit vectors
of length p and called the right singular vectors of X.
where is the square diagonal matrix with the singular values of X and the excess zeros chopped
off that satisfies . Comparison with the eigenvector factorization of XTX establishes
that the right singular vectors W of X are equivalent to the eigenvectors of XTX, while the singular
values σ(k) of are equal to the square-root of the eigenvalues λ(k) of XTX.
Using the singular value decomposition the score matrix T can be written
so each column of T is given by one of the left singular vectors of X multiplied by the
corresponding singular value. This form is also the polar decomposition of T.
Efficient algorithms exist to calculate the SVD of X without having to form the matrix XTX, so
computing the SVD is now the standard way to calculate a principal components analysis from a
data matrix, unless only a handful of components are required.
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The truncation of a matrix M or T using a truncated singular value decomposition in this way
produces a truncated matrix that is the nearest possible matrix of rank L to the original matrix, in
the sense of the difference between the two having the smallest possible Frobenius norm, a result
known as the Eckart–Young theorem [1936].
Further considerations
Given a set of points in Euclidean space, the first principal component corresponds to a line that
passes through the multidimensional mean and minimizes the sum of squares of the distances of
the points from the line. The second principal component corresponds to the same concept after
all correlation with the first principal component has been subtracted from the points. The
singular values (in Σ) are the square roots of the eigenvalues of the matrix XTX. Each eigenvalue is
proportional to the portion of the "variance" (more correctly of the sum of the squared distances of
the points from their multidimensional mean) that is associated with each eigenvector. The sum of
all the eigenvalues is equal to the sum of the squared distances of the points from their
multidimensional mean. PCA essentially rotates the set of points around their mean in order to
align with the principal components. This moves as much of the variance as possible (using an
orthogonal transformation) into the first few dimensions. The values in the remaining dimensions,
therefore, tend to be small and may be dropped with minimal loss of information (see below). PCA
is often used in this manner for dimensionality reduction. PCA has the distinction of being the
optimal orthogonal transformation for keeping the subspace that has largest "variance" (as defined
above). This advantage, however, comes at the price of greater computational requirements if
compared, for example, and when applicable, to the discrete cosine transform, and in particular to
the DCT-II which is simply known as the "DCT". Nonlinear dimensionality reduction techniques
tend to be more computationally demanding than PCA.
PCA is sensitive to the scaling of the variables. If we have just two variables and they have the same
sample variance and are positively correlated, then the PCA will entail a rotation by 45° and the
"weights" (they are the cosines of rotation) for the two variables with respect to the principal
component will be equal. But if we multiply all values of the first variable by 100, then the first
principal component will be almost the same as that variable, with a small contribution from the
other variable, whereas the second component will be almost aligned with the second original
variable. This means that whenever the different variables have different units (like temperature
and mass), PCA is a somewhat arbitrary method of analysis. (Different results would be obtained if
one used Fahrenheit rather than Celsius for example.) Pearson's original paper was entitled "On
Lines and Planes of Closest Fit to Systems of Points in Space" – "in space" implies physical
Euclidean space where such concerns do not arise. One way of making the PCA less arbitrary is to
use variables scaled so as to have unit variance, by standardizing the data and hence use the
autocorrelation matrix instead of the autocovariance matrix as a basis for PCA. However, this
compresses (or expands) the fluctuations in all dimensions of the signal space to unit variance.
Mean subtraction (a.k.a. "mean centering") is necessary for performing classical PCA to ensure
that the first principal component describes the direction of maximum variance. If mean
subtraction is not performed, the first principal component might instead correspond more or less
to the mean of the data. A mean of zero is needed for finding a basis that minimizes the mean
square error of the approximation of the data.[9]
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An autoencoder neural network with a linear hidden layer is similar to PCA. Upon convergence,
the weight vectors of the K neurons in the hidden layer will form a basis for the space spanned by
the first K principal components. Unlike PCA, this technique will not necessarily produce
orthogonal vectors, yet the principal components can easily be recovered from them using singular
value decomposition.[10]
PCA is a popular primary technique in pattern recognition. It is not, however, optimized for class
separability.[11] However, it has been used to quantify the distance between two or more classes by
calculating center of mass for each class in principal component space and reporting Euclidean
distance between center of mass of two or more classes.[12] The linear discriminant analysis is an
alternative which is optimized for class separability.
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vector of empirical means, one mean for each column j of the data
matrix
vector of empirical standard deviations, one standard deviation for
each column j of the data matrix
z-scores, computed using the mean and standard deviation for each
row m of the data matrix
covariance matrix
correlation matrix
matrix of basis vectors, one vector per column, where each basis
vector is one of the eigenvectors of C, and where the vectors in W
are a sub-set of those in V
matrix consisting of n row vectors, where each vector is the
projection of the corresponding data vector from matrix X onto the
basis vectors contained in the columns of matrix W.
Properties
Some properties of PCA include:[13]
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The statistical implication of this property is that the last few PCs are not simply unstructured left-
overs after removing the important PCs. Because these last PCs have variances as small as possible
they are useful in their own right. They can help to detect unsuspected near-constant linear
relationships between the elements of x, and they may also be useful in regression, in selecting a
subset of variables from x, and in outlier detection.
Then, perhaps the main statistical implication of the result is that not only can we decompose the
combined variances of all the elements of x into decreasing contributions due to each PC, but we
can also decompose the whole covariance matrix into contributions from each PC.
Although not strictly decreasing, the elements of will tend to become smaller as
increases, as is nonincreasing for increasing , whereas the elements of tend to stay
about the same size because of the normalization constraints: .
Limitations
As noted above, the results of PCA depend on the scaling of the variables. This can be cured by
scaling each feature by its standard deviation, so that one ends up with dimensionless features
with unital variance [14]
The applicability of PCA as described above is limited by certain (tacit) assumptions [15] made in
its derivation. In particular, PCA can capture linear correlations between the features but fails
when this assumption is violated (see Figure 6a in the reference). In some cases, coordinate
transformations can restore the linearity assumption and PCA can then be applied (see kernel
PCA).
Another limitation is the mean-removal process before constructing the covariance matrix for
PCA. In fields such as astronomy, all the signals are non-negative, and the mean-removal process
will force the mean of some astrophysical exposures to be zero, which consequently creates
unphysical negative fluxes,[16] and forward modeling has to be performed to recover the true
magnitude of the signals.[17] As an alternative method, non-negative matrix factorization focusing
only on the non-negative elements in the matrices, which is well-suited for astrophysical
observations.[18][19][20] See more at Relation between PCA and Non-negative Matrix Factorization.
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i.e., that the data vector is the sum of the desired information-bearing signal and a noise signal
one can show that PCA can be optimal for dimensionality reduction, from an information-
theoretic point-of-view.
In particular, Linsker showed that if is Gaussian and is Gaussian noise with a covariance
matrix proportional to the identity matrix, the PCA maximizes the mutual information
between the desired information and the dimensionality-reduced output .[21]
If the noise is still Gaussian and has a covariance matrix proportional to the identity matrix (i.e.,
the components of the vector are iid), but the information-bearing signal is non-Gaussian
(which is a common scenario), PCA at least minimizes an upper bound on the information loss,
which is defined as[22][23]
The optimality of PCA is also preserved if the noise is iid and at least more Gaussian (in terms of
the Kullback–Leibler divergence) than the information-bearing signal .[24] In general, even if the
above signal model holds, PCA loses its information-theoretic optimality as soon as the noise
becomes dependent.
The goal is to transform a given data set X of dimension p to an alternative data set Y of smaller
dimension L. Equivalently, we are seeking to find the matrix Y, where Y is the Karhunen–Loève
transform (KLT) of matrix X:
Place the calculated mean values into an empirical mean vector u of dimensions p × 1.
Subtract the empirical mean vector from each row of the data matrix X.
Store mean-subtracted data in the n × p matrix B.
where is the conjugate transpose operator. If B consists entirely of real numbers, which is
the case in many applications, the "conjugate transpose" is the same as the regular
transpose.
where D is the diagonal matrix of eigenvalues of C. This step will typically involve the use of
a computer-based algorithm for computing eigenvectors and eigenvalues. These algorithms
are readily available as sub-components of most matrix algebra systems, such as SAS,[27]
R, MATLAB,[28][29] Mathematica,[30] SciPy, IDL (Interactive Data Language), or GNU Octave
as well as OpenCV.
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Matrix V, also of dimension p × p, contains p column vectors, each of length p, which represent
the p eigenvectors of the covariance matrix C.
The eigenvalues and eigenvectors are ordered and paired. The jth eigenvalue corresponds to
the jth eigenvector.
Matrix V denotes the matrix of right eigenvectors (as opposed to left eigenvectors). In general,
the matrix of right eigenvectors need not be the (conjugate) transpose of the matrix of left
eigenvectors.
where
Use the vector g as a guide in choosing an appropriate value for L. The goal is to choose a
value of L as small as possible while achieving a reasonably high value of g on a percentage
basis. For example, you may want to choose L so that the cumulative energy g is above a
certain threshold, like 90 percent. In this case, choose the smallest value of L such that
The rows of matrix T represent the Kosambi-Karhunen–Loève transforms (KLT) of the data
vectors in the rows of matrix X.
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This is very constructive, as cov(X) is guaranteed to be a non-negative definite matrix and thus is
guaranteed to be diagonalisable by some unitary matrix.
Covariance-free computation
In practical implementations, especially with high dimensional data (large p), the naive covariance
method is rarely used because it is not efficient due to high computational and memory costs of
explicitly determining the covariance matrix. The covariance-free approach avoids the np2
operations of explicitly calculating and storing the covariance matrix XTX, instead utilizing one of
matrix-free methods, e.g., based on the function evaluating the product XT(X r) at the cost of 2np
operations.
Iterative computation
One way to compute the first principal component efficiently[31] is shown in the following pseudo-
code, for a data matrix X with zero mean, without ever computing its covariance matrix.
do c times:
s = 0 (a vector of length p)
for each row
exit if
return
This power iteration algorithm simply calculates the vector XT(X r), normalizes, and places the
result back in r. The eigenvalue is approximated by rT (XTX) r, which is the Rayleigh quotient on
the unit vector r for the covariance matrix XTX . If the largest singular value is well separated
from the next largest one, the vector r gets close to the first principal component of X within the
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number of iterations c, which is small relative to p, at the total cost 2cnp. The power iteration
convergence can be accelerated without noticeably sacrificing the small cost per iteration using
more advanced matrix-free methods, such as the Lanczos algorithm or the Locally Optimal Block
Preconditioned Conjugate Gradient (LOBPCG) method.
Online/sequential estimation
In an "online" or "streaming" situation with data arriving piece by piece rather than being stored in
a single batch, it is useful to make an estimate of the PCA projection that can be updated
sequentially. This can be done efficiently, but requires different algorithms.[35]
data were subjected to PCA for quantitative variables. When analyzing the results, it is natural to
connect the principal components to the qualitative variable species. For this, the following results
are produced.
Identification, on the factorial planes, of the different species e.g. using different colors.
Representation, on the factorial planes, of the centers of gravity of plants belonging to the
same species.
For each center of gravity and each axis, p-value to judge the significance of the difference
between the center of gravity and origin.
These results are what is called introducing a qualitative variable as supplementary element.
This procedure is detailed in and Husson, Lê & Pagès 2009 and Pagès 2013. Few software offer
this option in an "automatic" way. This is the case of SPAD (http://www.coheris.com/produits/an
alytics/logiciel-data-mining/) that historically, following the work of Ludovic Lebart, was the first
to propose this option, and the R package FactoMineR (http://factominer.free.fr/).
Applications
Quantitative finance
In quantitative finance, principal component analysis can be directly applied to the risk
management of interest rate derivative portfolios.[36] Trading multiple swap instruments which
are usually a function of 30-500 other market quotable swap instruments is sought to be reduced
to usually 3 or 4 principal components, representing the path of interest rates on a macro basis.
Converting risks to be represented as those to factor loadings (or multipliers) provides
assessments and understanding beyond that available to simply collectively viewing risks to
individual 30-500 buckets.
PCA has also been applied to equity portfolios in a similar fashion,[37] both to portfolio risk and to
risk return. One application is to reduce portfolio risk, where allocation strategies are applied to
the "principal portfolios" instead of the underlying stocks.[38] A second is to enhance portfolio
return, using the principal components to select stocks with upside potential.
Neuroscience
A variant of principal components analysis is used in neuroscience to identify the specific
properties of a stimulus that increase a neuron's probability of generating an action potential.[39]
This technique is known as spike-triggered covariance analysis. In a typical application an
experimenter presents a white noise process as a stimulus (usually either as a sensory input to a
test subject, or as a current injected directly into the neuron) and records a train of action
potentials, or spikes, produced by the neuron as a result. Presumably, certain features of the
stimulus make the neuron more likely to spike. In order to extract these features, the experimenter
calculates the covariance matrix of the spike-triggered ensemble, the set of all stimuli (defined and
discretized over a finite time window, typically on the order of 100 ms) that immediately preceded
a spike. The eigenvectors of the difference between the spike-triggered covariance matrix and the
covariance matrix of the prior stimulus ensemble (the set of all stimuli, defined over the same
length time window) then indicate the directions in the space of stimuli along which the variance
of the spike-triggered ensemble differed the most from that of the prior stimulus ensemble.
Specifically, the eigenvectors with the largest positive eigenvalues correspond to the directions
along which the variance of the spike-triggered ensemble showed the largest positive change
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compared to the variance of the prior. Since these were the directions in which varying the
stimulus led to a spike, they are often good approximations of the sought after relevant stimulus
features.
In neuroscience, PCA is also used to discern the identity of a neuron from the shape of its action
potential. Spike sorting is an important procedure because extracellular recording techniques
often pick up signals from more than one neuron. In spike sorting, one first uses PCA to reduce the
dimensionality of the space of action potential waveforms, and then performs clustering analysis
to associate specific action potentials with individual neurons.
Correspondence analysis
Correspondence analysis (CA) was developed by Jean-Paul Benzécri[41] and is conceptually similar
to PCA, but scales the data (which should be non-negative) so that rows and columns are treated
equivalently. It is traditionally applied to contingency tables. CA decomposes the chi-squared
statistic associated to this table into orthogonal factors.[42] Because CA is a descriptive technique,
it can be applied to tables for which the chi-squared statistic is appropriate or not. Several variants
of CA are available including detrended correspondence analysis and canonical correspondence
analysis. One special extension is multiple correspondence analysis, which may be seen as the
counterpart of principal component analysis for categorical data.[43]
Factor analysis
Principal component analysis creates variables that are linear combinations of the original
variables. The new variables have the property that the variables are all orthogonal. The PCA
transformation can be helpful as a pre-processing step before clustering. PCA is a variance-focused
approach seeking to reproduce the total variable variance, in which components reflect both
common and unique variance of the variable. PCA is generally preferred for purposes of data
reduction (i.e., translating variable space into optimal factor space) but not when the goal is to
detect the latent construct or factors.
Factor analysis is similar to principal component analysis, in that factor analysis also involves
linear combinations of variables. Different from PCA, factor analysis is a correlation-focused
approach seeking to reproduce the inter-correlations among variables, in which the factors
"represent the common variance of variables, excluding unique variance".[44] In terms of the
correlation matrix, this corresponds with focusing on explaining the off-diagonal terms (i.e. shared
co-variance), while PCA focuses on explaining the terms that sit on the diagonal. However, as a
side result, when trying to reproduce the on-diagonal terms, PCA also tends to fit relatively well
the off-diagonal correlations.[45] Results given by PCA and factor analysis are very similar in most
situations, but this is not always the case, and there are some problems where the results are
significantly different. Factor analysis is generally used when the research purpose is detecting
data structure (i.e., latent constructs or factors) or causal modeling.
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K-means clustering
It was asserted in [46][47] that the relaxed solution of k-means clustering, specified by the cluster
indicators, is given by the principal components, and the PCA subspace spanned by the principal
directions is identical to the cluster centroid subspace. However, that PCA is a useful relaxation of
k-means clustering was not a new result (see, for example,[48]), and it is straightforward to
uncover counterexamples to the statement that the cluster centroid subspace is spanned by the
principal directions.[49]
In PCA, the contribution of each component is ranked based on the magnitude of its
corresponding eigenvalue, which is equivalent to the fractional residual variance (FRV) in
analyzing empirical data.[16] For NMF, its components are ranked based only on the empirical
component number given a total of components, for PCA has a flat plateau, where no data is
captured to remove the quasi-static noise, then the curves dropped quickly as an indication of
over-fitting and captures random noise.[16] The FRV curves for NMF is decreasing continuously
[20] when the NMF components are constructed sequentially,[19] indicating the continuous
capturing of quasi-static noise; then converge to higher levels than PCA,[20] indicating the less
over-fitting property of NMF.
Generalizations
Sparse PCA
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A particular disadvantage of PCA is that the principal components are usually linear combinations
of all input variables. Sparse PCA overcomes this disadvantage by finding linear combinations that
contain just a few input variables. It extends the classic method of principal component analysis
(PCA) for the reduction of dimensionality of data by adding sparsity constraint on the input
variables. Several approaches have been proposed, including
a regression framework,[50]
a convex relaxation/semidefinite programming framework,[51]
a generalized power method framework[52]
an alternating maximization framework[53]
forward-backward greedy search and exact methods using branch-and-bound techniques,[54]
Bayesian formulation framework.[55]
The methodological and theoretical developments of Sparse PCA as well as its applications in
scientific studies are recently reviewed in a survey paper.[56]
Nonlinear PCA
Most of the modern methods for nonlinear dimensionality reduction find their theoretical and
algorithmic roots in PCA or K-means. Pearson's original idea was to take a straight line (or plane)
which will be "the best fit" to a set of data points. Principal curves and manifolds[60] give the
natural geometric framework for PCA generalization and extend the geometric interpretation of
PCA by explicitly constructing an embedded manifold for data approximation, and by encoding
using standard geometric projection onto the manifold, as it is illustrated by Fig. See also the
elastic map algorithm and principal geodesic analysis. Another popular generalization is kernel
PCA, which corresponds to PCA performed in a reproducing kernel Hilbert space associated with a
positive definite kernel.
In multilinear subspace learning,[61] PCA is generalized to multilinear PCA (MPCA) that extracts
features directly from tensor representations. MPCA is solved by performing PCA in each mode of
the tensor iteratively. MPCA has been applied to face recognition, gait recognition, etc. MPCA is
further extended to uncorrelated MPCA, non-negative MPCA and robust MPCA.
N-way principal component analysis may be performed with models such as Tucker
decomposition, PARAFAC, multiple factor analysis, co-inertia analysis, STATIS, and DISTATIS.
Robust PCA
While PCA finds the mathematically optimal method (as in minimizing the squared error), it is
still sensitive to outliers in the data that produce large errors, something that the method tries to
avoid in the first place. It is therefore common practice to remove outliers before computing PCA.
However, in some contexts, outliers can be difficult to identify. For example, in data mining
algorithms like correlation clustering, the assignment of points to clusters and outliers is not
known beforehand. A recently proposed generalization of PCA[62] based on a weighted PCA
increases robustness by assigning different weights to data objects based on their estimated
relevancy. Outlier-resistant versions of PCA have also been proposed on L1-norm formulations
(L1-PCA).[63]
Robust principal component analysis (RPCA) via decomposition in low-rank and sparse matrices
is a modification of PCA that works well with respect to grossly corrupted observations.[64][65][66]
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7.1.2020 Principal component analysis - Wikipedia
Similar techniques
See also
Correspondence analysis (for contingency tables)
Multiple correspondence analysis (for qualitative variables)
Factor analysis of mixed data (for quantitative and qualitative variables)
Canonical correlation
CUR matrix approximation (can replace of low-rank SVD approximation)
Detrended correspondence analysis
Dynamic mode decomposition
Eigenface
Exploratory factor analysis (Wikiversity)
Factorial code
Functional principal component analysis
Geometric data analysis
Independent component analysis
Kernel PCA
L1-norm principal component analysis
Low-rank approximation
Matrix decomposition
Non-negative matrix factorization
Nonlinear dimensionality reduction
Oja's rule
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7.1.2020 Principal component analysis - Wikipedia
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plus Additive Matrices for Background/Foreground Separation: A Review for a Comparative
Evaluation with a Large-Scale Dataset". Computer Science Review. 23: 1–71.
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"Network component analysis: Reconstruction of regulatory signals in biological systems" (htt
p://www.pnas.org/content/100/26/15522.full.pdf) (PDF). Proceedings of the National Academy
of Sciences. 100 (26): 15522–15527. Bibcode:2003PNAS..10015522L (https://ui.adsabs.harva
rd.edu/abs/2003PNAS..10015522L). doi:10.1073/pnas.2136632100 (https://doi.org/10.1073%2
Fpnas.2136632100). PMC 307600 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC307600).
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nalysis/). Institute for Digital Research and Education. UCLA. Retrieved 29 May 2018.
Further reading
Jackson, J.E. (1991). A User's Guide to Principal Components (Wiley).
Jolliffe, I. T. (1986). Principal Component Analysis (https://archive.org/details/principalcompone
00joll_0/page/487). Springer Series in Statistics. Springer-Verlag. pp. 487 (https://archive.org/d
etails/principalcompone00joll_0/page/487). CiteSeerX 10.1.1.149.8828 (https://citeseerx.ist.ps
u.edu/viewdoc/summary?doi=10.1.1.149.8828). doi:10.1007/b98835 (https://doi.org/10.1007%
2Fb98835). ISBN 978-0-387-95442-4.
Jolliffe, I.T. (2002). Principal Component Analysis, second edition (Springer).
Husson François, Lê Sébastien & Pagès Jérôme (2009). Exploratory Multivariate Analysis by
Example Using R. Chapman & Hall/CRC The R Series, London. 224p. ISBN 978-2-7535-
0938-2
Pagès Jérôme (2014). Multiple Factor Analysis by Example Using R (https://books.google.co
m/books?id=_RIeBQAAQBAJ&printsec=frontcover#v=snippet&q=%22principal%20componen
t%20analysis%22&f=false). Chapman & Hall/CRC The R Series London 272 p
External links
University of Copenhagen video by Rasmus Bro (https://www.youtube.com/watch?v=UUxIXU_
Ob6E) on YouTube
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