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Lecture16 PDF

This document discusses various methods for survival analysis, including Kaplan-Meier estimates, Cox proportional hazards models, and other approaches. It outlines key survival analysis concepts like the survival function, hazard function, and censoring. It also compares parametric and non-parametric survival models and discusses how to build multivariate models that account for dependencies between time intervals. The goal is to predict survival probabilities using patient data and evaluate model performance on new cases.

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69 views

Lecture16 PDF

This document discusses various methods for survival analysis, including Kaplan-Meier estimates, Cox proportional hazards models, and other approaches. It outlines key survival analysis concepts like the survival function, hazard function, and censoring. It also compares parametric and non-parametric survival models and discusses how to build multivariate models that account for dependencies between time intervals. The goal is to predict survival probabilities using patient data and evaluate model performance on new cases.

Uploaded by

markkkkkkkheeess
Copyright
© © All Rights Reserved
Available Formats
Download as PDF, TXT or read online on Scribd
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Survival Analysis

Decision Systems Group


Brigham and Womens Hospital

Harvard-MIT Division of Health Sciences and Technology


HST.951J: Medical Decision Support
Outline
Basic concepts & distributions

Survival, hazard
Parametric models
Non-parametric models
Simple models
Life-table
Product-limit
Multivariate models
Cox proportional hazard
Neural nets
What we are trying to do
Predict survival
Variable 1 Variable 2 days (or probability of survival)
Case 1
0.7 -0.2 8
Case 2
0.6 0.5 4
-0.6 0.1 2 and evaluate
0 -0.9 3
performance on
new cases
-0.4 0.4 2
-0.8 0.6 3 and determine
0.5 -0.7 4 which variables are
important
Using these

Survival function
Probability that an individual survives at least t

S(t) = P(T > t)


By definition, S(0) = 1 and S()=0
Estimated by (# survivors at t / total patients)
100

Survival
(%)

time

Unconditional failure rate

Probability density function (of death)


f(t) = lim t-> 0 P(individual dies (t,t+t))/ t
f(t) always non-negative
Area below density is 1
Estimated by

# patients dying in the interval/(total patients*interval_width)

Same as # patients dying per unit interval/total

Some other definitions

Just like S(t) is cumulative survival, F(t) is


cumulative death probability
S(t) = 1 F(t)
f(t) = - S(t)
Conditional failure rate
AKA Hazard function
h(t) = lim t-> 0 P(individual aged t dies (t,t+t))/ t
h(t) is instantaneous failure rate
Estimated by

# patients dying in the interval/(survivors at t *interval_width)

So can be estimated by
# patients dying per unit interval/survivors at t
h(t) = f(t)/S(t) h(t) = -S(t)/S(t) = -d log S(t)/dt
Parametric estimation

Example: Exponential
f(t) = e-t
S(t) = e-t
h(t) =
S(t) h(t)
1

t t

Weibull distribution
Generalization of the
exponential
h(t)
For , > 0

f(t) = (t) e-1 -t

S(t) = e -t =2 t

h(t) = (t) -1
S(t) h(t)
=1

t t

Non-Parametric estimation
Product-Limit (Kaplan-Meier)

S(ti) = (nj - dj )/ nj
S(t)

dj is the number of deaths in interval j


1 nj is the number of individuals at risk
Product is from time interval 1 to j
One interval per death time

2 4 5 8

Kaplan-Meier

Example
Deaths: 10, 37, 40, 80, 91,143, 164, 188, 188, 190,
192, 206,
Life-Tables
AKA actuarial method

S(ti) = (nj - dj )/ nj

dj is the number of deaths in interval j

nj is the number of individuals at risk

Product is from time interval 1 to j

Pre-defined intervals j are independent of death times

Kaplan-Meier
S(t) S(t)

1 1

2 2 1 2 3

Life-Table
hazard
survival

density

Simple models

Multiple strata

Multivariate models

Several strata, each defined by a set of


variable values
Could potentially go as far as one
stratum per case?
Can it do prediction for individuals?
Cox Proportional Hazards
Regression model
Can give estimate of hazard for a
particular individual relative to baseline
hazard at a particular point in time
Baseline hazard can be estimated by,
for example, by using survival from the
Kaplan-Meier method
Proportional Hazards

i = exi
where is baseline hazard and xi is covariate for patient

Cox proportional hazards


hi(t) = h0(t) e xi

Survival
exi
Si(t) = [S0(t)]
Cox Proportional Hazards

hi(t) = h0(t) e xi
New likelihood function is how we extimate
From the set of individuals at risk at time j (Rj), the probability of
picking exactly the one who died is

h0(t) e xi
m h0(t) e xm
Then likelihood function to maximize to all j is

L() = (e xi / m e xm )
Important details

Survival curves cant cross if hazards are


proportional
There is a common baseline h0, but we dont need to
know it to estimate the coefficients
We dont need to know the shape of hazard function
Cox model is commonly used to interpret importance
of covariates (amenable to variable selection
methods)
It is the most popular multivariate model for survival
Testing the proportionality assumption is difficult and
hardly ever done
Estimating survival for a

patient using the Cox model

Need to estimate the baseline


Can use parametric or non-parametric model
to estimate the baseline
Can then create a continuous survival curve
estimate for a patient
Baseline survival can be, for example:
the survival for a case in which all covariates are
set to their means
Kaplan-Meier estimate for all cases
What if the proportionality

assumption is not OK?

Survival curves may


cross
Other multivariate
models can be built
Survival at certain time
points are modeled and
combined100 A
Survival
(%)
B

time

0
Single-point models
Logistic regression
Neural nets

age
gender
blood pressure
CHD in ta

cholesterol
smoking
weight
Problems

Survival
(%)
Dependency nonmonotonic

between intervals is
curve

not modeled (no


links between
networks)
2 4
Nonmonotonic
1 3 5 6
Year
curves may appear S(1)=0.9 S(2)=0.6 S(3)=0.4 S(4)=0.3 S(5)=0.5 S(6)=0.3

How to evaluate?
patients
followed
for >1 year >2 years >3 years >4 years >5 years >6 years

input nodes: patient data

output nodes: probability of survival in a given time point

Accounting for dependencies

Survival (%)
Link networks
in some way to
account for monotonic
curve

dependencies

0 1 2 3 4 5
Year S(4)=0.2

S(3)=0.3

Output from lower network serves as


input for upper network.
Summary

Kaplan-Meier for simple descriptive


analysis
Cox Proportional for multivariate prediction
if survival curves dont cross
Other methods for multivariate survival
exist: logistic regression, neural nets,
CART, etc.
Censoring
Non-censored

Non-censored

Type I

Type II

Left

Study begin Study end

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