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Modelling Survival Prediction in Medical Data

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Hazlina Hamdan Jonathan Garibaldi

Universiti Putra Malaysia University of Nottingham
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 Modelling survival
prediction in medical data
By
Hazlina Hamdan
Dr. Jon Garibaldi

Hazlina Hamdan 1
31 March 2009

Presentation Content

Introduction
 Cancer and Breast Cancer
 Medical Prognosis
 Survival Analysis

Research Background
 Aims & Objectives

Understanding Previous Approach
 Artificial Neural Network
 PLANN

Analysis and Results

Conclusion

Future Work

Hazlina Hamdan 2
31 March 2009
 Cancer

Cancer is basically a disease which occurs when
cells behave abnormally and divide out of control
– form visible mass or tumour.

There are two general types of tumours namely:
 benign
 malignant

Breast cancer is the most common cancer
causing fatality amongst women.

Breast cancer is a malignant tumour that
develops from the uncontrolled growth of cells in
the breast.

Hazlina Hamdan 3
31 March 2009

Medical Prognosis

The principal factor in estimating of cure,
complication, disease recurrence or survival for a
patient or group of patients after treatment.

Prognosis is important because the type and
intensity of the medications are based on it.

Prognosis is only a prediction.

Hazlina Hamdan 4
31 March 2009
 Survival Analysis

The analysis of data that corresponds to the time
from when an individual enter a study until the
occurrence of some particular event or end-point.

Concerned with the comparison of survival curves
for different combinations of risk factors.

Data contains uncensored (reach until end point)
and censored (lost to follow-up or die from
unrelated cause) observations.

Hazlina Hamdan 5
31 March 2009

Survival Analysis – Survival Function

Probability an Cumulative Proportion Surviving (Kaplan-Meier)

individual survive at 1.0

Complete Censored

least up to a certain 0.9

time t. 0.8
Cumulative Proportion Surviving

0.7

S(tl)=P(T≥t) 0.6

0.5

0.4

Kaplan-Meier survival 0.3

0.2
curve. 0.1

0.0 Stage 1
Stage 2
-0.1 Stage 3
0 1 2 3 4 5 6 7 8 9 10 Stage 4
Time

Hazlina Hamdan 6
31 March 2009
Survival Analysis – Hazard Function

Probability an individual will die at a certain time,
conditioned on survival up to that time, and
denotes the instantaneous death rate. (Collet D.,
1994)
hl = P(T Є Al|T>tl-1) = fl /S(tl-1)
known also as conditional failure probability

Survival and Hazard function are related to each

other
S(t)=∏(1-hl)
l:tl≤t

Hazlina Hamdan 7
31 March 2009

Research Objectives

Understand previous approaches.

Apply previous approaches to our data.

Develop novel approaches based on Artificial
Neural Network (ANN) and Fuzzy method.

In clinical perspective is to assist doctor in
predicting survival of individual patients and
planning future treatments.

Hazlina Hamdan 8
31 March 2009
 Previous Approach
Artificial Neural Network (ANN)

Artificial Neural Network (ANN) is defined as an
information processing system inspired by the
structure of the human brain.

ANN gathers its knowledge by detecting a
common pattern and relationships in raw data,
then learning from such relationships and
adapting the results as required.

The knowledge is then used to predict the
outcome for new combinations of data.

Hazlina Hamdan 9
31 March 2009

Previous Approach - ANN

In the field of medicine, ANN have been used
since the late 1980s, initially as an aid to
diagnosis and treatment, and recently as a tool
for the analysis of survival data in the presence
of censorship.

The ability of neural networks to generalise to
new cases based on existing patterns is used as a
basis to compute and predict the survival of
individual patient or group of patients.

Hazlina Hamdan 10
31 March 2009
 Previous Approach-Feed-Forward ANN
Patients
Variables 1…x Inputs Hidden units Outputs
bias
bias

A A1… Ax
.
. .
.
.

. .
.
.
.
.
.

. .
.
.

N N1… Nx
Transfer Function
Hazlina Hamdan 11
31 March 2009

Previous Approaches-PLANN

Partial Logistic Artificial Neural Network

Proposed by Biganzoli et. al (1998)

Hazlina Hamdan 12
31 March 2009
 PLANN Model

Hazlina Hamdan 13
31 March 2009

PLANN Model-Pre-processing

Categorical variables indicator variables
Treatment Type Indicator variables

Radiotherapy 1 0 0

Hormone therapy 0 1 0

Chemotherapy 0 0 1

Continuous variables  range(-1,1) or (0,1)

Hazlina Hamdan 14
31 March 2009
 PLANN Model-Pre-processing

Training data - each subjects are replicated for all the
intervals in which the subjects is observed and coupled
with the event indicator
Time Size Treat1 Treat2 Treat3 Event
Subject1 3 1.0 1 0 0 1
Subject2 5 0.5 0 0 1 0

Time Size Treat1 Treat2 Treat3 Event

Subject1 1 1.0
2 1.0
3 1.0
Subject2 1 0.5
2 0.5
3 0.5
4 0.5
5 0.5
1 0 0 0
1 0 0 0
1 0 0 1
0 0 1 0
0 0 1 0
0 0 1 0
0 0 1 0
0 0 1 0

Hazlina Hamdan 15
31 March 2009

PLANN Model-Pre-processing

Testing – each subjects are replicated into full number of
time interval of observed with all event indicator as zero.
Time Size Treat1 Treat2 Treat3 Event
Subject1 3 1.0 1 0 0 1
Subject2 5 0.5 0 0 1 0

Time Size Treat1 Treat2 Treat3 Event

Subject1 1 1.0 1 0 0 0
2 1.0 1 0 0 0
3 1.0 1 0 0 0
4 1.0 1 0 0 0
5 1.0 1 0 0 0
Subject2 1 0.5 0 0 1 0
2 0.5 0 0 1 0
3 0.5 0 0 1 0
4 0.5 0 0 1 0
5 0.5 0 0 1 0

Hazlina Hamdan 16
31 March 2009
 PLANN Model-Post-processing

Predicted hazard is the mean calculated from the
distribution of the activation.

Hazlina Hamdan 17
31 March 2009

Analysis and Result

Head and Neck Cancer – disease recurrence

Radiation therapy Radiation +

(Arm A) Chemotherapy
(Arm B)
Total patients 51 45

End of time interval 47 76

(in month)
Total patient recur until end 42 31
interval
Total patient lost to follow 9 14
up
Total training replication 628 967

Total testing 47 76

Hazlina Hamdan 18
31 March 2009
 Analysis and Result

Hazlina Hamdan 19
31 March 2009

Analysis and Result

Hazlina Hamdan 20
31 March 2009
 Analysis and Result

Hazlina Hamdan 21
31 March 2009

Conclusion

ANN have been considered as alternative
methods for analysis of survival for individual
patient or group of patients.

A smooth discrete hazard possible be model by
treating the time interval and the covariates as
an input variable with standard feed forward
network and logistic activation function.

Hazlina Hamdan 22
31 March 2009
 Future Work

Implementing PLANN model to our data (breast
cancer data from QMC).

Develop fuzzy set rules in producing the survival
rate prediction for breast cancer patient.

Hazlina Hamdan 23
31 March 2009

References

Bishop, C. M. (1995). Neural Networks for Pattern Recognition, Oxford University
Press Inc., New York,.

Burke, H.B., Goodman, P.H., Rosen, D.B., Henson, D.E., Weinstein, J.N., Harrell,
F.E., Marks, J.R., Winchester, D.P. & Bostwick, D.G. (1997). Artificial neural network
improve the accuracy of cancer survival prediction. Cancer, vol. 79, pp.857-862

Collett, D. (1994). Modelling Survival Data In Medical Research. Chapman and Hall,
London.

Elia Biganzoli, P. B. L. M. E. M. (1998). "Feed forward neural networks for the
analysis of censored survival data: a partial logistic regression approach." Statistics
in Medicine 17(10): 1169-1186.

Lisboa, P. J. G., H. Wong, et al. (2003). "A Bayesian neural network approach for
modelling censored data with an application to prognosis after surgery for breast
cancer." Artificial Intelligence in Medicine 28(1): 1-25.

Ohno-Machado, L. (2001). "Modeling Medical Prognosis: Survival Analysis
Techniques." Journal of Biomedical Informatics 34(6): 428-439.

Ripley, R. M., A. L. Harris, et al. (1998). "Neural network models for breast cancer
prognosis." Neural Computing & Applications 7(4): 367-375.

Ravdin, P. and G. Clark (1992). "A practical application of neural network analysis for
predicting outcome of individual breast cancer patients." Breast Cancer Research and
Treatment 22(3): 285-293.

Hazlina Hamdan 24
31 March 2009

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