A Multitask Multiple Kernel Learning Algorithm for Survival Analysis with Application to Cancer Biology

Onur Dereli, Ceyda Oğuz, Mehmet Gönen
Proceedings of the 36th International Conference on Machine Learning, PMLR 97:1576-1585, 2019.

Abstract

Predictive performance of machine learning algorithms on related problems can be improved using multitask learning approaches. Rather than performing survival analysis on each data set to predict survival times of cancer patients, we developed a novel multitask approach based on multiple kernel learning (MKL). Our multitask MKL algorithm both works on multiple cancer data sets and integrates cancer-related pathways/gene sets into survival analysis. We tested our algorithm, which is named as Path2MSurv, on the Cancer Genome Atlas data sets analyzing gene expression profiles of 7,655 patients from 20 cancer types together with cancer-specific pathway/gene set collections. Path2MSurv obtained better or comparable predictive performance when benchmarked against random survival forest, survival support vector machine, and single-task variant of our algorithm. Path2MSurv has the ability to identify key pathways/gene sets in predicting survival times of patients from different cancer types.

Cite this Paper

BibTeX
@InProceedings{pmlr-v97-dereli19a, title = {A Multitask Multiple Kernel Learning Algorithm for Survival Analysis with Application to Cancer Biology}, author = {Dereli, Onur and O{\u{g}}uz, Ceyda and G{\"o}nen, Mehmet}, booktitle = {Proceedings of the 36th International Conference on Machine Learning}, pages = {1576--1585}, year = {2019}, editor = {Chaudhuri, Kamalika and Salakhutdinov, Ruslan}, volume = {97}, series = {Proceedings of Machine Learning Research}, month = {09--15 Jun}, publisher = {PMLR}, pdf = {http://proceedings.mlr.press/v97/dereli19a/dereli19a.pdf}, url = {https://proceedings.mlr.press/v97/dereli19a.html}, abstract = {Predictive performance of machine learning algorithms on related problems can be improved using multitask learning approaches. Rather than performing survival analysis on each data set to predict survival times of cancer patients, we developed a novel multitask approach based on multiple kernel learning (MKL). Our multitask MKL algorithm both works on multiple cancer data sets and integrates cancer-related pathways/gene sets into survival analysis. We tested our algorithm, which is named as Path2MSurv, on the Cancer Genome Atlas data sets analyzing gene expression profiles of 7,655 patients from 20 cancer types together with cancer-specific pathway/gene set collections. Path2MSurv obtained better or comparable predictive performance when benchmarked against random survival forest, survival support vector machine, and single-task variant of our algorithm. Path2MSurv has the ability to identify key pathways/gene sets in predicting survival times of patients from different cancer types.} }
Endnote
%0 Conference Paper %T A Multitask Multiple Kernel Learning Algorithm for Survival Analysis with Application to Cancer Biology %A Onur Dereli %A Ceyda Oğuz %A Mehmet Gönen %B Proceedings of the 36th International Conference on Machine Learning %C Proceedings of Machine Learning Research %D 2019 %E Kamalika Chaudhuri %E Ruslan Salakhutdinov %F pmlr-v97-dereli19a %I PMLR %P 1576--1585 %U https://proceedings.mlr.press/v97/dereli19a.html %V 97 %X Predictive performance of machine learning algorithms on related problems can be improved using multitask learning approaches. Rather than performing survival analysis on each data set to predict survival times of cancer patients, we developed a novel multitask approach based on multiple kernel learning (MKL). Our multitask MKL algorithm both works on multiple cancer data sets and integrates cancer-related pathways/gene sets into survival analysis. We tested our algorithm, which is named as Path2MSurv, on the Cancer Genome Atlas data sets analyzing gene expression profiles of 7,655 patients from 20 cancer types together with cancer-specific pathway/gene set collections. Path2MSurv obtained better or comparable predictive performance when benchmarked against random survival forest, survival support vector machine, and single-task variant of our algorithm. Path2MSurv has the ability to identify key pathways/gene sets in predicting survival times of patients from different cancer types.
APA
Dereli, O., Oğuz, C. & Gönen, M.. (2019). A Multitask Multiple Kernel Learning Algorithm for Survival Analysis with Application to Cancer Biology. Proceedings of the 36th International Conference on Machine Learning, in Proceedings of Machine Learning Research 97:1576-1585 Available from https://proceedings.mlr.press/v97/dereli19a.html.

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