Path2Surv: Pathway/gene set-based survival analysis using multiple kernel learning

Onur DereliMehmet Gönen


Survival analysis methods that integrate pathways/gene sets into their learning model could identify molecular mechanisms that determine survival characteristics of patients. Rather than first picking the predictive pathways/gene sets from a given collection and then training a predictive model on the subset of genomic features mapped to these selected pathways/gene sets, we developed a novel machine learning algorithm (Path2Surv) that conjointly performs these two steps using multiple kernel learning. We extensively tested our Path2Surv algorithm on 7655 patients from 20 cancer types using cancer-specific pathway/gene set collections and gene expression profiles of these patients. Path2Surv statistically significantly outperformed survival random forest (RF) on 12 out of 20 datasets and obtained comparable predictive performance against survival support vector machine (SVM) using significantly fewer gene expression features (i.e. less than 10% of what survival RF and survival SVM used). Our implementations of survival SVM and Path2Surv algorithms in R are available at together with the scripts that replicate the reported experiments. Supplementary data are available at Bioinformatics on...Continue Reading


Sep 8, 2004·Statistics in Medicine·Bart BakkerBert Kappen
Jan 24, 2007·Biometrical Journal. Biometrische Zeitschrift·Thomas A Gerds, Martin Schumacher
Jun 3, 2008·Bioinformatics·Ludger Evers, Claudia-Martina Messow
Oct 4, 2008·Nucleic Acids Research·Carl F SchaeferKenneth H Buetow
Nov 11, 2010·Bioinformatics·Vanya Van BelleJohan A K Suykens
Mar 4, 2011·European Journal of Human Genetics : EJHG·Herbert PangStéphane Minvielle
Aug 9, 2011·Artificial Intelligence in Medicine·Vanya Van BelleJohan A K Suykens
May 2, 2012·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Herbert PangTiejun Tong
Mar 20, 2013·Statistics in Medicine·Ulla B Mogensen, Thomas A Gerds
Jun 2, 2014·Nature Biotechnology·James C CostelloGustavo Stolovitzky
Apr 25, 2015·IEEE Transactions on Neural Networks and Learning Systems·Farkhondeh KiaeeSamaneh Eftekhari Mahabadi
Jan 16, 2016·Cell Systems·Arthur LiberzonPablo Tamayo
Mar 19, 2016·Statistical Methods in Medical Research·Andrea LamontM Lee Van Horn
Apr 18, 2018·Statistics in Medicine·Jennifer A Sinnott, Tianxi Cai

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