PLATYPUS: A Multiple-View Learning Predictive Framework for Cancer Drug Sensitivity Prediction

Pac Symp Biocomput. 2019:24:136-147.

Abstract

Cancer is a complex collection of diseases that are to some degree unique to each patient. Precision oncology aims to identify the best drug treatment regime using molecular data on tumor samples. While omics-level data is becoming more widely available for tumor specimens, the datasets upon which computational learning methods can be trained vary in coverage from sample to sample and from data type to data type. Methods that can 'connect the dots' to leverage more of the information provided by these studies could offer major advantages for maximizing predictive potential. We introduce a multi-view machinelearning strategy called PLATYPUS that builds 'views' from multiple data sources that are all used as features for predicting patient outcomes. We show that a learning strategy that finds agreement across the views on unlabeled data increases the performance of the learning methods over any single view. We illustrate the power of the approach by deriving signatures for drug sensitivity in a large cancer cell line database. Code and additional information are available from the PLATYPUS website https://sysbiowiki.soe.ucsc.edu/platypus.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antineoplastic Agents / therapeutic use
  • Cell Line, Tumor
  • Computational Biology / methods
  • Databases, Factual
  • Drug Resistance, Neoplasm* / genetics
  • Humans
  • Information Storage and Retrieval
  • Machine Learning* / statistics & numerical data
  • Neoplasms / drug therapy*
  • Neoplasms / genetics
  • Patient-Specific Modeling
  • Pharmacogenomic Variants
  • Precision Medicine
  • Software
  • Supervised Machine Learning / statistics & numerical data

Substances

  • Antineoplastic Agents