Predicting Synthetic Lethal Interactions using Heterogeneous Data Sources
Herty Liany, Anand Devaprasath D. Jeyasekharan, Vaibhav Rajan · bioRxiv (Cold Spring Harbor Laboratory) · 2019
Abstract Motivation A synthetic lethal (SL) interaction is a relationship between two functional entities where the loss of either one of the entities is viable but the loss of both entities is lethal to the cell. Such pairs can be used as drug targets in targeted anticancer therapies, and so, many methods have been developed to identify potential candidate SL pairs. However, these methods use only a subset of available data from multiple platforms, at genomic, epigenomic and transcriptomic levels; and hence are limited in their ability to learn from complex associations in heterogeneous data sources. Results In this paper we develop techniques that can seamlessly integrate multiple heterogeneous data sources to predict SL interactions. Our approach obtains latent representations by collective matrix factorization based techniques, which in turn are used for prediction through matrix completion. Our experiments, on a variety of biological datasets, illustrate the efficacy and versatility of our approach, that outperforms state-of-the-art methods for predicting SL interactions and can be used with heterogeneous data sources with minimal feature engineering. Availability Software available at https://github.com/lianyh Contact [email protected]