MAGICAL: A multi-class classifier to predict synthetic lethal and viable interactions using protein-protein interaction network

Synthetic lethality (SL) and synthetic viability (SV) are commonly studied genetic interactions in the targeted therapy approach in cancer. In SL, inhibiting either of the genes does not affect the cancer cell survival, but inhibiting both leads to a lethal phenotype. In SV, inhibiting the vulnerable gene makes the cancer cell sick; inhibiting the partner gene rescues and promotes cell viability. Many low and high-throughput experimental approaches have been employed to identify SLs and SVs, but they are time-consuming and expensive. The computational tools for SL prediction involve statistical and machine-learning approaches. Almost all machine learning tools are binary classifiers and involve only identifying SL pairs. Most importantly, there are limited properties known that best describe and discriminate SL from SV. We developed MAGICAL ( Multi-class Approach for Genetic Interaction in Cancer via Algorithm Learning ), a multi-class random forest based machine learning model for genetic interaction prediction. Network properties of protein derived from physical protein-protein interactions are used as features to classify SL and SV. The model results in an accuracy of ~80% for the training dataset (CGIdb, BioGRID, and SynLethDB) and performs well on DepMap and other experimentally derived reported datasets. Amongst all the network properties, the shortest path, average neighbor2, average betweenness, average triangle, and adhesion have significant discriminatory power. MAGICAL is the first multi-class model to identify discriminatory features of synthetic lethal and viable interactions. MAGICAL can predict SL and SV interactions with better accuracy and precision than any existing binary classifier.