Discovering the mechanism of action of drugs with a sparse explainable network

BACKGROUND: Although Deep Neural Networks (DDNs) have been successful in predicting the efficacy of cancer drugs, the lack of explainability in their decision-making process is a significant challenge. Previous research proposed mimicking the Gene Ontology structure to allow for interpretation of each neuron in the network. However, these previous approaches require huge amount of GPU resources and hinder its extension to genome-wide models. METHODS: We developed SparseGO, a sparse and interpretable neural network, for predicting drug response in cancer cell lines and their Mechanism of Action (MoA). To ensure model generalization, we trained it on multiple datasets and evaluated its performance using three cross-validation schemes. Its efficiency allows it to be used with gene expression. In addition, SparseGO integrates an eXplainable Artificial Intelligence (XAI) technique, DeepLIFT, with Support Vector Machines to computationally discover the MoA of drugs. FINDINGS: SparseGO's sparse implementation significantly reduced GPU memory usage and training speed compared to other methods, allowing it to process gene expression instead of mutations as input data. SparseGO using expression improved the accuracy and enabled its use on drug repositioning. Furthermore, gene expression allows the prediction of MoA using 265 drugs to train it. It was validated on understudied drugs such as parbendazole and PD153035. INTERPRETATION: SparseGO is an effective XAI method for predicting, but more importantly, understanding drug response. FUNDING: The Accelerator Award Programme funded by 10.13039/501100000289Cancer Research UK [C355/A26819], Fundación Científica de la AECC and Fondazione AIRC, Project PIBA_2020_1_0055 funded by the 10.13039/501100003086Basque Government and the Synlethal Project (RETOS Investigacion, Spanish Government).