Multi-view biomedical foundation models for molecule-target and property prediction
Parthasarathy Suryanarayanan, Yunguang Qiu, Shreyans Sethi, Diwakar Mahajan, Hongyang Li, Yuxin Yang, Elif Eyigoz, Aldo Guzman Saenz, Daniel E. Platt, Timothy H. Rumbell, Kenney Ng, Sanjoy Dey, Myson Burch, Bum Chul Kwon, Pablo Meyer, Feixiong Cheng, Jianying Hu, Joseph A. Morrone
Code Available — Be the first to reproduce this paper.
ReproduceCode
- github.com/BiomedSciAI/biomed-multi-viewOfficialpytorch★ 43
Abstract
Foundation models applied to bio-molecular space hold promise to accelerate drug discovery. Molecular representation is key to building such models. Previous works have typically focused on a single representation or view of the molecules. Here, we develop a multi-view foundation model approach, that integrates molecular views of graph, image and text. Single-view foundation models are each pre-trained on a dataset of up to 200M molecules and then aggregated into combined representations. Our multi-view model is validated on a diverse set of 18 tasks, encompassing ligand-protein binding, molecular solubility, metabolism and toxicity. We show that the multi-view models perform robustly and are able to balance the strengths and weaknesses of specific views. We then apply this model to screen compounds against a large (>100 targets) set of G Protein-Coupled receptors (GPCRs). From this library of targets, we identify 33 that are related to Alzheimer's disease. On this subset, we employ our model to identify strong binders, which are validated through structure-based modeling and identification of key binding motifs.