MolMVC: Enhancing molecular representations for drug-related tasks through multi-view contrastive learning

Page view(s)
17
Checked on Feb 03, 2025
MolMVC: Enhancing molecular representations for drug-related tasks through multi-view contrastive learning
Title:
MolMVC: Enhancing molecular representations for drug-related tasks through multi-view contrastive learning
Journal Title:
Bioinformatics
Keywords:
Publication Date:
02 September 2024
Citation:
Huang, Z., Fan, Z., Shen, S., Wu, M., & Deng, L. (2024). MolMVC: Enhancing molecular representations for drug-related tasks through multi-view contrastive learning. Bioinformatics, 40(Supplement_2), ii190–ii197. https://doi.org/10.1093/bioinformatics/btae386
Abstract:
Abstract Motivation Effective molecular representation is critical in drug development. The complex nature of molecules demands comprehensive multi-view representations, considering 1D, 2D, and 3D aspects, to capture diverse perspectives. Obtaining representations that encompass these varied structures is crucial for a holistic understanding of molecules in drug-related contexts. Results In this study, we introduce an innovative multi-view contrastive learning framework for molecular representation, denoted as MolMVC. Initially, we use a Transformer encoder to capture 1D sequence information and a Graph Transformer to encode the intricate 2D and 3D structural details of molecules. Our approach incorporates a novel attention-guided augmentation scheme, leveraging prior knowledge to create positive samples tailored to different molecular data views. To align multi-view molecular positive samples effectively in latent space, we introduce an adaptive multi-view contrastive loss (AMCLoss). In particular, we calculate AMCLoss at various levels within the model to effectively capture the hierarchical nature of the molecular information. Eventually, we pre-train the encoders via minimizing AMCLoss to obtain the molecular representation, which can be used for various down-stream tasks. In our experiments, we evaluate the performance of our MolMVC on multiple tasks, including molecular property prediction (MPP), drug-target binding affinity (DTA) prediction and cancer drug response (CDR) prediction. The results demonstrate that the molecular representation learned by our MolMVC can enhance the predictive accuracy on these tasks and also reduce the computational costs. Furthermore, we showcase MolMVC’s efficacy in drug repositioning across a spectrum of drug-related applications. Availability and implementation The code and pre-trained model are publicly available at https://github.com/Hhhzj-7/MolMVC.
License type:
Attribution 4.0 International (CC BY 4.0)
Funding Info:
This research is supported by core funding from: Institute for Infocomm Research
Grant Reference no. :

This work was supported by the National Natural Science Foundation of China under grants No.U23A20321 and No.62272490. This paper was published as part of a supplement financially supported by ECCB2024.
Description:
This article has been accepted for publication in [Bioinformatics] Published by Oxford University Press.
ISSN:
1367-4803
1367-4811