LRTM Left-Right Transition Matrices for Molecular Interaction Prediction

Authors

Kaitlin Zheng, Central South University
Guihua Duan, Central South University
Mengyun Yang, Shaoyang University
Wei Wu, Central South University
Yao-Hang Li, Old Dominion UniversityFollow
Jianxin Wang, Central South University

Document Type

Article

Publication Date

2025

DOI

10.1101/2025.02.06.636973

Publication Title

bioRxiv

Pages

1-9

Abstract

Molecular interactions are central to most biological processes. The discovery and identification of potential associations between molecules can provide insights into biological exploration, diagnostic and therapeutic interventions, and drug development. So far many relevant computational methods have been proposed, but most of them are usually limited to specific domains and rely on complex preprocessing procedures, which restricts the models’ ability to be applied to other tasks. Therefore, it remains a challenge to explore a generalized approach to accurately predicting potential associations. In this study, We propose Left-Right Transition Matrices (LRTM) for molecular interaction prediction. From the perspective on the diffusion model, we construct two transition matrices to model undirected graph information propagation. This allows modeling the transition probabilities of links, which facilitates link prediction in molecular bipartite networks. The extensive experimental results show that the proposed LRTM algorithm performs better than the compared methods. Also, the proposed algorithm has the potential for cross-task prediction. Furthermore, case studies show that LRTM is a powerful tool that can be effectively applied to practical applications.

Comments

This is a preprint article that has not undergone peer review.

Rights

© 2025 The Author.

The copyright holder for this preprint is the author/funder. It is made available under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC-BY-NC-ND 4.0) International License.

Original Publication Citation

Zheng, K., Duan, G., Yang, M., Wu, W., Li, Y., & Wang, J. (2025). LRTM: Left-right transition. BioRxiv. https://doi.org/10.1101/2025.02.06.636973

Repository Citation

Zheng, K., Duan, G., Yang, M., Wu, W., Li, Y., & Wang, J. (2025). LRTM: Left-right transition. BioRxiv. https://doi.org/10.1101/2025.02.06.636973

ORCID

0000-0002-7892-5295 (Li)