ModuLM: Enabling Modular and Multimodal Molecular Relational Learning with Large Language Models

Zhuo Chen, YIZHEN ZHENG, Huan Yee Koh, hongxin xiang, Linjiang Chen, Wenjie Du, Yang Wang

Keywords: Molecular Relational Learning, Large Language Models, Multimodality

TL;DR: We propose ModuLM, a flexible framework for LLM-based molecular relational learning, supporting multimodal inputs and dynamic model construction.

Abstract: Molecular Relational Learning (MRL) aims to understand interactions between molecular pairs, playing a critical role in advancing biochemical research. With the recent development of large language models (LLMs), a growing number of studies have explored the integration of MRL with LLMs and achieved promising results. However, the increasing availability of diverse LLMs and molecular structure encoders has significantly expanded the model space, presenting major challenges for benchmarking. Currently, there is no LLM framework that supports both flexible molecular input formats and dynamic architectural switching. To address these challenges, reduce redundant coding, and ensure fair model comparison, we propose ModuLM, a framework designed to support flexible LLM-based model construction and diverse molecular representations. ModuLM provides a rich suite of modular components, including 8 types of 2D molecular graph encoders, 11 types of 3D molecular conformation encoders, 7 types of interaction layers, and 7 mainstream LLM backbones. Owing to its highly flexible model assembly mechanism, ModuLM enables the dynamic construction of over 50,000 distinct model configurations. In addition, we provide comprehensive benchmark results to demonstrate the effectiveness of ModuLM in supporting LLM-based MRL tasks.

Code URL: https://github.com/ssjjjhw/ModuLM

Primary Area: Evaluation (e.g., data collection methodology, data processing methodology, data analysis methodology, meta studies on data sources, extracting signals from data, replicability of data collection and data analysis and validity of metrics, validity of data collection experiments, human-in-the-loop for data collection, human-in-the-loop for data evaluation)

Submission Number: 2276