Molecular Graph
Molecular graphs represent molecules as networks of atoms (nodes) and bonds (edges), enabling computational analysis of their structure and properties. Current research heavily utilizes graph neural networks (GNNs), often combined with large language models (LLMs) and other techniques like diffusion models, to predict molecular properties, generate novel molecules, and analyze molecular dynamics. This work focuses on improving the expressiveness of molecular representations, incorporating higher-order interactions and multi-scale information, and developing more efficient and interpretable models. These advancements have significant implications for drug discovery, materials science, and other fields reliant on understanding molecular behavior.
Papers
GraphXForm: Graph transformer for computer-aided molecular design with application to extraction
Jonathan Pirnay, Jan G. Rittig, Alexander B. Wolf, Martin Grohe, Jakob Burger, Alexander Mitsos, Dominik G. Grimm
Pre-trained Molecular Language Models with Random Functional Group Masking
Tianhao Peng, Yuchen Li, Xuhong Li, Jiang Bian, Zeke Xie, Ning Sui, Shahid Mumtaz, Yanwu Xu, Linghe Kong, Haoyi Xiong
Molecular Graph Representation Learning Integrating Large Language Models with Domain-specific Small Models
Tianyu Zhang, Yuxiang Ren, Chengbin Hou, Hairong Lv, Xuegong Zhang
Geometry Informed Tokenization of Molecules for Language Model Generation
Xiner Li, Limei Wang, Youzhi Luo, Carl Edwards, Shurui Gui, Yuchao Lin, Heng Ji, Shuiwang Ji