MolMetaLM: a Physicochemical Knowledge-Guided Molecular Meta Language Model (2411.15500v1)

Abstract: Most current molecular LLMs transfer the masked LLM or image-text generation model from natural language processing to molecular field. However, molecules are not solely characterized by atom/bond symbols; they encapsulate important physical/chemical properties. Moreover, normal LLMs bring grammar rules that are irrelevant for understanding molecules. In this study, we propose a novel physicochemical knowledge-guided molecular meta language framework MolMetaLM. We design a molecule-specialized meta language paradigm, formatted as multiple <S,P,O> (subject, predicate, object) knowledge triples sharing the same S (i.e., molecule) to enhance learning the semantic relationships between physicochemical knowledge and molecules. By introducing different molecular knowledge and noises, the meta language paradigm generates tens of thousands of pretraining tasks. By recovering the token/sequence/order-level noises, MolMetaLM exhibits proficiency in large-scale benchmark evaluations involving property prediction, molecule generation, conformation inference, and molecular optimization. Through MolMetaLM, we offer a new insight for designing LLMs.