Exploring Hierarchical Molecular Graph Representation in Multimodal LLMs

Following the milestones in large language models (LLMs) and multimodal models, we have seen a surge in applying LLMs to biochemical tasks. Leveraging graph features and molecular text representations, LLMs can tackle various tasks, such as predicting chemical reaction outcomes and describing molecular properties. However, most current work overlooks the multi-level nature of graph features. The impact of different feature levels on LLMs and the importance of each level remain unexplored, and it is possible that different chemistry tasks require different feature levels. In this work, we first investigate the effect of feature granularity by fusing GNN-generated feature tokens, discovering that even reducing all tokens to a single token does not significantly impact performance. We then explore the effect of various feature levels on performance, finding that both the quality of LLM-generated molecules and performance on different tasks benefit from different feature levels. We conclude with two key insights: (1) current molecular Multimodal LLMs(MLLMs) lack a comprehensive understanding of graph features, and (2) static processing is not sufficient for hierarchical graph feature. Our code will be publicly available soon.