Daily Papers

Language Models (LMs) have demonstrated impressive molecule understanding ability on various 1D text-related tasks. However, they inherently lack 2D graph perception - a critical ability of human professionals in comprehending molecules' topological structures. To bridge this gap, we propose MolCA: Molecular Graph-Language Modeling with Cross-Modal Projector and Uni-Modal Adapter. MolCA enables an LM (e.g., Galactica) to understand both text- and graph-based molecular contents via the cross-modal projector. Specifically, the cross-modal projector is implemented as a Q-Former to connect a graph encoder's representation space and an LM's text space. Further, MolCA employs a uni-modal adapter (i.e., LoRA) for the LM's efficient adaptation to downstream tasks. Unlike previous studies that couple an LM with a graph encoder via cross-modal contrastive learning, MolCA retains the LM's ability of open-ended text generation and augments it with 2D graph information. To showcase its effectiveness, we extensively benchmark MolCA on tasks of molecule captioning, IUPAC name prediction, and molecule-text retrieval, on which MolCA significantly outperforms the baselines. Our codes and checkpoints can be found at https://github.com/acharkq/MolCA.

Large Language Models (LLMs) have demonstrated remarkable generalization and instruction-following capabilities with instruction tuning. The advancements in LLMs and instruction tuning have led to the development of Large Vision-Language Models (LVLMs). However, the competency of the LLMs and instruction tuning have been less explored in the molecular domain. Thus, we propose LLaMo: Large Language Model-based Molecular graph assistant, which is an end-to-end trained large molecular graph-language model. To bridge the discrepancy between the language and graph modalities, we present the multi-level graph projector that transforms graph representations into graph tokens by abstracting the output representations of each GNN layer and motif representations with the cross-attention mechanism. We also introduce machine-generated molecular graph instruction data to instruction-tune the large molecular graph-language model for general-purpose molecule and language understanding. Our extensive experiments demonstrate that LLaMo shows the best performance on diverse tasks, such as molecular description generation, property prediction, and IUPAC name prediction. The code of LLaMo is available at https://github.com/mlvlab/LLaMo.