Improving Large Molecular Language Model via Relation-aware Multimodal Collaboration

Large language models (LLMs) have demonstrated their instruction-following capabilities and achieved powerful performance on various tasks. Inspired by their success, recent works in the molecular domain have led to the development of large molecular language models (LMLMs) that integrate 1D molecular strings or 2D molecular graphs into the language models. However, existing LMLMs often suffer from hallucination and limited robustness, largely due to inadequate integration of diverse molecular modalities such as 1D sequences, 2D molecular graphs, and 3D conformations. To address these limitations, we propose CoLLaMo, a large language model-based molecular assistant equipped with a multi-level molecular modality-collaborative projector. The relation-aware modality-collaborative attention mechanism in the projector facilitates fine-grained and relation-guided information exchange between atoms by incorporating 2D structural and 3D spatial relations. Furthermore, we present a molecule-centric new automatic measurement, including a hallucination assessment metric and GPT-based caption quality evaluation to address the limitations of token-based generic evaluation metrics (i.e., BLEU) widely used in assessing molecular comprehension of LMLMs. Our extensive experiments demonstrate that our CoLLaMo enhances the molecular modality generalization capabilities of LMLMs, achieving the best performance on multiple tasks, including molecule captioning, computed property QA, descriptive property QA, motif counting, and IUPAC name prediction.

TabFlash: Efficient Table Understanding with Progressive Question Conditioning and Token Focusing

Table images present unique challenges for effective and efficient understanding due to the need for question-specific focus and the presence of redundant background regions. Existing Multimodal Large Language Model (MLLM) approaches often overlook these characteristics, resulting in uninformative and redundant visual representations. To address these issues, we aim to generate visual features that are both informative and compact to improve table understanding. We first propose progressive question conditioning, which injects the question into Vision Transformer layers with gradually increasing frequency, considering each layer's capacity to handle additional information, to generate question-aware visual features. To reduce redundancy, we introduce a pruning strategy that discards background tokens, thereby improving efficiency. To mitigate information loss from pruning, we further propose token focusing, a training strategy that encourages the model to concentrate essential information in the retained tokens. By combining these approaches, we present TabFlash, an efficient and effective MLLM for table understanding. TabFlash achieves state-of-the-art performance, outperforming both open-source and proprietary MLLMs, while requiring 27% less FLOPs and 30% less memory usage compared to the second-best MLLM.

LLaMo: Large Language Model-based Molecular Graph Assistant

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.