MV-CLAM: Multi-View Molecular Interpretation with Cross-Modal Projection via Language Model

AbstractDeciphering molecular meaning in chemistry and biomedicine depends on context — a capability that large language models (LLMs) can enhance by aligning molecular structures with language. However, existing molecule-text models ignore complementary information in different molecular views and rely on single-view representations, limiting molecule structural understanding. Moreover, naïve multi-view alignment strategies face two challenges: (1) the aligned spaces differ across views due to inconsistent molecule-text mappings, and (2) existing loss objectives fail to preserve complementary information necessary for finegrained alignment. To enhance LLM’s ability to understand molecular structure, we propose MV-CLAM, a novel framework that aligns multi-view molecular representations into a unified textual space using a multi-querying transformer (MQ-Former). Our approach ensures cross-view consistency while the proposed token-level contrastive loss preserves diverse molecular features across textual queries. MV-CLAM enhances molecular reasoning, improving retrieval and captioning accuracy. The source code of MV-CLAM is available in https://github.com/sumin124/mv-clam.