Entropy-Guided Dynamic Tokens for Graph-LLM Alignment in Molecular Understanding

Molecular understanding is central to advancing areas such as scientific and drug discovery, yet Large Language Models (LLMs) struggle to understand molecular graphs effectively. Existing graph–LLM bridges often adapt the Q-Former-style connector with fixed-length static tokens, which is originally designed for vision tasks. These designs overlook stereochemistry and substructural context and typically require costly LLM-backbone fine-tuning, limiting efficiency and generalization. We introduce EDT-Former, an Entropy-guided Dynamic Token Transformer that generates tokens aligned with informative molecular patches, thereby preserving both local and global structural features for molecular graph understanding. Beyond prior approaches, EDT-Former enables alignment between frozen graph encoders and LLMs without tuning the LLM backbone (excluding the embedding layer), resulting in computationally efficient finetuning, and achieves state-of-the-art results on MoleculeQA, Mol-Instructions, and property prediction benchmarks (TDC, MoleculeNet), underscoring its effectiveness for scalable and generalizable multimodal molecular understanding.