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

arXiv: https://arxiv.org/abs/2602.02742 · HTML: https://mlsanity.com/paper/2602.02742/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 39 of its 55 references that are in the map.
- First posted on arXiv 2 Feb 2026.

## Builds on (most cited first, 30 of 39)

- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [The Llama 3 Herd of Models](https://mlsanity.com/paper/2407.21783/) (2024)
- [LLaMA: Open and Efficient Foundation Language Models](https://mlsanity.com/paper/2302.13971/) (2023)
- [Llama 2: Open Foundation and Fine-Tuned Chat Models](https://mlsanity.com/paper/2307.09288/) (2023)
- [Qwen3 Technical Report](https://mlsanity.com/paper/2505.09388/) (2025)
- [Judging LLM-as-a-Judge with MT-Bench and Chatbot Arena](https://mlsanity.com/paper/2306.05685/) (2023)
- [BLIP-2: Bootstrapping Language-Image Pre-training with Frozen Image Encoders and Large Language Models](https://mlsanity.com/paper/2301.12597/) (2023)
- [Flamingo: a Visual Language Model for Few-Shot Learning](https://mlsanity.com/paper/2204.14198/) (2022)
- [InstructBLIP: Towards General-purpose Vision-Language Models with Instruction Tuning](https://mlsanity.com/paper/2305.06500/) (2023)
- [BLOOM: A 176B-Parameter Open-Access Multilingual Language Model](https://mlsanity.com/paper/2211.05100/) (2022)
- [Pythia: A Suite for Analyzing Large Language Models Across Training and Scaling](https://mlsanity.com/paper/2304.01373/) (2023)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [Galactica: A Large Language Model for Science](https://mlsanity.com/paper/2211.09085/) (2022)
- [ChemCrow: Augmenting large-language models with chemistry tools](https://mlsanity.com/paper/2304.05376/) (2023)
- [Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development](https://mlsanity.com/paper/2102.09548/) (2021)
- [Multi-modal Molecule Structure-text Model for Text-based Retrieval and Editing](https://mlsanity.com/paper/2212.10789/) (2022)
- [Byte Latent Transformer: Patches Scale Better Than Tokens](https://mlsanity.com/paper/2412.09871/) (2024)
- [Mol-Instructions: A Large-Scale Biomolecular Instruction Dataset for Large Language Models](https://mlsanity.com/paper/2306.08018/) (2023)
- [ChemBERTa-2: Towards Chemical Foundation Models](https://mlsanity.com/paper/2209.01712/) (2022)
- [BioMedGPT: Open Multimodal Generative Pre-trained Transformer for BioMedicine](https://mlsanity.com/paper/2308.09442/) (2023)
- [GIMLET: A Unified Graph-Text Model for Instruction-Based Molecule Zero-Shot Learning](https://mlsanity.com/paper/2306.13089/) (2023)
- [Towards 3D Molecule-Text Interpretation in Language Models](https://mlsanity.com/paper/2401.13923/) (2024)
- [BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuning](https://mlsanity.com/paper/2402.17810/) (2024)
- [ProLLaMA: A Protein Large Language Model for Multi-Task Protein Language Processing](https://mlsanity.com/paper/2402.16445/) (2024)
- [MolFM: A Multimodal Molecular Foundation Model](https://mlsanity.com/paper/2307.09484/) (2023)
- [Molformer: Motif-based Transformer on 3D Heterogeneous Molecular Graphs](https://mlsanity.com/paper/2110.01191/) (2021)
- [UniMoT: Unified Molecule-Text Language Model with Discrete Token Representation](https://mlsanity.com/paper/2408.00863/) (2024)
- [MoleculeQA: A Dataset to Evaluate Factual Accuracy in Molecular Comprehension](https://mlsanity.com/paper/2403.08192/) (2024)
- [LLaMo: Large Language Model-based Molecular Graph Assistant](https://mlsanity.com/paper/2411.00871/) (2024)
- [Uni-Mol2: Exploring Molecular Pretraining Model at Scale](https://mlsanity.com/paper/2406.14969/) (2024)

## Built on by (most cited first, 1 of 1)

- [GraphReview: Scientific Paper Evaluation via LLM-based Graph Evidence Expansion](https://mlsanity.com/paper/2605.27204/) (2026)

## Abstract (arXiv)

Molecular understanding is central to advancing areas such as scientific 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 stateof-the-art results on MoleculeQA, Molecule-oriented Mol-Instructions, and property prediction benchmarks (TDC, MoleculeNet), underscoring its effectiveness for scalable and generalizable multimodal molecular understanding