# Mol-LLaMA: Towards General Understanding of Molecules in Large Molecular Language Model

arXiv: https://arxiv.org/abs/2502.13449 · HTML: https://mlsanity.com/paper/2502.13449/

## Key facts

- Cited by 17 papers in the map (data through 14 Oct 2026).
- Builds on 40 of its 72 references that are in the map.
- First posted on arXiv 19 Feb 2025.

## Builds on (most cited first, 30 of 40)

- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [The Llama 3 Herd of Models](https://mlsanity.com/paper/2407.21783/) (2024)
- [LoRA: Low-Rank Adaptation of Large Language Models](https://mlsanity.com/paper/2106.09685/) (2021)
- [Llama 2: Open Foundation and Fine-Tuned Chat Models](https://mlsanity.com/paper/2307.09288/) (2023)
- [Chain-of-Thought Prompting Elicits Reasoning in Large Language Models](https://mlsanity.com/paper/2201.11903/) (2022)
- [Judging LLM-as-a-Judge with MT-Bench and Chatbot Arena](https://mlsanity.com/paper/2306.05685/) (2023)
- [Visual Instruction Tuning](https://mlsanity.com/paper/2304.08485/) (2023)
- [BLIP-2: Bootstrapping Language-Image Pre-training with Frozen Image Encoders and Large Language Models](https://mlsanity.com/paper/2301.12597/) (2023)
- [GPT-4o System Card](https://mlsanity.com/paper/2410.21276/) (2024)
- [Improved Baselines with Visual Instruction Tuning](https://mlsanity.com/paper/2310.03744/) (2023)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [Video-LLaMA: An Instruction-tuned Audio-Visual Language Model for Video Understanding](https://mlsanity.com/paper/2306.02858/) (2023)
- [SciBERT: A Pretrained Language Model for Scientific Text](https://mlsanity.com/paper/1903.10676/) (2019)
- [Video-ChatGPT: Towards Detailed Video Understanding via Large Vision and Language Models](https://mlsanity.com/paper/2306.05424/) (2023)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing](https://mlsanity.com/paper/2007.15779/) (2020)
- [LLaVA-CoT: Let Vision Language Models Reason Step-by-Step](https://mlsanity.com/paper/2411.10440/) (2024)
- [ChemBERTa: Large-Scale Self-Supervised Pretraining for Molecular Property Prediction](https://mlsanity.com/paper/2010.09885/) (2020)
- [Translation between Molecules and Natural Language](https://mlsanity.com/paper/2204.11817/) (2022)
- [Multi-modal Molecule Structure-text Model for Text-based Retrieval and Editing](https://mlsanity.com/paper/2212.10789/) (2022)
- [Mol-Instructions: A Large-Scale Biomolecular Instruction Dataset for Large Language Models](https://mlsanity.com/paper/2306.08018/) (2023)
- [A Molecular Multimodal Foundation Model Associating Molecule Graphs with Natural Language](https://mlsanity.com/paper/2209.05481/) (2022)
- [MolCA: Molecular Graph-Language Modeling with Cross-Modal Projector and Uni-Modal Adapter](https://mlsanity.com/paper/2310.12798/) (2023)
- [LlaSMol: Advancing Large Language Models for Chemistry with a Large-Scale, Comprehensive, High-Quality Instruction Tuning Dataset](https://mlsanity.com/paper/2402.09391/) (2024)
- [VideoLLM: Modeling Video Sequence with Large Language Models](https://mlsanity.com/paper/2305.13292/) (2023)
- [The Impact of Large Language Models on Scientific Discovery: a Preliminary Study using GPT-4](https://mlsanity.com/paper/2311.07361/) (2023)
- [BioT5: Enriching Cross-modal Integration in Biology with Chemical Knowledge and Natural Language Associations](https://mlsanity.com/paper/2310.07276/) (2023)
- [Molecular representation learning with language models and domain-relevant auxiliary tasks](https://mlsanity.com/paper/2011.13230/) (2020)
- [Unifying Molecular and Textual Representations via Multi-task Language Modelling](https://mlsanity.com/paper/2301.12586/) (2023)
- [InstructMol: Multi-Modal Integration for Building a Versatile and Reliable Molecular Assistant in Drug Discovery](https://mlsanity.com/paper/2311.16208/) (2023)

## Built on by (most cited first, 17 of 17)

- [Graph is a Substrate Across Data Modalities](https://mlsanity.com/paper/2601.22384/) (2026)
- [MolReasoner: Toward Effective and Interpretable Reasoning for Molecular LLMs](https://mlsanity.com/paper/2508.02066/) (2025)
- [Multimodal Prompt Optimization: Why Not Leverage Multiple Modalities for MLLMs](https://mlsanity.com/paper/2510.09201/) (2025)
- [Flex-Judge: Text-Only Reasoning Unleashes Zero-Shot Multimodal Evaluators](https://mlsanity.com/paper/2505.18601/) (2025)
- [Breaking Bad Molecules: Are MLLMs Ready for Structure-Level Molecular Detoxification?](https://mlsanity.com/paper/2506.10912/) (2025)
- [ToxReason: A Benchmark for Mechanistic Chemical Toxicity Reasoning via Adverse Outcome Pathway](https://mlsanity.com/paper/2604.06264/) (2026)
- [MoRA: On-the-fly Molecule-aware Low-Rank Adaptation Framework for LLM-based Multi-Modal Molecular Assistant](https://mlsanity.com/paper/2510.12245/) (2025)
- [NMIRacle: Multi-modal Generative Molecular Elucidation from IR and NMR Spectra](https://mlsanity.com/paper/2512.19733/) (2025)
- [Entropy-Guided Dynamic Tokens for Graph-LLM Alignment in Molecular Understanding](https://mlsanity.com/paper/2602.02742/) (2026)
- [Heterogeneous Scientific Foundation Model Collaboration](https://mlsanity.com/paper/2604.27351/) (2026)
- [MoleCode unlocks structural intelligence in large language models](https://mlsanity.com/paper/2605.16480/) (2026)
- [MolLangData: A Large-Scale Dataset for Molecular Structure-Language Description via a Rule-Regularized Method](https://mlsanity.com/paper/2602.02320/) (2026)
- [Scaling-Aware Adapter for Structure-Grounded LLM Reasoning](https://mlsanity.com/paper/2602.02780/) (2026)
- [ES-Merging: Biological MLLM Merging via Embedding Space Signals](https://mlsanity.com/paper/2603.14405/) (2026)
- [MolRGen: A Training and Evaluation Setting for De Novo Molecular Generation with Reasonning Models](https://mlsanity.com/paper/2603.18256/) (2026)
- [Multi-Granular Rationale-Guided Molecular LLM for Property Prediction](https://mlsanity.com/paper/2608.10480/) (2026)
- [SafeMol: Dual-Modality Safety Alignment for Molecular Multimodal Models](https://mlsanity.com/paper/2609.33640/) (2026)

## Abstract (arXiv)

Understanding molecules is key to understanding organisms and driving advances in drug discovery, requiring interdisciplinary knowledge across chemistry and biology. Although large molecular language models have achieved notable success in task transfer, they often struggle to accurately analyze molecular features due to limited knowledge and reasoning capabilities. To address this issue, we present Mol-LLaMA, a large molecular language model that grasps the general knowledge centered on molecules and exhibits explainability and reasoning ability. To this end, we design key data types that encompass the fundamental molecular features, taking into account the essential abilities for molecular reasoning. Further, to improve molecular understanding, we propose a module that integrates complementary information from different molecular encoders, leveraging the distinct advantages of molecular representations. Our experimental results demonstrate that Mol-LLaMA is capable of comprehending the general features of molecules and providing informative responses, implying its potential as a general-purpose assistant for molecular analysis. Our project page is at https://mol-llama.github.io/.