# KnowMol: Advancing Molecular Large Language Models with Multi-Level Chemical Knowledge

arXiv: https://arxiv.org/abs/2510.19484 · HTML: https://mlsanity.com/paper/2510.19484/

## Key facts

- Cited by 7 papers in the map (data through 14 Oct 2026).
- Builds on 31 of its 55 references that are in the map.
- First posted on arXiv 22 Oct 2025.

## Builds on (most cited first, 30 of 31)

- [LoRA: Low-Rank Adaptation of Large Language Models](https://mlsanity.com/paper/2106.09685/) (2021)
- [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)
- [BLIP-2: Bootstrapping Language-Image Pre-training with Frozen Image Encoders and Large Language Models](https://mlsanity.com/paper/2301.12597/) (2023)
- [Neural Discrete Representation Learning](https://mlsanity.com/paper/1711.00937/) (2017)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [GLM-130B: An Open Bilingual Pre-trained Model](https://mlsanity.com/paper/2210.02414/) (2022)
- [Galactica: A Large Language Model for Science](https://mlsanity.com/paper/2211.09085/) (2022)
- [Pre-training Molecular Graph Representation with 3D Geometry](https://mlsanity.com/paper/2110.07728/) (2021)
- [What can Large Language Models do in chemistry? A comprehensive benchmark on eight tasks](https://mlsanity.com/paper/2305.18365/) (2023)
- [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)
- [Unifying Molecular and Textual Representations via Multi-task Language Modelling](https://mlsanity.com/paper/2301.12586/) (2023)
- [Empowering Molecule Discovery for Molecule-Caption Translation with Large Language Models: A ChatGPT Perspective](https://mlsanity.com/paper/2306.06615/) (2023)
- [InstructMol: Multi-Modal Integration for Building a Versatile and Reliable Molecular Assistant in Drug Discovery](https://mlsanity.com/paper/2311.16208/) (2023)
- [GIT-Mol: A Multi-modal Large Language Model for Molecular Science with Graph, Image, and Text](https://mlsanity.com/paper/2308.06911/) (2023)
- [MolXPT: Wrapping Molecules with Text for Generative Pre-training](https://mlsanity.com/paper/2305.10688/) (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)
- [MolFM: A Multimodal Molecular Foundation Model](https://mlsanity.com/paper/2307.09484/) (2023)
- [DrugChat: Towards Enabling ChatGPT-Like Capabilities on Drug Molecule Graphs](https://mlsanity.com/paper/2309.03907/) (2023)
- [UniMoT: Unified Molecule-Text Language Model with Discrete Token Representation](https://mlsanity.com/paper/2408.00863/) (2024)
- [L+M-24: Building a Dataset for Language + Molecules @ ACL 2024](https://mlsanity.com/paper/2403.00791/) (2024)
- [Specialist or Generalist? Instruction Tuning for Specific NLP Tasks](https://mlsanity.com/paper/2310.15326/) (2023)
- [Leveraging Biomolecule and Natural Language through Multi-Modal Learning: A Survey](https://mlsanity.com/paper/2403.01528/) (2024)
- [HIGHT: Hierarchical Graph Tokenization for Molecule-Language Alignment](https://mlsanity.com/paper/2406.14021/) (2024)
- [From Artificially Real to Real: Leveraging Pseudo Data from Large Language Models for Low-Resource Molecule Discovery](https://mlsanity.com/paper/2309.05203/) (2023)

## Built on by (most cited first, 7 of 7)

- [MolEmb: Multimodal Large Language Models Can Be Strong Molecular Embedding Models](https://mlsanity.com/paper/2608.23646/) (2026)
- [BioMatrix: Towards a Comprehensive Biological Foundation Model Spanning the Modality Matrix of Sequences, Structures, and Language](https://mlsanity.com/paper/2606.22138/) (2026)
- [MolLangData: A Large-Scale Dataset for Molecular Structure-Language Description via a Rule-Regularized Method](https://mlsanity.com/paper/2602.02320/) (2026)
- [Bolek: A Multimodal Language Model for Molecular Reasoning](https://mlsanity.com/paper/2605.02745/) (2026)
- [MolDeTox: Evaluating Language Model's Stepwise Fragment Editing for Molecular Detoxification](https://mlsanity.com/paper/2605.12181/) (2026)
- [LipoAgent: Coordinating Fine-Tuned LLM Agents for Safer Lipid Design](https://mlsanity.com/paper/2605.25250/) (2026)
- [MolSC: Leveraging Substituent Contributions to Enhance Fine-grained Molecular Understanding in LLMs](https://mlsanity.com/paper/2609.23073/) (2026)

## Abstract (arXiv)

The molecular large language models have garnered widespread attention due to their promising potential on molecular applications. However, current molecular large language models face significant limitations in understanding molecules due to inadequate textual descriptions and suboptimal molecular representation strategies during pretraining. To address these challenges, we introduce KnowMol-100K, a large-scale dataset with 100K fine-grained molecular annotations across multiple levels, bridging the gap between molecules and textual descriptions. Additionally, we propose chemically-informative molecular representation, effectively addressing limitations in existing molecular representation strategies. Building upon these innovations, we develop KnowMol, a state-of-the-art multi-modal molecular large language model. Extensive experiments demonstrate that KnowMol achieves superior performance across molecular understanding and generation tasks. GitHub: https://github.com/yzf-code/KnowMol Huggingface: https://hf.co/datasets/yzf1102/KnowMol-100K