# Mol-LLM: Multimodal Generalist Molecular LLM with Improved Graph Utilization

arXiv: https://arxiv.org/abs/2502.02810 · HTML: https://mlsanity.com/paper/2502.02810/

## Key facts

- Cited by 6 papers in the map (data through 14 Oct 2026).
- Builds on 32 of its 52 references that are in the map.
- First posted on arXiv 5 Feb 2025.

## Builds on (most cited first, 30 of 32)

- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [Exploring the Limits of Transfer Learning with a Unified Text-to-Text Transformer](https://mlsanity.com/paper/1910.10683/) (2019)
- [Direct Preference Optimization: Your Language Model is Secretly a Reward Model](https://mlsanity.com/paper/2305.18290/) (2023)
- [BLIP-2: Bootstrapping Language-Image Pre-training with Frozen Image Encoders and Large Language Models](https://mlsanity.com/paper/2301.12597/) (2023)
- [SciBERT: A Pretrained Language Model for Scientific Text](https://mlsanity.com/paper/1903.10676/) (2019)
- [Graph Contrastive Learning with Augmentations](https://mlsanity.com/paper/2010.13902/) (2020)
- [Deeper Insights into Graph Convolutional Networks for Semi-Supervised Learning](https://mlsanity.com/paper/1801.07606/) (2018)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [Strategies for Pre-training Graph Neural Networks](https://mlsanity.com/paper/1905.12265/) (2019)
- [SimPO: Simple Preference Optimization with a Reference-Free Reward](https://mlsanity.com/paper/2405.14734/) (2024)
- [Galactica: A Large Language Model for Science](https://mlsanity.com/paper/2211.09085/) (2022)
- [Aligning Modalities in Vision Large Language Models via Preference Fine-tuning](https://mlsanity.com/paper/2402.11411/) (2024)
- [Pure Transformers are Powerful Graph Learners](https://mlsanity.com/paper/2207.02505/) (2022)
- [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)
- [mDPO: Conditional Preference Optimization for Multimodal Large Language Models](https://mlsanity.com/paper/2406.11839/) (2024)
- [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)
- [Detecting and Mitigating Hallucination in Large Vision Language Models via Fine-Grained AI Feedback](https://mlsanity.com/paper/2404.14233/) (2024)
- [Strengthening Multimodal Large Language Model with Bootstrapped Preference Optimization](https://mlsanity.com/paper/2403.08730/) (2024)
- [Enhancing Large Vision Language Models with Self-Training on Image Comprehension](https://mlsanity.com/paper/2405.19716/) (2024)
- [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)
- [Developing ChemDFM as a large language foundation model for chemistry](https://mlsanity.com/paper/2401.14818/) (2024)

## Built on by (most cited first, 6 of 6)

- [Reasoning-Enhanced Large Language Models for Molecular Property Prediction](https://mlsanity.com/paper/2510.10248/) (2025)
- [Breaking Bad Molecules: Are MLLMs Ready for Structure-Level Molecular Detoxification?](https://mlsanity.com/paper/2506.10912/) (2025)
- [Round-trip Reinforcement Learning: Self-Consistent Training for Better Chemical LLMs](https://mlsanity.com/paper/2510.01527/) (2025)
- [RetroReasoner: A Reasoning LLM for Strategic Retrosynthesis Prediction](https://mlsanity.com/paper/2603.12666/) (2026)
- [MolDA: Molecular Understanding and Generation via Large Language Diffusion Model](https://mlsanity.com/paper/2604.04403/) (2026)
- [DrugGen 2: A disease-aware language model for enhancing drug discovery](https://mlsanity.com/paper/2607.08404/) (2026)

## Abstract (arXiv)

Recent advances in large language models (LLMs) have led to models that tackle diverse molecular tasks, such as chemical reaction prediction and molecular property prediction. Large-scale molecular instruction-tuning datasets have enabled sequence-only (e.g., SMILES or SELFIES) generalist molecular LLMs, and researchers are now exploring multimodal approaches that incorporate molecular structural information for further gains. However, a genuinely multimodal, generalist LLM that covers a broad spectrum of molecular tasks has yet to be fully investigated. We observe that naive next token prediction training ignores graph-structural information, limiting an LLM's ability to exploit molecular graphs. To address this, we propose (i) Molecular structure Preference Optimization (MolPO), which facilitates graph usage by optimizing preferences between pairs of correct and perturbed molecular structures, and (ii) an advanced graph encoder with a tailored pre-training strategy to improve the effect of graph utilization by MolPO. Building on these contributions, we introduce Mol-LLM, the first multimodal generalist model that (a) handles a broad spectrum of molecular tasks among molecular LLMs, (b) explicitly leverages molecular-structure information, and (c) takes advantage of extensive instruction tuning. Mol-LLM attains state-of-the-art or comparable results across the most comprehensive molecular-LLM benchmark-even on out-of-distribution datasets for reaction and property prediction, where it surpasses prior generalist molecular LLMs by a large margin.