# BioMedGPT-Mol: Multi-task Learning for Molecular Understanding and Generation

arXiv: https://arxiv.org/abs/2512.04629 · HTML: https://mlsanity.com/paper/2512.04629/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Builds on 35 of its 59 references that are in the map.
- First posted on arXiv 4 Dec 2025.

## Builds on (most cited first, 30 of 35)

- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [Chain-of-Thought Prompting Elicits Reasoning in Large Language Models](https://mlsanity.com/paper/2201.11903/) (2022)
- [Qwen3 Technical Report](https://mlsanity.com/paper/2505.09388/) (2025)
- [DeepSeek-R1: Incentivizing Reasoning Capability in LLMs via Reinforcement Learning](https://mlsanity.com/paper/2501.12948/) (2025)
- [Kimi k1.5: Scaling Reinforcement Learning with LLMs](https://mlsanity.com/paper/2501.12599/) (2025)
- [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)
- [Molecular Transformer - A Model for Uncertainty-Calibrated Chemical Reaction Prediction](https://mlsanity.com/paper/1811.02633/) (2018)
- [What can Large Language Models do in chemistry? A comprehensive benchmark on eight tasks](https://mlsanity.com/paper/2305.18365/) (2023)
- [Learning to Plan Chemical Syntheses](https://mlsanity.com/paper/1708.04202/) (2017)
- [Translation between Molecules and Natural Language](https://mlsanity.com/paper/2204.11817/) (2022)
- [Llama-Nemotron: Efficient Reasoning Models](https://mlsanity.com/paper/2505.00949/) (2025)
- [Mol-Instructions: A Large-Scale Biomolecular Instruction Dataset for Large Language Models](https://mlsanity.com/paper/2306.08018/) (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)
- [ChemLLM: A Chemical Large Language Model](https://mlsanity.com/paper/2402.06852/) (2024)
- [Retrosynthesis Prediction with Conditional Graph Logic Network](https://mlsanity.com/paper/2001.01408/) (2020)
- [BioMedGPT: Open Multimodal Generative Pre-trained Transformer for BioMedicine](https://mlsanity.com/paper/2308.09442/) (2023)
- [BioT5: Enriching Cross-modal Integration in Biology with Chemical Knowledge and Natural Language Associations](https://mlsanity.com/paper/2310.07276/) (2023)
- [Molecule Edit Graph Attention Network: Modeling Chemical Reactions as Sequences of Graph Edits](https://mlsanity.com/paper/2006.15426/) (2020)
- [A Graph to Graphs Framework for Retrosynthesis Prediction](https://mlsanity.com/paper/2003.12725/) (2020)
- [Retro*: Learning Retrosynthetic Planning with Neural Guided A* Search](https://mlsanity.com/paper/2006.15820/) (2020)
- [Learning Graph Models for Retrosynthesis Prediction](https://mlsanity.com/paper/2006.07038/) (2020)
- [DrugAssist: A Large Language Model for Molecule Optimization](https://mlsanity.com/paper/2401.10334/) (2023)
- [Training a Scientific Reasoning Model for Chemistry](https://mlsanity.com/paper/2506.17238/) (2025)
- [Root-aligned SMILES: A Tight Representation for Chemical Reaction Prediction](https://mlsanity.com/paper/2203.11444/) (2022)
- [Beyond Chemical QA: Evaluating LLM's Chemical Reasoning with Modular Chemical Operations](https://mlsanity.com/paper/2505.21318/) (2025)
- [RetroGraph: Retrosynthetic Planning with Graph Search](https://mlsanity.com/paper/2206.11477/) (2022)
- [Double-Ended Synthesis Planning with Goal-Constrained Bidirectional Search](https://mlsanity.com/paper/2407.06334/) (2024)
- [L+M-24: Building a Dataset for Language + Molecules @ ACL 2024](https://mlsanity.com/paper/2403.00791/) (2024)
- [GeLLMO: Generalizing Large Language Models for Multi-property Molecule Optimization](https://mlsanity.com/paper/2502.13398/) (2025)

## Built on by (most cited first, 3 of 3)

- [LatentChem: From Textual CoT to Latent Thinking in Chemical Reasoning](https://mlsanity.com/paper/2602.07075/) (2026)
- [BioMatrix: Towards a Comprehensive Biological Foundation Model Spanning the Modality Matrix of Sequences, Structures, and Language](https://mlsanity.com/paper/2606.22138/) (2026)
- [Reasoning4Sciences: Bridging Reasoning Language Models to All Scientific Branches](https://mlsanity.com/paper/2606.01145/) (2026)

## Abstract (arXiv)

Molecules play a crucial role in biomedical research and discovery, particularly in the field of small molecule drug development. Given the rapid advancements in large language models, especially the recent emergence of reasoning models, it is natural to explore how a general-purpose language model can be efficiently adapted for molecular science applications. In this work, we introduce BioMedGPT-Mol, a molecular language model designed to support molecular understanding and generation tasks. By curating and unifying existing public instruction datasets, we have assembled a large-scale, comprehensive, and high-quality training dataset. The model is then fine-tuned through a meticulously designed multi-task learning framework. On a consolidated benchmark derived from LlaSMol, TOMG-Bench, and MuMOInstruct, BioMedGPT-Mol achieves remarkable performance. Our experimental results demonstrate that a general-purpose reasoning model can be effectively and efficiently post-trained into a professional molecular language model through a well-structured multi-task curriculum. Leveraging these capabilities, we further apply the model to multi-step retrosynthetic planning, achieving state-of-the-art performance on RetroBench and demonstrating its superior efficacy as an end-to-end retrosynthetic planner. We anticipate that our approach can be extended to other biomedical scientific domains.