# MolReasoner: Toward Effective and Interpretable Reasoning for Molecular LLMs

arXiv: https://arxiv.org/abs/2508.02066 · HTML: https://mlsanity.com/paper/2508.02066/

## Key facts

- Cited by 12 papers in the map (data through 14 Oct 2026).
- Placed in Clinical and biomedical applications, one of 17 directions in LLM reasoning.
- Builds on 24 of its 41 references that are in the map.
- First posted on arXiv 4 Aug 2025.

## Placed in

- LLM reasoning / [Clinical and biomedical applications](https://mlsanity.com/lr/clinical-and-biomedical-applications/)

## Builds on (most cited first, 24 of 24)

- [Training language models to follow instructions with human feedback](https://mlsanity.com/paper/2203.02155/) (2022)
- [Proximal Policy Optimization Algorithms](https://mlsanity.com/paper/1707.06347/) (2017)
- [Exploring the Limits of Transfer Learning with a Unified Text-to-Text Transformer](https://mlsanity.com/paper/1910.10683/) (2019)
- [DeepSeekMath: Pushing the Limits of Mathematical Reasoning in Open Language Models](https://mlsanity.com/paper/2402.03300/) (2024)
- [Qwen3 Technical Report](https://mlsanity.com/paper/2505.09388/) (2025)
- [Think you have Solved Question Answering? Try ARC, the AI2 Reasoning Challenge](https://mlsanity.com/paper/1803.05457/) (2018)
- [HellaSwag: Can a Machine Really Finish Your Sentence?](https://mlsanity.com/paper/1905.07830/) (2019)
- [Can a Suit of Armor Conduct Electricity? A New Dataset for Open Book Question Answering](https://mlsanity.com/paper/1809.02789/) (2018)
- [Crowdsourcing Multiple Choice Science Questions](https://mlsanity.com/paper/1707.06209/) (2017)
- [Galactica: A Large Language Model for Science](https://mlsanity.com/paper/2211.09085/) (2022)
- [SFT Memorizes, RL Generalizes: A Comparative Study of Foundation Model Post-training](https://mlsanity.com/paper/2501.17161/) (2025)
- [What can Large Language Models do in chemistry? A comprehensive benchmark on eight tasks](https://mlsanity.com/paper/2305.18365/) (2023)
- [Multi-modal Molecule Structure-text Model for Text-based Retrieval and Editing](https://mlsanity.com/paper/2212.10789/) (2022)
- [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)
- [Fin-R1: A Large Language Model for Financial Reasoning through Reinforcement Learning](https://mlsanity.com/paper/2503.16252/) (2025)
- [SELFIES and the future of molecular string representations](https://mlsanity.com/paper/2204.00056/) (2022)
- [Towards 3D Molecule-Text Interpretation in Language Models](https://mlsanity.com/paper/2401.13923/) (2024)
- [Training a Scientific Reasoning Model for Chemistry](https://mlsanity.com/paper/2506.17238/) (2025)
- [BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuning](https://mlsanity.com/paper/2402.17810/) (2024)
- [CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph](https://mlsanity.com/paper/2406.10840/) (2024)
- [Mol-LLaMA: Towards General Understanding of Molecules in Large Molecular Language Model](https://mlsanity.com/paper/2502.13449/) (2025)
- [Structural Reasoning Improves Molecular Understanding of LLM](https://mlsanity.com/paper/2410.05610/) (2024)

## Built on by (most cited first, 12 of 12)

- [ReGuLaR: Variational Latent Reasoning Guided by Rendered Chain-of-Thought](https://mlsanity.com/paper/2601.23184/) (2026)
- [MolecularIQ: Characterizing Chemical Reasoning Capabilities Through Symbolic Verification on Molecular Graphs](https://mlsanity.com/paper/2601.15279/) (2026)
- [Reward Modeling for Reinforcement Learning-Based LLM Reasoning: Design, Challenges, and Evaluation](https://mlsanity.com/paper/2602.09305/) (2026)
- [Agentic reinforcement learning empowers next-generation chemical language models for molecular design and synthesis](https://mlsanity.com/paper/2601.17687/) (2026)
- [Chemical Chain-of-Thought Functions as a Hallucination-Prone Molecular Scratchpad](https://mlsanity.com/paper/2607.20935/) (2026)
- [DrugReasoner: Interpretable Drug Approval Prediction with a Reasoning-augmented Language Model](https://mlsanity.com/paper/2508.18579/) (2025)
- [Coder as Editor: Code-driven Interpretable Molecular Optimization](https://mlsanity.com/paper/2510.14455/) (2025)
- [Entropy-Guided Dynamic Tokens for Graph-LLM Alignment in Molecular Understanding](https://mlsanity.com/paper/2602.02742/) (2026)
- [A Scientific Reasoning Model for Organic Synthesis Procedure Generation](https://mlsanity.com/paper/2512.13668/) (2025)
- [SpecXMaster Technical Report](https://mlsanity.com/paper/2603.23101/) (2026)
- [MolGVR: A Chemistry-Grounded Framework for Text-to-Molecule Generation](https://mlsanity.com/paper/2607.29479/) (2026)
- [MolLean: A Process-Verifiable Language for Chemical Reasoning](https://mlsanity.com/paper/2610.20459/) (2026)

## Abstract (arXiv)

Large Language Models (LLMs) have shown impressive performance across various domains, but their ability to perform molecular reasoning remains underexplored. Existing methods mostly rely on general-purpose prompting, which lacks domain-specific molecular semantics, or fine-tuning, which faces challenges in interpretability and reasoning depth, often leading to structural and textual hallucinations. To address these issues, we introduce MolReasoner, a two-stage framework that transitions LLMs from memorization to high-fidelity chemical reasoning. In the Mol-SFT stage, knowledge-enhanced Chain-of-Thought (CoT) data provides a strong foundation, while the Mol-RL stage refines reasoning using a novel, task-adaptive reward system to mitigate hallucinations. Extensive evaluations demonstrate that MolReasoner significantly outperforms a wide range of strong baselines in both molecule generation and captioning tasks. Further analyses highlight the framework's synergistic design and its ability to produce more interpretable outputs. Our work presents a principled and effective new approach for advancing high-fidelity molecular reasoning.