# AttriLens-Mol: Attribute Guided Reinforcement Learning for Molecular Property Prediction with Large Language Models

arXiv: https://arxiv.org/abs/2508.04748 · HTML: https://mlsanity.com/paper/2508.04748/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Placed in Clinical and biomedical applications, one of 17 directions in LLM reasoning.
- Builds on 32 of its 44 references that are in the map.
- First posted on arXiv 6 Aug 2025.

## Placed in

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

## 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)
- [Training language models to follow instructions with human feedback](https://mlsanity.com/paper/2203.02155/) (2022)
- [The Llama 3 Herd of Models](https://mlsanity.com/paper/2407.21783/) (2024)
- [Chain-of-Thought Prompting Elicits Reasoning in Large Language Models](https://mlsanity.com/paper/2201.11903/) (2022)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [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)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [Finetuned Language Models Are Zero-Shot Learners](https://mlsanity.com/paper/2109.01652/) (2021)
- [DAPO: An Open-Source LLM Reinforcement Learning System at Scale](https://mlsanity.com/paper/2503.14476/) (2025)
- [Qwen2 Technical Report](https://mlsanity.com/paper/2407.10671/) (2024)
- [Rethinking the Role of Demonstrations: What Makes In-Context Learning Work?](https://mlsanity.com/paper/2202.12837/) (2022)
- [Calibrate Before Use: Improving Few-Shot Performance of Language Models](https://mlsanity.com/paper/2102.09690/) (2021)
- [Graph Contrastive Learning with Augmentations](https://mlsanity.com/paper/2010.13902/) (2020)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [SFT Memorizes, RL Generalizes: A Comparative Study of Foundation Model Post-training](https://mlsanity.com/paper/2501.17161/) (2025)
- [Do NOT Think That Much for 2+3=? On the Overthinking of o1-Like LLMs](https://mlsanity.com/paper/2412.21187/) (2024)
- [Pre-training Molecular Graph Representation with 3D Geometry](https://mlsanity.com/paper/2110.07728/) (2021)
- [Large-Scale Chemical Language Representations Capture Molecular Structure and Properties](https://mlsanity.com/paper/2106.09553/) (2021)
- [ChemRL-GEM: Geometry Enhanced Molecular Representation Learning for Property Prediction](https://mlsanity.com/paper/2106.06130/) (2021)
- [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)
- [ChemBERTa-2: Towards Chemical Foundation Models](https://mlsanity.com/paper/2209.01712/) (2022)
- [GeomGCL: Geometric Graph Contrastive Learning for Molecular Property Prediction](https://mlsanity.com/paper/2109.11730/) (2021)
- [Developing ChemDFM as a large language foundation model for chemistry](https://mlsanity.com/paper/2401.14818/) (2024)
- [MT-R1-Zero: Advancing LLM-based Machine Translation via R1-Zero-like Reinforcement Learning](https://mlsanity.com/paper/2504.10160/) (2025)
- [Let LRMs Break Free from Overthinking via Self-Braking Tuning](https://mlsanity.com/paper/2505.14604/) (2025)
- [Bidirectional Generation of Structure and Properties Through a Single Molecular Foundation Model](https://mlsanity.com/paper/2211.10590/) (2022)
- [GeLLMO: Generalizing Large Language Models for Multi-property Molecule Optimization](https://mlsanity.com/paper/2502.13398/) (2025)

## Built on by (most cited first, 2 of 2)

- [MolEvolve: LLM-Guided Evolutionary Search for Interpretable Molecular Optimization](https://mlsanity.com/paper/2603.24382/) (2026)
- [Probing Chemical Language Models: Effects of Pre-training and Fine-tuning](https://mlsanity.com/paper/2607.02140/) (2026)

## Abstract (arXiv)

Large Language Models (LLMs) have shown promise in assisting molecular property prediction tasks but often rely on human-crafted prompts and chain-of-thought templates. While recent advanced large reasoning models like DeepSeek-R1 employ reinforcement learning for an extended ``thinking'' process, their reasoning can be verbose and lack relevance. We introduce AttriLens-Mol, an attribute-guided reinforcement learning framework for molecular property prediction with LLMs. AttriLens-Mol steers the model's reasoning by using: (1) a format reward encouraging attribute-based structured output, (2) a count reward to avoid enumerating irrelevant attributes, and (3) a rationality reward using advanced LLMs and RDKit to verify the relatedness of the generated attributes. This approach implicitly elicits the model's inherent knowledge of relevant molecular attributes during reasoning, enables making predictions for the molecular property more effectively. Experiments on both in-distribution and out-of-distribution datasets show that, training both 7B-size R1-Distilled-Qwen2.5 and R1-Distilled-LLaMA3.1 models on 4,000 samples with our proposed AttriLens-Mol method significantly boosts the performance, getting comparable or better results than supervised fine-tuning models (Mol-Instructions, ChemDFM, etc.) and advanced models (GPT-3.5, GPT-4o, DeepSeek-V3, DeepSeek-R1, etc.). Further, our extracted attributes for the target property, when used as features for an interpretable decision tree model, yield superior performance compared to attributes generated by prompting LLMs. This shows that AttriLens-Mol effectively elicits more relevant and predictive molecular attributes, leading to enhanced interpretability and performance for property prediction. We release the code in https://github.com/szu-tera/AttriLens-Mol.