# Improving Molecular Property Prediction in Small Language Models Using Graph-based Tools

arXiv: https://arxiv.org/abs/2607.13115 · HTML: https://mlsanity.com/paper/2607.13115/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Placed in Medical and scientific domain agents, one of 16 directions in LLM agents and tool use.
- Builds on 16 of its 24 references that are in the map.
- First posted on arXiv 14 Jul 2026.

## Placed in

- LLM agents and tool use / [Medical and scientific domain agents](https://mlsanity.com/agents/medical-and-scientific-domain-agents/)

## Builds on (most cited first, 16 of 16)

- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [Large Language Models are Zero-Shot Reasoners](https://mlsanity.com/paper/2205.11916/) (2022)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [Convolutional Networks on Graphs for Learning Molecular Fingerprints](https://mlsanity.com/paper/1509.09292/) (2015)
- [Galactica: A Large Language Model for Science](https://mlsanity.com/paper/2211.09085/) (2022)
- [GNNExplainer: Generating Explanations for Graph Neural Networks](https://mlsanity.com/paper/1903.03894/) (2019)
- [The Mythos of Model Interpretability](https://mlsanity.com/paper/1606.03490/) (2016)
- [Parameterized Explainer for Graph Neural Network](https://mlsanity.com/paper/2011.04573/) (2020)
- [A Survey on Explainable Artificial Intelligence (XAI): Towards Medical XAI](https://mlsanity.com/paper/1907.07374/) (2019)
- [Analyzing Learned Molecular Representations for Property Prediction](https://mlsanity.com/paper/1904.01561/) (2019)
- [ChemBERTa: Large-Scale Self-Supervised Pretraining for Molecular Property Prediction](https://mlsanity.com/paper/2010.09885/) (2020)
- [DeepSeek-Coder-V2: Breaking the Barrier of Closed-Source Models in Code Intelligence](https://mlsanity.com/paper/2406.11931/) (2024)
- [Molecular Graph Convolutions: Moving Beyond Fingerprints](https://mlsanity.com/paper/1603.00856/) (2016)
- [MolCA: Molecular Graph-Language Modeling with Cross-Modal Projector and Uni-Modal Adapter](https://mlsanity.com/paper/2310.12798/) (2023)

## Built on by (most cited first, 1 of 1)

- [The Illusion of Replacement: Rethinking Specialized Machine Learning Models in the Foundation Model Era](https://mlsanity.com/paper/2608.28980/) (2026)

## Abstract (arXiv)

Small language models (SLMs) have shown promise for zero-shot molecular property prediction from SMILES strings, yet they often suffer from structural blindness because sequence representations under-specify key graph-topological cues. We propose a modular Context-Augmented Prompting framework that enables agentic tool use at inference time: a trained GNN expert model provides a predictive hint with confidence, and a GNN extracts an instance-specific explanatory subgraph (e.g., a subgraph SMILES and an accompanying explanatory paragraph). We evaluate three commonly used SLMs on MUTAG and Tox21 under five prompting configurations ranging from SMILES-only to using all available tools at hand. Across two datasets, enriching prompts with graph-derived context yields substantial accuracy gains, often exceeding 25% relative improvement and up to 74% on Tox21. We further validate the functional relevance of the extracted motifs via a necessity-based edge-drop intervention. Despite the observed gains, a persistent gap remains to specialized GNN models, highlighting both the value and limits of text-conditioned reasoning for molecular structure.