# MolDeTox: Evaluating Language Model's Stepwise Fragment Editing for Molecular Detoxification

arXiv: https://arxiv.org/abs/2605.12181 · HTML: https://mlsanity.com/paper/2605.12181/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 23 of its 54 references that are in the map.
- First posted on arXiv 12 May 2026.

## Builds on (most cited first, 23 of 23)

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- [CoTox: Chain-of-Thought-Based Molecular Toxicity Reasoning and Prediction](https://mlsanity.com/paper/2508.03159/) (2025)
- [Breaking Bad Molecules: Are MLLMs Ready for Structure-Level Molecular Detoxification?](https://mlsanity.com/paper/2506.10912/) (2025)
- [ToxReason: A Benchmark for Mechanistic Chemical Toxicity Reasoning via Adverse Outcome Pathway](https://mlsanity.com/paper/2604.06264/) (2026)

## Abstract (arXiv)

Large Language Models (LLMs) and Vision Language Models (VLMs) have recently shown promising capabilities in various scientific domain. In particular, these advances have opened new opportunities in drug discovery, where the ability to understand and modify molecular structures is critical for optimizing drug properties such as efficacy and toxicity. However, existing models and benchmarks often overlook toxicity-related challenges, focusing primarily on general property optimization without adequately addressing safety concerns. In addition, even existing toxicity repair benchmarks suffer from limited data diversity, low structural validity of generated molecules, and heavy reliance on proxy models for toxicity assessment. To address these limitations, we propose MolDeTox, a novel benchmark for molecular detoxification, designed to enable fine-grained and reliable evaluation of toxicity-aware molecular optimization across stepwise tasks. We evaluate a wide range of general-purpose LLMs and VLMs under diverse settings, and demonstrate that understanding and generating molecules at the fragment-level improves structural validity and enhances the quality of generated molecules. Moreover, through detailed task-level performance analysis, MolDeTox provides an interpretable benchmark that enables a deeper understanding of the detoxification process. Our dataset is available at : https://huggingface.co/datasets/MolDeTox/MolDeTox