# Breaking Bad Molecules: Are MLLMs Ready for Structure-Level Molecular Detoxification?

arXiv: https://arxiv.org/abs/2506.10912 · HTML: https://mlsanity.com/paper/2506.10912/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 67 of its 181 references that are in the map.
- First posted on arXiv 12 Jun 2025.

## Builds on (most cited first, 30 of 67)

- [Visual Instruction Tuning](https://mlsanity.com/paper/2304.08485/) (2023)
- [BLIP-2: Bootstrapping Language-Image Pre-training with Frozen Image Encoders and Large Language Models](https://mlsanity.com/paper/2301.12597/) (2023)
- [Qwen2.5-VL Technical Report](https://mlsanity.com/paper/2502.13923/) (2025)
- [BERTScore: Evaluating Text Generation with BERT](https://mlsanity.com/paper/1904.09675/) (2019)
- [GPT-4o System Card](https://mlsanity.com/paper/2410.21276/) (2024)
- [Improved Baselines with Visual Instruction Tuning](https://mlsanity.com/paper/2310.03744/) (2023)
- [BLIP: Bootstrapping Language-Image Pre-training for Unified Vision-Language Understanding and Generation](https://mlsanity.com/paper/2201.12086/) (2022)
- [Qwen2-VL: Enhancing Vision-Language Model's Perception of the World at Any Resolution](https://mlsanity.com/paper/2409.12191/) (2024)
- [Gemini 1.5: Unlocking multimodal understanding across millions of tokens of context](https://mlsanity.com/paper/2403.05530/) (2024)
- [UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction](https://mlsanity.com/paper/1802.03426/) (2018)
- [LLaVA-OneVision: Easy Visual Task Transfer](https://mlsanity.com/paper/2408.03326/) (2024)
- [InternVL: Scaling up Vision Foundation Models and Aligning for Generic Visual-Linguistic Tasks](https://mlsanity.com/paper/2312.14238/) (2023)
- [CLIPScore: A Reference-free Evaluation Metric for Image Captioning](https://mlsanity.com/paper/2104.08718/) (2021)
- [Qwen-VL: A Versatile Vision-Language Model for Understanding, Localization, Text Reading, and Beyond](https://mlsanity.com/paper/2308.12966/) (2023)
- [InternVL3: Exploring Advanced Training and Test-Time Recipes for Open-Source Multimodal Models](https://mlsanity.com/paper/2504.10479/) (2025)
- [MM-Vet: Evaluating Large Multimodal Models for Integrated Capabilities](https://mlsanity.com/paper/2308.02490/) (2023)
- [BLEURT: Learning Robust Metrics for Text Generation](https://mlsanity.com/paper/2004.04696/) (2020)
- [Yi: Open Foundation Models by 01.AI](https://mlsanity.com/paper/2403.04652/) (2024)
- [DeepSeek-VL2: Mixture-of-Experts Vision-Language Models for Advanced Multimodal Understanding](https://mlsanity.com/paper/2412.10302/) (2024)
- [Kimi-VL Technical Report](https://mlsanity.com/paper/2504.07491/) (2025)
- [GuacaMol: Benchmarking Models for De Novo Molecular Design](https://mlsanity.com/paper/1811.09621/) (2018)
- [Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models](https://mlsanity.com/paper/1811.12823/) (2018)
- [Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development](https://mlsanity.com/paper/2102.09548/) (2021)
- [Modeling polypharmacy side effects with graph convolutional networks](https://mlsanity.com/paper/1802.00543/) (2018)
- [Structure-based Drug Design with Equivariant Diffusion Models](https://mlsanity.com/paper/2210.13695/) (2022)
- [Fr'echet ChemNet Distance: A metric for generative models for molecules in drug discovery](https://mlsanity.com/paper/1803.09518/) (2018)
- [MMBench-Video: A Long-Form Multi-Shot Benchmark for Holistic Video Understanding](https://mlsanity.com/paper/2406.14515/) (2024)
- [Multi-modal Molecule Structure-text Model for Text-based Retrieval and Editing](https://mlsanity.com/paper/2212.10789/) (2022)
- [Sample Efficiency Matters: A Benchmark for Practical Molecular Optimization](https://mlsanity.com/paper/2206.12411/) (2022)
- [LlaSMol: Advancing Large Language Models for Chemistry with a Large-Scale, Comprehensive, High-Quality Instruction Tuning Dataset](https://mlsanity.com/paper/2402.09391/) (2024)

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

- [GenExam: A Multidisciplinary Text-to-Image Exam](https://mlsanity.com/paper/2509.14232/) (2025)
- [MolDeTox: Evaluating Language Model's Stepwise Fragment Editing for Molecular Detoxification](https://mlsanity.com/paper/2605.12181/) (2026)

## Abstract (arXiv)

Toxicity remains a leading cause of early-stage drug development failure. Despite advances in molecular design and property prediction, the task of molecular toxicity repair, generating structurally valid molecular alternatives with reduced toxicity, has not yet been systematically defined or benchmarked. To fill this gap, we introduce ToxiMol, the first benchmark task for general-purpose Multimodal Large Language Models (MLLMs) focused on molecular toxicity repair. We construct a standardized dataset covering 11 primary tasks and 660 representative toxic molecules spanning diverse mechanisms and granularities. We design a prompt annotation pipeline with mechanism-aware and task-adaptive capabilities, informed by expert toxicological knowledge. In parallel, we propose an automated evaluation framework, ToxiEval, which integrates toxicity endpoint prediction, synthetic accessibility, drug-likeness, and structural similarity into a high-throughput evaluation chain for repair success. We systematically assess 43 mainstream general-purpose MLLMs and conduct multiple ablation studies to analyze key issues, including evaluation metrics, candidate diversity, and failure attribution. Experimental results show that although current MLLMs still face significant challenges on this task, they begin to demonstrate promising capabilities in toxicity understanding, semantic constraint adherence, and structure-aware editing.