数据集 / HydroSophyTech/ToxiMol-benchmark

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ToxiMol: A Benchmark for Structure-Level Molecular Detoxification

arXiv Dataset

🔥 News

  • 🏆 ToxiMol has been accepted as an Oral presentation at the 32nd SIGKDD Conference on Knowledge Discovery and Data Mining (KDD 2026), AI for Sciences Track.

Overview

ToxiMol is the first comprehensive benchmark for molecular toxicity repair tailored to general-purpose Multimodal Large Language Models (MLLMs). This is the dataset repository for the paper "Breaking Bad Molecules: Are MLLMs Ready for Structure-Level Molecular Detoxification?".

Key Features

🧬 Comprehensive Dataset

  • 660 representative toxic molecules spanning diverse toxicity mechanisms and varying granularities
  • 11 primary toxicity repair tasks based on Therapeutics Data Commons (TDC) platform
  • Multi-granular coverage: Tox21 (12 sub-tasks), ToxCast (10 sub-tasks), and 9 additional datasets
  • Multimodal inputs: SMILES strings + 2D molecular structure images rendered using RDKit

🎯 Challenging Task Definition

The molecular toxicity repair task requires models to:

  1. Identify potential toxicity endpoints from molecular structures
  2. Interpret semantic constraints from natural language descriptions
  3. Generate structurally similar substitute molecules that eliminate toxic fragments
  4. Satisfy drug-likeness and synthetic feasibility requirements

📊 Systematic Evaluation

  • ToxiEval framework: Automated evaluation integrating toxicity prediction, synthetic accessibility, drug-likeness, and structural similarity
  • Comprehensive analysis: Evaluation of ~30 mainstream MLLMs with ablation studies
  • Multi-dimensional metrics: Success rate analysis across different evaluation criteria and failure modes

Dataset Structure

Task Overview

Dataset Task Type # Molecules Description
AMES Binary Classification 60 Mutagenicity testing
Carcinogens Binary Classification 60 Carcinogenicity prediction
ClinTox Binary Classification 60 Clinical toxicity data
DILI Binary Classification 60 Drug-induced liver injury
hERG Binary Classification 60 hERG channel inhibition
hERG_Central Binary Classification 60 Large-scale hERG database with integrated cardiac safety profiles
hERG_Karim Binary Classification 60 hERG data

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数据集版权信息

本数据集的许可证为 MIT License。如有违反相关条款，请联系 WEHUB，我们将及时处理。 查看许可证