ToxACoL: an endpoint-aware and task-focused compound representation learning paradigm for acute toxicity assessment

Jiang Lu, Lianlian Wu, Ruijiang Li, Mengxuan Wan, Jun Yang, Peng Zan, Hui Bai (), Song He () and Xiaochen Bo ()
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Jiang Lu: Tianjin University
Lianlian Wu: Tianjin University
Ruijiang Li: Academy of Military Medical Sciences
Mengxuan Wan: Shanghai University
Jun Yang: Central South University
Peng Zan: Shanghai University
Hui Bai: Tsinghua University
Song He: Academy of Military Medical Sciences
Xiaochen Bo: Tianjin University

Nature Communications, 2025, vol. 16, issue 1, 1-19

Abstract: Abstract Multi-species acute toxicity assessment forms the basis for chemical classification, labelling and risk management. Existing deep learning methods struggle with diverse experimental conditions, imbalanced data, and scarce target data, hindering their ability to reveal endpoint associations and accurately predict data-scarce endpoints. Here we propose a machine learning paradigm, Adjoint Correlation Learning, for multi-condition acute toxicity assessment (ToxACoL) to address these challenges. ToxACoL models endpoint associations via graph topology and achieves knowledge transfer via graph convolution. The adjoint correlation mechanism encodes compounds and endpoints synchronously, yielding endpoint-aware and task-focused representations. Comprehensive analyses demonstrate that ToxACoL yields 43%-87% improvements for data-scarce human endpoints, while reducing training data by 70% to 80%. Visualization of the learned top-level representation interprets structural alert mechanisms. Filled-in toxicity values highlight potential for extrapolating animal results to humans. Finally, we deploy ToxACoL as a free web platform for rapid prediction of multi-condition acute toxicities.

Date: 2025
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DOI: 10.1038/s41467-025-60989-7

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