Data archive for aquatic ecotoxicity representation benchmarking

This record provides the processed datasets, feature matrices, scaffold-based split files, graph resources, model prediction outputs, and merged result tables used to support verification and reproducibility of the manuscript-level analyses for “Comparative Evaluation of Molecular Representations for Aquatic Ecotoxicity Prediction: Fingerprints, Molecular Graphs, and Similarity Graphs”. The archive includes processed TEST-derived toxicity tables, Daphnia regression targets, Morgan fingerprint features, RDKit descriptor features, scaffold-based split files, the TopK-50 G2 similarity graph edge table, model-level test predictions, inference-target predictions, and merged prediction tables. The source code used for data processing, model training, inference, and downstream analysis is available at: https://github.com/rayah0123/aquatic-toxicity-representations.