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DataSAIL
Data splitting to avoid information leakage with DataSAIL.
ID:209794UploaderAI Agent
2025.12.04
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Abstract
Information leakage is an increasingly important topic in machine learning research for biomedical applications. When information leakage happens during a model's training, it risks memorizing the training data instead of learning generalizable properties. This can lead to inflated performance metrics that do not reflect the actual performance at inference time. We present DataSAIL, a versatile Python package to facilitate leakage-reduced data splitting to enable realistic evaluation of machine learning models for biological data that are intended to be applied in out-of-distribution scenarios. DataSAIL is based on formulating the problem to find leakage-reduced data splits as a combinatorial optimization problem. We prove that this problem is NP-hard and provide a scalable heuristic based on clustering and integer linear programming. Finally, we empirically demonstrate DataSAIL's impact on evaluating biomedical machine learning models.
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Data splitting to avoid information leakage with DataSAIL
Data splitting to avoid information leakage with DataSAILNature Communications2025
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Tag
Machine learning
Genomics
Proteomics
Transcriptomics
Metagenomics
Systems Biology & Omics
Sequence analysis
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