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arXiv · 2610.30104

BatchBench: Benchmarking AI Robustness to Batch Effects and Domain Shift in Biomedical Images - A JUMP Cell Painting Leaderboard

Sonja Topf·Ana Sanchez-Fernandez·Günter Klambauer
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Abstract

Despite recent advances, current AI systems remain highly susceptible to domain shifts, particularly in biomedical imaging, where images are usually acquired under substantially different experimental conditions. Although recent domain adaptation methods have made substantial progress, significant performance gaps under domain shift persist. To measure progress in this regard, we introduce BatchBench, a leaderboard that evaluates and compares the robustness of AI systems on biomedical images from unseen experimental batches and data sources. BatchBench is built on JUMP-CP, one of the largest publicly available biomedical imaging datasets. Generated using the Cell Painting assay, JUMP-CP exhibits pronounced batch effects and domain shifts, making it a challenging testbed for evaluating robustness to distributional changes.

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Sonja Topf, Ana Sanchez-Fernandez, Günter Klambauer. 2026-10-21. BatchBench: Benchmarking AI Robustness to Batch Effects and Domain Shift in Biomedical Images - A JUMP Cell Painting Leaderboard. https://arxiv.org/abs/2610.30104

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