Same Encoder, Different Winner: A Paired-View Framework for Cell Painting Encoder Evaluation
Read the original on arXiv Machine Learning →The paper introduces CP‑BG‑Bench, a paired‑view evaluation framework for Cell Painting vision encoders that fixes a central cell across four matched views (raw crop, segmented, and density‑augmented variants). Using this framework on three datasets and three encoders, the authors show that standard single‑metric rankings (e.g., replicate mAP) vary systematically across protocols, revealing disagreements along axes of cell versus background, morphology versus context, and within‑study versus across‑batch performance. The study demonstrates that segmented views can outperform crops in certain tasks and that background‑driven gains are largely determined by experimental design rather than encoder choice.
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