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arXiv · 2509.06986

CellPainTR: Generalizable Representation Learning for Cross-Dataset Cell Painting Analysis

Cedric Caruzzo·Jong Chul Ye
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Abstract

Large-scale biological discovery requires integrating massive, heterogeneous datasets like those from the JUMP Cell Painting consortium, but technical batch effects and a lack of generalizable models remain critical roadblocks. To address this, we introduce CellPainTR, a Transformer-based architecture designed to learn foundational representations of cellular morphology that are robust to batch effects. Unlike traditional methods that require retraining on new data, CellPainTR's design, featuring source-specific context tokens, allows for effective out-of-distribution (OOD) generalization to entirely unseen datasets without fine-tuning. We validate CellPainTR on the large-scale JUMP dataset, where it outperforms established methods like ComBat and Harmony in both batch integration and biological signal preservation. Critically, we demonstrate its robustness through a challenging OOD task on the unseen Bray et al. dataset, where it maintains high performance despite significant domain and feature shifts. Our work represents a significant step towards creating truly foundational models for image-based profiling, enabling more reliable and scalable cross-study biological analysis.

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Cedric Caruzzo, Jong Chul Ye. 2025-09-02. CellPainTR: Generalizable Representation Learning for Cross-Dataset Cell Painting Analysis. https://arxiv.org/abs/2509.06986

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