{"ID":2866453,"CreatedAt":"2026-06-01T04:54:23.091178241Z","UpdatedAt":"2026-06-01T04:54:23.091178241Z","DeletedAt":null,"paper_url":"https://arxiv.org/abs/2509.19896","arxiv_id":"2509.19896","title":"Efficient Cell Painting Image Representation Learning via Cross-Well Aligned Masked Siamese Network","abstract":"Computational models that predict cellular phenotypic responses to chemical and genetic perturbations can accelerate drug discovery by prioritizing therapeutic hypotheses and reducing costly wet-lab iteration. However, extracting biologically meaningful and batch-robust cell painting representations remains challenging. Conventional self-supervised and contrastive learning approaches often require a large-scale model and/or a huge amount of carefully curated data, still struggling with batch effects. We present Cross-Well Aligned Masked Siamese Network (CWA-MSN), a novel representation learning framework that aligns embeddings of cells subjected to the same perturbation across different wells, enforcing semantic consistency despite batch effects. Integrated into a masked siamese architecture, this alignment yields features that capture fine-grained morphology while remaining data- and parameter-efficient. For instance, in a gene-gene relationship retrieval benchmark, CWA-MSN outperforms the state-of-the-art publicly available self-supervised (OpenPhenom) and contrastive learning (CellCLIP) methods, improving the benchmark scores by +29\\% and +9\\%, respectively, while training on substantially fewer data (e.g., 0.2M images for CWA-MSN vs. 2.2M images for OpenPhenom) or smaller model size (e.g., 22M parameters for CWA-MSN vs. 1.48B parameters for CellCLIP). Extensive experiments demonstrate that CWA-MSN is a simple and effective way to learn cell image representation, enabling efficient phenotype modeling even under limited data and parameter budgets.","short_abstract":"Computational models that predict cellular phenotypic responses to chemical and genetic perturbations can accelerate drug discovery by prioritizing therapeutic hypotheses and reducing costly wet-lab iteration. However, extracting biologically meaningful and batch-robust cell painting representations remains challenging...","url_abs":"https://arxiv.org/abs/2509.19896","url_pdf":"https://arxiv.org/pdf/2509.19896v1","authors":"[\"Pin-Jui Huang\",\"Yu-Hsuan Liao\",\"SooHeon Kim\",\"NoSeong Park\",\"JongBae Park\",\"DongMyung Shin\"]","published":"2025-09-24T08:48:29Z","proceeding":"cs.CV","tasks":"[\"cs.CV\"]","methods":"[]","has_code":false}