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arXiv · 2609.36406

From Retrieval to Reasoning: Agentic Mechanism Prediction from Cell Painting Profiles

Jiayuan Chen·Botao Yu·Tianyu Liu·Thai-Hoang Pham·Meng Wu·Ping Zhang
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Abstract

Cell Painting is a high-content morphological profiling assay widely used for phenotype-based biological inference, with mechanism of action (MOA) prediction as a central application. Existing approaches largely formulate Cell Painting-based inference as representation matching, assigning predictions from nearby reference perturbations in morphological feature space. However, retrieved neighbors are often noisy and partially misleading evidence due to batch effects, non-specific cytotoxicity, phenotypic convergence, and source-dependent variability. We reformulate Cell Painting-based MOA prediction as a calibrated evidence reasoning problem, where retrieved neighbors are treated as uncertain observations that must be evaluated, compared, and sometimes rejected before supporting a mechanistic conclusion. We propose PhenoAIR, a reliability-aware multi-agent framework that maintains a candidate-centric evidence memory and performs controller-guided refinement over phenotype- and mechanism-side evidence. PhenoAIR uses offline reference-set calibration to weight evidence by source reliability, phenotype stability, and mechanism-level confusion. We evaluate PhenoAIR on a benchmark constructed from JUMP Cell Painting profiles and annotations, covering controlled, realistic, and discovery-oriented open-world MOA prediction settings. PhenoAIR outperforms representation-matching and LLM-based baselines across all settings.

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Jiayuan Chen, Botao Yu, Tianyu Liu, Thai-Hoang Pham, Meng Wu, Ping Zhang. 2026-09-29. From Retrieval to Reasoning: Agentic Mechanism Prediction from Cell Painting Profiles. https://arxiv.org/abs/2609.36406

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