# CP-Agent: Context-Aware Multimodal Reasoning for Cellular Morphological Profiling under Chemical Perturbations

arXiv: https://arxiv.org/abs/2606.03435 · HTML: https://mlsanity.com/paper/2606.03435/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Clinical and biomedical applications, one of 17 directions in LLM reasoning.
- Builds on 8 of its 64 references that are in the map.
- First posted on arXiv 2 Jun 2026.

## Placed in

- LLM reasoning / [Clinical and biomedical applications](https://mlsanity.com/lr/clinical-and-biomedical-applications/)
- LLM agents and tool use / [Medical and scientific domain agents](https://mlsanity.com/agents/medical-and-scientific-domain-agents/)

## Builds on (most cited first, 8 of 8)

- [MM-LLMs: Recent Advances in MultiModal Large Language Models](https://mlsanity.com/paper/2401.13601/) (2024)
- [Large Language Models(LLMs) on Tabular Data: Prediction, Generation, and Understanding -- A Survey](https://mlsanity.com/paper/2402.17944/) (2024)
- [LIDDIA: Language-based Intelligent Drug Discovery Agent](https://mlsanity.com/paper/2502.13959/) (2025)
- [μ-Bench: A Vision-Language Benchmark for Microscopy Understanding](https://mlsanity.com/paper/2407.01791/) (2024)
- [Geneverse: A collection of Open-source Multimodal Large Language Models for Genomic and Proteomic Research](https://mlsanity.com/paper/2406.15534/) (2024)
- [CellCLIP -- Learning Perturbation Effects in Cell Painting via Text-Guided Contrastive Learning](https://mlsanity.com/paper/2506.06290/) (2025)
- [GenoTEX: An LLM Agent Benchmark for Automated Gene Expression Data Analysis](https://mlsanity.com/paper/2406.15341/) (2024)
- [scI2CL: Effectively Integrating Single-cell Multi-omics by Intra- and Inter-omics Contrastive Learning](https://mlsanity.com/paper/2508.18304/) (2025)

## Abstract (arXiv)

Cell Painting combines multiplexed fluorescent staining, high-content imaging, and quantitative analysis to generate high-dimensional phenotypic readouts to support diverse downstream tasks such as mechanism-of-action (MoA) inference, toxicity prediction, and construction of drug-disease atlases. However, existing workflows are slow, costly and difficult to interpret. Approaches for drug screening modeling predominantly focus on molecular representation learning, while neglecting actual experimental context (e.g., cell line, dosing schedule, etc.), limiting generalization and MoA resolution. We introduce CP-Agent, an agentic multimodal large language model (MLLM) capable of generating mechanism-relevant, human-interpretable rationales for cell morphological changes under drug perturbations. At its core, CP-Agent leverages a context-aware alignment module, CP-CLIP, that jointly embeds high-content images and experimental metadata to enable robust treatment and MoA discrimination (achieving a maximum F1-score of 0.896). By integrating CP-CLIP outputs with agentic tool usage and reasoning, CP-Agent compiles rationales into a structured report to guide experimental design and hypothesis refinement. These capabilities highlight CP-Agent's potential to accelerate drug discovery by enabling more interpretable, scalable, and context-aware phenotypic screening -- streamlining iterative cycles of hypothesis generation in drug discovery.