Simple Agents Outperform Experts in Biomedical Imaging Workflow Optimization

• URL: http://arxiv.org/abs/2512.06006v1
• Date: Tue, 02 Dec 2025 18:42:26 GMT
• Title: Simple Agents Outperform Experts in Biomedical Imaging Workflow Optimization
• Authors: Xuefei, Wang, Kai A. Horstmann, Ethan Lin, Jonathan Chen, Alexander R. Farhang, Sophia Stiles, Atharva Sehgal, Jonathan Light, David Van Valen, Yisong Yue, Jennifer J. Sun,
• Abstract summary: Adapting production-level computer vision tools to bespoke scientific datasets is a critical "last mile" bottleneck.<n>We consider using AI agents to automate this manual coding, and focus on the open question of optimal agent design.<n>We demonstrate that a simple agent framework consistently generates adaptation code that outperforms human-expert solutions.
• Score: 69.36509281190662
• License: http://creativecommons.org/licenses/by-nc-sa/4.0/
• Abstract: Adapting production-level computer vision tools to bespoke scientific datasets is a critical "last mile" bottleneck. Current solutions are impractical: fine-tuning requires large annotated datasets scientists often lack, while manual code adaptation costs scientists weeks to months of effort. We consider using AI agents to automate this manual coding, and focus on the open question of optimal agent design for this targeted task. We introduce a systematic evaluation framework for agentic code optimization and use it to study three production-level biomedical imaging pipelines. We demonstrate that a simple agent framework consistently generates adaptation code that outperforms human-expert solutions. Our analysis reveals that common, complex agent architectures are not universally beneficial, leading to a practical roadmap for agent design. We open source our framework and validate our approach by deploying agent-generated functions into a production pipeline, demonstrating a clear pathway for real-world impact.

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