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bioRxiv · 10.64898/2026.05.13.724985

Evaluating open LLMs for agentic analysis orchestration in a typical biomedical lab

Nekrutenko, A.
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Abstract

Agentic tools -- software environments where a large language model plans, calls external tools, executes code, and iterates with minimal human intervention -- will run a substantial share of routine biomedical data analysis within the next few years. However, per-call inference cost on frontier models is the bottleneck and can add up quickly. Here, we tested whether a free, locally-runnable open-weight model could take over the repetitive execution steps at frontier accuracy. We used Claudes Opus to author plans of increasing detail for per-sample variant calling, and ran six 2026-release open-weight implementer LLMs against those plans on a set of desktop GPUs. qwen3.6:27b reproduced frontier accuracy on every plan and matched Opus cell-for-cell on a 36-cell error-injection matrix. A sub-$2,000 Jetson or Apple Mac Mini sufficed for the implementer side. The open-weight model landscape evolves on the order of months, so the specific implementer recommended here will be superseded; we provide the plans, harness, scoring code, and per-cell artifacts at https://github.com/nekrut/LLM-eval-paper as a framework for re-evaluating future models.

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Nekrutenko, A.. 2026-05-18. Evaluating open LLMs for agentic analysis orchestration in a typical biomedical lab. https://doi.org/10.64898/2026.05.13.724985

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