Evaluating and improving AI agents for sequencing protocol understanding

The paper introduces LibStructBench, a document‑grounded benchmark designed to assess whether AI agents can accurately reconstruct sequencing‑library structures and molecular workflows from protocols. Experiments reveal that current state‑of‑the‑art agents often generate roughly correct reconstructions but struggle with exact molecular‑state representation and workflow connectivity. The study also finds that changing the underlying language model yields larger performance differences than changing agent harnesses, and that additional knowledge only modestly improves oligo‑family recovery without affecting overall workflow accuracy.

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• llms
• agents
• benchmarks