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Evaluating and improving AI agents for sequencing protocol understanding
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First announced by arXiv: 2026-10-30 · Indexed by Pub-AI: 2026-10-30 UTC
Evaluating and improving AI agents for sequencing protocol understanding
First announced by arXiv: 2026-10-30 · Original record ↗
- arxiv
- 2610.37851
Explicit source versions (1)
- v1 · Date not supplied
- Preprint available
Source date: 2026-10-30 · First detected: 2026-10-30 UTC · Historical baseline
Source evidence (1)
- Official evidence ↗ · RSS guid=oai:arXiv.org:2610.37851v1; arxiv:announce_type=new; item pubDate (official metadata)
Abstract · arxiv
Existing scientific-agent benchmarks rarely evaluate whether agents can reconstruct the exact molecular structures and generation workflows specified by sequencing protocols, a capability critical for analyzing customized sequencing assays. We introduce LibStructBench, a document-grounded benchmark for reconstructing sequencing-library structures and molecular workflows. Our experiments show that frontier agents often produce approximately correct reconstructions but remain unreliable at exact reconstruction, particularly in molecular-state representation and workflow connectivity. Switching the underlying language model produced larger average performance differences than switching agent harnesses, with a statistically significant difference only for molecular-state reconstruction. Additional knowledge improved oligo-family recovery in a small pilot without improving mean molecular-workflow scores. Autonomous accumulation of procedural rules and cross-protocol examples showed non-monotonic validation performance and no mean held-out molecular-workflow improvement in the tested trajectory. These findings highlight the need for more controlled and verifiable approaches to scientific reasoning about molecular processes in complex experimental protocols.