Evaluating and improving AI agents for sequencing protocol understanding

arXiv:2610.37851v1 Announce Type: new Abstract: 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.