{"id":"https://openalex.org/W7224746293","doi":"https://doi.org/10.48550/arxiv.2610.37851","title":"Evaluating and improving AI agents for sequencing protocol understanding","display_name":"Evaluating and improving AI agents for sequencing protocol understanding","publication_year":2026,"publication_date":"2026-10-27","ids":{"openalex":"https://openalex.org/W7224746293","doi":"https://doi.org/10.48550/arxiv.2610.37851"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2610.37851","doi":null,"is_oa":true,"landing_page_url":"https://arxiv.org/abs/2610.37851","pdf_url":"https://arxiv.org/pdf/2610.37851","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2610.37851","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088660620","display_name":"Chi-Lam Poon","orcid":"https://orcid.org/0000-0001-6298-7099","observed_orcids":["https://orcid.org/0000-0001-6298-7099"]},"institutions":[{"id":"https://openalex.org/I1334819555","display_name":"Memorial Sloan Kettering Cancer Center","ror":"https://ror.org/02yrq0923","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1334819555"]},{"id":"https://openalex.org/I4387153466","display_name":"Weill Cornell Medicine","ror":"https://ror.org/02r109517","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295","https://openalex.org/I4387153466"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Poon, Chi-Lam","raw_affiliation_strings":["Memorial Sloan Kettering Cancer Center","Weill Cornell Medicine"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Memorial Sloan Kettering Cancer Center","institution_ids":["https://openalex.org/I1334819555"]},{"raw_affiliation_string":"Weill Cornell Medicine","institution_ids":["https://openalex.org/I4387153466"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5130898539","display_name":"Michael Goneos","orcid":"https://orcid.org/0009-0005-4907-0872","observed_orcids":["https://orcid.org/0009-0005-4907-0872"]},"institutions":[{"id":"https://openalex.org/I1280536761","display_name":"Ames Research Center","ror":"https://ror.org/02acart68","country_code":"US","type":"facility","lineage":["https://openalex.org/I1280536761","https://openalex.org/I4210124779"]},{"id":"https://openalex.org/I4387153466","display_name":"Weill Cornell Medicine","ror":"https://ror.org/02r109517","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295","https://openalex.org/I4387153466"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Goneos, Michael","raw_affiliation_strings":["NASA Ames Research Center","Weill Cornell Medicine"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NASA Ames Research Center","institution_ids":["https://openalex.org/I1280536761"]},{"raw_affiliation_string":"Weill Cornell Medicine","institution_ids":["https://openalex.org/I4387153466"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5144959374","display_name":"Zezheng Song","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Song, Zezheng","raw_affiliation_strings":["University of Maryland , College Park"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Maryland , College Park","institution_ids":["https://openalex.org/I66946132"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5160231351","display_name":"Xi Chen","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I3045169105","display_name":"Southern University of Science and Technology","ror":"https://ror.org/049tv2d57","country_code":"CN","type":"education","lineage":["https://openalex.org/I3045169105"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chen, Xi","raw_affiliation_strings":["Southern University of Science and Technology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Southern University of Science and Technology","institution_ids":["https://openalex.org/I3045169105"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.4787999987602234,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},"topics":[{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.4787999987602234,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.09950000047683716,"subfield":{"id":"https://openalex.org/subfields/2718","display_name":"Health Informatics"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11714","display_name":"Multimodal Machine Learning Applications","score":0.07590000331401825,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/sequencing-protocols","display_name":"sequencing protocols","score":0.8130000233650208},{"id":"https://openalex.org/keywords/agent-harnesses","display_name":"agent harnesses","score":0.6399999856948853},{"id":"https://openalex.org/keywords/scientific-reasoning","display_name":"scientific reasoning","score":0.5899999737739563}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.8633000254631042},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7031999826431274},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.6344000101089478},{"id":"https://openalex.org/C85847156","wikidata":"https://www.wikidata.org/wiki/Q59015987","display_name":"Verifiable secret sharing","level":3,"score":0.6208000183105469},{"id":"https://openalex.org/C2780385302","wikidata":"https://www.wikidata.org/wiki/Q367158","display_name":"Protocol (science)","level":3,"score":0.586899995803833},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4814999997615814},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.45100000500679016},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4408999979496002},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.3874000012874603},{"id":"https://openalex.org/C161301231","wikidata":"https://www.wikidata.org/wiki/Q3478658","display_name":"Knowledge representation and reasoning","level":2,"score":0.3727000057697296},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3569999933242798},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3409999907016754},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.3125},{"id":"https://openalex.org/C168167062","wikidata":"https://www.wikidata.org/wiki/Q1117970","display_name":"Component (thermodynamics)","level":2,"score":0.2881999909877777},{"id":"https://openalex.org/C2775851571","wikidata":"https://www.wikidata.org/wiki/Q6045205","display_name":"Interaction protocol","level":3,"score":0.27000001072883606},{"id":"https://openalex.org/C37335422","wikidata":"https://www.wikidata.org/wiki/Q6888134","display_name":"Model-based reasoning","level":3,"score":0.2590999901294708},{"id":"https://openalex.org/C41550386","wikidata":"https://www.wikidata.org/wiki/Q529909","display_name":"Multi-agent system","level":2,"score":0.25619998574256897}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2610.37851","doi":null,"is_oa":true,"landing_page_url":"https://arxiv.org/abs/2610.37851","pdf_url":"https://arxiv.org/pdf/2610.37851","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"doi:10.48550/arxiv.2610.37851","doi":"https://doi.org/10.48550/arxiv.2610.37851","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2610.37851","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2610.37851","doi":null,"is_oa":true,"landing_page_url":"https://arxiv.org/abs/2610.37851","pdf_url":"https://arxiv.org/pdf/2610.37851","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320309468","display_name":"Memorial Sloan-Kettering Cancer Center","ror":"https://ror.org/02yrq0923"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7224746293.pdf","grobid_xml":"https://content.openalex.org/works/W7224746293.grobid-xml"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W591959208","https://openalex.org/W1492083415","https://openalex.org/W2102212449","https://openalex.org/W2119204950","https://openalex.org/W2121690903","https://openalex.org/W2131356974","https://openalex.org/W2205615102","https://openalex.org/W2269040222","https://openalex.org/W2607278153","https://openalex.org/W2747545374","https://openalex.org/W2794083495","https://openalex.org/W2963367647","https://openalex.org/W3093858607","https://openalex.org/W3132562206","https://openalex.org/W3180741386","https://openalex.org/W4298003198","https://openalex.org/W4322768301","https://openalex.org/W4394735445","https://openalex.org/W4402345509","https://openalex.org/W4403324055","https://openalex.org/W4403799507","https://openalex.org/W4407012792","https://openalex.org/W4416043407","https://openalex.org/W7103754783","https://openalex.org/W7161178917","https://openalex.org/W7161734976","https://openalex.org/W7166807240","https://openalex.org/W7166851102","https://openalex.org/W7167845123"],"related_works":["https://openalex.org/W4415882201","https://openalex.org/W7141541063","https://openalex.org/W7204868117","https://openalex.org/W7161683797","https://openalex.org/W7167899806","https://openalex.org/W7214358173","https://openalex.org/W7222964624","https://openalex.org/W7118539294","https://openalex.org/W7077063820","https://openalex.org/W7162320531"],"abstract_inverted_index":{"Existing":[0],"scientific-agent":[1],"benchmarks":[2],"rarely":[3],"evaluate":[4],"whether":[5],"agents":[6,46],"can":[7],"reconstruct":[8],"the":[9,66,121,127],"exact":[10,56],"molecular":[11,39,139],"structures":[12,37],"and":[13,38,62,107,114,132],"generation":[14],"workflows":[15],"specified":[16],"by":[17],"sequencing":[18,26],"protocols,":[19],"a":[20,31,80,94],"capability":[21],"critical":[22],"for":[23,34,85,129],"analyzing":[24],"customized":[25],"assays.":[27],"We":[28],"introduce":[29],"LibStructBench,":[30],"document-grounded":[32],"benchmark":[33],"reconstructing":[35],"sequencing-library":[36],"workflows.":[40],"Our":[41],"experiments":[42],"show":[43],"that":[44],"frontier":[45],"often":[47],"produce":[48],"approximately":[49],"correct":[50],"reconstructions":[51],"but":[52],"remain":[53],"unreliable":[54],"at":[55],"reconstruction,":[57],"particularly":[58],"in":[59,93,120,141],"molecular-state":[60,86],"representation":[61],"workflow":[63],"connectivity.":[64],"Switching":[65],"underlying":[67],"language":[68],"model":[69],"produced":[70],"larger":[71],"average":[72],"performance":[73,113],"differences":[74],"than":[75],"switching":[76],"agent":[77],"harnesses,":[78],"with":[79],"statistically":[81],"significant":[82],"difference":[83],"only":[84],"reconstruction.":[87],"Additional":[88],"knowledge":[89],"improved":[90],"oligo-family":[91],"recovery":[92],"small":[95],"pilot":[96],"without":[97],"improving":[98],"mean":[99,116],"molecular-workflow":[100,118],"scores.":[101],"Autonomous":[102],"accumulation":[103],"of":[104],"procedural":[105],"rules":[106],"cross-protocol":[108],"examples":[109],"showed":[110],"non-monotonic":[111],"validation":[112],"no":[115],"held-out":[117],"improvement":[119],"tested":[122],"trajectory.":[123],"These":[124],"findings":[125],"highlight":[126],"need":[128],"more":[130],"controlled":[131],"verifiable":[133],"approaches":[134],"to":[135],"scientific":[136],"reasoning":[137],"about":[138],"processes":[140],"complex":[142],"experimental":[143],"protocols.":[144]},"counts_by_year":[],"updated_date":"2026-11-07T11:25:07.637180","created_date":"2026-10-31T00:00:00"}