{"id":"https://openalex.org/W7165741402","doi":"https://doi.org/10.48550/arxiv.2606.24779","title":"DeepBD: A Grounded Agentic Workflow for Variant Prioritization and Diagnosis of Genetic Birth Defects","display_name":"DeepBD: A Grounded Agentic Workflow for Variant Prioritization and Diagnosis of Genetic Birth Defects","publication_year":2026,"publication_date":"2026-06-23","ids":{"openalex":"https://openalex.org/W7165741402","doi":"https://doi.org/10.48550/arxiv.2606.24779"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2606.24779","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2606.24779","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,"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":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"},"type":"preprint","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.48550/arxiv.2606.24779","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5139261419","display_name":"Shiyu Li","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Li, Shiyu","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5139232876","display_name":"Ziqi Yan","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yan, Ziqi","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5139230518","display_name":"Zhihao Wu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wu, Zhihao","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023284940","display_name":"Jielong Lu","orcid":"https://orcid.org/0009-0008-4732-9686"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Lu, Jielong","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002439855","display_name":"Weiran Liao","orcid":"https://orcid.org/0000-0003-4536-5735"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Liao, Weiran","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107877612","display_name":"J. Yu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yu, Jiajun","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5139297932","display_name":"Genjie Li","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Li, Genjie","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5139273640","display_name":"Zeyu Chu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Chu, Zeyu","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052757755","display_name":"Jiajun Bu","orcid":"https://orcid.org/0000-0002-1097-2044"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bu, Jiajun","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5047118636","display_name":"Haishuai Wang","orcid":"https://orcid.org/0000-0003-1617-0920"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wang, Haishuai","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.9944000244140625,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.9944000244140625,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.0007999999797903001,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.0006000000284984708,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.8172000050544739},{"id":"https://openalex.org/keywords/exome-sequencing","display_name":"Exome sequencing","score":0.7333999872207642},{"id":"https://openalex.org/keywords/prioritization","display_name":"Prioritization","score":0.5903000235557556},{"id":"https://openalex.org/keywords/genetic-testing","display_name":"Genetic testing","score":0.4997999966144562},{"id":"https://openalex.org/keywords/whole-genome-sequencing","display_name":"Whole genome sequencing","score":0.4921000003814697},{"id":"https://openalex.org/keywords/exome","display_name":"Exome","score":0.4722000062465668},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.46650001406669617},{"id":"https://openalex.org/keywords/genetic-variants","display_name":"Genetic variants","score":0.3472999930381775},{"id":"https://openalex.org/keywords/relation","display_name":"Relation (database)","score":0.34389999508857727}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.8172000050544739},{"id":"https://openalex.org/C16671776","wikidata":"https://www.wikidata.org/wiki/Q5420592","display_name":"Exome sequencing","level":4,"score":0.7333999872207642},{"id":"https://openalex.org/C2777615720","wikidata":"https://www.wikidata.org/wiki/Q11888847","display_name":"Prioritization","level":2,"score":0.5903000235557556},{"id":"https://openalex.org/C2780673598","wikidata":"https://www.wikidata.org/wiki/Q285223","display_name":"Genetic testing","level":2,"score":0.4997999966144562},{"id":"https://openalex.org/C24432333","wikidata":"https://www.wikidata.org/wiki/Q2068526","display_name":"Whole genome sequencing","level":4,"score":0.4921000003814697},{"id":"https://openalex.org/C10590036","wikidata":"https://www.wikidata.org/wiki/Q417664","display_name":"Exome","level":5,"score":0.4722000062465668},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.46650001406669617},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.46309998631477356},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.42100000381469727},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4203999936580658},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40450000762939453},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.40119999647140503},{"id":"https://openalex.org/C2993967602","wikidata":"https://www.wikidata.org/wiki/Q5532932","display_name":"Genetic variants","level":4,"score":0.3472999930381775},{"id":"https://openalex.org/C25343380","wikidata":"https://www.wikidata.org/wiki/Q277521","display_name":"Relation (database)","level":2,"score":0.34389999508857727},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.3165999948978424},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.31439998745918274},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3140999972820282},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.30649998784065247},{"id":"https://openalex.org/C163763905","wikidata":"https://www.wikidata.org/wiki/Q17075943","display_name":"Precision medicine","level":2,"score":0.3034000098705292},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.30070000886917114},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.29010000824928284},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2865999937057495},{"id":"https://openalex.org/C156325361","wikidata":"https://www.wikidata.org/wiki/Q1152864","display_name":"Grounded theory","level":3,"score":0.2847000062465668},{"id":"https://openalex.org/C26207810","wikidata":"https://www.wikidata.org/wiki/Q1134884","display_name":"Pleiotropy","level":4,"score":0.2818000018596649},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.28139999508857727},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.26260000467300415},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.2572999894618988},{"id":"https://openalex.org/C2778279030","wikidata":"https://www.wikidata.org/wiki/Q1543380","display_name":"Live birth","level":3,"score":0.25679999589920044},{"id":"https://openalex.org/C72563966","wikidata":"https://www.wikidata.org/wiki/Q1303415","display_name":"Cohort","level":2,"score":0.2563000023365021},{"id":"https://openalex.org/C527412718","wikidata":"https://www.wikidata.org/wiki/Q855395","display_name":"Interpretation (philosophy)","level":2,"score":0.25060001015663147},{"id":"https://openalex.org/C64618202","wikidata":"https://www.wikidata.org/wiki/Q3733697","display_name":"Genetic heterogeneity","level":4,"score":0.2502000033855438}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2606.24779","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2606.24779","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,"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":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"doi:10.48550/arxiv.2606.24779","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2606.24779","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,"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":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Birth":[0],"defects":[1],"are":[2],"a":[3,71,93,101,199],"major":[4],"cause":[5],"of":[6,81,157],"fetal":[7,43,147],"loss,":[8],"neonatal":[9],"morbidity":[10],"and":[11,22,47,60,65,78,100,118,121,128,137,148,169,181,190,209],"long-term":[12],"disability.":[13],"In":[14],"the":[15,87,129],"subset":[16],"with":[17],"suspected":[18],"genetic":[19,82,218],"etiologies,":[20],"exome":[21],"genome":[23],"sequencing":[24],"have":[25],"moved":[26],"many":[27],"cases":[28],"from":[29,50,113,140],"variant":[30,76,111,215],"detection":[31],"to":[32],"post-sequencing":[33],"interpretation:":[34],"clinicians":[35],"must":[36],"rank":[37],"patient-specific":[38,110],"candidate":[39,178],"variants":[40],"under":[41],"incomplete":[42],"or":[44],"infant":[45,149],"phenotypes":[46],"heterogeneous":[48],"evidence":[49,95,98,107,205],"population":[51],"genetics,":[52],"variant-effect":[53,119],"prediction,":[54],"gene-disease":[55],"validity,":[56],"phenotype":[57],"ontologies,":[58],"cellular":[59],"pathway":[61],"context,":[62,124,189],"protein":[63],"structure":[64],"clinical":[66],"literature.":[67],"We":[68],"present":[69],"DeepBD,":[70],"grounded":[72,102,200],"agentic":[73,130,201],"workflow":[74,88,202],"for":[75,213],"prioritization":[77,216],"diagnostic":[79,103,211],"interpretation":[80],"birth":[83,219],"defects.":[84,220],"DeepBD":[85,154],"organizes":[86],"into":[89],"LLM-assisted":[90,210],"case":[91],"structuring,":[92],"pretrained":[94],"engine,":[96],"specialist":[97,126,191],"modules":[99,127],"review":[104,136,212],"layer.":[105],"The":[106],"engine":[108],"learns":[109],"scores":[112],"structured":[114],"rule":[115,186],"evidence,":[116,187],"sequence":[117],"representations":[120],"phenotype-conditioned":[122],"biological":[123],"whereas":[125],"layer":[131],"provide":[132,193],"tool-based":[133,207],"refinement,":[134,208],"candidate-pool":[135],"diagnosis-oriented":[138],"synthesis":[139],"ranked":[141],"candidates.":[142],"Developed":[143],"using":[144],"an":[145,160],"in-house":[146],"cohort":[150],"comprising":[151],"18,622":[152],"cases,":[153],"achieved":[155],"Recall@1/3/5/10":[156],"0.658/0.882/0.912/0.929":[158],"on":[159,175],"internal":[161],"held-out":[162],"solved-case":[163],"benchmark,":[164],"outperforming":[165],"standalone":[166],"Exomiser,":[167],"DeepRare":[168],"prompted":[170],"LLM":[171],"reranking":[172],"baselines":[173],"evaluated":[174],"Exomiser-derived":[176],"top-20":[177],"variants.":[179],"Ablation":[180],"overlap":[182],"analyses":[183],"show":[184],"that":[185,203],"mechanistic":[188],"refinement":[192],"complementary":[194],"signals.":[195],"These":[196],"findings":[197],"support":[198],"separates":[204],"integration,":[206],"retrospective":[214],"in":[217]},"counts_by_year":[],"updated_date":"2026-07-28T07:46:37.118299","created_date":"2026-06-25T00:00:00"}