{"id":"https://openalex.org/W4417283679","doi":"https://doi.org/10.1145/3748636.3762779","title":"A Probabilistic Framework for Imputing Genetic Distances in Spatiotemporal Pathogen Models","display_name":"A Probabilistic Framework for Imputing Genetic Distances in Spatiotemporal Pathogen Models","publication_year":2025,"publication_date":"2025-11-03","ids":{"openalex":"https://openalex.org/W4417283679","doi":"https://doi.org/10.1145/3748636.3762779"},"language":"en","primary_location":{"id":"doi:10.1145/3748636.3762779","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3748636.3762779","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3748636.3762779","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 33rd ACM International Conference on Advances in Geographic Information Systems","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["arxiv","crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://dl.acm.org/doi/pdf/10.1145/3748636.3762779","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5003188710","display_name":"Haley Stone","orcid":"https://orcid.org/0000-0003-1997-0042"},"institutions":[{"id":"https://openalex.org/I31746571","display_name":"UNSW Sydney","ror":"https://ror.org/03r8z3t63","country_code":"AU","type":"education","lineage":["https://openalex.org/I31746571"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Haley Stone","raw_affiliation_strings":["University of New South Wales, Sydney, Australia"],"raw_orcid":"https://orcid.org/0000-0003-1997-0042","affiliations":[{"raw_affiliation_string":"University of New South Wales, Sydney, Australia","institution_ids":["https://openalex.org/I31746571"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066174124","display_name":"Jing Du","orcid":"https://orcid.org/0000-0003-4113-0875"},"institutions":[{"id":"https://openalex.org/I31746571","display_name":"UNSW Sydney","ror":"https://ror.org/03r8z3t63","country_code":"AU","type":"education","lineage":["https://openalex.org/I31746571"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Jing Du","raw_affiliation_strings":["University of New South Wales, Sydney, Australia"],"raw_orcid":"https://orcid.org/0000-0003-4113-0875","affiliations":[{"raw_affiliation_string":"University of New South Wales, Sydney, Australia","institution_ids":["https://openalex.org/I31746571"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000564739","display_name":"Hao Xue","orcid":"https://orcid.org/0000-0003-1700-9215"},"institutions":[{"id":"https://openalex.org/I31746571","display_name":"UNSW Sydney","ror":"https://ror.org/03r8z3t63","country_code":"AU","type":"education","lineage":["https://openalex.org/I31746571"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Hao Xue","raw_affiliation_strings":["University of New South Wales, Sydney, Australia"],"raw_orcid":"https://orcid.org/0000-0003-1700-9215","affiliations":[{"raw_affiliation_string":"University of New South Wales, Sydney, Australia","institution_ids":["https://openalex.org/I31746571"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050090926","display_name":"Matthew Scotch","orcid":"https://orcid.org/0000-0001-5100-9724"},"institutions":[{"id":"https://openalex.org/I4210091789","display_name":"Arizona State Museum","ror":"https://ror.org/00g3q3z36","country_code":"US","type":"archive","lineage":["https://openalex.org/I4210091789"]},{"id":"https://openalex.org/I55732556","display_name":"Arizona State University","ror":"https://ror.org/03efmqc40","country_code":"US","type":"education","lineage":["https://openalex.org/I55732556"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matthew Scotch","raw_affiliation_strings":["Arizona State University, Arizona, Arizona, USA"],"raw_orcid":"https://orcid.org/0000-0001-5100-9724","affiliations":[{"raw_affiliation_string":"Arizona State University, Arizona, Arizona, USA","institution_ids":["https://openalex.org/I4210091789","https://openalex.org/I55732556"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002487990","display_name":"David Heslop","orcid":"https://orcid.org/0000-0002-1978-770X"},"institutions":[{"id":"https://openalex.org/I31746571","display_name":"UNSW Sydney","ror":"https://ror.org/03r8z3t63","country_code":"AU","type":"education","lineage":["https://openalex.org/I31746571"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"David Heslop","raw_affiliation_strings":["University of New South Wales, Sydney, Australia"],"raw_orcid":"https://orcid.org/0000-0002-1978-770X","affiliations":[{"raw_affiliation_string":"University of New South Wales, Sydney, Australia","institution_ids":["https://openalex.org/I31746571"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017299501","display_name":"Andreas Z\u00fcfle","orcid":"https://orcid.org/0000-0001-7001-4123"},"institutions":[{"id":"https://openalex.org/I150468666","display_name":"Emory University","ror":"https://ror.org/03czfpz43","country_code":"US","type":"education","lineage":["https://openalex.org/I150468666"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andreas Zufle","raw_affiliation_strings":["Emory University, Atlanta, Georgia, USA"],"raw_orcid":"https://orcid.org/0000-0001-7001-4123","affiliations":[{"raw_affiliation_string":"Emory University, Atlanta, Georgia, USA","institution_ids":["https://openalex.org/I150468666"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075730026","display_name":"C. Raina MacIntyre","orcid":"https://orcid.org/0000-0002-3060-0555"},"institutions":[{"id":"https://openalex.org/I31746571","display_name":"UNSW Sydney","ror":"https://ror.org/03r8z3t63","country_code":"AU","type":"education","lineage":["https://openalex.org/I31746571"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"C. Raina MacIntyre","raw_affiliation_strings":["University of New South Wales, Sydney, Australia"],"raw_orcid":"https://orcid.org/0000-0002-3060-0555","affiliations":[{"raw_affiliation_string":"University of New South Wales, Sydney, Australia","institution_ids":["https://openalex.org/I31746571"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5090893421","display_name":"Flora D. Salim","orcid":"https://orcid.org/0000-0002-1237-1664"},"institutions":[{"id":"https://openalex.org/I31746571","display_name":"UNSW Sydney","ror":"https://ror.org/03r8z3t63","country_code":"AU","type":"education","lineage":["https://openalex.org/I31746571"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Flora Salim","raw_affiliation_strings":["University of New South Wales, Sydney, Australia"],"raw_orcid":"https://orcid.org/0000-0002-1237-1664","affiliations":[{"raw_affiliation_string":"University of New South Wales, Sydney, Australia","institution_ids":["https://openalex.org/I31746571"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.45784695,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"646","last_page":"655"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10410","display_name":"COVID-19 epidemiological studies","score":0.2752000093460083,"subfield":{"id":"https://openalex.org/subfields/2611","display_name":"Modeling and Simulation"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10410","display_name":"COVID-19 epidemiological studies","score":0.2752000093460083,"subfield":{"id":"https://openalex.org/subfields/2611","display_name":"Modeling and Simulation"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10167","display_name":"Influenza Virus Research Studies","score":0.125900000333786,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"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/T11819","display_name":"Data-Driven Disease Surveillance","score":0.11640000343322754,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.70169997215271},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.6353999972343445},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.49050000309944153},{"id":"https://openalex.org/keywords/imputation","display_name":"Imputation (statistics)","score":0.40049999952316284},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.39800000190734863},{"id":"https://openalex.org/keywords/divergence","display_name":"Divergence (linguistics)","score":0.39719998836517334},{"id":"https://openalex.org/keywords/statistical-model","display_name":"Statistical model","score":0.3621000051498413},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.35600000619888306},{"id":"https://openalex.org/keywords/whole-genome-sequencing","display_name":"Whole genome sequencing","score":0.33959999680519104}],"concepts":[{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.70169997215271},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.6353999972343445},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.49050000309944153},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46779999136924744},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.41339999437332153},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4120999872684479},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4106999933719635},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.40290001034736633},{"id":"https://openalex.org/C58041806","wikidata":"https://www.wikidata.org/wiki/Q1660484","display_name":"Imputation (statistics)","level":3,"score":0.40049999952316284},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.39800000190734863},{"id":"https://openalex.org/C207390915","wikidata":"https://www.wikidata.org/wiki/Q1230525","display_name":"Divergence (linguistics)","level":2,"score":0.39719998836517334},{"id":"https://openalex.org/C114289077","wikidata":"https://www.wikidata.org/wiki/Q3284399","display_name":"Statistical model","level":2,"score":0.3621000051498413},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.35600000619888306},{"id":"https://openalex.org/C24432333","wikidata":"https://www.wikidata.org/wiki/Q2068526","display_name":"Whole genome sequencing","level":4,"score":0.33959999680519104},{"id":"https://openalex.org/C761482","wikidata":"https://www.wikidata.org/wiki/Q118093","display_name":"Transmission (telecommunications)","level":2,"score":0.3377000093460083},{"id":"https://openalex.org/C138592617","wikidata":"https://www.wikidata.org/wiki/Q748695","display_name":"Genetic distance","level":4,"score":0.3273000121116638},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.3262999951839447},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.31520000100135803},{"id":"https://openalex.org/C60782215","wikidata":"https://www.wikidata.org/wiki/Q3333679","display_name":"Probabilistic method","level":3,"score":0.30820000171661377},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.29510000348091125},{"id":"https://openalex.org/C2993807623","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genetic data","level":3,"score":0.2937000095844269},{"id":"https://openalex.org/C171578705","wikidata":"https://www.wikidata.org/wiki/Q5418700","display_name":"Evolutionary dynamics","level":3,"score":0.29179999232292175},{"id":"https://openalex.org/C109186463","wikidata":"https://www.wikidata.org/wiki/Q1230536","display_name":"Genetic divergence","level":4,"score":0.2913999855518341},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2816999852657318},{"id":"https://openalex.org/C21833749","wikidata":"https://www.wikidata.org/wiki/Q7189431","display_name":"Viral phylodynamics","level":4,"score":0.2809999883174896},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.2809000015258789},{"id":"https://openalex.org/C207201462","wikidata":"https://www.wikidata.org/wiki/Q182505","display_name":"Bayes' theorem","level":3,"score":0.2802000045776367},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.2782999873161316},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.2741999924182892},{"id":"https://openalex.org/C9357733","wikidata":"https://www.wikidata.org/wiki/Q6878417","display_name":"Missing data","level":2,"score":0.2718000113964081},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.2712000012397766},{"id":"https://openalex.org/C68873052","wikidata":"https://www.wikidata.org/wiki/Q349856","display_name":"Genetic variation","level":3,"score":0.2689000070095062},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.2648000121116638}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/3748636.3762779","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3748636.3762779","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3748636.3762779","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 33rd ACM International Conference on Advances in Geographic Information Systems","raw_type":"proceedings-article"},{"id":"pmh:oai:arXiv.org:2506.09076","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2506.09076","pdf_url":"https://arxiv.org/pdf/2506.09076","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"}],"best_oa_location":{"id":"doi:10.1145/3748636.3762779","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3748636.3762779","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3748636.3762779","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 33rd ACM International Conference on Advances in Geographic Information Systems","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6648413181","display_name":"Collaborative Research: NSF-CSIRO: HCC: Small: Understanding Bias in AI Models for the Prediction of Infectious Disease Spread","funder_award_id":"2302970","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7969191702","display_name":"Collaborative Research: NSF-CSIRO: HCC: Small: Understanding Bias in AI Models for the Prediction of Infectious Disease Spread","funder_award_id":"2302969","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320315885","display_name":"Australian Government","ror":"https://ror.org/0314h5y94"},{"id":"https://openalex.org/F4320320386","display_name":"Commonwealth Scientific and Industrial Research Organisation","ror":"https://ror.org/03qn8fb07"},{"id":"https://openalex.org/F4320320965","display_name":"University of New South Wales","ror":"https://ror.org/03r8z3t63"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4417283679.pdf","grobid_xml":"https://content.openalex.org/works/W4417283679.grobid-xml"},"referenced_works_count":11,"referenced_works":["https://openalex.org/W2011904222","https://openalex.org/W2065461553","https://openalex.org/W2070747934","https://openalex.org/W2134892520","https://openalex.org/W2141380436","https://openalex.org/W2149791927","https://openalex.org/W2298059330","https://openalex.org/W2510973425","https://openalex.org/W4224861332","https://openalex.org/W4367836877","https://openalex.org/W4395464415"],"related_works":[],"abstract_inverted_index":{"Pathogen":[0],"genome":[1],"data":[2],"offers":[3],"valuable":[4],"structure":[5],"for":[6,23],"spatial":[7],"models,":[8],"but":[9],"its":[10],"utility":[11],"is":[12],"limited":[13],"by":[14],"incomplete":[15],"sequencing":[16],"coverage.":[17],"We":[18],"propose":[19],"a":[20],"probabilistic":[21],"framework":[22],"inferring":[24],"genetic":[25,52],"distances":[26],"between":[27],"unsequenced":[28],"cases":[29,78],"and":[30,50,95],"known":[31,68],"sequences":[32],"within":[33],"defined":[34],"transmission":[35,69],"chains,":[36],"using":[37],"time-aware":[38],"evolutionary":[39,100],"distance":[40],"modeling.":[41],"The":[42],"method":[43],"estimates":[44],"pairwise":[45],"divergence":[46,61],"from":[47],"collection":[48],"dates":[49],"observed":[51,60],"distances,":[53],"enabling":[54],"biologically":[55],"plausible":[56],"imputation":[57],"grounded":[58],"in":[59,79,82],"patterns,":[62],"without":[63],"requiring":[64],"sequence":[65],"alignment":[66],"or":[67],"chains.":[70],"Applied":[71],"to":[72],"highly":[73],"pathogenic":[74],"avian":[75],"influenza":[76],"A/H5":[77],"wild":[80],"birds":[81],"the":[83,97],"United":[84],"States,":[85],"this":[86],"approach":[87],"supports":[88],"scalable,":[89],"uncertainty-aware":[90],"augmentation":[91],"of":[92,99],"genomic":[93],"datasets":[94],"enhances":[96],"integration":[98],"information":[101],"into":[102],"spatiotemporal":[103],"modeling":[104],"workflows.":[105]},"counts_by_year":[],"updated_date":"2026-08-05T07:39:15.569665","created_date":"2025-10-10T00:00:00"}
