{"id":"https://openalex.org/W4390489761","doi":"https://doi.org/10.48550/arxiv.2312.17506","title":"A graph neural network-based model with Out-of-Distribution Robustness for enhancing Antiretroviral Therapy Outcome Prediction for HIV-1","display_name":"A graph neural network-based model with Out-of-Distribution Robustness for enhancing Antiretroviral Therapy Outcome Prediction for HIV-1","publication_year":2023,"publication_date":"2023-12-29","ids":{"openalex":"https://openalex.org/W4390489761","doi":"https://doi.org/10.48550/arxiv.2312.17506"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2312.17506","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2312.17506","pdf_url":"https://arxiv.org/pdf/2312.17506","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2312.17506","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074443891","display_name":"Giulia Di Teodoro","orcid":"https://orcid.org/0000-0002-0418-0067"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Di Teodoro, Giulia","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074346581","display_name":"Federico Siciliano","orcid":"https://orcid.org/0000-0003-1339-6983"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Siciliano, Federico","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078765527","display_name":"Valerio Guarrasi","orcid":"https://orcid.org/0000-0002-1860-7447"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Guarrasi, Valerio","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065034994","display_name":"Anne\u2013Mieke Vandamme","orcid":"https://orcid.org/0000-0002-6594-2766"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Vandamme, Anne-Mieke","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050919587","display_name":"Valeria Ghisetti","orcid":"https://orcid.org/0000-0002-7808-190X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ghisetti, Valeria","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034073363","display_name":"Anders S\u00f6nnerborg","orcid":"https://orcid.org/0000-0001-8928-3374"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"S\u00f6nnerborg, Anders","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002487044","display_name":"Maurizio Zazzi","orcid":"https://orcid.org/0000-0002-0344-6281"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zazzi, Maurizio","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044165871","display_name":"Fabrizio Silvestri","orcid":"https://orcid.org/0000-0001-7669-9055"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Silvestri, Fabrizio","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5002827275","display_name":"Laura Palagi","orcid":"https://orcid.org/0000-0002-9496-6097"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Palagi, Laura","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5074443891"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":1,"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/T10112","display_name":"HIV Research and Treatment","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10112","display_name":"HIV Research and Treatment","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10526","display_name":"HIV/AIDS drug development and treatment","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"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/T10082","display_name":"HIV/AIDS Research and Interventions","score":0.9987999796867371,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"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/machine-learning","display_name":"Machine learning","score":0.6762121915817261},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.6547433733940125},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.604996383190155},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5649926662445068},{"id":"https://openalex.org/keywords/generalizability-theory","display_name":"Generalizability theory","score":0.4861885905265808},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.42897215485572815},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.40698787569999695},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12872982025146484},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.10404250025749207}],"concepts":[{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.6762121915817261},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.6547433733940125},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.604996383190155},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5649926662445068},{"id":"https://openalex.org/C27158222","wikidata":"https://www.wikidata.org/wiki/Q5532422","display_name":"Generalizability theory","level":2,"score":0.4861885905265808},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.42897215485572815},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.40698787569999695},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12872982025146484},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.10404250025749207},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2312.17506","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2312.17506","pdf_url":"https://arxiv.org/pdf/2312.17506","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"doi:10.48550/arxiv.2312.17506","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2312.17506","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"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":"article-journal"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2312.17506","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2312.17506","pdf_url":"https://arxiv.org/pdf/2312.17506","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.6399999856948853,"display_name":"Good health and well-being"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4390489761.pdf","grobid_xml":"https://content.openalex.org/works/W4390489761.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2118717649","https://openalex.org/W2413243053","https://openalex.org/W410723623","https://openalex.org/W2015341305","https://openalex.org/W2035068594","https://openalex.org/W4225593417","https://openalex.org/W2573498121","https://openalex.org/W3022298670","https://openalex.org/W3160494304","https://openalex.org/W3006162251"],"abstract_inverted_index":{"Predicting":[0],"the":[1,16,33,40,121,134,161,169,174,180,187],"outcome":[2],"of":[3,26,35,182],"antiretroviral":[4],"therapies":[5],"(ART)":[6],"for":[7,114,148],"HIV-1":[8],"is":[9,214],"a":[10,36,65,74,81,87,100,132],"pressing":[11],"clinical":[12,48,52,205],"challenge,":[13],"especially":[14],"when":[15],"ART":[17],"includes":[18],"drugs":[19,159],"with":[20,54,207],"limited":[21,45,208],"effectiveness":[22],"data.":[23],"This":[24],"scarcity":[25],"data":[27,95,144,209],"can":[28],"arise":[29],"either":[30],"due":[31,43],"to":[32,39,44,140,142],"introduction":[34],"new":[37],"drug":[38],"market":[41],"or":[42],"use":[46],"in":[47,51,86,160,186,200,202],"settings,":[49],"resulting":[50],"dataset":[53],"highly":[55],"unbalanced":[56],"therapy":[57],"representation.":[58],"To":[59],"tackle":[60],"this":[61,127],"issue,":[62],"we":[63],"introduce":[64],"novel":[66],"joint":[67],"fusion":[68],"model,":[69,188],"which":[70,109],"combines":[71],"features":[72],"from":[73,104],"Fully":[75],"Connected":[76],"(FC)":[77],"Neural":[78,83],"Network":[79,84],"and":[80,99,146,193],"Graph":[82],"(GNN)":[85],"multi-modality":[88],"fashion.":[89],"Our":[90,164],"model":[91,139,171],"uses":[92],"both":[93],"tabular":[94],"about":[96],"genetic":[97,123],"sequences":[98],"knowledge":[101,128],"base":[102,129],"derived":[103],"Stanford":[105,184],"drug-resistance":[106],"mutation":[107],"tables,":[108],"serve":[110],"as":[111,131],"benchmark":[112],"references":[113],"deducing":[115],"in-vivo":[116],"treatment":[117],"efficacy":[118],"based":[119],"on":[120],"viral":[122],"sequence.":[124],"By":[125],"leveraging":[126],"structured":[130],"graph,":[133],"GNN":[135],"component":[136],"enables":[137],"our":[138],"adapt":[141],"imbalanced":[143],"distributions":[145],"account":[147],"Out-of-Distribution":[149],"(OoD)":[150],"drugs.":[151],"We":[152],"evaluated":[153],"these":[154],"models'":[155],"robustness":[156],"against":[157],"OoD":[158],"test":[162],"set.":[163],"comprehensive":[165],"analysis":[166],"demonstrates":[167],"that":[168],"proposed":[170],"consistently":[172],"outperforms":[173],"FC":[175],"model.":[176],"These":[177],"results":[178],"underscore":[179],"advantage":[181],"integrating":[183],"scores":[185],"thereby":[189],"enhancing":[190],"its":[191,198],"generalizability":[192],"robustness,":[194],"but":[195],"also":[196],"extending":[197],"utility":[199],"contributing":[201],"more":[203],"informed":[204],"decisions":[206],"availability.":[210],"The":[211],"source":[212],"code":[213],"available":[215],"at":[216],"https://github.com/federicosiciliano/graph-ood-hiv":[217]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-03-10T16:38:18.471706","created_date":"2025-10-10T00:00:00"}
