{"id":"https://openalex.org/W4288421310","doi":"https://doi.org/10.1145/3535508.3545542","title":"Neighborhood embedding and re-ranking of disease genes with ADAGIO","display_name":"Neighborhood embedding and re-ranking of disease genes with ADAGIO","publication_year":2022,"publication_date":"2022-07-28","ids":{"openalex":"https://openalex.org/W4288421310","doi":"https://doi.org/10.1145/3535508.3545542"},"language":"en","primary_location":{"id":"doi:10.1145/3535508.3545542","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3535508.3545542","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3535508.3545542","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 13th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://dl.acm.org/doi/pdf/10.1145/3535508.3545542","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5028761606","display_name":"Mert Erden","orcid":"https://orcid.org/0000-0003-4718-9181"},"institutions":[{"id":"https://openalex.org/I121934306","display_name":"Tufts University","ror":"https://ror.org/05wvpxv85","country_code":"US","type":"education","lineage":["https://openalex.org/I121934306"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mert Erden","raw_affiliation_strings":["Tufts University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tufts University","institution_ids":["https://openalex.org/I121934306"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022777811","display_name":"Megan Gelement","orcid":null},"institutions":[{"id":"https://openalex.org/I121934306","display_name":"Tufts University","ror":"https://ror.org/05wvpxv85","country_code":"US","type":"education","lineage":["https://openalex.org/I121934306"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Megan Gelement","raw_affiliation_strings":["Tufts University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tufts University","institution_ids":["https://openalex.org/I121934306"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038502642","display_name":"Sarrah M. Hakimjee","orcid":null},"institutions":[{"id":"https://openalex.org/I121934306","display_name":"Tufts University","ror":"https://ror.org/05wvpxv85","country_code":"US","type":"education","lineage":["https://openalex.org/I121934306"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sarrah Hakimjee","raw_affiliation_strings":["Tufts University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tufts University","institution_ids":["https://openalex.org/I121934306"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5094255540","display_name":"Kyla H. Levin","orcid":"https://orcid.org/0009-0005-2533-7499"},"institutions":[{"id":"https://openalex.org/I121934306","display_name":"Tufts University","ror":"https://ror.org/05wvpxv85","country_code":"US","type":"education","lineage":["https://openalex.org/I121934306"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kyla Levin","raw_affiliation_strings":["Tufts University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tufts University","institution_ids":["https://openalex.org/I121934306"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002716091","display_name":"Mary-Joy Sidhom","orcid":null},"institutions":[{"id":"https://openalex.org/I121934306","display_name":"Tufts University","ror":"https://ror.org/05wvpxv85","country_code":"US","type":"education","lineage":["https://openalex.org/I121934306"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mary-Joy Sidhom","raw_affiliation_strings":["Tufts University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tufts University","institution_ids":["https://openalex.org/I121934306"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036303987","display_name":"Kapil Devkota","orcid":"https://orcid.org/0000-0002-6093-6260"},"institutions":[{"id":"https://openalex.org/I121934306","display_name":"Tufts University","ror":"https://ror.org/05wvpxv85","country_code":"US","type":"education","lineage":["https://openalex.org/I121934306"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kapil Devkota","raw_affiliation_strings":["Tufts University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tufts University","institution_ids":["https://openalex.org/I121934306"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5026411021","display_name":"Lenore Cowen","orcid":"https://orcid.org/0000-0001-6698-6413"},"institutions":[{"id":"https://openalex.org/I121934306","display_name":"Tufts University","ror":"https://ror.org/05wvpxv85","country_code":"US","type":"education","lineage":["https://openalex.org/I121934306"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lenore J. Cowen","raw_affiliation_strings":["Tufts University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tufts University","institution_ids":["https://openalex.org/I121934306"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"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":0.0765428,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"11"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9997000098228455,"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"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9997000098228455,"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/T10086","display_name":"Alzheimer's disease research and treatments","score":0.9926999807357788,"subfield":{"id":"https://openalex.org/subfields/2737","display_name":"Physiology"},"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9847999811172485,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/benchmark","display_name":"Benchmark (surveying)","score":0.7281391620635986},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.6823476552963257},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.646658718585968},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.5918962359428406},{"id":"https://openalex.org/keywords/measure","display_name":"Measure (data warehouse)","score":0.584740400314331},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5546051859855652},{"id":"https://openalex.org/keywords/disease","display_name":"Disease","score":0.5412449836730957},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5326891541481018},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5218999981880188},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5071938037872314},{"id":"https://openalex.org/keywords/interconnection","display_name":"Interconnection","score":0.480352520942688},{"id":"https://openalex.org/keywords/similarity-measure","display_name":"Similarity measure","score":0.4192933440208435},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.37782153487205505},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.28025150299072266},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.26530396938323975},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.26212388277053833},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.1726371943950653},{"id":"https://openalex.org/keywords/computer-network","display_name":"Computer network","score":0.08034947514533997},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.06502681970596313}],"concepts":[{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.7281391620635986},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.6823476552963257},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.646658718585968},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.5918962359428406},{"id":"https://openalex.org/C2780009758","wikidata":"https://www.wikidata.org/wiki/Q6804172","display_name":"Measure (data warehouse)","level":2,"score":0.584740400314331},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5546051859855652},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.5412449836730957},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5326891541481018},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5218999981880188},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5071938037872314},{"id":"https://openalex.org/C123745756","wikidata":"https://www.wikidata.org/wiki/Q1665949","display_name":"Interconnection","level":2,"score":0.480352520942688},{"id":"https://openalex.org/C2776517306","wikidata":"https://www.wikidata.org/wiki/Q29017317","display_name":"Similarity measure","level":2,"score":0.4192933440208435},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.37782153487205505},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.28025150299072266},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.26530396938323975},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.26212388277053833},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.1726371943950653},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.08034947514533997},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.06502681970596313},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3535508.3545542","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3535508.3545542","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3535508.3545542","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 13th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/3535508.3545542","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3535508.3545542","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3535508.3545542","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 13th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2904832559","display_name":null,"funder_award_id":"DMS-1812503","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3651390770","display_name":"Mining Multi-Layer Protein-Protein Association Networks: An Integrated Spectral Approach","funder_award_id":"1812503","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4572708944","display_name":null,"funder_award_id":"1934553","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7900601331","display_name":null,"funder_award_id":"CCF-1934553","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"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4288421310.pdf","grobid_xml":"https://content.openalex.org/works/W4288421310.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W1812073992","https://openalex.org/W1989536974","https://openalex.org/W1993812537","https://openalex.org/W2036568936","https://openalex.org/W2038122249","https://openalex.org/W2048555293","https://openalex.org/W2086254934","https://openalex.org/W2118607021","https://openalex.org/W2119220491","https://openalex.org/W2122801779","https://openalex.org/W2124649441","https://openalex.org/W2146980885","https://openalex.org/W2246559112","https://openalex.org/W2624021832","https://openalex.org/W2763172433","https://openalex.org/W2772875656","https://openalex.org/W2789374663","https://openalex.org/W2808435921","https://openalex.org/W2952588534","https://openalex.org/W3043771525","https://openalex.org/W3092119378","https://openalex.org/W3165506417","https://openalex.org/W3190631166","https://openalex.org/W6682156016"],"related_works":["https://openalex.org/W2319693127","https://openalex.org/W2111173507","https://openalex.org/W4248020907","https://openalex.org/W2606618787","https://openalex.org/W1992371859","https://openalex.org/W121350374","https://openalex.org/W3142162173","https://openalex.org/W3015424904","https://openalex.org/W2135077600","https://openalex.org/W2072263576"],"abstract_inverted_index":{"We":[0,23,48],"present":[1],"ADAGIO,":[2],"a":[3,37],"new":[4,54],"method":[5],"for":[6,31,44],"network-based":[7],"disease":[8,34,55],"gene":[9,56],"prioritization":[10],"that":[11],"balances":[12],"network":[13,21],"interconnection":[14],"structure":[15],"with":[16],"an":[17],"embedding":[18],"measure":[19],"of":[20],"similarity.":[22],"show":[24],"ADAGIO":[25,50],"performs":[26],"better":[27],"than":[28],"previous":[29],"methods":[30],"recovering":[32],"known":[33],"genes":[35,43],"in":[36,58],"recent":[38],"benchmark":[39],"set":[40],"encompassing":[41],"disease-associated":[42],"22":[45],"polygenic":[46],"diseases.":[47,63],"find":[49],"discovers":[51],"some":[52],"interesting":[53],"candidates":[57],"both":[59],"Alzheimer's":[60],"and":[61],"Parkinson's":[62]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
