{"id":"https://openalex.org/W2799305836","doi":"https://doi.org/10.1109/jbhi.2018.2830806","title":"PathEmb: Random Walk Based Document Embedding for Global Pathway Similarity Search","display_name":"PathEmb: Random Walk Based Document Embedding for Global Pathway Similarity Search","publication_year":2018,"publication_date":"2018-04-27","ids":{"openalex":"https://openalex.org/W2799305836","doi":"https://doi.org/10.1109/jbhi.2018.2830806","mag":"2799305836","pmid":"https://pubmed.ncbi.nlm.nih.gov/29993756"},"language":"en","primary_location":{"id":"doi:10.1109/jbhi.2018.2830806","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2018.2830806","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100317587","display_name":"Jiao Zhang","orcid":"https://orcid.org/0000-0001-8218-3688"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Jiao Zhang","raw_affiliation_strings":["Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong"],"raw_orcid":"https://orcid.org/0000-0001-8218-3688","affiliations":[{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008386708","display_name":"Sam Kwong","orcid":"https://orcid.org/0000-0001-7484-7261"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Sam Kwong","raw_affiliation_strings":["Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong"],"raw_orcid":"https://orcid.org/0000-0001-7484-7261","affiliations":[{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101657809","display_name":"Guangming Liu","orcid":"https://orcid.org/0000-0002-5630-7445"},"institutions":[{"id":"https://openalex.org/I21193070","display_name":"Beijing Jiaotong University","ror":"https://ror.org/01yj56c84","country_code":"CN","type":"education","lineage":["https://openalex.org/I21193070"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guangming Liu","raw_affiliation_strings":["School of Computer and Information Technology, Beijing Jiaotong University, Beijing, China"],"raw_orcid":"https://orcid.org/0000-0002-5630-7445","affiliations":[{"raw_affiliation_string":"School of Computer and Information Technology, Beijing Jiaotong University, Beijing, China","institution_ids":["https://openalex.org/I21193070"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066935890","display_name":"Qiuzhen Lin","orcid":"https://orcid.org/0000-0003-2415-0401"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qiuzhen Lin","raw_affiliation_strings":["College of Computer Science and Software Engineering, Shenzhen University, 518060, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Software Engineering, Shenzhen University, 518060, China","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5030015771","display_name":"Ka\u2010Chun Wong","orcid":"https://orcid.org/0000-0001-6062-733X"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Ka-Chun Wong","raw_affiliation_strings":["Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong"],"raw_orcid":"https://orcid.org/0000-0001-6062-733X","affiliations":[{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong","institution_ids":["https://openalex.org/I168719708"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.4511,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.61711968,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"23","issue":"3","first_page":"1329","last_page":"1335"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9995999932289124,"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":0.9995999932289124,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9968000054359436,"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/T11273","display_name":"Advanced Graph Neural Networks","score":0.993399977684021,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/computer-science","display_name":"Computer science","score":0.6619672775268555},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5949611067771912},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.5755658745765686},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.5493506789207458},{"id":"https://openalex.org/keywords/nearest-neighbor-search","display_name":"Nearest neighbor search","score":0.4894646406173706},{"id":"https://openalex.org/keywords/search-algorithm","display_name":"Search algorithm","score":0.41401174664497375},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.35534462332725525},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2890215814113617},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.20669350028038025}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6619672775268555},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5949611067771912},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.5755658745765686},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.5493506789207458},{"id":"https://openalex.org/C116738811","wikidata":"https://www.wikidata.org/wiki/Q608751","display_name":"Nearest neighbor search","level":2,"score":0.4894646406173706},{"id":"https://openalex.org/C125583679","wikidata":"https://www.wikidata.org/wiki/Q755673","display_name":"Search algorithm","level":2,"score":0.41401174664497375},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35534462332725525},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2890215814113617},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.20669350028038025},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002417","descriptor_name":"Cattle","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002417","descriptor_name":"Cattle","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002417","descriptor_name":"Cattle","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/jbhi.2018.2830806","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2018.2830806","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"},{"id":"pmid:29993756","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29993756","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE journal of biomedical and health informatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":66,"referenced_works":["https://openalex.org/W36903255","https://openalex.org/W168564468","https://openalex.org/W1490161904","https://openalex.org/W1509240356","https://openalex.org/W1588865119","https://openalex.org/W1614298861","https://openalex.org/W1641749581","https://openalex.org/W1854214752","https://openalex.org/W1888005072","https://openalex.org/W1966893452","https://openalex.org/W1976511318","https://openalex.org/W1977431865","https://openalex.org/W1988790447","https://openalex.org/W2004559608","https://openalex.org/W2012066443","https://openalex.org/W2013497015","https://openalex.org/W2040676413","https://openalex.org/W2055043387","https://openalex.org/W2056124433","https://openalex.org/W2063658018","https://openalex.org/W2066506515","https://openalex.org/W2070491228","https://openalex.org/W2078542889","https://openalex.org/W2080829915","https://openalex.org/W2099991711","https://openalex.org/W2100586946","https://openalex.org/W2105302963","https://openalex.org/W2112262143","https://openalex.org/W2124045889","https://openalex.org/W2128408632","https://openalex.org/W2131744502","https://openalex.org/W2132231137","https://openalex.org/W2142965177","https://openalex.org/W2147913014","https://openalex.org/W2153929049","https://openalex.org/W2154851992","https://openalex.org/W2155834877","https://openalex.org/W2159899793","https://openalex.org/W2167139431","https://openalex.org/W2167222948","https://openalex.org/W2168209541","https://openalex.org/W2340796580","https://openalex.org/W2366717601","https://openalex.org/W2508901223","https://openalex.org/W2550782081","https://openalex.org/W2556519015","https://openalex.org/W2557385283","https://openalex.org/W2584628929","https://openalex.org/W2586247031","https://openalex.org/W2598679590","https://openalex.org/W2767112182","https://openalex.org/W2950577311","https://openalex.org/W2962756421","https://openalex.org/W2963514026","https://openalex.org/W3104097132","https://openalex.org/W3105705953","https://openalex.org/W4236236547","https://openalex.org/W4248437541","https://openalex.org/W4249723702","https://openalex.org/W6601546654","https://openalex.org/W6606906144","https://openalex.org/W6636510571","https://openalex.org/W6639055396","https://openalex.org/W6680870402","https://openalex.org/W6721529736","https://openalex.org/W6830460197"],"related_works":["https://openalex.org/W3083116277","https://openalex.org/W2550092706","https://openalex.org/W2097704312","https://openalex.org/W2046947721","https://openalex.org/W2098392074","https://openalex.org/W3131368048","https://openalex.org/W1498782543","https://openalex.org/W3082644980","https://openalex.org/W2089099363","https://openalex.org/W2363946901"],"abstract_inverted_index":{"Pathway":[0],"analysis":[1],"is":[2,58,86,95,139,151,159],"a":[3,14,29,35,37,73,98,102,128,142,152],"cornerstone":[4],"of":[5,193,202],"system":[6],"biology.":[7],"In":[8,68],"particular,":[9],"pathway":[10,31,38,55,78,94,111,138,154,164,179],"similarity":[11,39,56,79,155],"search":[12,40,57,156,197],"plays":[13],"key":[15],"role":[16],"in":[17,191],"establishing":[18],"structural,":[19],"functional,":[20],"and":[21,173,196],"evolutionary":[22],"relationships":[23],"between":[24],"different":[25],"biological":[26],"entities.":[27],"Given":[28],"query":[30,51],"as":[32,34,97,122,127],"well":[33],"database,":[36],"aims":[41],"to":[42,49,62,88,108,161],"identify":[43],"novel":[44,74],"pathways":[45],"that":[46,185],"are":[47,120,125,204],"homologous":[48],"the":[50,54,63,89,132,136,188],"pathway.":[52],"Unfortunately,":[53],"computationally":[59],"inefficient":[60],"due":[61],"NP-complete":[64],"graph":[65],"isomorphism":[66],"problem.":[67],"this":[69],"study,":[70],"we":[71],"introduce":[72],"algorithmic":[75],"framework":[76],"for":[77,135,146],"search,":[80],"named":[81],"PathEmb":[82,100,150,172,186,203],"(Pathway":[83],"Embedding),":[84],"which":[85,124,158],"analogous":[87],"Skip-gram":[90],"model":[91],"where":[92],"each":[93],"represented":[96],"\"document.\"":[99],"exploits":[101],"second":[103],"order":[104],"random":[105,118],"walk":[106],"strategy":[107],"explore":[109],"diverse":[110],"patterns.":[112],"All":[113],"signaling":[114],"paths":[115],"traversed":[116],"from":[117],"walks":[119],"regarded":[121],"\"sentences,\"":[123],"constituted":[126],"\"document\"":[129,133],"afterwards.":[130],"Then,":[131],"pattern":[134],"individual":[137],"mapped":[140],"into":[141],"low-dimensional":[143],"feature":[144],"space":[145],"downstream":[147],"tasks.":[148],"Furthermore,":[149],"topology-free":[153],"algorithm,":[157],"feasible":[160],"handle":[162],"any":[163],"with":[165],"arbitrary":[166],"structure.":[167],"We":[168],"have":[169],"extensively":[170],"evaluated":[171],"other":[174],"cutting-edge":[175],"methods":[176,190],"on":[177],"three":[178],"datasets.":[180],"The":[181,199],"experimental":[182],"results":[183],"demonstrate":[184],"outperforms":[187],"existing":[189],"terms":[192],"computational":[194],"efficiency":[195],"accuracy.":[198],"source":[200],"code":[201],"freely":[205],"available":[206],"online":[207],"https://github.com/zhangjiaobxy/PathEmb.":[208]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":3}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
