{"id":"https://openalex.org/W3092319880","doi":"https://doi.org/10.1093/bioinformatics/btaa881","title":"Learning graph representations of biochemical networks and its application to enzymatic link prediction","display_name":"Learning graph representations of biochemical networks and its application to enzymatic link prediction","publication_year":2020,"publication_date":"2020-09-29","ids":{"openalex":"https://openalex.org/W3092319880","doi":"https://doi.org/10.1093/bioinformatics/btaa881","mag":"3092319880","pmid":"https://pubmed.ncbi.nlm.nih.gov/33051674"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa881","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa881","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/6/793/37809498/btaa881.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/37/6/793/37809498/btaa881.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053492559","display_name":"Julie Jiang","orcid":"https://orcid.org/0000-0003-4260-282X"},"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":"Julie Jiang","raw_affiliation_strings":["Department of Computer Science, Tufts University , Medford 02155, USA"],"raw_orcid":"https://orcid.org/0000-0003-4260-282X","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Tufts University , Medford 02155, USA","institution_ids":["https://openalex.org/I121934306"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100352436","display_name":"Liping Liu","orcid":"https://orcid.org/0000-0002-3690-3928"},"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":true,"raw_author_name":"Li-Ping Liu","raw_affiliation_strings":["Department of Computer Science, Tufts University , Medford 02155, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Tufts University , Medford 02155, USA","institution_ids":["https://openalex.org/I121934306"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5048817284","display_name":"Soha Hassoun","orcid":"https://orcid.org/0000-0001-9477-2199"},"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":true,"raw_author_name":"Soha Hassoun","raw_affiliation_strings":["Department of Chemical and Biological Engineering, Tufts University , Medford 02155, USA","Department of Computer Science, Tufts University , Medford 02155, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical and Biological Engineering, Tufts University , Medford 02155, USA","institution_ids":["https://openalex.org/I121934306"]},{"raw_affiliation_string":"Department of Computer Science, Tufts University , Medford 02155, USA","institution_ids":["https://openalex.org/I121934306"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5048817284","https://openalex.org/A5100352436"],"corresponding_institution_ids":["https://openalex.org/I121934306"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.5837,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.65753775,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"37","issue":"6","first_page":"793","last_page":"799"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9333000183105469,"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":0.9333000183105469,"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":0.014399999752640724,"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"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.011599999852478504,"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/computer-science","display_name":"Computer science","score":0.6502041816711426},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.6344285011291504},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.6245869398117065},{"id":"https://openalex.org/keywords/graph-embedding","display_name":"Graph embedding","score":0.4425433278083801},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.41487038135528564},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.379251092672348},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.37005487084388733},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32196152210235596},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22967100143432617}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6502041816711426},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.6344285011291504},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.6245869398117065},{"id":"https://openalex.org/C75564084","wikidata":"https://www.wikidata.org/wiki/Q5597085","display_name":"Graph embedding","level":3,"score":0.4425433278083801},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.41487038135528564},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.379251092672348},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.37005487084388733},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32196152210235596},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22967100143432617}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaa881","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa881","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/6/793/37809498/btaa881.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33051674","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33051674","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:8097755","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8097755","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa881","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa881","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/6/793/37809498/btaa881.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2731872532","display_name":"CRII: RI: Self-Attention through the Bayesian Lens","funder_award_id":"1850358","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3748230582","display_name":"FET: Small: Tools and Experimental Validation for Predicting Enzymatic Promiscuity and its Products","funder_award_id":"1909536","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5172521839","display_name":null,"funder_award_id":"R01GM132391","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5775615792","display_name":null,"funder_award_id":"R01 GM132391","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6739667390","display_name":null,"funder_award_id":"R01GM132391","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G8180145166","display_name":"CISE: RI: Small: Amortized Inference for Large-Scale Graphical Models","funder_award_id":"1908617","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/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3092319880.pdf","grobid_xml":"https://content.openalex.org/works/W3092319880.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W1976308333","https://openalex.org/W1996830618","https://openalex.org/W2002560900","https://openalex.org/W2018045523","https://openalex.org/W2030342799","https://openalex.org/W2034994407","https://openalex.org/W2037933327","https://openalex.org/W2043799214","https://openalex.org/W2058141842","https://openalex.org/W2066220968","https://openalex.org/W2112933939","https://openalex.org/W2114013202","https://openalex.org/W2120745758","https://openalex.org/W2128312954","https://openalex.org/W2134441341","https://openalex.org/W2137650465","https://openalex.org/W2159482845","https://openalex.org/W2159899793","https://openalex.org/W2177317049","https://openalex.org/W2187089797","https://openalex.org/W2200017991","https://openalex.org/W2201696856","https://openalex.org/W2441233433","https://openalex.org/W2485621561","https://openalex.org/W2512660405","https://openalex.org/W2612872092","https://openalex.org/W2764075199","https://openalex.org/W2811057373","https://openalex.org/W2899210162","https://openalex.org/W2908591635","https://openalex.org/W2909668868","https://openalex.org/W2962756421","https://openalex.org/W2963224980","https://openalex.org/W2977707586","https://openalex.org/W3100545487","https://openalex.org/W4232932184","https://openalex.org/W4239499371","https://openalex.org/W4294216483"],"related_works":["https://openalex.org/W3036264823","https://openalex.org/W3206528106","https://openalex.org/W2123605750","https://openalex.org/W2912814903","https://openalex.org/W2088740331","https://openalex.org/W2950907416","https://openalex.org/W3038102983","https://openalex.org/W2082479932","https://openalex.org/W4281484020","https://openalex.org/W2932872266"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,204],"complete":[2],"characterization":[3],"of":[4,33,95,164,169,184,190],"enzymatic":[5,25,35,42,72],"activities":[6],"between":[7,37],"molecules":[8],"remains":[9],"incomplete,":[10],"hindering":[11],"biological":[12,16],"engineering":[13],"and":[14,71,89,116,138,161,178,206],"limiting":[15],"discovery.":[17],"We":[18,79,101,145,151],"develop":[19],"in":[20,45,58,85,130,158,166,187],"this":[21],"work":[22],"a":[23,50],"technique,":[24],"link":[26,126],"prediction":[27,127],"(ELP),":[28],"for":[29,155,162],"predicting":[30,156],"the":[31,46,86,96,182,188],"likelihood":[32],"an":[34],"transformation":[36],"two":[38],"molecules.":[39],"ELP":[40,52,104,147,154],"models":[41],"reactions":[43],"cataloged":[44],"KEGG":[47],"database":[48],"as":[49],"graph.":[51],"is":[53],"innovative":[54],"over":[55,134,141],"prior":[56],"works":[57],"using":[59,112],"graph":[60,76,114,123,185,196],"embedding":[61,124,186,197],"to":[62],"learn":[63],"molecular":[64,70],"representations":[65],"that":[66,103,122],"capture":[67],"not":[68,93],"only":[69],"attributes":[73],"but":[74],"also":[75,152],"connectivity.":[77],"RESULTS:":[78],"explore":[80],"transductive":[81],"(test":[82,91],"nodes":[83,92],"included":[84],"training":[87,97],"graph)":[88,98],"inductive":[90],"part":[94],"learning":[99,109],"models.":[100],"show":[102,121],"achieves":[105],"high":[106],"AUC":[107],"when":[108],"node":[110,117],"embeddings":[111],"both":[113],"connectivity":[115],"attributes.":[118],"Further,":[119],"we":[120,193],"improves":[125],"by":[128,139],"30%":[129],"area":[131],"under":[132],"curve":[133],"fingerprint-based":[135],"similarity":[136],"approaches":[137],"8%":[140],"support":[142],"vector":[143],"machines.":[144],"compare":[146],"against":[148],"rule-based":[149],"methods.":[150],"evaluate":[153],"links":[157],"pathway":[159],"maps":[160],"reconstruction":[163],"edges":[165],"reaction":[167],"networks":[168],"four":[170],"common":[171],"gut":[172],"microbiota":[173],"phyla:":[174],"actinobacteria,":[175],"bacteroidetes,":[176],"firmicutes":[177],"proteobacteria.":[179],"To":[180],"emphasize":[181],"importance":[183],"context":[189],"biochemical":[191],"networks,":[192],"illustrate":[194],"how":[195],"can":[198],"guide":[199],"visualization.":[200],"AVAILABILITY":[201],"AND":[202],"IMPLEMENTATION:":[203],"code":[205],"datasets":[207],"are":[208],"available":[209],"through":[210],"https://github.com/HassounLab/ELP.":[211]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}