{"id":"https://openalex.org/W3206782361","doi":"https://doi.org/10.1093/bioinformatics/btab729","title":"HPODNets: deep graph convolutional networks for predicting human protein\u2013phenotype associations","display_name":"HPODNets: deep graph convolutional networks for predicting human protein\u2013phenotype associations","publication_year":2021,"publication_date":"2021-10-18","ids":{"openalex":"https://openalex.org/W3206782361","doi":"https://doi.org/10.1093/bioinformatics/btab729","mag":"3206782361","pmid":"https://pubmed.ncbi.nlm.nih.gov/34672333"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab729","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab729","pdf_url":null,"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":null,"license_id":null,"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":"green","oa_url":"https://research.aalto.fi/en/publications/482e0620-a406-4549-af32-dc9ee71e9c5d","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5029384246","display_name":"Lizhi Liu","orcid":"https://orcid.org/0000-0002-6983-4914"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lizhi Liu","raw_affiliation_strings":["School of Computer Science, Fudan University , Shanghai 200433, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science, Fudan University , Shanghai 200433, China","institution_ids":["https://openalex.org/I24943067"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059001924","display_name":"Hiroshi Mamitsuka","orcid":"https://orcid.org/0000-0002-6607-5617"},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]},{"id":"https://openalex.org/I4399598384","display_name":"Kyoto University Institute for Chemical Research","ror":"https://ror.org/0349bbg69","country_code":null,"type":"facility","lineage":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]},{"id":"https://openalex.org/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]}],"countries":["FI","JP"],"is_corresponding":false,"raw_author_name":"Hiroshi Mamitsuka","raw_affiliation_strings":["Bioinformatics Center, Institute for Chemical Research, Kyoto University , Uji, Kyoto Prefecture 611-0011, Japan","Department of Computer Science, Aalto University , Espoo 02150, Finland"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Center, Institute for Chemical Research, Kyoto University , Uji, Kyoto Prefecture 611-0011, Japan","institution_ids":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]},{"raw_affiliation_string":"Department of Computer Science, Aalto University , Espoo 02150, Finland","institution_ids":["https://openalex.org/I9927081"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5045866167","display_name":"Shanfeng Zhu","orcid":"https://orcid.org/0000-0002-6067-5312"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I2802974365","display_name":"Shanghai Innovative Research Center of Traditional Chinese Medicine","ror":"https://ror.org/01gnagj68","country_code":"CN","type":"facility","lineage":["https://openalex.org/I2802974365"]},{"id":"https://openalex.org/I4210085920","display_name":"Shanghai Institute for Science of Science","ror":"https://ror.org/004srxn73","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210085920"]},{"id":"https://openalex.org/I4210164150","display_name":"Shanghai Center for Brain Science and Brain-Inspired Technology","ror":"https://ror.org/0551a0y31","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210164150"]},{"id":"https://openalex.org/I881766915","display_name":"Nanjing University","ror":"https://ror.org/01rxvg760","country_code":"CN","type":"education","lineage":["https://openalex.org/I881766915"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Shanfeng Zhu","raw_affiliation_strings":["Institute of Artificial Intelligence Biomedicine, Nanjing University , Nanjing 210032, China","Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University , Shanghai 200433, China","Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai 200433, China","MOE Frontiers Center for Brain Science, Fudan University , Shanghai 200433, China","Shanghai Key Lab of Intelligent Information Processing, Fudan University , Shanghai 200433, China","Zhangjiang Fudan International Innovation Center , Shanghai 200433, China"],"affiliations":[{"raw_affiliation_string":"Institute of Artificial Intelligence Biomedicine, Nanjing University , Nanjing 210032, China","institution_ids":["https://openalex.org/I881766915"]},{"raw_affiliation_string":"Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University , Shanghai 200433, China","institution_ids":["https://openalex.org/I4210164150","https://openalex.org/I4210085920","https://openalex.org/I24943067"]},{"raw_affiliation_string":"Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai 200433, China","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"MOE Frontiers Center for Brain Science, Fudan University , Shanghai 200433, China","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"Shanghai Key Lab of Intelligent Information Processing, Fudan University , Shanghai 200433, China","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"Zhangjiang Fudan International Innovation Center , Shanghai 200433, China","institution_ids":["https://openalex.org/I2802974365"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5045866167"],"corresponding_institution_ids":["https://openalex.org/I24943067","https://openalex.org/I2802974365","https://openalex.org/I4210085920","https://openalex.org/I4210164150","https://openalex.org/I881766915"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.4869,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.62585561,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"38","issue":"3","first_page":"799","last_page":"808"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998999834060669,"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":0.9998999834060669,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9965000152587891,"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":0.9937999844551086,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.700596034526825},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5876443386077881},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5871002078056335},{"id":"https://openalex.org/keywords/phenotype","display_name":"Phenotype","score":0.5650409460067749},{"id":"https://openalex.org/keywords/protein-function-prediction","display_name":"Protein function prediction","score":0.51076340675354},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.4863434433937073},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.4371614456176758},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.43371325731277466},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.42398664355278015},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4225025475025177},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3993712067604065},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32478728890419006},{"id":"https://openalex.org/keywords/protein-function","display_name":"Protein function","score":0.24202626943588257},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2139148712158203},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19650059938430786},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.15568900108337402},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08850803971290588}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.700596034526825},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5876443386077881},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5871002078056335},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.5650409460067749},{"id":"https://openalex.org/C207060522","wikidata":"https://www.wikidata.org/wiki/Q7251473","display_name":"Protein function prediction","level":4,"score":0.51076340675354},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.4863434433937073},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.4371614456176758},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.43371325731277466},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.42398664355278015},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4225025475025177},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3993712067604065},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32478728890419006},{"id":"https://openalex.org/C2986374874","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Protein function","level":3,"score":0.24202626943588257},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2139148712158203},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19650059938430786},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.15568900108337402},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08850803971290588}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btab729","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab729","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34672333","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34672333","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:aaltodoc.aalto.fi:123456789/115753","is_oa":true,"landing_page_url":"https://research.aalto.fi/en/publications/482e0620-a406-4549-af32-dc9ee71e9c5d","pdf_url":null,"source":{"id":"https://openalex.org/S4306401663","display_name":"Aaltodoc (Aalto University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I9927081","host_organization_name":"Aalto University","host_organization_lineage":["https://openalex.org/I9927081"],"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":null,"raw_type":"acceptedVersion"}],"best_oa_location":{"id":"pmh:oai:aaltodoc.aalto.fi:123456789/115753","is_oa":true,"landing_page_url":"https://research.aalto.fi/en/publications/482e0620-a406-4549-af32-dc9ee71e9c5d","pdf_url":null,"source":{"id":"https://openalex.org/S4306401663","display_name":"Aaltodoc (Aalto University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I9927081","host_organization_name":"Aalto University","host_organization_lineage":["https://openalex.org/I9927081"],"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":null,"raw_type":"acceptedVersion"},"sustainable_development_goals":[{"score":0.47999998927116394,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[{"id":"https://openalex.org/G5527349350","display_name":null,"funder_award_id":"315896","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G6060234","display_name":null,"funder_award_id":"61872094","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6370758788","display_name":null,"funder_award_id":"B18015","funder_id":"https://openalex.org/F4320327912","funder_display_name":"Higher Education Discipline Innovation Project"}],"funders":[{"id":"https://openalex.org/F4320319772","display_name":"Shanghai Center for Brain Science and Brain-Inspired Technology","ror":null},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321108","display_name":"Academy of Finland","ror":"https://ror.org/05k73zm37"},{"id":"https://openalex.org/F4320321133","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35"},{"id":"https://openalex.org/F4320327912","display_name":"Higher Education Discipline Innovation Project","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":48,"referenced_works":["https://openalex.org/W1482169241","https://openalex.org/W1926568554","https://openalex.org/W1996212779","https://openalex.org/W2007477772","https://openalex.org/W2020301095","https://openalex.org/W2031966872","https://openalex.org/W2055043387","https://openalex.org/W2083045667","https://openalex.org/W2090146405","https://openalex.org/W2094129019","https://openalex.org/W2095705004","https://openalex.org/W2101220662","https://openalex.org/W2103017472","https://openalex.org/W2120688086","https://openalex.org/W2124649441","https://openalex.org/W2162813650","https://openalex.org/W2187089797","https://openalex.org/W2227395312","https://openalex.org/W2418684121","https://openalex.org/W2556519015","https://openalex.org/W2577502906","https://openalex.org/W2608690367","https://openalex.org/W2761208857","https://openalex.org/W2786016794","https://openalex.org/W2794479004","https://openalex.org/W2796502523","https://openalex.org/W2801795754","https://openalex.org/W2809000676","https://openalex.org/W2887905891","https://openalex.org/W2899728356","https://openalex.org/W2900569176","https://openalex.org/W2951422523","https://openalex.org/W2965085020","https://openalex.org/W2975578922","https://openalex.org/W2997462854","https://openalex.org/W3006418437","https://openalex.org/W3022179362","https://openalex.org/W3036409928","https://openalex.org/W3042221936","https://openalex.org/W3045552416","https://openalex.org/W3045843906","https://openalex.org/W3098485826","https://openalex.org/W3106811464","https://openalex.org/W3145736512","https://openalex.org/W3164046276","https://openalex.org/W4205666823","https://openalex.org/W4248234957","https://openalex.org/W6674330103"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W4226493464","https://openalex.org/W4312417841","https://openalex.org/W3193565141","https://openalex.org/W3133861977","https://openalex.org/W3167935049","https://openalex.org/W3029198973"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2}],"updated_date":"2026-03-29T08:15:47.926485","created_date":"2025-10-10T00:00:00"}
