{"id":"https://openalex.org/W7165373194","doi":"https://doi.org/10.1093/bib/bbag313","title":"The role of protein embeddings for protein\u2013protein interaction prediction with graph neural networks","display_name":"The role of protein embeddings for protein\u2013protein interaction prediction with graph neural networks","publication_year":2026,"publication_date":"2026-05-01","ids":{"openalex":"https://openalex.org/W7165373194","doi":"https://doi.org/10.1093/bib/bbag313","pmid":"https://pubmed.ncbi.nlm.nih.gov/42319252"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbag313","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag313","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bib/bbag313","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014010817","display_name":"Laura Balbi","orcid":"https://orcid.org/0000-0002-1116-3476"},"institutions":[{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Laura Balbi","raw_affiliation_strings":["LASIGE, Faculdade de Ci\u00eancias da Universidade de Lisboa , Campo Grande, 1749-016 Lisbon ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LASIGE, Faculdade de Ci\u00eancias da Universidade de Lisboa , Campo Grande, 1749-016 Lisbon ,","institution_ids":["https://openalex.org/I141596103"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063408223","display_name":"Rita T. Sousa","orcid":"https://orcid.org/0000-0002-7241-8970"},"institutions":[{"id":"https://openalex.org/I112756935","display_name":"Technische Hochschule Mannheim","ror":"https://ror.org/04p61dj41","country_code":"DE","type":"education","lineage":["https://openalex.org/I112756935"]},{"id":"https://openalex.org/I177802217","display_name":"University of Mannheim","ror":"https://ror.org/031bsb921","country_code":"DE","type":"education","lineage":["https://openalex.org/I177802217"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Rita T Sousa","raw_affiliation_strings":["University of Mannheim , 68131 Mannheim ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Mannheim , 68131 Mannheim ,","institution_ids":["https://openalex.org/I112756935","https://openalex.org/I177802217"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135657439","display_name":"Pedro Cotovio","orcid":"https://orcid.org/0000-0001-6724-899X"},"institutions":[{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]},{"id":"https://openalex.org/I165862685","display_name":"St George's, University of London","ror":"https://ror.org/040f08y74","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I165862685"]},{"id":"https://openalex.org/I180825142","display_name":"City, University of London","ror":"https://ror.org/04489at23","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I180825142"]}],"countries":["GB","PT"],"is_corresponding":false,"raw_author_name":"Pedro Cotovio","raw_affiliation_strings":["Department of Computer Science , City St George\u2019s, University of London, EC1V 0HB ,","LASIGE, Faculdade de Ci\u00eancias da Universidade de Lisboa , Campo Grande, 1749-016 Lisbon ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science , City St George\u2019s, University of London, EC1V 0HB ,","institution_ids":["https://openalex.org/I165862685","https://openalex.org/I180825142"]},{"raw_affiliation_string":"LASIGE, Faculdade de Ci\u00eancias da Universidade de Lisboa , Campo Grande, 1749-016 Lisbon ,","institution_ids":["https://openalex.org/I141596103"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5034898355","display_name":"C\u00e1tia Pesquita","orcid":"https://orcid.org/0000-0002-1847-9393"},"institutions":[{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Catia Pesquita","raw_affiliation_strings":["LASIGE, Faculdade de Ci\u00eancias da Universidade de Lisboa , Campo Grande, 1749-016 Lisbon ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LASIGE, Faculdade de Ci\u00eancias da Universidade de Lisboa , Campo Grande, 1749-016 Lisbon ,","institution_ids":["https://openalex.org/I141596103"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.67837268,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"27","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9363999962806702,"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":0.9363999962806702,"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":0.0215000007301569,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.010999999940395355,"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/exploit","display_name":"Exploit","score":0.7479000091552734},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.6004999876022339},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5397999882698059},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.48159998655319214},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.4526999890804291},{"id":"https://openalex.org/keywords/deep-neural-networks","display_name":"Deep neural networks","score":0.35850000381469727}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.769599974155426},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.7479000091552734},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.6004999876022339},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5692999958992004},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5397999882698059},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.48159998655319214},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.4526999890804291},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4431000053882599},{"id":"https://openalex.org/C2984842247","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep neural networks","level":3,"score":0.35850000381469727},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3424000144004822},{"id":"https://openalex.org/C58642233","wikidata":"https://www.wikidata.org/wiki/Q8269924","display_name":"Taxonomy (biology)","level":2,"score":0.3116999864578247},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2867000102996826},{"id":"https://openalex.org/C146380142","wikidata":"https://www.wikidata.org/wiki/Q1137726","display_name":"Directed graph","level":2,"score":0.27219998836517334},{"id":"https://openalex.org/C88230418","wikidata":"https://www.wikidata.org/wiki/Q131476","display_name":"Graph theory","level":2,"score":0.2712000012397766},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.2547000050544739}],"mesh":[{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","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":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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbag313","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag313","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:42319252","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42319252","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":"Briefings in bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13280947","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13280947/","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":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbag313","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag313","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":144,"referenced_works":["https://openalex.org/W580415724","https://openalex.org/W1995932087","https://openalex.org/W2007245700","https://openalex.org/W2009672036","https://openalex.org/W2056092504","https://openalex.org/W2076048958","https://openalex.org/W2085497102","https://openalex.org/W2090891622","https://openalex.org/W2095867585","https://openalex.org/W2103017472","https://openalex.org/W2107340752","https://openalex.org/W2108984616","https://openalex.org/W2111823238","https://openalex.org/W2116341502","https://openalex.org/W2116447934","https://openalex.org/W2132582966","https://openalex.org/W2139906443","https://openalex.org/W2146545950","https://openalex.org/W2147526198","https://openalex.org/W2154851992","https://openalex.org/W2163485494","https://openalex.org/W2164353258","https://openalex.org/W2171403830","https://openalex.org/W2184957013","https://openalex.org/W2287132924","https://openalex.org/W2338910273","https://openalex.org/W2393319904","https://openalex.org/W2461928526","https://openalex.org/W2534390616","https://openalex.org/W2558748708","https://openalex.org/W2582372140","https://openalex.org/W2615066396","https://openalex.org/W2770983033","https://openalex.org/W2786016794","https://openalex.org/W2790952361","https://openalex.org/W2889626364","https://openalex.org/W2901568326","https://openalex.org/W2913256647","https://openalex.org/W2948220209","https://openalex.org/W2949564348","https://openalex.org/W2949867299","https://openalex.org/W2950374603","https://openalex.org/W2950595506","https://openalex.org/W2950742983","https://openalex.org/W2952317511","https://openalex.org/W2957436444","https://openalex.org/W2962756421","https://openalex.org/W2962969117","https://openalex.org/W2963224980","https://openalex.org/W2963610729","https://openalex.org/W2964198126","https://openalex.org/W2966164316","https://openalex.org/W2969644707","https://openalex.org/W2971405760","https://openalex.org/W2995514860","https://openalex.org/W2996970264","https://openalex.org/W2999044305","https://openalex.org/W3003315801","https://openalex.org/W3011576596","https://openalex.org/W3015964336","https://openalex.org/W3033814770","https://openalex.org/W3033896008","https://openalex.org/W3045012301","https://openalex.org/W3081019734","https://openalex.org/W3087257704","https://openalex.org/W3092613928","https://openalex.org/W3112306601","https://openalex.org/W3112600195","https://openalex.org/W3133653953","https://openalex.org/W3134013259","https://openalex.org/W3134084134","https://openalex.org/W3134169372","https://openalex.org/W3136655674","https://openalex.org/W3146944767","https://openalex.org/W3177500196","https://openalex.org/W3177828909","https://openalex.org/W3185942550","https://openalex.org/W3186179742","https://openalex.org/W3188579603","https://openalex.org/W3194156258","https://openalex.org/W3198168376","https://openalex.org/W3202711716","https://openalex.org/W3205907523","https://openalex.org/W3209369100","https://openalex.org/W3210147532","https://openalex.org/W4205102440","https://openalex.org/W4205177317","https://openalex.org/W4213131528","https://openalex.org/W4220824576","https://openalex.org/W4223581484","https://openalex.org/W4223644783","https://openalex.org/W4225687252","https://openalex.org/W4225868104","https://openalex.org/W4233120011","https://openalex.org/W4236728335","https://openalex.org/W4237335579","https://openalex.org/W4240943811","https://openalex.org/W4280617006","https://openalex.org/W4283019243","https://openalex.org/W4283586679","https://openalex.org/W4296032638","https://openalex.org/W4306317025","https://openalex.org/W4307370003","https://openalex.org/W4307717106","https://openalex.org/W4313597598","https://openalex.org/W4317703013","https://openalex.org/W4317867801","https://openalex.org/W4318756918","https://openalex.org/W4318816694","https://openalex.org/W4321769975","https://openalex.org/W4323348775","https://openalex.org/W4324143928","https://openalex.org/W4353066697","https://openalex.org/W4362663312","https://openalex.org/W4385073318","https://openalex.org/W4386161992","https://openalex.org/W4387865568","https://openalex.org/W4387966974","https://openalex.org/W4388024559","https://openalex.org/W4388144391","https://openalex.org/W4388718657","https://openalex.org/W4388979610","https://openalex.org/W4389098833","https://openalex.org/W4389614980","https://openalex.org/W4389742650","https://openalex.org/W4391133455","https://openalex.org/W4391431830","https://openalex.org/W4392500220","https://openalex.org/W4392633839","https://openalex.org/W4392858197","https://openalex.org/W4395663162","https://openalex.org/W4396762078","https://openalex.org/W4396896506","https://openalex.org/W4400576356","https://openalex.org/W4400984795","https://openalex.org/W4401617485","https://openalex.org/W4403777291","https://openalex.org/W4403972634","https://openalex.org/W4406748499","https://openalex.org/W4407242483","https://openalex.org/W4407352079","https://openalex.org/W4408524736","https://openalex.org/W4409339885","https://openalex.org/W4410233685"],"related_works":[],"abstract_inverted_index":{"Graph":[0],"neural":[1],"networks":[2],"are":[3],"a":[4,49,77,90,139,145],"natural":[5],"fit":[6],"for":[7,133,148,157],"protein-protein":[8],"interaction":[9],"(PPI)":[10],"prediction":[11,160],"because":[12],"they":[13,26],"exploit":[14],"the":[15,46,128,143],"graph":[16,61],"structure":[17],"of":[18,34,142],"interactomes,":[19],"yet":[20],"it":[21],"remains":[22],"unclear":[23],"how":[24],"much":[25],"benefit":[27],"from":[28],"protein-level":[29,64,131],"representations":[30,125,132],"and":[31,44,59,68,70,86,103,112,154],"which":[32],"sources":[33],"protein":[35],"information":[36],"matter":[37],"most.":[38],"We":[39,88],"address":[40],"this":[41],"by":[42],"surveying":[43],"organizing":[45],"field":[47],"into":[48],"coherent":[50],"taxonomy":[51],"that":[52,73,80,98,117],"describes":[53],"three":[54],"paradigms:":[55],"network-level":[56],"approaches":[57,65],"(shallow":[58],"deep":[60],"representation":[62],"learning),":[63],"(sequence,":[66],"structure,":[67],"function),":[69],"hybrid":[71,118],"methods":[72,102,119,151],"combine":[74],"both":[75],"paradigms-providing":[76],"cohesive":[78],"synthesis":[79],"highlights":[81],"their":[82],"respective":[83],"strengths,":[84],"complementarities,":[85],"tradeoffs.":[87],"developed":[89],"unified":[91],"framework":[92,147],"to":[93],"systematically":[94],"compare":[95],"these":[96],"paradigms":[97],"incorporates":[99],"multiple":[100],"representative":[101,150],"evaluates":[104],"them":[105],"on":[106],"two":[107],"widely":[108],"used":[109],"benchmarks:":[110],"OGBl-ppa":[111],"HuRI.":[113],"Our":[114],"results":[115],"indicate":[116],"have":[120],"improved":[121],"performance,":[122],"with":[123],"function-driven":[124],"emerging":[126],"as":[127],"most":[129],"informative":[130],"PPI":[134,159],"prediction.":[135],"This":[136],"work":[137],"provides":[138],"taxonomical":[140],"map":[141],"field,":[144],"reproducible":[146],"evaluating":[149],"across":[152],"paradigms,":[153],"practical":[155],"guidance":[156],"future":[158],"efforts.":[161]},"counts_by_year":[],"updated_date":"2026-07-27T08:26:11.824852","created_date":"2026-06-20T00:00:00"}