{"id":"https://openalex.org/W4385373640","doi":"https://doi.org/10.48550/arxiv.2307.14367","title":"Prot2Text: Multimodal Protein's Function Generation with GNNs and Transformers","display_name":"Prot2Text: Multimodal Protein's Function Generation with GNNs and Transformers","publication_year":2023,"publication_date":"2023-07-25","ids":{"openalex":"https://openalex.org/W4385373640","doi":"https://doi.org/10.48550/arxiv.2307.14367"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2307.14367","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2307.14367","pdf_url":"https://arxiv.org/pdf/2307.14367","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-sa","license_id":"https://openalex.org/licenses/cc-by-nc-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2307.14367","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5012412123","display_name":"Hadi Abdine","orcid":"https://orcid.org/0009-0001-3944-4747"},"institutions":[{"id":"https://openalex.org/I142476485","display_name":"\u00c9cole Polytechnique","ror":"https://ror.org/05hy3tk52","country_code":"FR","type":"education","lineage":["https://openalex.org/I142476485","https://openalex.org/I4210145102"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Abdine, Hadi","raw_affiliation_strings":["DaSciM, LIX, \u00c9cole Polytechnique, Institut Polytechnique de Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"DaSciM, LIX, \u00c9cole Polytechnique, Institut Polytechnique de Paris, France","institution_ids":["https://openalex.org/I142476485"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072113617","display_name":"Michail Chatzianastasis","orcid":"https://orcid.org/0000-0002-9905-1646"},"institutions":[{"id":"https://openalex.org/I142476485","display_name":"\u00c9cole Polytechnique","ror":"https://ror.org/05hy3tk52","country_code":"FR","type":"education","lineage":["https://openalex.org/I142476485","https://openalex.org/I4210145102"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Chatzianastasis, Michail","raw_affiliation_strings":["DaSciM, LIX, \u00c9cole Polytechnique, Institut Polytechnique de Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"DaSciM, LIX, \u00c9cole Polytechnique, Institut Polytechnique de Paris, France","institution_ids":["https://openalex.org/I142476485"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023347965","display_name":"Costas Bouyioukos","orcid":"https://orcid.org/0000-0002-7443-3736"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]},{"id":"https://openalex.org/I34771391","display_name":"University of Cyprus","ror":"https://ror.org/02qjrjx09","country_code":"CY","type":"education","lineage":["https://openalex.org/I34771391"]},{"id":"https://openalex.org/I4210131858","display_name":"Epig\u00e9n\u00e9tique et Destin Cellulaire","ror":"https://ror.org/03dbsav41","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I204730241","https://openalex.org/I4210096427","https://openalex.org/I4210131858"]}],"countries":["CY","FR"],"is_corresponding":false,"raw_author_name":"Bouyioukos, Costas","raw_affiliation_strings":["Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, CY 1678, Cyprus","Epigenetics and Cell Fate, CNRS UMR7216, Universit\u00e9 Paris Cit\u00e9, F-75013 Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, CY 1678, Cyprus","institution_ids":["https://openalex.org/I34771391"]},{"raw_affiliation_string":"Epigenetics and Cell Fate, CNRS UMR7216, Universit\u00e9 Paris Cit\u00e9, F-75013 Paris, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I204730241","https://openalex.org/I4210131858"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085652160","display_name":"Michalis Vazirgiannis","orcid":null},"institutions":[{"id":"https://openalex.org/I142476485","display_name":"\u00c9cole Polytechnique","ror":"https://ror.org/05hy3tk52","country_code":"FR","type":"education","lineage":["https://openalex.org/I142476485","https://openalex.org/I4210145102"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Vazirgiannis, Michalis","raw_affiliation_strings":["DaSciM, LIX, \u00c9cole Polytechnique, Institut Polytechnique de Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"DaSciM, LIX, \u00c9cole Polytechnique, Institut Polytechnique de Paris, France","institution_ids":["https://openalex.org/I142476485"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9977999925613403,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9977999925613403,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9976000189781189,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.996999979019165,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials 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":0.7157166600227356},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.556987464427948},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5401315689086914},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.46306127309799194},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4284573495388031},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.41152423620224},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.4104287922382355},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.1588393747806549},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.07253777980804443}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7157166600227356},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.556987464427948},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5401315689086914},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.46306127309799194},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4284573495388031},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.41152423620224},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.4104287922382355},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.1588393747806549},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.07253777980804443},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.0},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2307.14367","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2307.14367","pdf_url":"https://arxiv.org/pdf/2307.14367","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-sa","license_id":"https://openalex.org/licenses/cc-by-nc-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"doi:10.48550/arxiv.2307.14367","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2307.14367","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2307.14367","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2307.14367","pdf_url":"https://arxiv.org/pdf/2307.14367","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-sa","license_id":"https://openalex.org/licenses/cc-by-nc-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[{"score":0.49000000953674316,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4385373640.pdf","grobid_xml":"https://content.openalex.org/works/W4385373640.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W1982597966","https://openalex.org/W2116341502","https://openalex.org/W2154652894","https://openalex.org/W2156125289","https://openalex.org/W2584305206","https://openalex.org/W2604314403","https://openalex.org/W2739999456","https://openalex.org/W2896457183","https://openalex.org/W2908510526","https://openalex.org/W2911489562","https://openalex.org/W2936695845","https://openalex.org/W2943203634","https://openalex.org/W2943495267","https://openalex.org/W2947926079","https://openalex.org/W2950277699","https://openalex.org/W2960216239","https://openalex.org/W2964015378","https://openalex.org/W2965857891","https://openalex.org/W3034999214","https://openalex.org/W3092867907","https://openalex.org/W3093934881","https://openalex.org/W3094502228","https://openalex.org/W3109892317","https://openalex.org/W3113698408","https://openalex.org/W3164046276","https://openalex.org/W3188579603","https://openalex.org/W3211795435","https://openalex.org/W4205773061","https://openalex.org/W4233120011","https://openalex.org/W4236358448","https://openalex.org/W4281478251","https://openalex.org/W4288089799","https://openalex.org/W4288090629","https://openalex.org/W4288099645","https://openalex.org/W4288419255","https://openalex.org/W4292779060","https://openalex.org/W4310273071","https://openalex.org/W4315928370","https://openalex.org/W4318751307","https://openalex.org/W4320342754","https://openalex.org/W4327550249","https://openalex.org/W4382239070","https://openalex.org/W4385245566","https://openalex.org/W4385572894","https://openalex.org/W4387805937"],"related_works":["https://openalex.org/W2062195135","https://openalex.org/W2795079307","https://openalex.org/W2961085424","https://openalex.org/W2793058541","https://openalex.org/W1983629434","https://openalex.org/W2055929693","https://openalex.org/W4224009465","https://openalex.org/W4324271173","https://openalex.org/W1967645776","https://openalex.org/W2352227742"],"abstract_inverted_index":{"In":[0,39],"recent":[1],"years,":[2],"significant":[3],"progress":[4],"has":[5],"been":[6],"made":[7],"in":[8,53,75],"the":[9,16,27,60,107,130,137,144],"field":[10],"of":[11,18,103,109,132,140,146,160],"protein":[12,87,123],"function":[13,52,158],"prediction":[14,159],"with":[15,152],"development":[17],"various":[19],"machine-learning":[20],"approaches.":[21],"However,":[22],"most":[23],"existing":[24,161],"methods":[25],"formulate":[26],"task":[28],"as":[29,162,164],"a":[30,44,50,54,100,121],"multi-classification":[31],"problem,":[32],"i.e.":[33],"assigning":[34],"predefined":[35],"labels":[36],"to":[37],"proteins.":[38,166],"this":[40],"work,":[41],"we":[42,119],"propose":[43],"novel":[45],"approach,":[46],"Prot2Text,":[47],"which":[48],"predicts":[49],"protein's":[51],"free":[55],"text":[56],"style,":[57],"moving":[58],"beyond":[59],"conventional":[61],"binary":[62],"or":[63],"categorical":[64],"classifications.":[65],"By":[66],"combining":[67],"Graph":[68],"Neural":[69],"Networks(GNNs)":[70],"and":[71,90,93,111,127,148],"Large":[72],"Language":[73],"Models(LLMs),":[74],"an":[76],"encoder-decoder":[77],"framework,":[78],"our":[79,117],"model":[80],"effectively":[81],"integrates":[82],"diverse":[83],"data":[84],"types":[85],"including":[86],"sequence,":[88],"structure,":[89],"textual":[91],"annotation":[92],"description.":[94],"This":[95],"multimodal":[96,122,141],"approach":[97],"allows":[98],"for":[99,155],"holistic":[101],"representation":[102],"proteins'":[104],"functions,":[105],"enabling":[106],"generation":[108],"detailed":[110],"accurate":[112,157],"functional":[113],"descriptions.":[114],"To":[115],"evaluate":[116],"model,":[118],"extracted":[120],"dataset":[124],"from":[125],"SwissProt,":[126],"demonstrate":[128],"empirically":[129],"effectiveness":[131],"Prot2Text.":[133],"These":[134],"results":[135],"highlight":[136],"transformative":[138],"impact":[139],"models,":[142],"specifically":[143],"fusion":[145],"GNNs":[147],"LLMs,":[149],"empowering":[150],"researchers":[151],"powerful":[153],"tools":[154],"more":[156],"well":[163],"first-to-see":[165]},"counts_by_year":[{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":1}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2024-03-26T00:00:00"}
