{"id":"https://openalex.org/W2772596531","doi":"https://doi.org/10.1515/jib-2017-0055","title":"Protein-Protein Interaction Article Classification Using a Convolutional Recurrent Neural Network with Pre-trained Word Embeddings","display_name":"Protein-Protein Interaction Article Classification Using a Convolutional Recurrent Neural Network with Pre-trained Word Embeddings","publication_year":2017,"publication_date":"2017-12-13","ids":{"openalex":"https://openalex.org/W2772596531","doi":"https://doi.org/10.1515/jib-2017-0055","mag":"2772596531","pmid":"https://pubmed.ncbi.nlm.nih.gov/29236678"},"language":"en","primary_location":{"id":"doi:10.1515/jib-2017-0055","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2017-0055","pdf_url":"http://www.degruyter.com/downloadpdf/j/jib.2017.14.issue-4/jib-2017-0055/jib-2017-0055.xml","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"http://www.degruyter.com/downloadpdf/j/jib.2017.14.issue-4/jib-2017-0055/jib-2017-0055.xml","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5073280030","display_name":"S\u00e9rgio Matos","orcid":"https://orcid.org/0000-0003-1941-3983"},"institutions":[{"id":"https://openalex.org/I60858718","display_name":"University of Aveiro","ror":"https://ror.org/00nt41z93","country_code":"PT","type":"education","lineage":["https://openalex.org/I60858718"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"S\u00e9rgio Matos","raw_affiliation_strings":["DETI/IEETA, University of Aveiro, 3810-193Aveiro, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"DETI/IEETA, University of Aveiro, 3810-193Aveiro, Portugal","institution_ids":["https://openalex.org/I60858718"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5053662030","display_name":"Rui Antunes","orcid":"https://orcid.org/0000-0003-3533-8872"},"institutions":[{"id":"https://openalex.org/I60858718","display_name":"University of Aveiro","ror":"https://ror.org/00nt41z93","country_code":"PT","type":"education","lineage":["https://openalex.org/I60858718"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Rui Antunes","raw_affiliation_strings":["DETI/IEETA, University of Aveiro, 3810-193Aveiro, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"DETI/IEETA, University of Aveiro, 3810-193Aveiro, Portugal","institution_ids":["https://openalex.org/I60858718"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5073280030"],"corresponding_institution_ids":["https://openalex.org/I60858718"],"apc_list":null,"apc_paid":null,"fwci":0.2027,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.53711642,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"14","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9991000294685364,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9991000294685364,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9865000247955322,"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"}},{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.9671000242233276,"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":0.8079717755317688},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.6912606954574585},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.6840587854385376},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6266783475875854},{"id":"https://openalex.org/keywords/word","display_name":"Word (group theory)","score":0.5827000141143799},{"id":"https://openalex.org/keywords/recall","display_name":"Recall","score":0.5666124820709229},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.49103569984436035},{"id":"https://openalex.org/keywords/recurrent-neural-network","display_name":"Recurrent neural network","score":0.4771439731121063},{"id":"https://openalex.org/keywords/f1-score","display_name":"F1 score","score":0.44894832372665405},{"id":"https://openalex.org/keywords/precision-and-recall","display_name":"Precision and recall","score":0.44797414541244507},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.41853398084640503},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.40840673446655273},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.06278917193412781}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8079717755317688},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.6912606954574585},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.6840587854385376},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6266783475875854},{"id":"https://openalex.org/C90805587","wikidata":"https://www.wikidata.org/wiki/Q10944557","display_name":"Word (group theory)","level":2,"score":0.5827000141143799},{"id":"https://openalex.org/C100660578","wikidata":"https://www.wikidata.org/wiki/Q18733","display_name":"Recall","level":2,"score":0.5666124820709229},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.49103569984436035},{"id":"https://openalex.org/C147168706","wikidata":"https://www.wikidata.org/wiki/Q1457734","display_name":"Recurrent neural network","level":3,"score":0.4771439731121063},{"id":"https://openalex.org/C148524875","wikidata":"https://www.wikidata.org/wiki/Q6975395","display_name":"F1 score","level":2,"score":0.44894832372665405},{"id":"https://openalex.org/C81669768","wikidata":"https://www.wikidata.org/wiki/Q2359161","display_name":"Precision and recall","level":2,"score":0.44797414541244507},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.41853398084640503},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.40840673446655273},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.06278917193412781},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0}],"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":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1515/jib-2017-0055","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2017-0055","pdf_url":"http://www.degruyter.com/downloadpdf/j/jib.2017.14.issue-4/jib-2017-0055/jib-2017-0055.xml","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29236678","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29236678","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":"Journal of integrative bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:5327946","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6042813","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:6cbb0439831d48589a9073ab6cccd3d1","is_oa":false,"landing_page_url":"https://doaj.org/article/6cbb0439831d48589a9073ab6cccd3d1","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Integrative Bioinformatics, Vol 14, Iss 4, Pp 1-72 (2017)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1515/jib-2017-0055","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2017-0055","pdf_url":"http://www.degruyter.com/downloadpdf/j/jib.2017.14.issue-4/jib-2017-0055/jib-2017-0055.xml","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.41999998688697815,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320334779","display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","ror":"https://ror.org/00snfqn58"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2772596531.pdf","grobid_xml":"https://content.openalex.org/works/W2772596531.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W1525672751","https://openalex.org/W1825157170","https://openalex.org/W1832693441","https://openalex.org/W1996002274","https://openalex.org/W2001668098","https://openalex.org/W2082782306","https://openalex.org/W2101234009","https://openalex.org/W2104768328","https://openalex.org/W2108108770","https://openalex.org/W2112543617","https://openalex.org/W2114669670","https://openalex.org/W2116261113","https://openalex.org/W2121029939","https://openalex.org/W2125413176","https://openalex.org/W2127603354","https://openalex.org/W2140679639","https://openalex.org/W2168066604","https://openalex.org/W2170738476","https://openalex.org/W2252215182","https://openalex.org/W2516150684","https://openalex.org/W2734608416","https://openalex.org/W2919115771","https://openalex.org/W2949541494","https://openalex.org/W2950133940","https://openalex.org/W2963587816","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2358294942","https://openalex.org/W4367460280","https://openalex.org/W4328049145","https://openalex.org/W4206165639","https://openalex.org/W2050712820","https://openalex.org/W4387490204","https://openalex.org/W3212239346","https://openalex.org/W4386414453","https://openalex.org/W4388937883","https://openalex.org/W4385625287"],"abstract_inverted_index":{"Curation":[0],"of":[1,19,36,88,95],"protein":[2,70],"interactions":[3],"from":[4],"scientific":[5],"articles":[6,65],"is":[7],"an":[8,82,99],"important":[9],"task,":[10],"since":[11],"interaction":[12],"networks":[13],"are":[14],"essential":[15],"for":[16,28,62,66],"the":[17,31,34,73,85],"understanding":[18],"biological":[20],"processes":[21],"associated":[22],"with":[23],"disease":[24],"or":[25],"pharmacological":[26],"action":[27],"example.":[29],"However,":[30],"increase":[32],"in":[33],"number":[35],"publications":[37],"that":[38],"potentially":[39],"contain":[40],"relevant":[41,64],"information":[42,68],"turns":[43],"this":[44,53],"into":[45],"a":[46,57,91],"very":[47],"challenging":[48],"and":[49,90],"expensive":[50],"task.":[51],"In":[52],"work":[54],"we":[55,80],"used":[56],"convolutional":[58],"recurrent":[59],"neural":[60],"network":[61],"identifying":[63],"extracting":[67],"regarding":[69],"interactions.":[71],"Using":[72],"BioCreative":[74],"III":[75],"Article":[76],"Classification":[77],"Task":[78],"dataset,":[79],"achieved":[81],"area":[83],"under":[84],"precision-recall":[86],"curve":[87],"0.715":[89],"Matthew's":[92],"correlation":[93],"coefficient":[94],"0.600,":[96],"which":[97],"represents":[98],"improvement":[100],"over":[101],"previous":[102],"works.":[103]},"counts_by_year":[{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2017-12-22T00:00:00"}
