{"id":"https://openalex.org/W2886936867","doi":"https://doi.org/10.1109/icosc.2019.8665584","title":"Identifying Protein-Protein Interaction Using Tree LSTM and Structured Attention","display_name":"Identifying Protein-Protein Interaction Using Tree LSTM and Structured Attention","publication_year":2019,"publication_date":"2019-01-01","ids":{"openalex":"https://openalex.org/W2886936867","doi":"https://doi.org/10.1109/icosc.2019.8665584","mag":"2886936867"},"language":"en","primary_location":{"id":"doi:10.1109/icosc.2019.8665584","is_oa":false,"landing_page_url":"https://doi.org/10.1109/icosc.2019.8665584","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE 13th International Conference on Semantic Computing (ICSC)","raw_type":"proceedings-article"},"type":"preprint","indexed_in":["arxiv","crossref","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/1808.03227","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5018961302","display_name":"Mahtab Ahmed","orcid":"https://orcid.org/0000-0002-0915-6904"},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Mahtab Ahmed","raw_affiliation_strings":["Department of Computer Science, University of Western Ontario, London, Ontario, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Western Ontario, London, Ontario, Canada","institution_ids":["https://openalex.org/I125749732"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023276757","display_name":"Jumayel Islam","orcid":null},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Jumayel Islam","raw_affiliation_strings":["Department of Computer Science, University of Western Ontario, London, Ontario, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Western Ontario, London, Ontario, Canada","institution_ids":["https://openalex.org/I125749732"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031103421","display_name":"Muhammad Rifayat Samee","orcid":null},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Muhammad Rifayat Samee","raw_affiliation_strings":["Department of Computer Science, University of Western Ontario, London, Ontario, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Western Ontario, London, Ontario, Canada","institution_ids":["https://openalex.org/I125749732"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056001196","display_name":"Robert E. Mercer","orcid":"https://orcid.org/0000-0002-0080-715X"},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Robert E. Mercer","raw_affiliation_strings":["Department of Computer Science, University of Western Ontario, London, Ontario, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Western Ontario, London, Ontario, Canada","institution_ids":["https://openalex.org/I125749732"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5018961302"],"corresponding_institution_ids":["https://openalex.org/I125749732"],"apc_list":null,"apc_paid":null,"fwci":0.2569,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.54838495,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"224","last_page":"231"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9976999759674072,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9961000084877014,"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/benchmark","display_name":"Benchmark (surveying)","score":0.7837257385253906},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7466903924942017},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.6600743532180786},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6391800045967102},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.6185646653175354},{"id":"https://openalex.org/keywords/recurrent-neural-network","display_name":"Recurrent neural network","score":0.6055870056152344},{"id":"https://openalex.org/keywords/recall","display_name":"Recall","score":0.5084115862846375},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.4705299139022827},{"id":"https://openalex.org/keywords/precision-and-recall","display_name":"Precision and recall","score":0.4410487115383148},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.43433475494384766},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.39115267992019653},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.37465283274650574},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3396235406398773},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.07753944396972656}],"concepts":[{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.7837257385253906},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7466903924942017},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.6600743532180786},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6391800045967102},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.6185646653175354},{"id":"https://openalex.org/C147168706","wikidata":"https://www.wikidata.org/wiki/Q1457734","display_name":"Recurrent neural network","level":3,"score":0.6055870056152344},{"id":"https://openalex.org/C100660578","wikidata":"https://www.wikidata.org/wiki/Q18733","display_name":"Recall","level":2,"score":0.5084115862846375},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.4705299139022827},{"id":"https://openalex.org/C81669768","wikidata":"https://www.wikidata.org/wiki/Q2359161","display_name":"Precision and recall","level":2,"score":0.4410487115383148},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.43433475494384766},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.39115267992019653},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.37465283274650574},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3396235406398773},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.07753944396972656},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","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/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1109/icosc.2019.8665584","is_oa":false,"landing_page_url":"https://doi.org/10.1109/icosc.2019.8665584","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE 13th International Conference on Semantic Computing (ICSC)","raw_type":"proceedings-article"},{"id":"pmh:oai:arXiv.org:1808.03227","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1808.03227","pdf_url":"https://arxiv.org/pdf/1808.03227","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"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":"mag:2886936867","is_oa":true,"landing_page_url":"https://arxiv.org/pdf/1808.03227.pdf","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"arXiv (Cornell University)","raw_type":null},{"id":"doi:10.48550/arxiv.1808.03227","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.1808.03227","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"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"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:1808.03227","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1808.03227","pdf_url":"https://arxiv.org/pdf/1808.03227","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"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":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2886936867.pdf","grobid_xml":"https://content.openalex.org/works/W2886936867.grobid-xml"},"referenced_works_count":49,"referenced_works":["https://openalex.org/W992532482","https://openalex.org/W1574662932","https://openalex.org/W1850865022","https://openalex.org/W1972340877","https://openalex.org/W1986704581","https://openalex.org/W1990794790","https://openalex.org/W1996787131","https://openalex.org/W2003756933","https://openalex.org/W2048059249","https://openalex.org/W2064030835","https://openalex.org/W2079735306","https://openalex.org/W2096951189","https://openalex.org/W2097960255","https://openalex.org/W2121844933","https://openalex.org/W2122904379","https://openalex.org/W2134036914","https://openalex.org/W2135186741","https://openalex.org/W2148004186","https://openalex.org/W2166111585","https://openalex.org/W2166474856","https://openalex.org/W2250861254","https://openalex.org/W2251713149","https://openalex.org/W2264517602","https://openalex.org/W2342313026","https://openalex.org/W2370746078","https://openalex.org/W2414378847","https://openalex.org/W2512456704","https://openalex.org/W2527712604","https://openalex.org/W2549835527","https://openalex.org/W2559034752","https://openalex.org/W2560748602","https://openalex.org/W2586559132","https://openalex.org/W2623425365","https://openalex.org/W2773368817","https://openalex.org/W2795129839","https://openalex.org/W2949674892","https://openalex.org/W2949952998","https://openalex.org/W2951381434","https://openalex.org/W2963355447","https://openalex.org/W2964308564","https://openalex.org/W2964348125","https://openalex.org/W4297809627","https://openalex.org/W6634388643","https://openalex.org/W6675354045","https://openalex.org/W6682691769","https://openalex.org/W6685182218","https://openalex.org/W6691723933","https://openalex.org/W6746720330","https://openalex.org/W6748327556"],"related_works":["https://openalex.org/W2945221272","https://openalex.org/W2096693449","https://openalex.org/W3020030373","https://openalex.org/W3024981952","https://openalex.org/W2608694595","https://openalex.org/W3170752662","https://openalex.org/W3154537295","https://openalex.org/W3209279086","https://openalex.org/W3211193901","https://openalex.org/W2966117709","https://openalex.org/W2952997929","https://openalex.org/W3094508997","https://openalex.org/W2725541287","https://openalex.org/W3103900065","https://openalex.org/W2761525601","https://openalex.org/W2893292317","https://openalex.org/W3173178406","https://openalex.org/W3200181563","https://openalex.org/W3103358463","https://openalex.org/W3167717463"],"abstract_inverted_index":{"Identifying":[0],"interactions":[1],"between":[2],"proteins":[3],"is":[4,20],"important":[5],"to":[6,102],"understand":[7],"underlying":[8],"biological":[9],"processes.":[10],"Extracting":[11],"a":[12,41,78],"protein-protein":[13],"interaction":[14],"(PPI)":[15],"from":[16],"the":[17,59,67,107],"raw":[18],"text":[19],"often":[21],"very":[22],"difficult.":[23],"Previous":[24],"supervised":[25,108],"learning":[26],"methods":[27],"have":[28,98],"used":[29],"handcrafted":[30],"features":[31],"on":[32,66],"human-annotated":[33],"data":[34,72],"sets.":[35,73],"In":[36],"this":[37],"paper,":[38],"we":[39],"propose":[40],"novel":[42],"tree":[43,103],"recurrent":[44,96,104],"neural":[45],"network":[46],"with":[47],"structured":[48],"attention":[49],"architecture":[50,55],"for":[51,106],"doing":[52],"PPI.":[53],"Our":[54,90],"achieves":[56],"state":[57],"of":[58],"art":[60],"results":[61,92],"(precision,":[62],"recall,":[63],"and":[64,69],"F1-score)":[65],"AIMed":[68],"BioInfer":[70],"benchmark":[71],"Moreover,":[74],"our":[75],"models":[76,84],"achieve":[77],"significant":[79],"improvement":[80],"over":[81],"previous":[82],"best":[83],"without":[85],"any":[86],"explicit":[87],"feature":[88],"extraction.":[89],"experimental":[91],"show":[93],"that":[94],"traditional":[95],"networks":[97,105],"inferior":[99],"performance":[100],"compared":[101],"PPI":[109],"problem.":[110]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2019,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
