{"id":"https://openalex.org/W2511500211","doi":"https://doi.org/10.18653/v1/w16-3009","title":"Deep Learning with Minimal Training Data: TurkuNLP Entry in the BioNLP Shared Task 2016","display_name":"Deep Learning with Minimal Training Data: TurkuNLP Entry in the BioNLP Shared Task 2016","publication_year":2016,"publication_date":"2016-01-01","ids":{"openalex":"https://openalex.org/W2511500211","doi":"https://doi.org/10.18653/v1/w16-3009","mag":"2511500211"},"language":"en","primary_location":{"id":"doi:10.18653/v1/w16-3009","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/w16-3009","pdf_url":"https://www.aclweb.org/anthology/W16-3009.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 4th BioNLP Shared Task Workshop","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.aclweb.org/anthology/W16-3009.pdf","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086256360","display_name":"Farrokh Mehryary","orcid":"https://orcid.org/0000-0002-5555-2828"},"institutions":[{"id":"https://openalex.org/I1323252656","display_name":"Information Technology University","ror":"https://ror.org/00ngv8j44","country_code":"PK","type":"education","lineage":["https://openalex.org/I1323252656"]},{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]}],"countries":["FI","PK"],"is_corresponding":false,"raw_author_name":"Farrokh Mehryary","raw_affiliation_strings":["Department of Information Technology, University of Turku","Faculty of Mathematics and Natural Sciences, FI-20014, Turku, Finland","University of Turku Graduate School (UTUGS)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information Technology, University of Turku","institution_ids":["https://openalex.org/I1323252656","https://openalex.org/I155660961"]},{"raw_affiliation_string":"Faculty of Mathematics and Natural Sciences, FI-20014, Turku, Finland","institution_ids":["https://openalex.org/I155660961"]},{"raw_affiliation_string":"University of Turku Graduate School (UTUGS)","institution_ids":["https://openalex.org/I155660961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049143500","display_name":"Jari Bj\u00f6rne","orcid":"https://orcid.org/0000-0003-1722-6404"},"institutions":[{"id":"https://openalex.org/I1323252656","display_name":"Information Technology University","ror":"https://ror.org/00ngv8j44","country_code":"PK","type":"education","lineage":["https://openalex.org/I1323252656"]},{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]},{"id":"https://openalex.org/I183173800","display_name":"Turku Centre for Computer Science","ror":"https://ror.org/00vy7ed73","country_code":"FI","type":"facility","lineage":["https://openalex.org/I130217899","https://openalex.org/I155660961","https://openalex.org/I183173800"]}],"countries":["FI","PK"],"is_corresponding":false,"raw_author_name":"Jari Bj\u00f6rne","raw_affiliation_strings":["Department of Information Technology, University of Turku","Faculty of Mathematics and Natural Sciences, FI-20014, Turku, Finland","Turku Centre for Computer Science (TUCS)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information Technology, University of Turku","institution_ids":["https://openalex.org/I1323252656","https://openalex.org/I155660961"]},{"raw_affiliation_string":"Faculty of Mathematics and Natural Sciences, FI-20014, Turku, Finland","institution_ids":["https://openalex.org/I155660961"]},{"raw_affiliation_string":"Turku Centre for Computer Science (TUCS)","institution_ids":["https://openalex.org/I183173800"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066925770","display_name":"Sampo Pyysalo","orcid":"https://orcid.org/0000-0002-6279-5000"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I4210107233","display_name":"Language Science (South Korea)","ror":"https://ror.org/01h9v1373","country_code":"KR","type":"company","lineage":["https://openalex.org/I4210107233"]}],"countries":["GB","KR"],"is_corresponding":false,"raw_author_name":"Sampo Pyysalo","raw_affiliation_strings":["Language Technology Lab, DTAL, University of Cambridge"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Language Technology Lab, DTAL, University of Cambridge","institution_ids":["https://openalex.org/I4210107233","https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5105839982","display_name":"Tapio Salakoski","orcid":null},"institutions":[{"id":"https://openalex.org/I1323252656","display_name":"Information Technology University","ror":"https://ror.org/00ngv8j44","country_code":"PK","type":"education","lineage":["https://openalex.org/I1323252656"]},{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]},{"id":"https://openalex.org/I183173800","display_name":"Turku Centre for Computer Science","ror":"https://ror.org/00vy7ed73","country_code":"FI","type":"facility","lineage":["https://openalex.org/I130217899","https://openalex.org/I155660961","https://openalex.org/I183173800"]}],"countries":["FI","PK"],"is_corresponding":false,"raw_author_name":"Tapio Salakoski","raw_affiliation_strings":["Turku Centre for Computer Science (TUCS)","Faculty of Mathematics and Natural Sciences, FI-20014, Turku, Finland","Department of Information Technology, University of Turku"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Turku Centre for Computer Science (TUCS)","institution_ids":["https://openalex.org/I183173800"]},{"raw_affiliation_string":"Faculty of Mathematics and Natural Sciences, FI-20014, Turku, Finland","institution_ids":["https://openalex.org/I155660961"]},{"raw_affiliation_string":"Department of Information Technology, University of Turku","institution_ids":["https://openalex.org/I1323252656","https://openalex.org/I155660961"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5019929457","display_name":"Filip Ginter","orcid":"https://orcid.org/0000-0002-5484-6103"},"institutions":[{"id":"https://openalex.org/I1323252656","display_name":"Information Technology University","ror":"https://ror.org/00ngv8j44","country_code":"PK","type":"education","lineage":["https://openalex.org/I1323252656"]},{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]},{"id":"https://openalex.org/I183173800","display_name":"Turku Centre for Computer Science","ror":"https://ror.org/00vy7ed73","country_code":"FI","type":"facility","lineage":["https://openalex.org/I130217899","https://openalex.org/I155660961","https://openalex.org/I183173800"]}],"countries":["FI","PK"],"is_corresponding":false,"raw_author_name":"Filip Ginter","raw_affiliation_strings":["Faculty of Mathematics and Natural Sciences, FI-20014, Turku, Finland","Turku Centre for Computer Science (TUCS)","Department of Information Technology, University of Turku"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Mathematics and Natural Sciences, FI-20014, Turku, Finland","institution_ids":["https://openalex.org/I155660961"]},{"raw_affiliation_string":"Turku Centre for Computer Science (TUCS)","institution_ids":["https://openalex.org/I183173800"]},{"raw_affiliation_string":"Department of Information Technology, University of Turku","institution_ids":["https://openalex.org/I1323252656","https://openalex.org/I155660961"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":48,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9994999766349792,"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":0.9994999766349792,"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/T10028","display_name":"Topic Modeling","score":0.9902999997138977,"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/T10215","display_name":"Semantic Web and Ontologies","score":0.9829999804496765,"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":0.788088321685791},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.7534976005554199},{"id":"https://openalex.org/keywords/training","display_name":"Training (meteorology)","score":0.562192440032959},{"id":"https://openalex.org/keywords/training-set","display_name":"Training set","score":0.5325056314468384},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4767131209373474},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3426920771598816},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.069175124168396}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.788088321685791},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.7534976005554199},{"id":"https://openalex.org/C2777211547","wikidata":"https://www.wikidata.org/wiki/Q17141490","display_name":"Training (meteorology)","level":2,"score":0.562192440032959},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.5325056314468384},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4767131209373474},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3426920771598816},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.069175124168396},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C153294291","wikidata":"https://www.wikidata.org/wiki/Q25261","display_name":"Meteorology","level":1,"score":0.0},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.18653/v1/w16-3009","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/w16-3009","pdf_url":"https://www.aclweb.org/anthology/W16-3009.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 4th BioNLP Shared Task Workshop","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.18653/v1/w16-3009","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/w16-3009","pdf_url":"https://www.aclweb.org/anthology/W16-3009.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 4th BioNLP Shared Task Workshop","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4293880762","display_name":null,"funder_award_id":"MR/M013049","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G4498546091","display_name":"Literature-based discovery for cancer biology","funder_award_id":"MR/M013049/1","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"}],"funders":[{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"},{"id":"https://openalex.org/F4320323313","display_name":"Turun Yliopisto","ror":"https://ror.org/05vghhr25"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2511500211.pdf","grobid_xml":"https://content.openalex.org/works/W2511500211.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W50348749","https://openalex.org/W122290181","https://openalex.org/W1508977358","https://openalex.org/W1522301498","https://openalex.org/W1606347560","https://openalex.org/W2032566933","https://openalex.org/W2042972234","https://openalex.org/W2051718393","https://openalex.org/W2064675550","https://openalex.org/W2094061585","https://openalex.org/W2095705004","https://openalex.org/W2107530479","https://openalex.org/W2107878631","https://openalex.org/W2108791029","https://openalex.org/W2121844933","https://openalex.org/W2127080518","https://openalex.org/W2138627627","https://openalex.org/W2153579005","https://openalex.org/W2163362093","https://openalex.org/W2166111585","https://openalex.org/W2171283231","https://openalex.org/W2250232417","https://openalex.org/W2251279337","https://openalex.org/W2738031524","https://openalex.org/W2916355958","https://openalex.org/W2964121744","https://openalex.org/W2964217331","https://openalex.org/W4294170691"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W3046775127","https://openalex.org/W3107602296","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W4364306694","https://openalex.org/W4312192474","https://openalex.org/W4283697347","https://openalex.org/W4210805261"],"abstract_inverted_index":{"We":[0,17,62],"present":[1],"the":[2,6,42,50,54,59,107,110],"TurkuNLP":[3],"entry":[4],"to":[5,23,72,109],"BioNLP":[7],"Shared":[8],"Task":[9],"2016":[10],"Bacteria":[11],"Biotopes":[12],"event":[13,24],"extraction":[14,25],"(BB3-event)":[15],"subtask.":[16],"propose":[18],"a":[19,27,80],"deep":[20],"learningbased":[21],"approach":[22],"using":[26],"combination":[28],"of":[29,84,116],"several":[30],"Long":[31],"Short-Term":[32],"Memory":[33],"(LSTM)":[34],"networks":[35],"over":[36],"syntactic":[37],"dependency":[38,60,93],"graphs.":[39],"Features":[40],"for":[41],"proposed":[43],"neural":[44],"network":[45,67],"are":[46,87],"generated":[47],"based":[48],"on":[49],"shortest":[51],"path":[52],"connecting":[53],"two":[55],"candidate":[56],"entities":[57],"in":[58],"graph.":[61],"further":[63],"detail":[64],"how":[65],"this":[66],"can":[68],"be":[69,98],"efficiently":[70],"trained":[71],"have":[73],"good":[74],"generalization":[75],"performance":[76],"even":[77],"when":[78],"only":[79],"very":[81],"limited":[82],"number":[83],"training":[85],"examples":[86],"available":[88],"and":[89,92,121],"part-of-speech":[90],"(POS)":[91],"type":[94],"feature":[95],"representations":[96],"must":[97],"learned":[99],"from":[100],"scratch.":[101],"Our":[102],"method":[103],"ranked":[104],"second":[105],"among":[106],"entries":[108],"shared":[111],"task,":[112],"achieving":[113],"an":[114],"F-score":[115],"52.1%":[117],"with":[118],"62.3%":[119],"precision":[120],"44.8%":[122],"recall.":[123]},"counts_by_year":[{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":19},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":9},{"year":2016,"cited_by_count":1}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
