{"id":"https://openalex.org/W1988647655","doi":"https://doi.org/10.1186/1471-2105-11-s5-p8","title":"A fast and effective dependency graph kernel for PPI relation extraction","display_name":"A fast and effective dependency graph kernel for PPI relation extraction","publication_year":2010,"publication_date":"2010-10-01","ids":{"openalex":"https://openalex.org/W1988647655","doi":"https://doi.org/10.1186/1471-2105-11-s5-p8","mag":"1988647655"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-11-s5-p8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-s5-p8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-S5-P8","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-S5-P8","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5070226189","display_name":"Domonkos Tikk","orcid":null},"institutions":[{"id":"https://openalex.org/I29770179","display_name":"Budapest University of Technology and Economics","ror":"https://ror.org/02w42ss30","country_code":"HU","type":"education","lineage":["https://openalex.org/I29770179"]},{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]}],"countries":["DE","HU"],"is_corresponding":true,"raw_author_name":"Domonkos Tikk","raw_affiliation_strings":["Department of Telecommunications and Media Informatics, Budapest University of Technology and Economics, H-1117, Budapest, Magyar Tud\u00f3sok krt 2, Hungary","Knowledge Management in Bioinformatics, Institute for Computer Science, Humboldt-Universit\u00e4t zu Berlin, Unter den Linden 6, 10099, Berlin, Germany","Knowledge Management in Bioinformatics, Institute for Computer Science, Humboldt-Universit\u00e4t zu Berlin, Berlin, Germany","Department of Telecommunications and Media Informatics, Budapest University of Technology and Economics, Budapest, Hungary"],"affiliations":[{"raw_affiliation_string":"Department of Telecommunications and Media Informatics, Budapest University of Technology and Economics, H-1117, Budapest, Magyar Tud\u00f3sok krt 2, Hungary","institution_ids":["https://openalex.org/I29770179"]},{"raw_affiliation_string":"Knowledge Management in Bioinformatics, Institute for Computer Science, Humboldt-Universit\u00e4t zu Berlin, Unter den Linden 6, 10099, Berlin, Germany","institution_ids":["https://openalex.org/I39343248"]},{"raw_affiliation_string":"Knowledge Management in Bioinformatics, Institute for Computer Science, Humboldt-Universit\u00e4t zu Berlin, Berlin, Germany","institution_ids":["https://openalex.org/I39343248"]},{"raw_affiliation_string":"Department of Telecommunications and Media Informatics, Budapest University of Technology and Economics, Budapest, Hungary","institution_ids":["https://openalex.org/I29770179"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067194946","display_name":"Peter Palaga","orcid":null},"institutions":[{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Peter Palaga","raw_affiliation_strings":["Knowledge Management in Bioinformatics, Institute for Computer Science, Humboldt-Universit\u00e4t zu Berlin, Unter den Linden 6, 10099, Berlin, Germany","Knowledge Management in Bioinformatics, Institute for Computer Science, Humboldt-Universit\u00e4t zu Berlin, Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Knowledge Management in Bioinformatics, Institute for Computer Science, Humboldt-Universit\u00e4t zu Berlin, Unter den Linden 6, 10099, Berlin, Germany","institution_ids":["https://openalex.org/I39343248"]},{"raw_affiliation_string":"Knowledge Management in Bioinformatics, Institute for Computer Science, Humboldt-Universit\u00e4t zu Berlin, Berlin, Germany","institution_ids":["https://openalex.org/I39343248"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055236937","display_name":"Ulf Leser","orcid":"https://orcid.org/0000-0003-2166-9582"},"institutions":[{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Ulf Leser","raw_affiliation_strings":["Knowledge Management in Bioinformatics, Institute for Computer Science, Humboldt-Universit\u00e4t zu Berlin, Unter den Linden 6, 10099, Berlin, Germany","Knowledge Management in Bioinformatics, Institute for Computer Science, Humboldt-Universit\u00e4t zu Berlin, Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Knowledge Management in Bioinformatics, Institute for Computer Science, Humboldt-Universit\u00e4t zu Berlin, Unter den Linden 6, 10099, Berlin, Germany","institution_ids":["https://openalex.org/I39343248"]},{"raw_affiliation_string":"Knowledge Management in Bioinformatics, Institute for Computer Science, Humboldt-Universit\u00e4t zu Berlin, Berlin, Germany","institution_ids":["https://openalex.org/I39343248"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5070226189"],"corresponding_institution_ids":["https://openalex.org/I29770179","https://openalex.org/I39343248"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.2643,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.57059572,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"11","issue":"S5","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":0.9995999932289124,"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":0.9995999932289124,"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":0.9753000140190125,"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":0.9700000286102295,"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/relationship-extraction","display_name":"Relationship extraction","score":0.8493214845657349},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8212110996246338},{"id":"https://openalex.org/keywords/parsing","display_name":"Parsing","score":0.6661030054092407},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.6516212224960327},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.643528163433075},{"id":"https://openalex.org/keywords/parse-tree","display_name":"Parse tree","score":0.6409437656402588},{"id":"https://openalex.org/keywords/tree-kernel","display_name":"Tree kernel","score":0.6167318224906921},{"id":"https://openalex.org/keywords/sentence","display_name":"Sentence","score":0.5573849081993103},{"id":"https://openalex.org/keywords/kernel","display_name":"Kernel (algebra)","score":0.5473679304122925},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5161250829696655},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4946291148662567},{"id":"https://openalex.org/keywords/syntax","display_name":"Syntax","score":0.49170762300491333},{"id":"https://openalex.org/keywords/abstract-syntax-tree","display_name":"Abstract syntax tree","score":0.4678668975830078},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.462560772895813},{"id":"https://openalex.org/keywords/dependency","display_name":"Dependency (UML)","score":0.4494766592979431},{"id":"https://openalex.org/keywords/dependency-grammar","display_name":"Dependency grammar","score":0.42554253339767456},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.3228057026863098},{"id":"https://openalex.org/keywords/kernel-method","display_name":"Kernel method","score":0.30100777745246887},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.24382489919662476},{"id":"https://openalex.org/keywords/radial-basis-function-kernel","display_name":"Radial basis function kernel","score":0.15397852659225464},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.10730302333831787},{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"Support vector machine","score":0.09737169742584229}],"concepts":[{"id":"https://openalex.org/C153604712","wikidata":"https://www.wikidata.org/wiki/Q7310755","display_name":"Relationship extraction","level":3,"score":0.8493214845657349},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8212110996246338},{"id":"https://openalex.org/C186644900","wikidata":"https://www.wikidata.org/wiki/Q194152","display_name":"Parsing","level":2,"score":0.6661030054092407},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.6516212224960327},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.643528163433075},{"id":"https://openalex.org/C2781466058","wikidata":"https://www.wikidata.org/wiki/Q627921","display_name":"Parse tree","level":3,"score":0.6409437656402588},{"id":"https://openalex.org/C140417398","wikidata":"https://www.wikidata.org/wiki/Q16933942","display_name":"Tree kernel","level":5,"score":0.6167318224906921},{"id":"https://openalex.org/C2777530160","wikidata":"https://www.wikidata.org/wiki/Q41796","display_name":"Sentence","level":2,"score":0.5573849081993103},{"id":"https://openalex.org/C74193536","wikidata":"https://www.wikidata.org/wiki/Q574844","display_name":"Kernel (algebra)","level":2,"score":0.5473679304122925},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5161250829696655},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4946291148662567},{"id":"https://openalex.org/C60048249","wikidata":"https://www.wikidata.org/wiki/Q37437","display_name":"Syntax","level":2,"score":0.49170762300491333},{"id":"https://openalex.org/C58646249","wikidata":"https://www.wikidata.org/wiki/Q127380","display_name":"Abstract syntax tree","level":3,"score":0.4678668975830078},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.462560772895813},{"id":"https://openalex.org/C19768560","wikidata":"https://www.wikidata.org/wiki/Q320727","display_name":"Dependency (UML)","level":2,"score":0.4494766592979431},{"id":"https://openalex.org/C164883195","wikidata":"https://www.wikidata.org/wiki/Q674834","display_name":"Dependency grammar","level":3,"score":0.42554253339767456},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.3228057026863098},{"id":"https://openalex.org/C122280245","wikidata":"https://www.wikidata.org/wiki/Q620622","display_name":"Kernel method","level":3,"score":0.30100777745246887},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.24382489919662476},{"id":"https://openalex.org/C75866337","wikidata":"https://www.wikidata.org/wiki/Q7280263","display_name":"Radial basis function kernel","level":4,"score":0.15397852659225464},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.10730302333831787},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.09737169742584229},{"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/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"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/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"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":"doi:10.1186/1471-2105-11-s5-p8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-s5-p8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-S5-P8","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:europepmc.org:1967532","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2956401","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"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-11-s5-p8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-s5-p8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-S5-P8","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6899999976158142,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1988647655.pdf","grobid_xml":"https://content.openalex.org/works/W1988647655.grobid-xml"},"referenced_works_count":4,"referenced_works":["https://openalex.org/W636969833","https://openalex.org/W1493270114","https://openalex.org/W2143954109","https://openalex.org/W2166111585"],"related_works":["https://openalex.org/W2188063681","https://openalex.org/W2108059661","https://openalex.org/W1525618684","https://openalex.org/W2027424931","https://openalex.org/W2794309877","https://openalex.org/W4234806381","https://openalex.org/W185385371","https://openalex.org/W2152269015","https://openalex.org/W2476066186","https://openalex.org/W2042972234"],"abstract_inverted_index":{"Background":[0],"Extraction":[1],"of":[2,14,34,63,96],"protein-protein":[3],"interactions":[4],"(PPIs)":[5],"reported":[6],"in":[7,70],"scientific":[8],"publications":[9],"is":[10,21],"a":[11,24],"core":[12],"topic":[13],"biomedical":[15],"text":[16,36],"mining.":[17],"The":[18],"ultimate":[19],"goal":[20],"to":[22,47,90],"devise":[23],"PPI":[25,48],"extraction":[26,49],"method":[27],"that":[28],"performs":[29],"well":[30],"on":[31,51,59],"large":[32],"amount":[33],"unseen":[35],"independently":[37],"from":[38,86],"the":[39,52,60,72,83,87,97],"training":[40],"corpus.":[41],"One":[42],"popular,":[43],"machine-learning":[44],"based":[45],"approach":[46],"builds":[50],"convolution":[53],"kernels,":[54],"i.e.,":[55],"similarity":[56,98],"functions":[57,68],"defined":[58],"parse-based":[61],"representation":[62,75,89],"sentences":[64],"and":[65,93],"interactions.":[66],"Kernel":[67],"differ":[69],"(1)":[71],"underlying":[73],"sentence":[74,88],"(bag-of-words,":[76],"syntax":[77],"tree":[78],"parse,":[79],"dependency":[80],"graphs),":[81],"(2)":[82],"substructures":[84],"retrieved":[85],"define":[91],"interactions,":[92],"(3)":[94],"calculation":[95],"function.":[99]},"counts_by_year":[{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}