{"id":"https://openalex.org/W2166657393","doi":"https://doi.org/10.1109/cbms.2009.5255388","title":"Extraction of coexpression relationship among genes from biomedical text using dynamic conditional random fields","display_name":"Extraction of coexpression relationship among genes from biomedical text using dynamic conditional random fields","publication_year":2009,"publication_date":"2009-08-01","ids":{"openalex":"https://openalex.org/W2166657393","doi":"https://doi.org/10.1109/cbms.2009.5255388","mag":"2166657393"},"language":"en","primary_location":{"id":"doi:10.1109/cbms.2009.5255388","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cbms.2009.5255388","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2009 22nd IEEE International Symposium on Computer-Based Medical Systems","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5109408655","display_name":"Richa Tiwari","orcid":"https://orcid.org/0000-0003-3069-8510"},"institutions":[{"id":"https://openalex.org/I17301866","display_name":"University of Alabama","ror":"https://ror.org/03xrrjk67","country_code":"US","type":"education","lineage":["https://openalex.org/I17301866"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Richa Tiwari","raw_affiliation_strings":["Department of Computer and Information Sciences, University of Alabama, Birmingham, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer and Information Sciences, University of Alabama, Birmingham, USA","institution_ids":["https://openalex.org/I17301866"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061568662","display_name":"Chengcui Zhang","orcid":"https://orcid.org/0000-0002-5868-6450"},"institutions":[{"id":"https://openalex.org/I17301866","display_name":"University of Alabama","ror":"https://ror.org/03xrrjk67","country_code":"US","type":"education","lineage":["https://openalex.org/I17301866"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chengcui Zhang","raw_affiliation_strings":["Department of Computer and Information Sciences, University of Alabama, Birmingham, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer and Information Sciences, University of Alabama, Birmingham, USA","institution_ids":["https://openalex.org/I17301866"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5072192748","display_name":"Wei-Bang Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I17301866","display_name":"University of Alabama","ror":"https://ror.org/03xrrjk67","country_code":"US","type":"education","lineage":["https://openalex.org/I17301866"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wei-Bang Chen","raw_affiliation_strings":["Department of Computer and Information Sciences, University of Alabama, Birmingham, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer and Information Sciences, University of Alabama, Birmingham, USA","institution_ids":["https://openalex.org/I17301866"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5109408655"],"corresponding_institution_ids":["https://openalex.org/I17301866"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.15938078,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":95},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"4"},"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/T10028","display_name":"Topic Modeling","score":0.9976000189781189,"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/T10181","display_name":"Natural Language Processing Techniques","score":0.9951000213623047,"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/conditional-random-field","display_name":"Conditional random field","score":0.8313672542572021},{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"Support vector machine","score":0.6884074211120605},{"id":"https://openalex.org/keywords/generalization","display_name":"Generalization","score":0.6467879414558411},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6446088552474976},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.5804405212402344},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5451734066009521},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.49235570430755615},{"id":"https://openalex.org/keywords/biomedical-text-mining","display_name":"Biomedical text mining","score":0.48931166529655457},{"id":"https://openalex.org/keywords/word","display_name":"Word (group theory)","score":0.48146358132362366},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4673141837120056},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.45933571457862854},{"id":"https://openalex.org/keywords/random-forest","display_name":"Random forest","score":0.42856478691101074},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.4145805537700653},{"id":"https://openalex.org/keywords/crfs","display_name":"CRFS","score":0.41312357783317566},{"id":"https://openalex.org/keywords/text-mining","display_name":"Text mining","score":0.37668538093566895},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.336394727230072},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3361356854438782},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18707504868507385},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1664511263370514},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13660377264022827}],"concepts":[{"id":"https://openalex.org/C152565575","wikidata":"https://www.wikidata.org/wiki/Q1124538","display_name":"Conditional random field","level":2,"score":0.8313672542572021},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.6884074211120605},{"id":"https://openalex.org/C177148314","wikidata":"https://www.wikidata.org/wiki/Q170084","display_name":"Generalization","level":2,"score":0.6467879414558411},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6446088552474976},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.5804405212402344},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5451734066009521},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.49235570430755615},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.48931166529655457},{"id":"https://openalex.org/C90805587","wikidata":"https://www.wikidata.org/wiki/Q10944557","display_name":"Word (group theory)","level":2,"score":0.48146358132362366},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4673141837120056},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.45933571457862854},{"id":"https://openalex.org/C169258074","wikidata":"https://www.wikidata.org/wiki/Q245748","display_name":"Random forest","level":2,"score":0.42856478691101074},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.4145805537700653},{"id":"https://openalex.org/C2775953691","wikidata":"https://www.wikidata.org/wiki/Q5013874","display_name":"CRFS","level":3,"score":0.41312357783317566},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.37668538093566895},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.336394727230072},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3361356854438782},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18707504868507385},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1664511263370514},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13660377264022827},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"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/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/cbms.2009.5255388","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cbms.2009.5255388","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2009 22nd IEEE International Symposium on Computer-Based Medical Systems","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","score":0.75,"display_name":"Quality Education"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320337398","display_name":"Division of Biological Infrastructure","ror":"https://ror.org/04qn9mx93"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W189514790","https://openalex.org/W2036935277","https://openalex.org/W2072944755","https://openalex.org/W2115936127","https://openalex.org/W2126813895","https://openalex.org/W2132870739","https://openalex.org/W2141099517","https://openalex.org/W2147880316","https://openalex.org/W2152463966","https://openalex.org/W2156515921","https://openalex.org/W2158823144","https://openalex.org/W6607642809","https://openalex.org/W6682082992"],"related_works":["https://openalex.org/W2055466819","https://openalex.org/W50079190","https://openalex.org/W2356597680","https://openalex.org/W1492005981","https://openalex.org/W189110383","https://openalex.org/W4250494529","https://openalex.org/W2027233318","https://openalex.org/W2937192905","https://openalex.org/W2148251896","https://openalex.org/W1663435917"],"abstract_inverted_index":{"Text":[0],"mining":[1],"tools":[2,20],"and":[3,33,73,84,103,146,152],"algorithms":[4],"are":[5],"being":[6],"successfully":[7],"used":[8],"for":[9],"information":[10,25],"extraction":[11,26],"especially":[12],"on":[13],"large":[14],"corpus":[15],"like":[16],"biomedical":[17,39],"publications.":[18],"These":[19],"not":[21],"only":[22],"aid":[23],"in":[24,29,89,104],"but":[27],"also":[28],"forming":[30],"new":[31],"theories":[32],"relationships":[34],"between":[35,83],"various":[36],"fields":[37],"of":[38,42,97,141],"research.":[40],"Extraction":[41],"gene-gene":[43],"or":[44],"gene-disease":[45],"relationship":[46,82],"is":[47],"one":[48],"such":[49,93],"application.":[50],"In":[51],"this":[52],"paper,":[53],"we":[54],"introduce":[55],"a":[56],"method":[57],"to":[58,111,156],"detect":[59],"coexpressed":[60],"genes":[61,86,118],"from":[62,128,132],"text,":[63],"using":[64],"the":[65,69,80,95,117,123,126],"grammatical":[66],"dependencies":[67],"among":[68,85],"words":[70],"within":[71],"sentences":[72,114],"Dynamic":[74],"Conditional":[75],"Random":[76],"Fields":[77],"(DCRFs).":[78],"Determining":[79],"coexpression":[81],"can":[87],"help":[88],"identifying":[90],"important":[91],"concepts":[92],"as":[94,120,122],"functionality":[96],"gene(s)":[98],"involved,":[99],"their":[100],"pathogenic":[101],"mechanism,":[102],"deciphering":[105],"protein-protein":[106],"interactions.":[107],"This":[108],"work":[109],"attempts":[110],"extract":[112],"relevant":[113],"by":[115],"labeling":[116],"involved":[119],"well":[121],"word":[124],"representing":[125],"relationship,":[127],"full-length":[129],"papers":[130],"collected":[131],"PubMed.":[133],"The":[134],"results":[135],"obtained":[136],"were":[137],"compared":[138],"with":[139,149],"that":[140],"Support":[142],"Vector":[143],"Machine":[144],"(SVM)":[145],"Nearest":[147],"Neighbor":[148],"generalization":[150],"(NNge),":[151],"have":[153],"been":[154],"found":[155],"outperform":[157],"both.":[158]},"counts_by_year":[{"year":2021,"cited_by_count":2},{"year":2013,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
