{"id":"https://openalex.org/W3004748909","doi":"https://doi.org/10.1109/bibm47256.2019.8983234","title":"Extracting Molecular Entities and Their Interactions from Pathway Figures Based on Deep Learning","display_name":"Extracting Molecular Entities and Their Interactions from Pathway Figures Based on Deep Learning","publication_year":2019,"publication_date":"2019-11-01","ids":{"openalex":"https://openalex.org/W3004748909","doi":"https://doi.org/10.1109/bibm47256.2019.8983234","mag":"3004748909"},"language":"en","primary_location":{"id":"doi:10.1109/bibm47256.2019.8983234","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm47256.2019.8983234","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","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/A5087149818","display_name":"Fei He","orcid":"https://orcid.org/0000-0002-3284-9506"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Fei He","raw_affiliation_strings":["Christopher S. Bond Life Sciences Center, University of Missouri,Dept. of Electrical Engineering and Computer Science,Columbia,MO,USA","Dept. of Electrical Engineering and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA"],"affiliations":[{"raw_affiliation_string":"Christopher S. Bond Life Sciences Center, University of Missouri,Dept. of Electrical Engineering and Computer Science,Columbia,MO,USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Dept. of Electrical Engineering and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003943520","display_name":"Duolin Wang","orcid":"https://orcid.org/0000-0003-1649-460X"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Duolin Wang","raw_affiliation_strings":["Christopher S. Bond Life Sciences Center, University of Missouri,Dept. of Electrical Engineering and Computer Science,Columbia,MO,USA","Dept. of Electrical Engineering and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA"],"affiliations":[{"raw_affiliation_string":"Christopher S. Bond Life Sciences Center, University of Missouri,Dept. of Electrical Engineering and Computer Science,Columbia,MO,USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Dept. of Electrical Engineering and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065455945","display_name":"Yulia Innokenteva","orcid":null},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yulia Innokenteva","raw_affiliation_strings":["Christopher S. Bond Life Sciences Center, University of Missouri,Dept. of Electrical Engineering and Computer Science,Columbia,MO,USA","Dept. of Electrical Engineering and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA"],"affiliations":[{"raw_affiliation_string":"Christopher S. Bond Life Sciences Center, University of Missouri,Dept. of Electrical Engineering and Computer Science,Columbia,MO,USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Dept. of Electrical Engineering and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052141799","display_name":"Olha Kholod","orcid":"https://orcid.org/0000-0001-6257-4948"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Olha Kholod","raw_affiliation_strings":["Christopher S. Bond Life Sciences Center, University of Missouri,Dept. of Electrical Engineering and Computer Science,Columbia,MO,USA","Dept. of Electrical Engineering and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA"],"affiliations":[{"raw_affiliation_string":"Christopher S. Bond Life Sciences Center, University of Missouri,Dept. of Electrical Engineering and Computer Science,Columbia,MO,USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Dept. of Electrical Engineering and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034457600","display_name":"Dmitriy Shin","orcid":"https://orcid.org/0000-0002-5571-9384"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dmitriy Shin","raw_affiliation_strings":["Christopher S. Bond Life Sciences Center, University of Missouri,Dept. of Electrical Engineering and Computer Science,Columbia,MO,USA","Dept. of Electrical Engineering and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA"],"affiliations":[{"raw_affiliation_string":"Christopher S. Bond Life Sciences Center, University of Missouri,Dept. of Electrical Engineering and Computer Science,Columbia,MO,USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Dept. of Electrical Engineering and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082428303","display_name":"Dong Xu","orcid":"https://orcid.org/0000-0002-4809-0514"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dong Xu","raw_affiliation_strings":["Christopher S. Bond Life Sciences Center, University of Missouri,Dept. of Electrical Engineering and Computer Science,Columbia,MO,USA","Dept. of Electrical Engineering and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA"],"affiliations":[{"raw_affiliation_string":"Christopher S. Bond Life Sciences Center, University of Missouri,Dept. of Electrical Engineering and Computer Science,Columbia,MO,USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Dept. of Electrical Engineering and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5087149818"],"corresponding_institution_ids":["https://openalex.org/I76835614"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.13827488,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"1191","last_page":"1193"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998000264167786,"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":0.9998000264167786,"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/T13083","display_name":"Advanced Text Analysis Techniques","score":0.9861000180244446,"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":0.9835000038146973,"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/pipeline","display_name":"Pipeline (software)","score":0.8068262934684753},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7431321144104004},{"id":"https://openalex.org/keywords/pace","display_name":"Pace","score":0.6133652329444885},{"id":"https://openalex.org/keywords/data-curation","display_name":"Data curation","score":0.598146915435791},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.5388924479484558},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4972706139087677},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.4684581756591797},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3598218560218811}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.8068262934684753},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7431321144104004},{"id":"https://openalex.org/C2777526511","wikidata":"https://www.wikidata.org/wiki/Q691543","display_name":"Pace","level":2,"score":0.6133652329444885},{"id":"https://openalex.org/C91632574","wikidata":"https://www.wikidata.org/wiki/Q15088675","display_name":"Data curation","level":2,"score":0.598146915435791},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5388924479484558},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4972706139087677},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.4684581756591797},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3598218560218811},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","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},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm47256.2019.8983234","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm47256.2019.8983234","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education","score":0.6800000071525574}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":7,"referenced_works":["https://openalex.org/W943972918","https://openalex.org/W2114363816","https://openalex.org/W2148083369","https://openalex.org/W2156651988","https://openalex.org/W2325767305","https://openalex.org/W2566288590","https://openalex.org/W2595875793"],"related_works":["https://openalex.org/W2386723501","https://openalex.org/W2387879414","https://openalex.org/W2390304029","https://openalex.org/W2354923724","https://openalex.org/W2146830340","https://openalex.org/W2377101853","https://openalex.org/W4306317641","https://openalex.org/W1488337274","https://openalex.org/W4287611188","https://openalex.org/W2216178707"],"abstract_inverted_index":{"Many":[0],"new":[1],"molecular":[2,132],"mechanisms":[3,175],"of":[4,40,59,107],"genomics,":[5],"pharmacogenomics,":[6],"immunology,":[7],"and":[8,16,95,105,134,172],"other":[9],"fields":[10],"are":[11,32],"reflected":[12],"in":[13,25,34,50,71,110,153],"pathway":[14,48,68,80,108,138,174],"figures":[15,49,69,119,139],"need":[17],"to":[18,74,100,151,168],"be":[19],"curated":[20],"for":[21,66],"various":[22],"applications,":[23],"especially":[24],"precision":[26],"medicine.":[27],"Current":[28],"manual":[29],"curation":[30,81],"approaches":[31],"inadequate":[33],"keeping":[35],"up":[36],"with":[37,45,89,165],"the":[38,51,60,102,111,118],"pace":[39],"biomedical":[41,52],"literature":[42,53,155],"growth.":[43],"Compared":[44],"textual":[46],"representations,":[47],"often":[54],"contain":[55],"more":[56,176],"direct":[57],"representations":[58],"mechanisms.":[61],"However,":[62],"no":[63],"systematic":[64],"method":[65,94,164],"curating":[67],"exists":[70],"publications":[72],"due":[73],"date.":[75],"Here,":[76],"we":[77,160],"propose":[78],"a":[79,85,141,148],"pipeline,":[82],"which":[83],"integrates":[84],"deep":[86],"learning":[87],"model":[88,128],"an":[90,96],"optical":[91],"character":[92],"recognition":[93],"image":[97],"processing":[98],"strategy":[99],"capture":[101],"locations,":[103],"names,":[104],"interactions":[106,136],"entities":[109,133],"figure.":[112],"Our":[113],"pipeline":[114,146],"was":[115],"evaluated":[116],"on":[117],"from":[120,137],"PubMed":[121],"publications.":[122],"The":[123,144],"results":[124],"demonstrate":[125],"that":[126],"our":[127,163],"can":[129],"effectively":[130],"retrieve":[131],"their":[135],"at":[140],"large":[142],"scale.":[143],"proposed":[145],"provides":[147],"complementary":[149],"approach":[150],"text-mining":[152,166],"biological":[154],"mining.":[156],"In":[157],"future":[158],"work,":[159],"will":[161],"combine":[162],"tools":[167],"enrich":[169],"extracted":[170],"information":[171],"reconstruct":[173],"precisely.":[177]},"counts_by_year":[{"year":2023,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
