{"id":"https://openalex.org/W2905949160","doi":"https://doi.org/10.1186/s12859-018-2511-9","title":"Scalable deep text comprehension for Cancer surveillance on high-performance computing","display_name":"Scalable deep text comprehension for Cancer surveillance on high-performance computing","publication_year":2018,"publication_date":"2018-12-01","ids":{"openalex":"https://openalex.org/W2905949160","doi":"https://doi.org/10.1186/s12859-018-2511-9","mag":"2905949160","pmid":"https://pubmed.ncbi.nlm.nih.gov/30577743"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-018-2511-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2511-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2511-9","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","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2511-9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5002942001","display_name":"John X. Qiu","orcid":null},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"John X. Qiu","raw_affiliation_strings":["Biomedical Sciences, Engineering, and Computing Group, Health Data Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Sciences, Engineering, and Computing Group, Health Data Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, USA","institution_ids":["https://openalex.org/I1289243028"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054049458","display_name":"Hong\u2010Jun Yoon","orcid":"https://orcid.org/0000-0002-5450-5878"},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hong-Jun Yoon","raw_affiliation_strings":["Biomedical Sciences, Engineering, and Computing Group, Health Data Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, USA. yoonh@ornl.gov","Biomedical Sciences, Engineering, and Computing Group, Health Data Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Sciences, Engineering, and Computing Group, Health Data Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, USA. yoonh@ornl.gov","institution_ids":[]},{"raw_affiliation_string":"Biomedical Sciences, Engineering, and Computing Group, Health Data Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, USA","institution_ids":["https://openalex.org/I1289243028"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030803191","display_name":"Kshitij Srivastava","orcid":"https://orcid.org/0000-0002-3658-0815"},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kshitij Srivastava","raw_affiliation_strings":["Biomedical Sciences, Engineering, and Computing Group, Health Data Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Sciences, Engineering, and Computing Group, Health Data Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, USA","institution_ids":["https://openalex.org/I1289243028"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055914870","display_name":"Thomas P. Watson","orcid":null},"institutions":[{"id":"https://openalex.org/I94658018","display_name":"University of Memphis","ror":"https://ror.org/01cq23130","country_code":"US","type":"education","lineage":["https://openalex.org/I94658018"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thomas P. Watson","raw_affiliation_strings":["Herff College of Engineering, University of Memphis, Memphis, TN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Herff College of Engineering, University of Memphis, Memphis, TN, USA","institution_ids":["https://openalex.org/I94658018"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037444677","display_name":"J. Blair Christian","orcid":"https://orcid.org/0000-0002-4658-1635"},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J. Blair Christian","raw_affiliation_strings":["Biomedical Sciences, Engineering, and Computing Group, Health Data Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Sciences, Engineering, and Computing Group, Health Data Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, USA","institution_ids":["https://openalex.org/I1289243028"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028188095","display_name":"Arvind Ramanathan","orcid":"https://orcid.org/0000-0002-1622-5488"},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Arvind Ramanathan","raw_affiliation_strings":["Biomedical Sciences, Engineering, and Computing Group, Health Data Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Sciences, Engineering, and Computing Group, Health Data Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, USA","institution_ids":["https://openalex.org/I1289243028"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087581630","display_name":"Xiao Wu","orcid":"https://orcid.org/0009-0000-4601-7930"},"institutions":[{"id":"https://openalex.org/I75420490","display_name":"Louisiana State University Health Sciences Center New Orleans","ror":"https://ror.org/01qv8fp92","country_code":"US","type":"education","lineage":["https://openalex.org/I75420490"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiao C. Wu","raw_affiliation_strings":["Louisiana Tumor Registry, Louisiana State University Health Sciences Center, New Orleans, LA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Louisiana Tumor Registry, Louisiana State University Health Sciences Center, New Orleans, LA, USA","institution_ids":["https://openalex.org/I75420490"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058728327","display_name":"Paul Fearn","orcid":null},"institutions":[{"id":"https://openalex.org/I4210140884","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paul A. Fearn","raw_affiliation_strings":["Surveillance Research Program, National Cancer Institute, Bethesda, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Surveillance Research Program, National Cancer Institute, Bethesda, MD, USA","institution_ids":["https://openalex.org/I4210140884"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014968146","display_name":"Georgia D. Tourassi","orcid":"https://orcid.org/0000-0002-9418-9638"},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Georgia D. Tourassi","raw_affiliation_strings":["Biomedical Sciences, Engineering, and Computing Group, Health Data Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Sciences, Engineering, and Computing Group, Health Data Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, USA","institution_ids":["https://openalex.org/I1289243028"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5002942001"],"corresponding_institution_ids":["https://openalex.org/I1289243028"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.0207,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.76708493,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"19","issue":"S18","first_page":"488","last_page":"488"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.10769999772310257,"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":0.10769999772310257,"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":0.10159999877214432,"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/T10862","display_name":"AI in cancer detection","score":0.0917000025510788,"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":0.8620091676712036},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.8014962673187256},{"id":"https://openalex.org/keywords/stochastic-gradient-descent","display_name":"Stochastic gradient descent","score":0.6019715666770935},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.5901327729225159},{"id":"https://openalex.org/keywords/titan","display_name":"Titan (rocket family)","score":0.5271810293197632},{"id":"https://openalex.org/keywords/message-passing-interface","display_name":"Message Passing Interface","score":0.5184159278869629},{"id":"https://openalex.org/keywords/workload","display_name":"Workload","score":0.5150477886199951},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5031725764274597},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.4992537498474121},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.4597696363925934},{"id":"https://openalex.org/keywords/gpu-cluster","display_name":"GPU cluster","score":0.45950740575790405},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.4432443082332611},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4397905766963959},{"id":"https://openalex.org/keywords/data-parallelism","display_name":"Data parallelism","score":0.43279391527175903},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.3950938582420349},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3924518823623657},{"id":"https://openalex.org/keywords/parallelism","display_name":"Parallelism (grammar)","score":0.31029626727104187},{"id":"https://openalex.org/keywords/message-passing","display_name":"Message passing","score":0.26715195178985596},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.1727702021598816},{"id":"https://openalex.org/keywords/cuda","display_name":"CUDA","score":0.13155877590179443}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8620091676712036},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.8014962673187256},{"id":"https://openalex.org/C206688291","wikidata":"https://www.wikidata.org/wiki/Q7617819","display_name":"Stochastic gradient descent","level":3,"score":0.6019715666770935},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.5901327729225159},{"id":"https://openalex.org/C50805821","wikidata":"https://www.wikidata.org/wiki/Q1136670","display_name":"Titan (rocket family)","level":2,"score":0.5271810293197632},{"id":"https://openalex.org/C166782233","wikidata":"https://www.wikidata.org/wiki/Q127879","display_name":"Message Passing Interface","level":3,"score":0.5184159278869629},{"id":"https://openalex.org/C2778476105","wikidata":"https://www.wikidata.org/wiki/Q628539","display_name":"Workload","level":2,"score":0.5150477886199951},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5031725764274597},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.4992537498474121},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.4597696363925934},{"id":"https://openalex.org/C2781335571","wikidata":"https://www.wikidata.org/wiki/Q2633544","display_name":"GPU cluster","level":3,"score":0.45950740575790405},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.4432443082332611},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4397905766963959},{"id":"https://openalex.org/C61483411","wikidata":"https://www.wikidata.org/wiki/Q3124522","display_name":"Data parallelism","level":3,"score":0.43279391527175903},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.3950938582420349},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3924518823623657},{"id":"https://openalex.org/C2781172179","wikidata":"https://www.wikidata.org/wiki/Q853109","display_name":"Parallelism (grammar)","level":2,"score":0.31029626727104187},{"id":"https://openalex.org/C854659","wikidata":"https://www.wikidata.org/wiki/Q1859284","display_name":"Message passing","level":2,"score":0.26715195178985596},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.1727702021598816},{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.13155877590179443},{"id":"https://openalex.org/C146978453","wikidata":"https://www.wikidata.org/wiki/Q3798668","display_name":"Aerospace engineering","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":false},{"descriptor_ui":"D003205","descriptor_name":"Computing Methodologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003205","descriptor_name":"Computing Methodologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003205","descriptor_name":"Computing Methodologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D032882","descriptor_name":"Comprehension","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D032882","descriptor_name":"Comprehension","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D032882","descriptor_name":"Comprehension","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/s12859-018-2511-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2511-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2511-9","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":"pmid:30577743","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30577743","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:osti.gov:1491345","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1491345","pdf_url":"https://www.osti.gov/servlets/purl/1491345","source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"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":null},{"id":"pmh:oai:doaj.org/article:6684208320a84967842d0cd01bbb996c","is_oa":true,"landing_page_url":"https://doaj.org/article/6684208320a84967842d0cd01bbb996c","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 19, Iss S18, Pp 99-110 (2018)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5287164","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6302459","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:6302459","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6302459","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-018-2511-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2511-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2511-9","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":[{"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education","score":0.4000000059604645}],"awards":[{"id":"https://openalex.org/G1220351962","display_name":null,"funder_award_id":"DE-AC5206NA25396","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G1313983767","display_name":null,"funder_award_id":"DE-AC02","funder_id":"https://openalex.org/F4320338284","funder_display_name":"Argonne National Laboratory"},{"id":"https://openalex.org/G1489425746","display_name":null,"funder_award_id":"DE-AC05-00OR22725","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G1528409558","display_name":null,"funder_award_id":"No. DE-AC05-00OR22725","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G1645119126","display_name":null,"funder_award_id":"AC05-00OR22725","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G1716777315","display_name":null,"funder_award_id":"DE-AC52-07NA27344","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1719536385","display_name":null,"funder_award_id":"DE-AC05-00OR22725","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G1899543020","display_name":null,"funder_award_id":"DE-AC5206NA25396","funder_id":"https://openalex.org/F4320338304","funder_display_name":"Los Alamos National Laboratory"},{"id":"https://openalex.org/G2082431150","display_name":null,"funder_award_id":"DE-AC52-07NA27344","funder_id":"https://openalex.org/F4320316892","funder_display_name":"UT-Battelle"},{"id":"https://openalex.org/G2569679037","display_name":null,"funder_award_id":"JDACS4C","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G2584197162","display_name":null,"funder_award_id":"DE-AC05-00OR22725","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3005847338","display_name":null,"funder_award_id":"JDACS4C","funder_id":"https://openalex.org/F4320338304","funder_display_name":"Los Alamos National Laboratory"},{"id":"https://openalex.org/G3049477530","display_name":null,"funder_award_id":"Contract No. DE-AC05-00OR22725","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G314071323","display_name":null,"funder_award_id":"JDACS4C","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G3548842975","display_name":null,"funder_award_id":"Contract DE-AC05-00OR22725","funder_id":"https://openalex.org/F4320316892","funder_display_name":"UT-Battelle"},{"id":"https://openalex.org/G4017386982","display_name":null,"funder_award_id":"DE-AC52-07NA27344","funder_id":"https://openalex.org/F4320338287","funder_display_name":"Oak Ridge National Laboratory"},{"id":"https://openalex.org/G4343739756","display_name":null,"funder_award_id":"Contract DE-AC52-07NA27344","funder_id":"https://openalex.org/F4320338286","funder_display_name":"Lawrence Livermore National Laboratory"},{"id":"https://openalex.org/G4423657506","display_name":null,"funder_award_id":"AC05-00OR22725","funder_id":"https://openalex.org/F4320338287","funder_display_name":"Oak Ridge National Laboratory"},{"id":"https://openalex.org/G4957472368","display_name":null,"funder_award_id":". DE-AC05-00OR22725","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G498139845","display_name":null,"funder_award_id":"DE-AC02","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G5359441962","display_name":null,"funder_award_id":"DE-AC5206NA25396","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G5726405315","display_name":null,"funder_award_id":"DE-AC05","funder_id":"https://openalex.org/F4320306250","funder_display_name":"Battelle"},{"id":"https://openalex.org/G574795485","display_name":null,"funder_award_id":"DE-AC52-07NA27344","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G5783643890","display_name":null,"funder_award_id":"DE-AC02-06-CH11357","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G5816449448","display_name":null,"funder_award_id":"DE-AC52-07NA27344","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G5840121450","display_name":null,"funder_award_id":"DE-AC05-00OR22725","funder_id":"https://openalex.org/F4320338304","funder_display_name":"Los Alamos National Laboratory"},{"id":"https://openalex.org/G5869080520","display_name":null,"funder_award_id":"DE-AC52-07NA27344","funder_id":"https://openalex.org/F4320306250","funder_display_name":"Battelle"},{"id":"https://openalex.org/G6086734019","display_name":null,"funder_award_id":"DE-AC05-00OR22725","funder_id":"https://openalex.org/F4320338286","funder_display_name":"Lawrence Livermore National Laboratory"},{"id":"https://openalex.org/G6129992089","display_name":null,"funder_award_id":"DE-AC05-","funder_id":"https://openalex.org/F4320316892","funder_display_name":"UT-Battelle"},{"id":"https://openalex.org/G632693473","display_name":null,"funder_award_id":"DE-AC52-07NA27344","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G6474786868","display_name":null,"funder_award_id":"DE-AC5206NA25396","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6486853205","display_name":null,"funder_award_id":"Contract No. DE-AC05-00OR22725","funder_id":"https://openalex.org/F4320338287","funder_display_name":"Oak Ridge National Laboratory"},{"id":"https://openalex.org/G6558272803","display_name":null,"funder_award_id":"DE-AC02","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G6640896145","display_name":null,"funder_award_id":"Contract DE-AC5206NA25396","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G675320460","display_name":null,"funder_award_id":"DE-AC05-00OR22725","funder_id":"https://openalex.org/F4320338287","funder_display_name":"Oak Ridge National Laboratory"},{"id":"https://openalex.org/G6864165199","display_name":null,"funder_award_id":"DE-AC05-00OR22725","funder_id":"https://openalex.org/F4320306250","funder_display_name":"Battelle"},{"id":"https://openalex.org/G6911681599","display_name":null,"funder_award_id":"No. DE-AC05-00OR22725","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G69709960","display_name":null,"funder_award_id":"Contract DE-AC52-07NA27344","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G7186599013","display_name":null,"funder_award_id":"under Contract DE-AC05-00OR22725","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G7769062580","display_name":null,"funder_award_id":"No. DE-AC05-00OR22725","funder_id":"https://openalex.org/F4320316892","funder_display_name":"UT-Battelle"},{"id":"https://openalex.org/G7989027471","display_name":null,"funder_award_id":"DE-AC52-07NA27344","funder_id":"https://openalex.org/F4320338304","funder_display_name":"Los Alamos National Laboratory"},{"id":"https://openalex.org/G7995982022","display_name":null,"funder_award_id":"DE-AC05","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G8269158468","display_name":null,"funder_award_id":"AC05-00OR22725","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G8374966015","display_name":null,"funder_award_id":"AC52-07NA27344","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G8595310706","display_name":null,"funder_award_id":"DE-AC02-06-CH11357","funder_id":"https://openalex.org/F4320338284","funder_display_name":"Argonne National Laboratory"},{"id":"https://openalex.org/G8666256197","display_name":null,"funder_award_id":"DE-AC52-07NA27344","funder_id":"https://openalex.org/F4320338284","funder_display_name":"Argonne National Laboratory"},{"id":"https://openalex.org/G8906985441","display_name":null,"funder_award_id":"00OR22725","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G8943143067","display_name":null,"funder_award_id":"AC05-00OR22725","funder_id":"https://openalex.org/F4320316892","funder_display_name":"UT-Battelle"},{"id":"https://openalex.org/G969889393","display_name":null,"funder_award_id":"DE-AC02-","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G991281326","display_name":null,"funder_award_id":"AC52-07NA27344","funder_id":"https://openalex.org/F4320338286","funder_display_name":"Lawrence Livermore National Laboratory"}],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320306250","display_name":"Battelle","ror":"https://ror.org/01h5tnr73"},{"id":"https://openalex.org/F4320316892","display_name":"UT-Battelle","ror":"https://ror.org/04nza6677"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332359","display_name":"Office of Science","ror":"https://ror.org/00mmn6b08"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320338284","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63"},{"id":"https://openalex.org/F4320338286","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53"},{"id":"https://openalex.org/F4320338287","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56"},{"id":"https://openalex.org/F4320338304","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2905949160.pdf","grobid_xml":"https://content.openalex.org/works/W2905949160.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W6908809","https://openalex.org/W114517082","https://openalex.org/W182110599","https://openalex.org/W1832693441","https://openalex.org/W2102017903","https://openalex.org/W2109722477","https://openalex.org/W2124061625","https://openalex.org/W2149527488","https://openalex.org/W2153579005","https://openalex.org/W2154834860","https://openalex.org/W2158922990","https://openalex.org/W2163229756","https://openalex.org/W2165612380","https://openalex.org/W2168231600","https://openalex.org/W2215206286","https://openalex.org/W2235523093","https://openalex.org/W2311607323","https://openalex.org/W2402144811","https://openalex.org/W2493134281","https://openalex.org/W2559997609","https://openalex.org/W2611254939","https://openalex.org/W2778119792","https://openalex.org/W2790740913","https://openalex.org/W2919115771","https://openalex.org/W2963083845","https://openalex.org/W4210348154","https://openalex.org/W4255155743","https://openalex.org/W4294170691","https://openalex.org/W6600195515","https://openalex.org/W6600258949","https://openalex.org/W6676367512","https://openalex.org/W6684620663","https://openalex.org/W6684859321","https://openalex.org/W6713134421"],"related_works":["https://openalex.org/W2963113252","https://openalex.org/W2782867136","https://openalex.org/W2991615366","https://openalex.org/W3200042011","https://openalex.org/W2564229740","https://openalex.org/W3045212162","https://openalex.org/W4287235399","https://openalex.org/W2030707850","https://openalex.org/W3187255235","https://openalex.org/W2078397179"],"abstract_inverted_index":{"BACKGROUND:":[0],"Deep":[1],"Learning":[2],"(DL)":[3],"has":[4,13],"advanced":[5],"the":[6,37,48,72,89,107,115,141,173,201,214],"state-of-the-art":[7],"capabilities":[8],"in":[9,15,205],"bioinformatics":[10],"applications":[11],"which":[12],"resulted":[14],"trends":[16],"of":[17,39,94,101,131,138,143,196],"increasingly":[18],"sophisticated":[19],"and":[20,27,70,114,134,148,198],"computationally":[21],"demanding":[22],"models":[23],"trained":[24],"by":[25],"larger":[26,28],"data":[29,58,79,111],"sets.":[30],"This":[31],"vastly":[32],"increased":[33],"computational":[34,50],"demand":[35],"challenges":[36],"feasibility":[38],"conducting":[40],"cutting-edge":[41],"research.":[42],"One":[43],"solution":[44],"is":[45,218],"to":[46,81,203,235],"distribute":[47],"vast":[49],"workload":[51],"across":[52,220],"multiple":[53,221],"computing":[54],"cluster":[55],"nodes":[56,133,223],"with":[57,225],"parallelism":[59,80,112],"algorithms.":[60],"In":[61],"this":[62],"study,":[63],"we":[64,127],"used":[65,128],"a":[66,83,98,136,160,183,193,236],"High-Performance":[67],"Computing":[68,122],"environment":[69],"implemented":[71],"Downpour":[73],"Stochastic":[74],"Gradient":[75],"Descent":[76],"algorithm":[77],"for":[78,88],"train":[82],"Convolutional":[84],"Neural":[85],"Network":[86],"(CNN)":[87],"natural":[90],"language":[91],"processing":[92],"task":[93],"information":[95],"extraction":[96],"from":[97],"massive":[99],"dataset":[100],"cancer":[102],"pathology":[103],"reports.":[104],"We":[105,152,211],"evaluated":[106],"scalability":[108],"improvements":[109],"using":[110,192],"training":[113,145,170,208,216],"Titan":[116],"supercomputer":[117],"at":[118,159],"Oak":[119],"Ridge":[120],"Leadership":[121],"Facility.":[123],"To":[124],"evaluate":[125],"scalability,":[126],"different":[129,144],"numbers":[130],"worker":[132],"performed":[135],"set":[137],"experiments":[139],"comparing":[140],"effects":[142],"batch":[146,194],"sizes":[147],"optimizer":[149,180],"functions.":[150],"RESULTS:":[151],"found":[153],"that":[154,213],"Adadelta":[155],"would":[156],"consistently":[157,181],"converge":[158,204],"lower":[161],"validation":[162,188],"loss,":[163],"though":[164],"requiring":[165],"over":[166],"twice":[167],"as":[168,172],"many":[169],"epochs":[171],"fastest":[174],"converging":[175],"optimizer,":[176],"RMSProp.":[177],"The":[178],"Adam":[179],"achieved":[182],"close":[184],"2nd":[185],"place":[186],"minimum":[187],"loss":[189],"significantly":[190],"faster;":[191],"size":[195],"16":[197],"32":[199],"allowed":[200],"network":[202],"only":[206],"4.5":[207],"epochs.":[209],"CONCLUSIONS:":[210],"demonstrated":[212],"networked":[215],"process":[217],"scalable":[219],"compute":[222],"communicating":[224],"message":[226],"passing":[227],"interface":[228],"while":[229],"achieving":[230],"higher":[231],"classification":[232],"accuracy":[233],"compared":[234],"traditional":[237],"machine":[238],"learning":[239],"algorithm.":[240]},"counts_by_year":[{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":3}],"updated_date":"2026-05-07T13:39:58.223016","created_date":"2025-10-10T00:00:00"}
