{"id":"https://openalex.org/W2963029044","doi":"https://doi.org/10.1186/s12859-019-2957-4","title":"Visualizing complex feature interactions and feature sharing in genomic deep neural networks","display_name":"Visualizing complex feature interactions and feature sharing in genomic deep neural networks","publication_year":2019,"publication_date":"2019-07-19","ids":{"openalex":"https://openalex.org/W2963029044","doi":"https://doi.org/10.1186/s12859-019-2957-4","mag":"2963029044","pmid":"https://pubmed.ncbi.nlm.nih.gov/31324140"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-019-2957-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2957-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2957-4","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/s12859-019-2957-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100731233","display_name":"Ge Liu","orcid":"https://orcid.org/0009-0008-5124-9929"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ge Liu","raw_affiliation_strings":["Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA"],"affiliations":[{"raw_affiliation_string":"Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015255518","display_name":"Haoyang Zeng","orcid":"https://orcid.org/0000-0003-1057-2865"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Haoyang Zeng","raw_affiliation_strings":["Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA"],"affiliations":[{"raw_affiliation_string":"Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5037283552","display_name":"David K. Gifford","orcid":"https://orcid.org/0000-0003-1709-4034"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David K. Gifford","raw_affiliation_strings":["Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. gifford@mit.edu","Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA"],"affiliations":[{"raw_affiliation_string":"Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. gifford@mit.edu","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA","institution_ids":["https://openalex.org/I63966007"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5100731233"],"corresponding_institution_ids":["https://openalex.org/I63966007"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.5459,"has_fulltext":true,"cited_by_count":25,"citation_normalized_percentile":{"value":0.83210808,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"20","issue":"1","first_page":"401","last_page":"401"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9979000091552734,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9979000091552734,"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":0.9961000084877014,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9915000200271606,"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/computer-science","display_name":"Computer science","score":0.7116393446922302},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.6446625590324402},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.6441566944122314},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5272566080093384},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.5084575414657593},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.45851871371269226},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.4542056918144226},{"id":"https://openalex.org/keywords/interpretability","display_name":"Interpretability","score":0.41783416271209717},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4036811888217926}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7116393446922302},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6446625590324402},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.6441566944122314},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5272566080093384},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.5084575414657593},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.45851871371269226},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.4542056918144226},{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.41783416271209717},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4036811888217926},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006657","descriptor_name":"Histones","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006657","descriptor_name":"Histones","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006657","descriptor_name":"Histones","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006657","descriptor_name":"Histones","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D042421","descriptor_name":"Histone Code","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D042421","descriptor_name":"Histone Code","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D042421","descriptor_name":"Histone Code","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D042421","descriptor_name":"Histone Code","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-019-2957-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2957-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2957-4","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:31324140","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31324140","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:doaj.org/article:c64c7d1f60f746bbbe83a3a758dbef28","is_oa":true,"landing_page_url":"https://doaj.org/article/c64c7d1f60f746bbbe83a3a758dbef28","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"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 20, Iss 1, Pp 1-14 (2019)","raw_type":"article"},{"id":"pmh:oai:dspace.mit.edu:1721.1/126253","is_oa":true,"landing_page_url":"https://hdl.handle.net/1721.1/126253","pdf_url":null,"source":{"id":"https://openalex.org/S4306400425","display_name":"DSpace@MIT (Massachusetts Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I63966007","host_organization_name":"Massachusetts Institute of Technology","host_organization_lineage":["https://openalex.org/I63966007"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BioMed Central","raw_type":"http://purl.org/eprint/type/JournalArticle"},{"id":"pmh:oai:pubmedcentral.nih.gov:6642501","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6642501","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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/s12859-019-2957-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2957-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2957-4","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":0.75,"display_name":"Peace, Justice and strong institutions","id":"https://metadata.un.org/sdg/16"}],"awards":[{"id":"https://openalex.org/G6288217157","display_name":null,"funder_award_id":"R01CA218094","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6542914005","display_name":null,"funder_award_id":"U01HG007037","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337253","display_name":"Instituto de Ciencias del Mar y Limnolog\u00eda, Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2963029044.pdf","grobid_xml":"https://content.openalex.org/works/W2963029044.grobid-xml"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1686810756","https://openalex.org/W1787224781","https://openalex.org/W1849277567","https://openalex.org/W1932198206","https://openalex.org/W1970746718","https://openalex.org/W2006594553","https://openalex.org/W2029799334","https://openalex.org/W2040391822","https://openalex.org/W2097117768","https://openalex.org/W2103777723","https://openalex.org/W2111709760","https://openalex.org/W2133564696","https://openalex.org/W2134957137","https://openalex.org/W2163605009","https://openalex.org/W2163605769","https://openalex.org/W2169393322","https://openalex.org/W2171888347","https://openalex.org/W2185037267","https://openalex.org/W2198606573","https://openalex.org/W2282821441","https://openalex.org/W2293078015","https://openalex.org/W2345512687","https://openalex.org/W2433743436","https://openalex.org/W2528491735","https://openalex.org/W2546542913","https://openalex.org/W2592030644","https://openalex.org/W2605409611","https://openalex.org/W2618851150","https://openalex.org/W2949197630","https://openalex.org/W2949888546","https://openalex.org/W2951212842","https://openalex.org/W2951218167","https://openalex.org/W2951410692","https://openalex.org/W2951760474","https://openalex.org/W2952239877","https://openalex.org/W2952935243","https://openalex.org/W2953262163","https://openalex.org/W2963468488"],"related_works":["https://openalex.org/W2905433371","https://openalex.org/W2888392564","https://openalex.org/W4226493464","https://openalex.org/W4312417841","https://openalex.org/W3193565141","https://openalex.org/W3133861977","https://openalex.org/W2951211570","https://openalex.org/W3103566983","https://openalex.org/W3167935049","https://openalex.org/W3029198973"],"abstract_inverted_index":{"DeepResolve":[0,35],"is":[1,36],"capable":[2],"of":[3],"visualizing":[4],"complex":[5],"feature":[6,10,25],"contribution":[7],"patterns":[8],"and":[9,27,42],"interactions":[11],"that":[12],"contribute":[13],"to":[14],"decision":[15],"making":[16],"in":[17],"genomic":[18],"deep":[19],"convolutional":[20],"networks.":[21],"It":[22],"also":[23],"recovers":[24],"sharing":[26],"class":[28],"similarities":[29],"which":[30],"suggest":[31],"interesting":[32],"biological":[33],"mechanisms.":[34],"compatible":[37],"with":[38],"existing":[39],"visualization":[40],"tools":[41],"provides":[43],"complementary":[44],"insights.":[45]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":1}],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-10-10T00:00:00"}
