{"id":"https://openalex.org/W4385563407","doi":"https://doi.org/10.1093/bib/bbad286","title":"HEAP: a task adaptive-based explainable deep learning framework for enhancer activity prediction","display_name":"HEAP: a task adaptive-based explainable deep learning framework for enhancer activity prediction","publication_year":2023,"publication_date":"2023-08-03","ids":{"openalex":"https://openalex.org/W4385563407","doi":"https://doi.org/10.1093/bib/bbad286","pmid":"https://pubmed.ncbi.nlm.nih.gov/37539835"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad286","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad286","pdf_url":"https://academic.oup.com/bib/article-pdf/24/5/bbad286/51710990/bbad286.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/24/5/bbad286/51710990/bbad286.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100420960","display_name":"Yuhang Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I24201400","display_name":"Chengdu University of Information Technology","ror":"https://ror.org/01yxwrh59","country_code":"CN","type":"education","lineage":["https://openalex.org/I24201400"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuhang Liu","raw_affiliation_strings":["School of Computer Science, Chengdu University of Information Technology , 610225, Chengdu , China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science, Chengdu University of Information Technology , 610225, Chengdu , China","institution_ids":["https://openalex.org/I24201400"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115602493","display_name":"Zixuan Wang","orcid":"https://orcid.org/0009-0007-6723-1822"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zixuan Wang","raw_affiliation_strings":["College of Electronics and Information Engieering, Sichuan University , 610065, Chengdu , China"],"affiliations":[{"raw_affiliation_string":"College of Electronics and Information Engieering, Sichuan University , 610065, Chengdu , China","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101881297","display_name":"Hao Yuan","orcid":"https://orcid.org/0009-0009-7192-0254"},"institutions":[{"id":"https://openalex.org/I24201400","display_name":"Chengdu University of Information Technology","ror":"https://ror.org/01yxwrh59","country_code":"CN","type":"education","lineage":["https://openalex.org/I24201400"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hao Yuan","raw_affiliation_strings":["School of Computer Science, Chengdu University of Information Technology , 610225, Chengdu , China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science, Chengdu University of Information Technology , 610225, Chengdu , China","institution_ids":["https://openalex.org/I24201400"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000700564","display_name":"Guiquan Zhu","orcid":"https://orcid.org/0000-0002-8316-5809"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guiquan Zhu","raw_affiliation_strings":["West China Hospital of Stomatology, Sichuan University , 610041, Chengdu , China"],"affiliations":[{"raw_affiliation_string":"West China Hospital of Stomatology, Sichuan University , 610041, Chengdu , China","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100741917","display_name":"Yongqing Zhang","orcid":"https://orcid.org/0000-0003-3422-8305"},"institutions":[{"id":"https://openalex.org/I24201400","display_name":"Chengdu University of Information Technology","ror":"https://ror.org/01yxwrh59","country_code":"CN","type":"education","lineage":["https://openalex.org/I24201400"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yongqing Zhang","raw_affiliation_strings":["School of Computer Science, Chengdu University of Information Technology , 610225, Chengdu , China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science, Chengdu University of Information Technology , 610225, Chengdu , China","institution_ids":["https://openalex.org/I24201400"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5100741917"],"corresponding_institution_ids":["https://openalex.org/I24201400"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":1.2153,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.79383327,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"24","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","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/T10222","display_name":"Genomics and Chromatin Dynamics","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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9968000054359436,"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/T10604","display_name":"RNA Research and Splicing","score":0.9955000281333923,"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/enhancer","display_name":"Enhancer","score":0.8022024631500244},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7404475212097168},{"id":"https://openalex.org/keywords/heap","display_name":"Heap (data structure)","score":0.5958058834075928},{"id":"https://openalex.org/keywords/grammar","display_name":"Grammar","score":0.549492359161377},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5117576122283936},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.44961753487586975},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17412865161895752},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.16937124729156494},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.12198415398597717},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.11690494418144226},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08809590339660645}],"concepts":[{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.8022024631500244},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7404475212097168},{"id":"https://openalex.org/C134757568","wikidata":"https://www.wikidata.org/wiki/Q274089","display_name":"Heap (data structure)","level":2,"score":0.5958058834075928},{"id":"https://openalex.org/C26022165","wikidata":"https://www.wikidata.org/wiki/Q8091","display_name":"Grammar","level":2,"score":0.549492359161377},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5117576122283936},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.44961753487586975},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17412865161895752},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.16937124729156494},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.12198415398597717},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.11690494418144226},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08809590339660645},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbad286","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad286","pdf_url":"https://academic.oup.com/bib/article-pdf/24/5/bbad286/51710990/bbad286.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37539835","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37539835","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bib/bbad286","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad286","pdf_url":"https://academic.oup.com/bib/article-pdf/24/5/bbad286/51710990/bbad286.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6399999856948853,"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4"}],"awards":[{"id":"https://openalex.org/G1121271761","display_name":null,"funder_award_id":"Program","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G1231421488","display_name":null,"funder_award_id":"under","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2087396116","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5939423041","display_name":null,"funder_award_id":"Technology","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5994120800","display_name":null,"funder_award_id":"Natural","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6126170064","display_name":null,"funder_award_id":"2022001","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7726157001","display_name":null,"funder_award_id":"Grant No.","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8617958116","display_name":null,"funder_award_id":"62272067","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320311826","display_name":"Chengdu University of Information Technology","ror":"https://ror.org/01yxwrh59"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320328111","display_name":"Chengdu University","ror":"https://ror.org/034z67559"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4385563407.pdf"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1986865417","https://openalex.org/W2067786443","https://openalex.org/W2102619694","https://openalex.org/W2103777723","https://openalex.org/W2183523328","https://openalex.org/W2198606573","https://openalex.org/W2259938310","https://openalex.org/W2338148720","https://openalex.org/W2341539131","https://openalex.org/W2581468399","https://openalex.org/W2591130492","https://openalex.org/W2790244616","https://openalex.org/W2924377282","https://openalex.org/W2962862931","https://openalex.org/W2968775930","https://openalex.org/W2972720099","https://openalex.org/W2989837622","https://openalex.org/W2997580108","https://openalex.org/W2998882284","https://openalex.org/W3012001726","https://openalex.org/W3045910546","https://openalex.org/W3096505797","https://openalex.org/W3117490633","https://openalex.org/W3122486793","https://openalex.org/W3129125493","https://openalex.org/W3133716533","https://openalex.org/W3162028695","https://openalex.org/W3179235883","https://openalex.org/W3180669414","https://openalex.org/W3196944487","https://openalex.org/W4213068753","https://openalex.org/W4213355816","https://openalex.org/W4220872625","https://openalex.org/W4224127506","https://openalex.org/W4280563114","https://openalex.org/W4385245566","https://openalex.org/W6736518430","https://openalex.org/W6737947904","https://openalex.org/W6739901393","https://openalex.org/W6749694348","https://openalex.org/W6770304583","https://openalex.org/W6772444045","https://openalex.org/W6791304746","https://openalex.org/W6809921208"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W3046775127","https://openalex.org/W3107602296","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W4313488044","https://openalex.org/W3209574120","https://openalex.org/W4312192474","https://openalex.org/W4210805261"],"abstract_inverted_index":{"Enhancers":[0],"are":[1],"crucial":[2],"cis-regulatory":[3],"elements":[4],"that":[5,64,129],"control":[6],"gene":[7],"expression":[8],"in":[9,23,101],"a":[10,28,86,108,173,191],"cell-type-specific":[11],"manner.":[12],"Despite":[13],"extensive":[14],"genetic":[15],"and":[16,30,55,77,134,169,179],"computational":[17],"studies,":[18],"accurately":[19],"predicting":[20,53],"enhancer":[21,44,57,69,180,201],"activity":[22,45],"different":[24,102],"cell":[25,103],"types":[26],"remains":[27],"challenge,":[29],"the":[31,136,139,149,160,183,197],"grammar":[32],"of":[33,138,176,185,200],"enhancers":[34,54,100],"is":[35],"still":[36],"poorly":[37],"understood.":[38],"Here,":[39],"we":[40,116],"present":[41],"HEAP":[42,130,152,188],"(high-resolution":[43],"prediction),":[46],"an":[47],"explainable":[48,150],"deep":[49],"learning":[50,90],"framework":[51,60,151],"for":[52,68,142,194],"exploring":[56],"grammar.":[58,181],"The":[59,71],"includes":[61],"three":[62,164],"modules":[63],"use":[65,85],"grammar-based":[66],"reasoning":[67],"prediction.":[70],"algorithm":[72],"can":[73],"incorporate":[74],"DNA":[75],"sequences":[76],"epigenetic":[78],"modifications":[79],"to":[80,97,118,156,172],"obtain":[81],"better":[82,174],"accuracy.":[83],"We":[84,105],"novel":[87],"two-step":[88],"multi-task":[89],"method,":[91],"task":[92],"adaptive":[93],"parameter":[94],"sharing":[95],"(TAPS),":[96],"efficiently":[98],"predict":[99],"types.":[104],"first":[106],"train":[107],"shared":[109],"model":[110,167,177],"with":[111,144],"all":[112],"cell-type":[113],"datasets.":[114],"Then":[115],"adapt":[117],"specific":[119],"tasks":[120],"by":[121],"adding":[122],"several":[123],"task-specific":[124],"subset":[125],"layers.":[126],"Experiments":[127],"demonstrate":[128],"outperforms":[131],"published":[132],"methods":[133],"showcases":[135],"effectiveness":[137],"TAPS,":[140],"especially":[141],"those":[143],"limited":[145],"training":[146],"samples.":[147],"Notably,":[148],"utilizes":[153],"post-hoc":[154],"interpretation":[155],"provide":[157],"insights":[158],"into":[159,196],"prediction":[161],"mechanisms":[162,199],"from":[163],"perspectives:":[165],"data,":[166],"architecture":[168],"algorithm,":[170],"leading":[171],"understanding":[175],"decisions":[178],"To":[182],"best":[184],"our":[186],"knowledge,":[187],"will":[189],"be":[190],"valuable":[192],"tool":[193],"insight":[195],"complex":[198],"activity.":[202]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3}],"updated_date":"2026-04-13T07:58:08.660418","created_date":"2025-10-10T00:00:00"}
