{"id":"https://openalex.org/W4404927047","doi":"https://doi.org/10.1007/s10489-024-05848-6","title":"LOCO-EPI: Leave-one-chromosome-out (LOCO) as a benchmarking paradigm for deep learning based prediction of enhancer-promoter interactions","display_name":"LOCO-EPI: Leave-one-chromosome-out (LOCO) as a benchmarking paradigm for deep learning based prediction of enhancer-promoter interactions","publication_year":2024,"publication_date":"2024-12-02","ids":{"openalex":"https://openalex.org/W4404927047","doi":"https://doi.org/10.1007/s10489-024-05848-6"},"language":"en","primary_location":{"id":"doi:10.1007/s10489-024-05848-6","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10489-024-05848-6","pdf_url":null,"source":{"id":"https://openalex.org/S74726891","display_name":"Applied Intelligence","issn_l":"0924-669X","issn":["0924-669X","1573-7497"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Applied Intelligence","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2504.00306","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5078898675","display_name":"Muhammad Tahir","orcid":"https://orcid.org/0000-0002-7450-5840"},"institutions":[{"id":"https://openalex.org/I46247651","display_name":"University of Manitoba","ror":"https://ror.org/02gfys938","country_code":"CA","type":"education","lineage":["https://openalex.org/I46247651"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Muhammad Tahir","raw_affiliation_strings":["Department of Electrical and Computer Engineering, University of Manitoba, R3T 5V6, Winnipeg, MB, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, University of Manitoba, R3T 5V6, Winnipeg, MB, Canada","institution_ids":["https://openalex.org/I46247651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045267281","display_name":"Shehroz S. Khan","orcid":"https://orcid.org/0000-0002-1195-4999"},"institutions":[{"id":"https://openalex.org/I2803079837","display_name":"American University of the Middle East","ror":"https://ror.org/02gqgne03","country_code":"KW","type":"education","lineage":["https://openalex.org/I2803079837"]}],"countries":["KW"],"is_corresponding":false,"raw_author_name":"Shehroz S. Khan","raw_affiliation_strings":["College of Engineering and Technology, American University of the Middle East, Kuwait city, Kuwait"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Engineering and Technology, American University of the Middle East, Kuwait city, Kuwait","institution_ids":["https://openalex.org/I2803079837"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048849645","display_name":"James Davie","orcid":"https://orcid.org/0000-0002-0420-6888"},"institutions":[{"id":"https://openalex.org/I46247651","display_name":"University of Manitoba","ror":"https://ror.org/02gfys938","country_code":"CA","type":"education","lineage":["https://openalex.org/I46247651"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"James Davie","raw_affiliation_strings":["Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada","institution_ids":["https://openalex.org/I46247651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058429468","display_name":"Soichiro Yamanaka","orcid":"https://orcid.org/0000-0003-0210-0382"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Soichiro Yamanaka","raw_affiliation_strings":["Graduate School of Science, Department of Biophysics and Biochemistry, University of Tokyo, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate School of Science, Department of Biophysics and Biochemistry, University of Tokyo, Tokyo, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042544444","display_name":"Ahmed Ashraf","orcid":"https://orcid.org/0000-0002-0463-4102"},"institutions":[{"id":"https://openalex.org/I46247651","display_name":"University of Manitoba","ror":"https://ror.org/02gfys938","country_code":"CA","type":"education","lineage":["https://openalex.org/I46247651"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Ahmed Ashraf","raw_affiliation_strings":["Department of Electrical and Computer Engineering, University of Manitoba, R3T 5V6, Winnipeg, MB, Canada"],"raw_orcid":"https://orcid.org/0000-0002-0463-4102","affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, University of Manitoba, R3T 5V6, Winnipeg, MB, Canada","institution_ids":["https://openalex.org/I46247651"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5042544444"],"corresponding_institution_ids":["https://openalex.org/I46247651"],"apc_list":{"value":2990,"currency":"USD","value_usd":2990},"apc_paid":null,"fwci":0.9632,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.74507103,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"55","issue":"1","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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9993000030517578,"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":0.9991999864578247,"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":0.7750450968742371},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7479343414306641},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.742296040058136},{"id":"https://openalex.org/keywords/chromosome","display_name":"Chromosome","score":0.47086966037750244},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4068794846534729},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3456885516643524},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24734187126159668},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1856936812400818},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12029987573623657},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.09055250883102417}],"concepts":[{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.7750450968742371},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7479343414306641},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.742296040058136},{"id":"https://openalex.org/C30481170","wikidata":"https://www.wikidata.org/wiki/Q37748","display_name":"Chromosome","level":3,"score":0.47086966037750244},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4068794846534729},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3456885516643524},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24734187126159668},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1856936812400818},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12029987573623657},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.09055250883102417},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1007/s10489-024-05848-6","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10489-024-05848-6","pdf_url":null,"source":{"id":"https://openalex.org/S74726891","display_name":"Applied Intelligence","issn_l":"0924-669X","issn":["0924-669X","1573-7497"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Applied Intelligence","raw_type":"journal-article"},{"id":"pmh:oai:arXiv.org:2504.00306","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2504.00306","pdf_url":"https://arxiv.org/pdf/2504.00306","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":"text"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2504.00306","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2504.00306","pdf_url":"https://arxiv.org/pdf/2504.00306","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":"text"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320334506","display_name":"Canadian Institutes of Health Research","ror":"https://ror.org/01gavpb45"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":58,"referenced_works":["https://openalex.org/W1149957381","https://openalex.org/W1941076503","https://openalex.org/W1973062929","https://openalex.org/W1981276685","https://openalex.org/W1987371782","https://openalex.org/W1999532833","https://openalex.org/W2011463791","https://openalex.org/W2020217377","https://openalex.org/W2099521715","https://openalex.org/W2114024619","https://openalex.org/W2124266758","https://openalex.org/W2136170142","https://openalex.org/W2139166279","https://openalex.org/W2145144631","https://openalex.org/W2324629078","https://openalex.org/W2328176404","https://openalex.org/W2333286569","https://openalex.org/W2413285763","https://openalex.org/W2470258573","https://openalex.org/W2553838260","https://openalex.org/W2564164333","https://openalex.org/W2742892125","https://openalex.org/W2768844315","https://openalex.org/W2782196652","https://openalex.org/W2800857888","https://openalex.org/W2883604250","https://openalex.org/W2892079508","https://openalex.org/W2903262559","https://openalex.org/W2911079020","https://openalex.org/W2951218167","https://openalex.org/W2968830255","https://openalex.org/W2971769670","https://openalex.org/W2993022331","https://openalex.org/W3044447231","https://openalex.org/W3093812284","https://openalex.org/W3096005429","https://openalex.org/W3096831136","https://openalex.org/W3099969680","https://openalex.org/W3104691427","https://openalex.org/W3115055674","https://openalex.org/W3156113107","https://openalex.org/W3196444943","https://openalex.org/W3209882608","https://openalex.org/W4205411722","https://openalex.org/W4205953903","https://openalex.org/W4234866497","https://openalex.org/W4282984452","https://openalex.org/W4285094511","https://openalex.org/W4293868238","https://openalex.org/W4297253404","https://openalex.org/W4308139740","https://openalex.org/W4309400060","https://openalex.org/W4310675782","https://openalex.org/W4317476838","https://openalex.org/W4362523448","https://openalex.org/W4362673322","https://openalex.org/W4396495316","https://openalex.org/W4399783809"],"related_works":["https://openalex.org/W4238897586","https://openalex.org/W435179959","https://openalex.org/W2619091065","https://openalex.org/W2059640416","https://openalex.org/W1490753184","https://openalex.org/W2284465472","https://openalex.org/W2152841149","https://openalex.org/W2586783543","https://openalex.org/W4387598842","https://openalex.org/W2973036402"],"abstract_inverted_index":null,"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":1}],"updated_date":"2026-08-05T07:39:15.569665","created_date":"2025-10-10T00:00:00"}
