{"id":"https://openalex.org/W6949179217","doi":"https://doi.org/10.5281/zenodo.14622041","title":"UniversalEPI: a generalized attention-based deep ensemble model to accurately predict enhancer-promoter interactions across diverse cell types and conditions","display_name":"UniversalEPI: a generalized attention-based deep ensemble model to accurately predict enhancer-promoter interactions across diverse cell types and conditions","publication_year":2025,"publication_date":"2025-01-09","ids":{"openalex":"https://openalex.org/W6949179217","doi":"https://doi.org/10.5281/zenodo.14622041"},"language":"en","primary_location":{"id":"doi:10.5281/zenodo.14622041","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.14622041","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},"type":"other","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.5281/zenodo.14622041","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Grover, Aayush","orcid":"https://orcid.org/0000-0002-5201-0070"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Grover, Aayush","raw_affiliation_strings":["ETH Z\u00fcrich"],"raw_orcid":"https://orcid.org/0000-0002-5201-0070","affiliations":[{"raw_affiliation_string":"ETH Z\u00fcrich","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Zhang, Lin","orcid":"https://orcid.org/0000-0001-5245-4766"},"institutions":[{"id":"https://openalex.org/I4210122261","display_name":"Swiss Data Science Center","ror":"https://ror.org/02hdt9m26","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I2799323385","https://openalex.org/I35440088","https://openalex.org/I4210122261","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Zhang, Lin","raw_affiliation_strings":["Swiss Data Science Center"],"raw_orcid":"https://orcid.org/0000-0001-5245-4766","affiliations":[{"raw_affiliation_string":"Swiss Data Science Center","institution_ids":["https://openalex.org/I4210122261"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Muser, Till","orcid":"https://orcid.org/0000-0002-9856-4554"},"institutions":[{"id":"https://openalex.org/I4210122261","display_name":"Swiss Data Science Center","ror":"https://ror.org/02hdt9m26","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I2799323385","https://openalex.org/I35440088","https://openalex.org/I4210122261","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Muser, Till","raw_affiliation_strings":["Swiss Data Science Center"],"raw_orcid":"https://orcid.org/0000-0002-9856-4554","affiliations":[{"raw_affiliation_string":"Swiss Data Science Center","institution_ids":["https://openalex.org/I4210122261"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Haefliger, Simeon","orcid":null},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Haefliger, Simeon","raw_affiliation_strings":["ETH Zurich"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ETH Zurich","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Wang, Minjia","orcid":"https://orcid.org/0000-0002-7847-4818"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Wang, Minjia","raw_affiliation_strings":["ETH Zurich"],"raw_orcid":"https://orcid.org/0000-0002-7847-4818","affiliations":[{"raw_affiliation_string":"ETH Zurich","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Yates, Josephine","orcid":"https://orcid.org/0000-0001-8346-4502"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Yates, Josephine","raw_affiliation_strings":["ETH Zurich"],"raw_orcid":"https://orcid.org/0000-0001-8346-4502","affiliations":[{"raw_affiliation_string":"ETH Zurich","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Van Allen, Eliezer","orcid":"https://orcid.org/0000-0002-0201-4444"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Van Allen, Eliezer","raw_affiliation_strings":["Broad Institute"],"raw_orcid":"https://orcid.org/0000-0002-0201-4444","affiliations":[{"raw_affiliation_string":"Broad Institute","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Theis, Fabian","orcid":"https://orcid.org/0000-0002-2419-1943"},"institutions":[{"id":"https://openalex.org/I3018134672","display_name":"Helmholtz Zentrum M\u00fcnchen","ror":"https://ror.org/00cfam450","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I3018134672"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Theis, Fabian","raw_affiliation_strings":["Helmholtz Zentrum M\u00fcnchen"],"raw_orcid":"https://orcid.org/0000-0002-2419-1943","affiliations":[{"raw_affiliation_string":"Helmholtz Zentrum M\u00fcnchen","institution_ids":["https://openalex.org/I3018134672"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Ibarra, Ignacio","orcid":"https://orcid.org/0000-0002-0582-002X"},"institutions":[{"id":"https://openalex.org/I3018134672","display_name":"Helmholtz Zentrum M\u00fcnchen","ror":"https://ror.org/00cfam450","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I3018134672"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Ibarra, Ignacio","raw_affiliation_strings":["Helmholtz Zentrum M\u00fcnchen"],"raw_orcid":"https://orcid.org/0000-0002-0582-002X","affiliations":[{"raw_affiliation_string":"Helmholtz Zentrum M\u00fcnchen","institution_ids":["https://openalex.org/I3018134672"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Krymova, Ekaterina","orcid":"https://orcid.org/0000-0002-5313-3451"},"institutions":[{"id":"https://openalex.org/I4210122261","display_name":"Swiss Data Science Center","ror":"https://ror.org/02hdt9m26","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I2799323385","https://openalex.org/I35440088","https://openalex.org/I4210122261","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Krymova, Ekaterina","raw_affiliation_strings":["Swiss Data Science Center"],"raw_orcid":"https://orcid.org/0000-0002-5313-3451","affiliations":[{"raw_affiliation_string":"Swiss Data Science Center","institution_ids":["https://openalex.org/I4210122261"]}]},{"author_position":"last","author":{"id":null,"display_name":"Boeva, Valentina","orcid":"https://orcid.org/0000-0002-4382-7185"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Boeva, Valentina","raw_affiliation_strings":["ETH Zurich"],"raw_orcid":"https://orcid.org/0000-0002-4382-7185","affiliations":[{"raw_affiliation_string":"ETH Zurich","institution_ids":["https://openalex.org/I35440088"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":11,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I35440088"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":true,"primary_topic":null,"topics":[],"keywords":[{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.47850000858306885},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4731999933719635},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.4578000009059906},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.41769999265670776},{"id":"https://openalex.org/keywords/type","display_name":"Type (biology)","score":0.39340001344680786},{"id":"https://openalex.org/keywords/data-type","display_name":"Data type","score":0.35339999198913574}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5925999879837036},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5259000062942505},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.47850000858306885},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4731999933719635},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.4578000009059906},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.41769999265670776},{"id":"https://openalex.org/C2777299769","wikidata":"https://www.wikidata.org/wiki/Q3707858","display_name":"Type (biology)","level":2,"score":0.39340001344680786},{"id":"https://openalex.org/C138958017","wikidata":"https://www.wikidata.org/wiki/Q190087","display_name":"Data type","level":2,"score":0.35339999198913574},{"id":"https://openalex.org/C119898033","wikidata":"https://www.wikidata.org/wiki/Q3433888","display_name":"Ensemble forecasting","level":2,"score":0.34700000286102295},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.34369999170303345},{"id":"https://openalex.org/C45942800","wikidata":"https://www.wikidata.org/wiki/Q245652","display_name":"Ensemble learning","level":2,"score":0.34150001406669617},{"id":"https://openalex.org/C5274069","wikidata":"https://www.wikidata.org/wiki/Q2285707","display_name":"Categorical variable","level":2,"score":0.29159998893737793},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.2847999930381775},{"id":"https://openalex.org/C189014844","wikidata":"https://www.wikidata.org/wiki/Q189118","display_name":"Cell type","level":3,"score":0.28189998865127563},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2800000011920929},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.25850000977516174}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.5281/zenodo.14622041","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.14622041","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"doi:10.5281/zenodo.14622041","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.14622041","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"UniversalEPI":[0],"is":[1],"an":[2],"attention-based":[3],"deep":[4],"ensemble":[5],"designed":[6],"to":[7,12,40],"predict":[8],"enhancer-promoter":[9],"interactions":[10],"up":[11],"2":[13],"Mb,":[14],"which":[15],"can":[16],"generalize":[17],"across":[18],"unseen":[19],"cell":[20],"types":[21],"using":[22],"only":[23],"DNA":[24],"sequence":[25],"and":[26,36],"chromatin":[27],"accessibility":[28],"(ATAC-seq)":[29],"data":[30],"as":[31],"input.":[32],"The":[33],"source":[34],"code":[35],"model":[37],"checkpoints":[38],"corresponding":[39],"the":[41],"main":[42],"manuscript":[43],"are":[44],"released":[45],"here.":[46]},"counts_by_year":[],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
