{"id":"https://openalex.org/W4385715465","doi":"https://doi.org/10.1093/bioinformatics/btad479","title":"BEENE: deep learning-based nonlinear embedding improves batch effect estimation","display_name":"BEENE: deep learning-based nonlinear embedding improves batch effect estimation","publication_year":2023,"publication_date":"2023-08-01","ids":{"openalex":"https://openalex.org/W4385715465","doi":"https://doi.org/10.1093/bioinformatics/btad479","pmid":"https://pubmed.ncbi.nlm.nih.gov/37561107"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad479","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad479","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad479/51088291/btad479.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad479/51088291/btad479.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101726125","display_name":"Md Ashiqur Rahman","orcid":"https://orcid.org/0000-0002-2933-2637"},"institutions":[{"id":"https://openalex.org/I219193219","display_name":"Purdue University West Lafayette","ror":"https://ror.org/02dqehb95","country_code":"US","type":"education","lineage":["https://openalex.org/I219193219"]},{"id":"https://openalex.org/I183697816","display_name":"Bangladesh University of Engineering and Technology","ror":"https://ror.org/05a1qpv97","country_code":"BD","type":"education","lineage":["https://openalex.org/I183697816"]}],"countries":["BD","US"],"is_corresponding":true,"raw_author_name":"Md Ashiqur Rahman","raw_affiliation_strings":["Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology , Dhaka 1205, Bangladesh","Department of Computer Science, Purdue University , West Lafayette, IN 47907, United States"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology , Dhaka 1205, Bangladesh","institution_ids":["https://openalex.org/I183697816"]},{"raw_affiliation_string":"Department of Computer Science, Purdue University , West Lafayette, IN 47907, United States","institution_ids":["https://openalex.org/I219193219"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043716996","display_name":"Abdullah Aman Tutul","orcid":null},"institutions":[{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]},{"id":"https://openalex.org/I183697816","display_name":"Bangladesh University of Engineering and Technology","ror":"https://ror.org/05a1qpv97","country_code":"BD","type":"education","lineage":["https://openalex.org/I183697816"]}],"countries":["BD","US"],"is_corresponding":false,"raw_author_name":"Abdullah Aman Tutul","raw_affiliation_strings":["Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology , Dhaka 1205, Bangladesh","Department of Computer Science and Engineering, Texas A&M University , College Station, TX 77843, United States"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology , Dhaka 1205, Bangladesh","institution_ids":["https://openalex.org/I183697816"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, Texas A&M University , College Station, TX 77843, United States","institution_ids":["https://openalex.org/I91045830"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113826906","display_name":"Mahfuza Sharmin","orcid":null},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mahfuza Sharmin","raw_affiliation_strings":["Department of Genetics, Stanford University , Stanford, CA 94305, United States"],"affiliations":[{"raw_affiliation_string":"Department of Genetics, Stanford University , Stanford, CA 94305, United States","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063693993","display_name":"Md. Shamsuzzoha Bayzid","orcid":"https://orcid.org/0000-0002-5640-0615"},"institutions":[{"id":"https://openalex.org/I183697816","display_name":"Bangladesh University of Engineering and Technology","ror":"https://ror.org/05a1qpv97","country_code":"BD","type":"education","lineage":["https://openalex.org/I183697816"]}],"countries":["BD"],"is_corresponding":false,"raw_author_name":"Md Shamsuzzoha Bayzid","raw_affiliation_strings":["Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology , Dhaka 1205, Bangladesh"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology , Dhaka 1205, Bangladesh","institution_ids":["https://openalex.org/I183697816"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5101726125"],"corresponding_institution_ids":["https://openalex.org/I183697816","https://openalex.org/I219193219"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.3907,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.81369743,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"39","issue":"8","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9983999729156494,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9983999729156494,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9696000218391418,"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/T12676","display_name":"Machine Learning and ELM","score":0.9492999911308289,"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/embedding","display_name":"Embedding","score":0.7293588519096375},{"id":"https://openalex.org/keywords/estimation","display_name":"Estimation","score":0.6660043597221375},{"id":"https://openalex.org/keywords/nonlinear-system","display_name":"Nonlinear system","score":0.6410219669342041},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6203361749649048},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6180787086486816},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.59267258644104},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.43094420433044434},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3896154761314392},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.06360363960266113}],"concepts":[{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.7293588519096375},{"id":"https://openalex.org/C96250715","wikidata":"https://www.wikidata.org/wiki/Q965330","display_name":"Estimation","level":2,"score":0.6660043597221375},{"id":"https://openalex.org/C158622935","wikidata":"https://www.wikidata.org/wiki/Q660848","display_name":"Nonlinear system","level":2,"score":0.6410219669342041},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6203361749649048},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6180787086486816},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.59267258644104},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.43094420433044434},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3896154761314392},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.06360363960266113},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","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":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007963","descriptor_name":"Leukocytes, Mononuclear","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007963","descriptor_name":"Leukocytes, Mononuclear","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007963","descriptor_name":"Leukocytes, Mononuclear","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad479","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad479","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad479/51088291/btad479.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37561107","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37561107","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10448987","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10448987","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10448987/pdf/btad479.pdf","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad479","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad479","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad479/51088291/btad479.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.41999998688697815},{"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17","score":0.4099999964237213}],"awards":[{"id":"https://openalex.org/G7192019233","display_name":null,"funder_award_id":"2021-01-016","funder_id":"https://openalex.org/F4320325821","funder_display_name":"Bangladesh University of Engineering and Technology"}],"funders":[{"id":"https://openalex.org/F4320316680","display_name":"University of Engineering and Technology, Lahore","ror":"https://ror.org/0051w2v06"},{"id":"https://openalex.org/F4320325821","display_name":"Bangladesh University of Engineering and Technology","ror":"https://ror.org/05a1qpv97"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4385715465.pdf"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W1987971958","https://openalex.org/W2039521726","https://openalex.org/W2043904301","https://openalex.org/W2049446938","https://openalex.org/W2095705004","https://openalex.org/W2096192437","https://openalex.org/W2107665951","https://openalex.org/W2122982115","https://openalex.org/W2135937351","https://openalex.org/W2146512944","https://openalex.org/W2187089797","https://openalex.org/W2512452276","https://openalex.org/W2612519453","https://openalex.org/W2794480084","https://openalex.org/W2794521141","https://openalex.org/W2889326414","https://openalex.org/W2902382430","https://openalex.org/W2905317377","https://openalex.org/W2913340405","https://openalex.org/W2949067670","https://openalex.org/W2968352143","https://openalex.org/W2984472267","https://openalex.org/W3002417351","https://openalex.org/W3021272327","https://openalex.org/W3088521497","https://openalex.org/W4213108508","https://openalex.org/W4235169531","https://openalex.org/W4244364296","https://openalex.org/W4256361765","https://openalex.org/W6674330103","https://openalex.org/W6756351969"],"related_works":["https://openalex.org/W2081900870","https://openalex.org/W4375867731","https://openalex.org/W2183306018","https://openalex.org/W2549990292","https://openalex.org/W2345479200","https://openalex.org/W2951819827","https://openalex.org/W2849310602","https://openalex.org/W2611989081","https://openalex.org/W2419146053","https://openalex.org/W4380075502"],"abstract_inverted_index":{"BEENE":[0],"is":[1],"freely":[2],"available":[3],"as":[4],"an":[5],"open":[6],"source":[7],"project":[8],"at":[9],"https://github.com/ashiq24/BEENE.":[10]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":2}],"updated_date":"2026-03-26T15:22:09.906841","created_date":"2025-10-10T00:00:00"}
