{"id":"https://openalex.org/W7126066062","doi":"https://doi.org/10.1109/bibm66473.2025.11356776","title":"PlantBiMoE: A Bidirectional Foundation Model with Sparsemoe for Plant Genomes","display_name":"PlantBiMoE: A Bidirectional Foundation Model with Sparsemoe for Plant Genomes","publication_year":2025,"publication_date":"2025-12-15","ids":{"openalex":"https://openalex.org/W7126066062","doi":"https://doi.org/10.1109/bibm66473.2025.11356776"},"language":null,"primary_location":{"id":"doi:10.1109/bibm66473.2025.11356776","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356776","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Kepeng Lin","orcid":null},"institutions":[{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Kepeng Lin","raw_affiliation_strings":["School of Electronic Information and Communications, Huazhong University of Science and Technology,Wuhan,China,430074"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Electronic Information and Communications, Huazhong University of Science and Technology,Wuhan,China,430074","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028190701","display_name":"Qizhe Zhang","orcid":"https://orcid.org/0000-0003-2286-3029"},"institutions":[{"id":"https://openalex.org/I37461747","display_name":"Wuhan University","ror":"https://ror.org/033vjfk17","country_code":"CN","type":"education","lineage":["https://openalex.org/I37461747"]},{"id":"https://openalex.org/I4210114190","display_name":"Shanghai Zhangjiang Laboratory","ror":"https://ror.org/0208qbg77","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210114190"]},{"id":"https://openalex.org/I4210125402","display_name":"Hubei Zhongshan Hospital","ror":"https://ror.org/02xhgjz70","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210125402"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qizhe Zhang","raw_affiliation_strings":["Hubei Hongshan Laboratory,Wuhan,China,430070"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hubei Hongshan Laboratory,Wuhan,China,430070","institution_ids":["https://openalex.org/I4210125402","https://openalex.org/I37461747","https://openalex.org/I4210114190"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124265284","display_name":"Rui Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I37461747","display_name":"Wuhan University","ror":"https://ror.org/033vjfk17","country_code":"CN","type":"education","lineage":["https://openalex.org/I37461747"]},{"id":"https://openalex.org/I4210114190","display_name":"Shanghai Zhangjiang Laboratory","ror":"https://ror.org/0208qbg77","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210114190"]},{"id":"https://openalex.org/I4210125402","display_name":"Hubei Zhongshan Hospital","ror":"https://ror.org/02xhgjz70","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210125402"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Rui Wang","raw_affiliation_strings":["Hubei Hongshan Laboratory,Wuhan,China,430070"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hubei Hongshan Laboratory,Wuhan,China,430070","institution_ids":["https://openalex.org/I4210125402","https://openalex.org/I37461747","https://openalex.org/I4210114190"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124194705","display_name":"Xuehai Hu","orcid":null},"institutions":[{"id":"https://openalex.org/I37461747","display_name":"Wuhan University","ror":"https://ror.org/033vjfk17","country_code":"CN","type":"education","lineage":["https://openalex.org/I37461747"]},{"id":"https://openalex.org/I4210114190","display_name":"Shanghai Zhangjiang Laboratory","ror":"https://ror.org/0208qbg77","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210114190"]},{"id":"https://openalex.org/I4210125402","display_name":"Hubei Zhongshan Hospital","ror":"https://ror.org/02xhgjz70","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210125402"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuehai Hu","raw_affiliation_strings":["Hubei Hongshan Laboratory,Wuhan,China,430070"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hubei Hongshan Laboratory,Wuhan,China,430070","institution_ids":["https://openalex.org/I4210125402","https://openalex.org/I37461747","https://openalex.org/I4210114190"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100738462","display_name":"Wei Xu","orcid":"https://orcid.org/0000-0003-0816-6016"},"institutions":[{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wei Xu","raw_affiliation_strings":["School of Electronic Information and Communications, Huazhong University of Science and Technology,Wuhan,China,430074"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Electronic Information and Communications, Huazhong University of Science and Technology,Wuhan,China,430074","institution_ids":["https://openalex.org/I47720641"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1765","last_page":"1770"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.19979999959468842,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.19979999959468842,"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":0.1956000030040741,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.10949999839067459,"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/benchmark","display_name":"Benchmark (surveying)","score":0.6830000281333923},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6782000064849854},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.48660001158714294},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.40619999170303345},{"id":"https://openalex.org/keywords/computational-model","display_name":"Computational model","score":0.3937999904155731},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.38830000162124634},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.3634999990463257}],"concepts":[{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.6830000281333923},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6782000064849854},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6327999830245972},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.48660001158714294},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.48249998688697815},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.40619999170303345},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.3937999904155731},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.38830000162124634},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.3634999990463257},{"id":"https://openalex.org/C179799912","wikidata":"https://www.wikidata.org/wiki/Q205084","display_name":"Computational complexity theory","level":2,"score":0.33869999647140503},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.3147999942302704},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3133000135421753},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3070000112056732},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.30059999227523804},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.29260000586509705},{"id":"https://openalex.org/C105565629","wikidata":"https://www.wikidata.org/wiki/Q1248292","display_name":"Gene prediction","level":4,"score":0.2827000021934509},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.2743000090122223},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.26109999418258667},{"id":"https://openalex.org/C125411270","wikidata":"https://www.wikidata.org/wiki/Q18653","display_name":"Encoding (memory)","level":2,"score":0.258899986743927},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.2563000023365021},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.25380000472068787},{"id":"https://openalex.org/C39238701","wikidata":"https://www.wikidata.org/wiki/Q2091816","display_name":"Computational genomics","level":5,"score":0.25110000371932983}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm66473.2025.11356776","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356776","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5448909361","display_name":null,"funder_award_id":"2023YFD1202903","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"}],"funders":[{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":15,"referenced_works":["https://openalex.org/W1978654848","https://openalex.org/W2063291945","https://openalex.org/W2064675550","https://openalex.org/W2150884987","https://openalex.org/W2477453901","https://openalex.org/W2962834855","https://openalex.org/W3127238141","https://openalex.org/W3164328317","https://openalex.org/W3165538067","https://openalex.org/W4400451184","https://openalex.org/W4400580495","https://openalex.org/W4404349982","https://openalex.org/W4404821554","https://openalex.org/W4405175768","https://openalex.org/W4411141228"],"related_works":[],"abstract_inverted_index":{"Understanding":[0],"the":[1,37,73,82,92,111,147,157],"underlying":[2],"linguistic":[3],"rules":[4],"of":[5,40,94,153],"plant":[6,55,177,195],"genomes":[7],"remains":[8],"a":[9,51,64,182],"fundamental":[10],"challenge":[11],"in":[12],"computational":[13,98,184],"biology.":[14,201],"Recent":[15],"advances":[16],"including":[17],"AgroNT":[18],"and":[19,32,53,63,84,106,156,199],"PDLLMs":[20],"have":[21],"made":[22],"notable":[23],"progress":[24],"although,":[25],"they":[26],"suffer":[27],"from":[28,134],"excessive":[29],"parameter":[30],"size":[31],"limited":[33],"ability":[34],"to":[35,75,136,194],"model":[36,58,74,109,173],"bidirectional":[38,61,70],"nature":[39],"DNA":[41,86],"strands":[42],"respectively.":[43],"To":[44],"address":[45],"these":[46],"limitations,":[47],"we":[48],"propose":[49],"PlantBiMoE,":[50],"lightweight":[52],"expressive":[54],"genome":[56],"language":[57],"that":[59,144,171],"integrates":[60],"Mamba":[62,71],"Sparse":[65],"Mixture-of-Experts":[66],"(SparseMoE)":[67],"framework.":[68],"The":[69,202],"enables":[72],"effectively":[76,175],"capture":[77],"structural":[78],"dependencies":[79],"across":[80,125],"both":[81],"forward":[83],"reverse":[85],"strands,":[87],"while":[88,190],"SparseMoE":[89],"significantly":[90],"reduces":[91],"number":[93],"active":[95],"parameters,":[96],"improving":[97],"efficiency":[99],"without":[100],"sacrificing":[101],"modeling":[102],"capacity.":[103],"We":[104],"evaluated":[105],"tested":[107],"our":[108,172],"on":[110,150],"Modified":[112],"Plants":[113],"Genome":[114],"Benchmark":[115],"(MPGB),":[116],"an":[117],"enhanced":[118],"genomic":[119,178,188],"benchmark,":[120],"which":[121],"consolidates":[122],"31":[123,154],"datasets":[124,155],"11":[126],"representative":[127],"tasks,":[128,189],"with":[129,162],"input":[130],"sequence":[131],"lengths":[132],"ranging":[133],"50":[135],"<tex":[137],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[138],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">$6,000":[139],"\\text{bp}$</tex>.":[140],"Experimental":[141],"results":[142,169],"demonstrate":[143,170],"PlantBiMoE":[145],"achieves":[146],"best":[148,159],"performance":[149],"20":[151],"out":[152],"average":[158],"when":[160],"comparing":[161],"existing":[163],"models.":[164],"In":[165],"summary,":[166],"all":[167],"above":[168],"can":[174],"represent":[176],"sequences,":[179],"serving":[180],"as":[181],"robust":[183],"tool":[185],"for":[186],"diverse":[187],"making":[191],"substantive":[192],"contributions":[193],"genomics,":[196],"gene":[197],"editing,":[198],"synthetic":[200],"code":[203],"is":[204],"available":[205],"at:":[206],"https://github.com/HUST-Keep-Lin/PlantBiMoE.":[207]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2026-01-30T00:00:00"}
