{"id":"https://openalex.org/W2973033739","doi":"https://doi.org/10.1145/3307339.3342140","title":"Transmembrane Topology Identification by Fusing Evolutionary and Co-evolutionary Information with Cascaded Bidirectional Transformers","display_name":"Transmembrane Topology Identification by Fusing Evolutionary and Co-evolutionary Information with Cascaded Bidirectional Transformers","publication_year":2019,"publication_date":"2019-09-04","ids":{"openalex":"https://openalex.org/W2973033739","doi":"https://doi.org/10.1145/3307339.3342140","mag":"2973033739"},"language":"en","primary_location":{"id":"doi:10.1145/3307339.3342140","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3307339.3342140","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"type":"article","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":"https://openalex.org/A5100332625","display_name":"Zhen Li","orcid":"https://orcid.org/0000-0002-7669-2686"},"institutions":[{"id":"https://openalex.org/I4210116924","display_name":"Chinese University of Hong Kong, Shenzhen","ror":"https://ror.org/02d5ks197","country_code":"CN","type":"education","lineage":["https://openalex.org/I177725633","https://openalex.org/I180726961","https://openalex.org/I4210116924"]},{"id":"https://openalex.org/I160992636","display_name":"Toyota Technological Institute at Chicago","ror":"https://ror.org/02sn5gb64","country_code":"US","type":"education","lineage":["https://openalex.org/I160992636"]},{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"CN","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["CN","US"],"is_corresponding":true,"raw_author_name":"Zhen Li","raw_affiliation_strings":["The Chinese University of Hong Kong & Toyota Technological Institute at Chicago, Shenzhen, IL, China"],"affiliations":[{"raw_affiliation_string":"The Chinese University of Hong Kong & Toyota Technological Institute at Chicago, Shenzhen, IL, China","institution_ids":["https://openalex.org/I177725633","https://openalex.org/I160992636","https://openalex.org/I4210116924"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002842265","display_name":"Chongming Ni","orcid":null},"institutions":[{"id":"https://openalex.org/I160992636","display_name":"Toyota Technological Institute at Chicago","ror":"https://ror.org/02sn5gb64","country_code":"US","type":"education","lineage":["https://openalex.org/I160992636"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chongming Ni","raw_affiliation_strings":["Toyota Technological Institute at Chicago, Chicago, IL, China"],"affiliations":[{"raw_affiliation_string":"Toyota Technological Institute at Chicago, Chicago, IL, China","institution_ids":["https://openalex.org/I160992636"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019398608","display_name":"Jinbo Xu","orcid":"https://orcid.org/0000-0001-7111-4839"},"institutions":[{"id":"https://openalex.org/I160992636","display_name":"Toyota Technological Institute at Chicago","ror":"https://ror.org/02sn5gb64","country_code":"US","type":"education","lineage":["https://openalex.org/I160992636"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jinbo Xu","raw_affiliation_strings":["Toyota Technological Institute at Chicago, Chicago, IL, USA"],"affiliations":[{"raw_affiliation_string":"Toyota Technological Institute at Chicago, Chicago, IL, USA","institution_ids":["https://openalex.org/I160992636"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100618900","display_name":"Xin Gao","orcid":"https://orcid.org/0000-0002-7108-3574"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Xin Gao","raw_affiliation_strings":["King Abdullah University of Science and Technology, Thuwal, IL, Saudi Arabia"],"affiliations":[{"raw_affiliation_string":"King Abdullah University of Science and Technology, Thuwal, IL, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009164482","display_name":"Shuguang Cui","orcid":"https://orcid.org/0000-0003-2608-775X"},"institutions":[{"id":"https://openalex.org/I4210099586","display_name":"Shenzhen Research Institute of Big Data","ror":"https://ror.org/00z1gwf89","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210099586"]},{"id":"https://openalex.org/I4210116924","display_name":"Chinese University of Hong Kong, Shenzhen","ror":"https://ror.org/02d5ks197","country_code":"CN","type":"education","lineage":["https://openalex.org/I177725633","https://openalex.org/I180726961","https://openalex.org/I4210116924"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shuguang Cui","raw_affiliation_strings":["The Chinese University of Hong Kong & Shenzhen Research Institute of Big Data, Shenzhen, IL, China"],"affiliations":[{"raw_affiliation_string":"The Chinese University of Hong Kong & Shenzhen Research Institute of Big Data, Shenzhen, IL, China","institution_ids":["https://openalex.org/I4210116924","https://openalex.org/I4210099586"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100371324","display_name":"Sheng Wang","orcid":"https://orcid.org/0000-0003-4210-1670"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Sheng Wang","raw_affiliation_strings":["King Abdullah University of Science and Technology & amp; Toyota Technological Institute at Chicago, Thuwal, Saudi Arabia","King Abdullah University of Science and Technology & amp"],"affiliations":[{"raw_affiliation_string":"King Abdullah University of Science and Technology & amp; Toyota Technological Institute at Chicago, Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]},{"raw_affiliation_string":"King Abdullah University of Science and Technology & amp","institution_ids":["https://openalex.org/I71920554"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5100332625"],"corresponding_institution_ids":["https://openalex.org/I160992636","https://openalex.org/I177725633","https://openalex.org/I4210116924"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.08475122,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"136","last_page":"143"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9995999932289124,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9975000023841858,"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/topology","display_name":"Topology (electrical circuits)","score":0.705085039138794},{"id":"https://openalex.org/keywords/transmembrane-protein","display_name":"Transmembrane protein","score":0.64975506067276},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.6303554177284241},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6133396625518799},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.563190758228302},{"id":"https://openalex.org/keywords/network-topology","display_name":"Network topology","score":0.4657714068889618},{"id":"https://openalex.org/keywords/transmembrane-domain","display_name":"Transmembrane domain","score":0.42468762397766113},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3373318910598755},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2587631344795227},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.11595296859741211},{"id":"https://openalex.org/keywords/computer-network","display_name":"Computer network","score":0.11098843812942505},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10080352425575256},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.0932762622833252},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.06483939290046692}],"concepts":[{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.705085039138794},{"id":"https://openalex.org/C24530287","wikidata":"https://www.wikidata.org/wiki/Q424204","display_name":"Transmembrane protein","level":3,"score":0.64975506067276},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.6303554177284241},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6133396625518799},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.563190758228302},{"id":"https://openalex.org/C199845137","wikidata":"https://www.wikidata.org/wiki/Q145490","display_name":"Network topology","level":2,"score":0.4657714068889618},{"id":"https://openalex.org/C118892022","wikidata":"https://www.wikidata.org/wiki/Q7834587","display_name":"Transmembrane domain","level":3,"score":0.42468762397766113},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3373318910598755},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2587631344795227},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.11595296859741211},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.11098843812942505},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10080352425575256},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0932762622833252},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.06483939290046692},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3307339.3342140","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3307339.3342140","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.6899999976158142,"id":"https://metadata.un.org/sdg/10","display_name":"Reduced inequalities"}],"awards":[{"id":"https://openalex.org/G1758905538","display_name":"INSTRUCTIONAL SCIENTIFIC EQUIPMENT PROGRAM","funder_award_id":"7251409","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2229035017","display_name":null,"funder_award_id":"R01GM089753","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2294964640","display_name":null,"funder_award_id":"50 and","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2533753470","display_name":null,"funder_award_id":"KQTD201503311441545","funder_id":"https://openalex.org/F4320335803","funder_display_name":"Shenzhen Fundamental Research and Discipline Layout project"},{"id":"https://openalex.org/G2627567548","display_name":"Guiding Understanding via Information from Digital Environments (GUIDE)","funder_award_id":"1503311","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3033157081","display_name":"Collaborative Research: Dayside Field-Aligned Current (FAC) Source Regions of Extreme Poynting Flux Events and the Response of the Magnetosphere-Ionosphere-Thermosphere System","funder_award_id":"1144154","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3611247453","display_name":null,"funder_award_id":"R01GM","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3910867469","display_name":null,"funder_award_id":"2017072","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4688678934","display_name":"ABI Development: Developing RaptorX Web Portal for Protein Structure and Functional Study","funder_award_id":"1564955","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5685904344","display_name":null,"funder_award_id":"2017ZT07X152","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G575036185","display_name":null,"funder_award_id":"FCC/1/197","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"},{"id":"https://openalex.org/G743072215","display_name":null,"funder_award_id":"No. KQTD2015033114415450 No. ZDSYS201707251409055 No. 2017ZT07X152","funder_id":"https://openalex.org/F4320335803","funder_display_name":"Shenzhen Fundamental Research and Discipline Layout project"},{"id":"https://openalex.org/G7805870020","display_name":null,"funder_award_id":"KQTD2015033114415450","funder_id":"https://openalex.org/F4320335803","funder_display_name":"Shenzhen Fundamental Research and Discipline Layout project"},{"id":"https://openalex.org/G7989544831","display_name":null,"funder_award_id":"ZDSYS201707251409055","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G982156559","display_name":null,"funder_award_id":"ZDSYS201707251409055","funder_id":"https://openalex.org/F4320335803","funder_display_name":"Shenzhen Fundamental Research and Discipline Layout project"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320322320","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320335803","display_name":"Shenzhen Fundamental Research and Discipline Layout project","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W1938173378","https://openalex.org/W1982583124","https://openalex.org/W2034566079","https://openalex.org/W2051210555","https://openalex.org/W2065921821","https://openalex.org/W2104467962","https://openalex.org/W2105537627","https://openalex.org/W2114340287","https://openalex.org/W2117539524","https://openalex.org/W2145336405","https://openalex.org/W2150853746","https://openalex.org/W2151156268","https://openalex.org/W2164025376","https://openalex.org/W2194775991","https://openalex.org/W2345051977","https://openalex.org/W2489780108","https://openalex.org/W2557728737","https://openalex.org/W2565639579","https://openalex.org/W2626778328","https://openalex.org/W2751052002","https://openalex.org/W2760320363","https://openalex.org/W2795783309","https://openalex.org/W2886725294","https://openalex.org/W2949867299","https://openalex.org/W2953106684","https://openalex.org/W2963341956","https://openalex.org/W2963457143","https://openalex.org/W4250482878"],"related_works":["https://openalex.org/W3099772455","https://openalex.org/W3172198228","https://openalex.org/W2129301794","https://openalex.org/W1986078734","https://openalex.org/W1540599686","https://openalex.org/W2016396528","https://openalex.org/W2261012589","https://openalex.org/W4377101717","https://openalex.org/W2584604027","https://openalex.org/W1925092754"],"abstract_inverted_index":{"The":[0],"transmembrane":[1,51,106,148],"topology":[2,22,52],"is":[3,34],"the":[4,8,20,50,61,63,69,93,99,104,111,118,123,128,147,152,157,165,184],"key":[5],"to":[6,48,96,114],"understand":[7],"3D":[9],"structures":[10],"of":[11,19,27,139,164],"multi-pass":[12],"Transmembrane":[13],"Proteins":[14],"(mTPs).":[15],"However,":[16],"accurate":[17,87],"prediction":[18],"1D":[21,84,129],"label":[23,88],"for":[24,86,142],"each":[25],"residue":[26],"an":[28,54],"mTP":[29],"from":[30,68,117],"evolutionary":[31],"information":[32],"alone":[33],"very":[35],"challenging,":[36],"if":[37],"not":[38],"infeasible.":[39],"In":[40],"this":[41],"work,":[42],"we":[43,91,132],"propose":[44],"a":[45],"novel":[46],"approach":[47,171],"identify":[49],"under":[53],"object":[55],"detection":[56],"framework":[57],"that":[58,78,102],"takes":[59],"as":[60,108,110],"input":[62],"predicted":[64],"2D":[65,82,124],"distance":[66],"matrix":[67],"co-evolutionary":[70],"information,":[71],"followed":[72],"by":[73],"several":[74,134],"bidirectional":[75,135],"Transformer":[76,136],"blocks":[77,137],"effectively":[79],"fuse":[80],"both":[81],"and":[83,127,156,174,180],"features":[85,126],"prediction.":[89],"Specifically,":[90],"employ":[92],"Faster-RCNN":[94],"module":[95],"simultaneously":[97],"predict":[98],"rectangular":[100],"bounds":[101],"cover":[103],"interacted":[105],"regions,":[107],"well":[109],"confidence":[112],"scores":[113],"discriminate":[115],"them":[116],"non-transmembrane":[119],"regions.":[120],"To":[121],"integrate":[122],"pairwise":[125],"sequential":[130],"features,":[131],"establish":[133],"consisting":[138],"self-attention":[140],"units":[141],"capturing":[143],"long-range":[144],"dependencies":[145],"in":[146,162],"topology.":[149],"Tested":[150],"on":[151],"330":[153],"non-redundant":[154],"mTPs":[155],"newly":[158],"released":[159],"45":[160],"mTPs,":[161],"terms":[163],"Segment":[166],"OVerlap":[167],"(SOV)":[168],"score,":[169],"our":[170],"achieves":[172],"0.927":[173],"0.843,":[175],"which":[176],"are":[177],"about":[178],"4.5%":[179],"6.6%":[181],"better":[182],"than":[183],"cutting-edge":[185],"consensus":[186],"methods,":[187],"respectively.":[188]},"counts_by_year":[],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}