{"id":"https://openalex.org/W4413336899","doi":"https://doi.org/10.1186/s13321-025-01078-1","title":"xBitterT5: an explainable transformer-based framework with multimodal inputs for identifying bitter-taste peptides","display_name":"xBitterT5: an explainable transformer-based framework with multimodal inputs for identifying bitter-taste peptides","publication_year":2025,"publication_date":"2025-08-20","ids":{"openalex":"https://openalex.org/W4413336899","doi":"https://doi.org/10.1186/s13321-025-01078-1","pmid":"https://pubmed.ncbi.nlm.nih.gov/40835950"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-025-01078-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01078-1","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01078-1","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01078-1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103040369","display_name":"Nguyen Doan Hieu Nguyen","orcid":"https://orcid.org/0009-0003-9259-8600"},"institutions":[{"id":"https://openalex.org/I848706","display_name":"Sungkyunkwan University","ror":"https://ror.org/04q78tk20","country_code":"KR","type":"education","lineage":["https://openalex.org/I848706"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Nguyen Doan Hieu Nguyen","raw_affiliation_strings":["Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, Gyeonggi-do, 16419, Republic of Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, Gyeonggi-do, 16419, Republic of Korea","institution_ids":["https://openalex.org/I848706"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091402542","display_name":"Nhat Truong Pham","orcid":"https://orcid.org/0000-0002-8086-6722"},"institutions":[{"id":"https://openalex.org/I848706","display_name":"Sungkyunkwan University","ror":"https://ror.org/04q78tk20","country_code":"KR","type":"education","lineage":["https://openalex.org/I848706"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Nhat Truong Pham","raw_affiliation_strings":["Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, Gyeonggi-do, 16419, Republic of Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, Gyeonggi-do, 16419, Republic of Korea","institution_ids":["https://openalex.org/I848706"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008749744","display_name":"Duong Thanh Tran","orcid":"https://orcid.org/0009-0003-5096-8167"},"institutions":[{"id":"https://openalex.org/I848706","display_name":"Sungkyunkwan University","ror":"https://ror.org/04q78tk20","country_code":"KR","type":"education","lineage":["https://openalex.org/I848706"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Duong Thanh Tran","raw_affiliation_strings":["Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, Gyeonggi-do, 16419, Republic of Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, Gyeonggi-do, 16419, Republic of Korea","institution_ids":["https://openalex.org/I848706"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033232360","display_name":"Leyi Wei","orcid":"https://orcid.org/0000-0003-1444-190X"},"institutions":[{"id":"https://openalex.org/I49835588","display_name":"Macao Polytechnic University","ror":"https://ror.org/02sf5td35","country_code":"MO","type":"education","lineage":["https://openalex.org/I49835588"]}],"countries":["MO"],"is_corresponding":false,"raw_author_name":"Leyi Wei","raw_affiliation_strings":["Center for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Science, Macao Polytechnic University, Macau, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Science, Macao Polytechnic University, Macau, China","institution_ids":["https://openalex.org/I49835588"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042243661","display_name":"Adeel Malik","orcid":"https://orcid.org/0000-0002-3453-6001"},"institutions":[{"id":"https://openalex.org/I157264075","display_name":"Sangmyung University","ror":"https://ror.org/01x4whx42","country_code":"KR","type":"education","lineage":["https://openalex.org/I157264075"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Adeel Malik","raw_affiliation_strings":["Institute of Intelligence Informatics Technology, Sangmyung University, Seoul, 03016, Republic of Korea. adeel@procarb.org","Institute of Intelligence Informatics Technology, Sangmyung University, Seoul, 03016, Republic of Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Intelligence Informatics Technology, Sangmyung University, Seoul, 03016, Republic of Korea. adeel@procarb.org","institution_ids":[]},{"raw_affiliation_string":"Institute of Intelligence Informatics Technology, Sangmyung University, Seoul, 03016, Republic of Korea","institution_ids":["https://openalex.org/I157264075"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040180866","display_name":"Balachandran Manavalan","orcid":"https://orcid.org/0000-0003-0697-9419"},"institutions":[{"id":"https://openalex.org/I848706","display_name":"Sungkyunkwan University","ror":"https://ror.org/04q78tk20","country_code":"KR","type":"education","lineage":["https://openalex.org/I848706"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Balachandran Manavalan","raw_affiliation_strings":["Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, Gyeonggi-do, 16419, Republic of Korea. bala2022@skku.edu","Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, Gyeonggi-do, 16419, Republic of Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, Gyeonggi-do, 16419, Republic of Korea. bala2022@skku.edu","institution_ids":[]},{"raw_affiliation_string":"Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, Gyeonggi-do, 16419, Republic of Korea","institution_ids":["https://openalex.org/I848706"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5042243661"],"corresponding_institution_ids":["https://openalex.org/I157264075"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":2.9321,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.90868231,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"17","issue":"1","first_page":"127","last_page":"127"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11584","display_name":"Biochemical Analysis and Sensing Techniques","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/2916","display_name":"Nutrition and Dietetics"},"field":{"id":"https://openalex.org/fields/29","display_name":"Nursing"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11584","display_name":"Biochemical Analysis and Sensing Techniques","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/2916","display_name":"Nutrition and Dietetics"},"field":{"id":"https://openalex.org/fields/29","display_name":"Nursing"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11667","display_name":"Advanced Chemical Sensor Technologies","score":0.9882000088691711,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.972599983215332,"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/computer-science","display_name":"Computer science","score":0.6858247518539429},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.5775514245033264},{"id":"https://openalex.org/keywords/bitter-taste","display_name":"Bitter taste","score":0.558949887752533},{"id":"https://openalex.org/keywords/taste","display_name":"Taste","score":0.5356094241142273},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.14367827773094177},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.08821886777877808},{"id":"https://openalex.org/keywords/food-science","display_name":"Food science","score":0.06777974963188171},{"id":"https://openalex.org/keywords/electrical-engineering","display_name":"Electrical engineering","score":0.06104475259780884}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6858247518539429},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.5775514245033264},{"id":"https://openalex.org/C3020017864","wikidata":"https://www.wikidata.org/wiki/Q124794","display_name":"Bitter taste","level":3,"score":0.558949887752533},{"id":"https://openalex.org/C8868529","wikidata":"https://www.wikidata.org/wiki/Q124794","display_name":"Taste","level":2,"score":0.5356094241142273},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.14367827773094177},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.08821886777877808},{"id":"https://openalex.org/C31903555","wikidata":"https://www.wikidata.org/wiki/Q1637030","display_name":"Food science","level":1,"score":0.06777974963188171},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.06104475259780884},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-025-01078-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01078-1","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01078-1","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:40835950","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40835950","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":"Journal of cheminformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:e24b19efabf44534b87dcb4690121a9c","is_oa":true,"landing_page_url":"https://doaj.org/article/e24b19efabf44534b87dcb4690121a9c","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 17, Iss 1, Pp 1-15 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12366191","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12366191","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Cheminform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13321-025-01078-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01078-1","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01078-1","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5899999737739563,"display_name":"Zero hunger","id":"https://metadata.un.org/sdg/2"}],"awards":[{"id":"https://openalex.org/G30685149","display_name":null,"funder_award_id":"BK21 FOUR","funder_id":"https://openalex.org/F4320320671","funder_display_name":"National Research Foundation"},{"id":"https://openalex.org/G6306751561","display_name":null,"funder_award_id":"RS-2024-00344752","funder_id":"https://openalex.org/F4320322120","funder_display_name":"National Research Foundation of Korea"},{"id":"https://openalex.org/G8818205549","display_name":null,"funder_award_id":"BK21 FOUR","funder_id":"https://openalex.org/F4320321378","funder_display_name":"Sungkyunkwan University"}],"funders":[{"id":"https://openalex.org/F4320320671","display_name":"National Research Foundation","ror":"https://ror.org/05s0g1g46"},{"id":"https://openalex.org/F4320321378","display_name":"Sungkyunkwan University","ror":"https://ror.org/04q78tk20"},{"id":"https://openalex.org/F4320322120","display_name":"National Research Foundation of Korea","ror":"https://ror.org/013aysd81"},{"id":"https://openalex.org/F4320328359","display_name":"Ministry of Science and ICT, South Korea","ror":"https://ror.org/01wpjm123"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4413336899.pdf","grobid_xml":"https://content.openalex.org/works/W4413336899.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W280389901","https://openalex.org/W1508604947","https://openalex.org/W1975147762","https://openalex.org/W2030452273","https://openalex.org/W2037591739","https://openalex.org/W2102461176","https://openalex.org/W2255466643","https://openalex.org/W2465717638","https://openalex.org/W2733626550","https://openalex.org/W2807896518","https://openalex.org/W2895677720","https://openalex.org/W2942801317","https://openalex.org/W2949342052","https://openalex.org/W2949685204","https://openalex.org/W2953008890","https://openalex.org/W3009321976","https://openalex.org/W3013552211","https://openalex.org/W3045928028","https://openalex.org/W3111866356","https://openalex.org/W3131121088","https://openalex.org/W3177500196","https://openalex.org/W3194214681","https://openalex.org/W4200115265","https://openalex.org/W4206500608","https://openalex.org/W4225008496","https://openalex.org/W4281654920","https://openalex.org/W4285731555","https://openalex.org/W4289525677","https://openalex.org/W4301397797","https://openalex.org/W4312113926","https://openalex.org/W4318046551","https://openalex.org/W4361989906","https://openalex.org/W4385572894","https://openalex.org/W4386376633","https://openalex.org/W4387373991","https://openalex.org/W4389524207","https://openalex.org/W4390591106","https://openalex.org/W4400000389","https://openalex.org/W4401857142","https://openalex.org/W4402492525","https://openalex.org/W4402669707","https://openalex.org/W4402669727","https://openalex.org/W4402670712","https://openalex.org/W4402683143","https://openalex.org/W4404470798"],"related_works":["https://openalex.org/W1972417599","https://openalex.org/W1603393798","https://openalex.org/W3135026916","https://openalex.org/W2978452059","https://openalex.org/W4237724796","https://openalex.org/W1596800225","https://openalex.org/W2185122967","https://openalex.org/W4250387097","https://openalex.org/W2784542306","https://openalex.org/W2594921673"],"abstract_inverted_index":{"Bitter":[0],"peptides":[1,91],"(BPs),":[2],"derived":[3],"from":[4,115],"the":[5,64,82,87,118,146,151],"hydrolysis":[6],"of":[7,33,66,90,120],"proteins":[8],"in":[9,15,27,198],"food,":[10],"play":[11],"a":[12,101,181],"crucial":[13],"role":[14],"both":[16,130,192],"food":[17,39,200],"science":[18],"and":[19,25,41,77,92,104,123,133,180,195,201],"biomedicine":[20],"by":[21],"influencing":[22],"taste":[23],"perception":[24],"participating":[26],"various":[28],"physiological":[29],"processes.":[30],"Accurate":[31],"identification":[32,51,109],"BPs":[34],"is":[35],"essential":[36],"for":[37,49,107],"understanding":[38],"quality":[40],"potential":[42],"health":[43],"impacts.":[44],"Traditional":[45],"machine":[46],"learning":[47],"approaches":[48,79],"BP":[50,108],"have":[52,80],"relied":[53],"on":[54,145],"conventional":[55],"feature":[56],"descriptors,":[57],"achieving":[58],"moderate":[59],"success":[60],"but":[61,84],"struggling":[62],"with":[63,117],"complexities":[65],"biological":[67],"sequence":[68,122],"data.":[69],"Recent":[70],"advances":[71],"utilizing":[72],"protein":[73],"language":[74],"model":[75,152],"embedding":[76],"meta-learning":[78],"improved":[81],"accuracy,":[83],"frequently":[85],"neglect":[86],"molecular":[88,126,135],"representations":[89],"lack":[93],"interpretability.":[94],"In":[95],"this":[96],"study,":[97],"we":[98],"propose":[99],"xBitterT5,":[100],"novel":[102],"multimodal":[103],"interpretable":[105],"framework":[106],"that":[110,160],"integrates":[111],"pretrained":[112],"transformer-based":[113],"embeddings":[114],"BioT5+":[116],"combination":[119],"peptide":[121,131],"its":[124,164],"SELFIES":[125],"representation.":[127],"Specifically,":[128],"incorporating":[129],"sequences":[132],"their":[134],"strings,":[136],"xBitterT5":[137],"demonstrates":[138],"superior":[139],"performance":[140],"compared":[141],"to":[142,163,190],"previous":[143],"methods":[144],"same":[147],"benchmark":[148],"datasets.":[149],"Importantly,":[150],"provides":[153],"residue-level":[154],"interpretability,":[155],"highlighting":[156],"chemically":[157],"meaningful":[158],"substructures":[159],"significantly":[161],"contribute":[162],"bitterness,":[165],"thus":[166],"offering":[167],"mechanistic":[168],"insights":[169],"beyond":[170],"black-box":[171],"predictions.":[172],"A":[173],"user-friendly":[174],"web":[175],"server":[176],"(":[177,184],"https://balalab-skku.org/xBitterT5/":[178],")":[179,186],"standalone":[182],"version":[183],"https://github.com/cbbl-skku-org/xBitterT5/":[185],"are":[187],"freely":[188],"available":[189],"support":[191],"computational":[193],"biologists":[194],"experimental":[196],"researchers":[197],"peptide-based":[199],"biomedicine.":[202]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1}],"updated_date":"2026-05-02T08:42:23.175194","created_date":"2025-10-10T00:00:00"}
