{"id":"https://openalex.org/W4391248838","doi":"https://doi.org/10.1109/jbhi.2024.3358842","title":"TEPI: <u>T</u>axonomy-Aware <u>E</u>mbedding and <u>P</u>seudo-<u>I</u>maging for Scarcely-Labeled Zero-Shot Genome Classification","display_name":"TEPI: <u>T</u>axonomy-Aware <u>E</u>mbedding and <u>P</u>seudo-<u>I</u>maging for Scarcely-Labeled Zero-Shot Genome Classification","publication_year":2024,"publication_date":"2024-01-26","ids":{"openalex":"https://openalex.org/W4391248838","doi":"https://doi.org/10.1109/jbhi.2024.3358842"},"language":"en","primary_location":{"id":"doi:10.1109/jbhi.2024.3358842","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2024.3358842","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-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/A5080710999","display_name":"Sathyanarayanan N. Aakur","orcid":"https://orcid.org/0000-0003-1062-8929"},"institutions":[{"id":"https://openalex.org/I82497590","display_name":"Auburn University","ror":"https://ror.org/02v80fc35","country_code":"US","type":"education","lineage":["https://openalex.org/I82497590"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sathyanarayanan N. Aakur","raw_affiliation_strings":["Department of Computer Science and Software Engineering, Auburn University, Auburn, AL, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Software Engineering, Auburn University, Auburn, AL, USA","institution_ids":["https://openalex.org/I82497590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058097248","display_name":"Vishalini R. Laguduva","orcid":null},"institutions":[{"id":"https://openalex.org/I82497590","display_name":"Auburn University","ror":"https://ror.org/02v80fc35","country_code":"US","type":"education","lineage":["https://openalex.org/I82497590"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vishalini R. Laguduva","raw_affiliation_strings":["Department of Computer Science and Software Engineering, Auburn University, Auburn, AL, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Software Engineering, Auburn University, Auburn, AL, USA","institution_ids":["https://openalex.org/I82497590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087680931","display_name":"Priyadharsini Ramamurthy","orcid":"https://orcid.org/0009-0007-7181-4967"},"institutions":[{"id":"https://openalex.org/I115475287","display_name":"Oklahoma State University","ror":"https://ror.org/01g9vbr38","country_code":"US","type":"education","lineage":["https://openalex.org/I115475287"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Priyadharsini Ramamurthy","raw_affiliation_strings":["Department of Computer Science, Oklahoma State University, Stillwater, OK, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Oklahoma State University, Stillwater, OK, USA","institution_ids":["https://openalex.org/I115475287"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006895637","display_name":"Akhilesh Ramachandran","orcid":"https://orcid.org/0000-0001-9744-3905"},"institutions":[{"id":"https://openalex.org/I115475287","display_name":"Oklahoma State University","ror":"https://ror.org/01g9vbr38","country_code":"US","type":"education","lineage":["https://openalex.org/I115475287"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Akhilesh Ramachandran","raw_affiliation_strings":["Oklahoma Animal Disease Diagnostics Laboratory, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, USA"],"affiliations":[{"raw_affiliation_string":"Oklahoma Animal Disease Diagnostics Laboratory, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, USA","institution_ids":["https://openalex.org/I115475287"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5080710999"],"corresponding_institution_ids":["https://openalex.org/I82497590"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0088428,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"28","issue":"4","first_page":"2385","last_page":"2396"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994999766349792,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994999766349792,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9983000159263611,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9925000071525574,"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/genome","display_name":"Genome","score":0.5472672581672668},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.5368216037750244},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5320305228233337},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5246149301528931},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.4684959053993225},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.4533076882362366},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.38078099489212036},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3416803181171417},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2743954360485077},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.17095276713371277},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13096129894256592},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.12134429812431335}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5472672581672668},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.5368216037750244},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5320305228233337},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5246149301528931},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.4684959053993225},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.4533076882362366},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.38078099489212036},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3416803181171417},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2743954360485077},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17095276713371277},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13096129894256592},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.12134429812431335}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/jbhi.2024.3358842","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2024.3358842","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3625790698","display_name":null,"funder_award_id":"B000C011","funder_id":"https://openalex.org/F4320306114","funder_display_name":"U.S. Department of Agriculture"},{"id":"https://openalex.org/G5894997987","display_name":null,"funder_award_id":"AP20VSD","funder_id":"https://openalex.org/F4320306114","funder_display_name":"U.S. Department of Agriculture"}],"funders":[{"id":"https://openalex.org/F4320306114","display_name":"U.S. Department of Agriculture","ror":"https://ror.org/01na82s61"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":56,"referenced_works":["https://openalex.org/W1686810756","https://openalex.org/W1991330646","https://openalex.org/W2003453203","https://openalex.org/W2020302957","https://openalex.org/W2064675550","https://openalex.org/W2082825869","https://openalex.org/W2096718691","https://openalex.org/W2122467784","https://openalex.org/W2142678031","https://openalex.org/W2152869198","https://openalex.org/W2157036763","https://openalex.org/W2159954944","https://openalex.org/W2163922914","https://openalex.org/W2173732482","https://openalex.org/W2194775991","https://openalex.org/W2407797316","https://openalex.org/W2470052926","https://openalex.org/W2497697626","https://openalex.org/W2520774990","https://openalex.org/W2596142952","https://openalex.org/W2739996966","https://openalex.org/W2809485291","https://openalex.org/W2895428268","https://openalex.org/W2899728356","https://openalex.org/W2912633045","https://openalex.org/W2951160681","https://openalex.org/W2951934944","https://openalex.org/W2953000767","https://openalex.org/W2961729414","https://openalex.org/W2962756421","https://openalex.org/W2963804400","https://openalex.org/W2990618091","https://openalex.org/W2991464892","https://openalex.org/W2997591727","https://openalex.org/W3008594856","https://openalex.org/W3010360466","https://openalex.org/W3023822817","https://openalex.org/W3024771599","https://openalex.org/W3025462460","https://openalex.org/W3094502228","https://openalex.org/W3096281419","https://openalex.org/W3108028701","https://openalex.org/W3108877114","https://openalex.org/W3109684201","https://openalex.org/W3130086149","https://openalex.org/W3165170361","https://openalex.org/W3199096350","https://openalex.org/W3202036388","https://openalex.org/W3211537242","https://openalex.org/W4242110084","https://openalex.org/W4294170691","https://openalex.org/W4385245566","https://openalex.org/W6637373629","https://openalex.org/W6752901131","https://openalex.org/W6776700526","https://openalex.org/W6785034178"],"related_works":["https://openalex.org/W2081900870","https://openalex.org/W4312203868","https://openalex.org/W2389214306","https://openalex.org/W2069013776","https://openalex.org/W2038264393","https://openalex.org/W4235240664","https://openalex.org/W2059637021","https://openalex.org/W2965083567","https://openalex.org/W2037549926","https://openalex.org/W1838576100"],"abstract_inverted_index":{"A":[0],"species'":[1],"genetic":[2,22],"code":[3],"or":[4],"genome":[5,44,111],"encodes":[6],"valuable":[7],"evolutionary,":[8],"biological,":[9],"and":[10,20,27,57,99,114,124,131,150],"phylogenetic":[11,132],"information":[12],"that":[13],"aids":[14],"in":[15,39,138],"species":[16,35],"recognition,":[17],"taxonomic":[18],"classification,":[19],"understanding":[21],"predispositions":[23],"like":[24],"drug":[25],"resistance":[26],"virulence.":[28],"However,":[29],"the":[30,69],"vast":[31],"number":[32],"of":[33,71,134],"potential":[34],"poses":[36],"significant":[37],"challenges":[38],"developing":[40],"a":[41,118],"general-purpose":[42],"whole":[43],"classification":[45,73],"tool.":[46],"Traditional":[47],"bioinformatics":[48],"tools":[49],"have":[50],"made":[51],"notable":[52],"progress":[53],"but":[54,66],"lack":[55],"scalability":[56],"are":[58],"computationally":[59],"expensive.":[60],"Machine":[61],"learning-based":[62],"frameworks":[63],"show":[64],"promise":[65],"must":[67],"address":[68],"issue":[70],"large":[72],"vocabularies":[74],"with":[75],"long-tail":[76],"distributions.":[77],"In":[78],"this":[79,84],"study,":[80],"we":[81],"propose":[82],"addressing":[83],"problem":[85],"through":[86],"zero-shot":[87,148],"learning":[88],"using":[89,145],"TEPI,":[90],"<underline":[91,95,100,104],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[92,96,101,105],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">T</u>":[93],"axonomy-aware":[94],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">E</u>":[97],"mbedding":[98],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">P</u>":[102],"seudo-":[103],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">I</u>":[106],"maging.":[107],"We":[108,142],"represent":[109],"each":[110],"as":[112],"pseudo-images":[113],"map":[115],"them":[116],"to":[117],"taxonomy-aware":[119],"embedding":[120,127],"space":[121,128],"for":[122],"reasoning":[123],"classification.":[125],"This":[126],"captures":[129],"compositional":[130],"relationships":[133],"species,":[135],"enabling":[136],"predictions":[137],"extensive":[139],"search":[140],"spaces.":[141],"evaluate":[143],"TEPI":[144],"two":[146],"rigorous":[147],"settings":[149],"demonstrate":[151],"its":[152],"generalization":[153],"capabilities":[154],"qualitatively":[155],"on":[156],"curated,":[157],"large-scale,":[158],"publicly":[159],"sourced":[160],"data.":[161]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
