{"id":"https://openalex.org/W7135208526","doi":"https://doi.org/10.1109/tcbbio.2026.3673740","title":"Biologically Constrained DNA Encoding With Triplet Networks for Similarity Image Retrieval","display_name":"Biologically Constrained DNA Encoding With Triplet Networks for Similarity Image Retrieval","publication_year":2026,"publication_date":"2026-03-13","ids":{"openalex":"https://openalex.org/W7135208526","doi":"https://doi.org/10.1109/tcbbio.2026.3673740","pmid":"https://pubmed.ncbi.nlm.nih.gov/41824343"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2026.3673740","is_oa":true,"landing_page_url":"https://doi.org/10.1109/tcbbio.2026.3673740","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1109/tcbbio.2026.3673740","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5114249411","display_name":"Tatsuya Koike","orcid":"https://orcid.org/0009-0006-4730-4505"},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]},{"id":"https://openalex.org/I39012071","display_name":"Kyoto College of Graduate Studies for Informatics","ror":"https://ror.org/05mzj8a56","country_code":"JP","type":"education","lineage":["https://openalex.org/I39012071"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Takefumi Koike","raw_affiliation_strings":["Graduate School of Informatics, Kyoto University, Kyoto, Japan"],"raw_orcid":"https://orcid.org/0009-0006-4730-4505","affiliations":[{"raw_affiliation_string":"Graduate School of Informatics, Kyoto University, Kyoto, Japan","institution_ids":["https://openalex.org/I22299242","https://openalex.org/I39012071"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5129071073","display_name":"Hiromitsu Awano","orcid":null},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]},{"id":"https://openalex.org/I39012071","display_name":"Kyoto College of Graduate Studies for Informatics","ror":"https://ror.org/05mzj8a56","country_code":"JP","type":"education","lineage":["https://openalex.org/I39012071"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Hiromitsu Awano","raw_affiliation_strings":["Graduate School of Informatics, Kyoto University, Kyoto, Japan"],"raw_orcid":"https://orcid.org/0000-0002-3674-4584","affiliations":[{"raw_affiliation_string":"Graduate School of Informatics, Kyoto University, Kyoto, Japan","institution_ids":["https://openalex.org/I22299242","https://openalex.org/I39012071"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5129011126","display_name":"Takashi Sato","orcid":null},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]},{"id":"https://openalex.org/I39012071","display_name":"Kyoto College of Graduate Studies for Informatics","ror":"https://ror.org/05mzj8a56","country_code":"JP","type":"education","lineage":["https://openalex.org/I39012071"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Takashi Sato","raw_affiliation_strings":["Graduate School of Informatics, Kyoto University, Kyoto, Japan"],"raw_orcid":"https://orcid.org/0000-0002-1577-8259","affiliations":[{"raw_affiliation_string":"Graduate School of Informatics, Kyoto University, Kyoto, Japan","institution_ids":["https://openalex.org/I22299242","https://openalex.org/I39012071"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.22720828,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"23","issue":"3","first_page":"1240","last_page":"1252"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12946","display_name":"Fractal and DNA sequence analysis","score":0.2815000116825104,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.2815000116825104,"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":0.131400004029274,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.05959999933838844,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/encoding","display_name":"Encoding (memory)","score":0.5228999853134155},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4966000020503998},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.46560001373291016},{"id":"https://openalex.org/keywords/image-retrieval","display_name":"Image retrieval","score":0.4577000141143799},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.4546999931335449}],"concepts":[{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5864999890327454},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5827999711036682},{"id":"https://openalex.org/C125411270","wikidata":"https://www.wikidata.org/wiki/Q18653","display_name":"Encoding (memory)","level":2,"score":0.5228999853134155},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4966000020503998},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.46560001373291016},{"id":"https://openalex.org/C1667742","wikidata":"https://www.wikidata.org/wiki/Q10927554","display_name":"Image retrieval","level":3,"score":0.4577000141143799},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.4546999931335449},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.3921000063419342},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3452000021934509},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.2921000123023987},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.2915000021457672},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.25999999046325684}],"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":"D000098415","descriptor_name":"Convolutional Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098415","descriptor_name":"Convolutional Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001482","descriptor_name":"Base Composition","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001482","descriptor_name":"Base Composition","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbbio.2026.3673740","is_oa":true,"landing_page_url":"https://doi.org/10.1109/tcbbio.2026.3673740","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41824343","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41824343","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":"IEEE transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":{"id":"doi:10.1109/tcbbio.2026.3673740","is_oa":true,"landing_page_url":"https://doi.org/10.1109/tcbbio.2026.3673740","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":34,"referenced_works":["https://openalex.org/W1975517671","https://openalex.org/W2018255407","https://openalex.org/W2091266578","https://openalex.org/W2096733369","https://openalex.org/W2118509786","https://openalex.org/W2120865268","https://openalex.org/W2123229215","https://openalex.org/W2130660124","https://openalex.org/W2138621090","https://openalex.org/W2147069236","https://openalex.org/W2157364932","https://openalex.org/W2194775991","https://openalex.org/W2333320475","https://openalex.org/W2531409750","https://openalex.org/W2767325013","https://openalex.org/W2788257106","https://openalex.org/W2892361591","https://openalex.org/W2944582089","https://openalex.org/W2951269465","https://openalex.org/W2963775347","https://openalex.org/W3003918453","https://openalex.org/W3086108252","https://openalex.org/W3193252214","https://openalex.org/W4213203727","https://openalex.org/W4239015296","https://openalex.org/W4280595066","https://openalex.org/W4372335309","https://openalex.org/W4378175706","https://openalex.org/W4385830440","https://openalex.org/W4386424884","https://openalex.org/W4389117782","https://openalex.org/W4393040418","https://openalex.org/W4401391440","https://openalex.org/W4404133616"],"related_works":[],"abstract_inverted_index":{"As":[0],"the":[1,36,87,91,97,100,114,135,139,143,158],"volume":[2],"of":[3,90,99,138,150],"digital":[4],"data":[5,19,30],"continues":[6],"to":[7,22,127,167],"grow":[8],"exponentially,":[9],"DNA":[10,51,93,145],"has":[11],"emerged":[12],"as":[13],"a":[14,40,46,50,131],"promising":[15],"medium":[16],"for":[17,49],"long-term":[18],"storage":[20],"due":[21],"its":[23],"high":[24],"density":[25],"and":[26,57,82,116,130,153],"durability.":[27],"For":[28],"enabling":[29],"retrieval":[31,63],"via":[32],"DNA's":[33],"biochemical":[34,88],"reactions,":[35],"encoding":[37],"strategy":[38],"plays":[39],"critical":[41],"role.":[42],"This":[43],"paper":[44],"proposes":[45],"training":[47,58,136],"framework":[48],"encoder":[52],"that":[53,75,120],"improves":[54],"both":[55],"accuracy":[56,125],"efficiency":[59],"in":[60],"content-based":[61],"image":[62,109],"by":[64],"incorporating":[65],"deep":[66],"metric":[67],"learning.":[68],"In":[69],"addition,":[70],"we":[71,103],"introduce":[72],"loss":[73],"functions":[74],"enforce":[76],"biological":[77,164],"constraints,":[78],"specifically":[79],"homopolymer":[80,151],"length":[81,152],"GC":[83,155],"content,":[84],"thereby":[85],"improving":[86,163],"stability":[89],"generated":[92,144],"sequences.":[94],"To":[95],"evaluate":[96],"effectiveness":[98],"proposed":[101],"method,":[102],"conduct":[104],"quantitative":[105],"assessments":[106],"based":[107],"on":[108,113],"classification":[110,124],"performance.":[111],"Simulations":[112],"CIFAR-10":[115],"CIFAR-100":[117],"datasets":[118],"demonstrate":[119],"our":[121],"method":[122],"achieves":[123],"comparable":[126],"CNN-based":[128],"baselines":[129],"20-fold":[132],"speedup":[133],"over":[134],"time":[137],"existing":[140],"method.":[141],"Moreover,":[142],"sequences":[146],"enable":[147],"strict":[148],"control":[149],"maintain":[154],"content":[156],"within":[157],"optimal":[159],"40-60%":[160],"range,":[161],"significantly":[162],"feasibility":[165],"compared":[166],"baseline":[168],"methods.":[169]},"counts_by_year":[],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2026-03-14T00:00:00"}