{"id":"https://openalex.org/W3159986226","doi":"https://doi.org/10.1109/isit45174.2021.9517821","title":"Trellis BMA: Coded Trace Reconstruction on IDS Channels for DNA Storage","display_name":"Trellis BMA: Coded Trace Reconstruction on IDS Channels for DNA Storage","publication_year":2021,"publication_date":"2021-07-12","ids":{"openalex":"https://openalex.org/W3159986226","doi":"https://doi.org/10.1109/isit45174.2021.9517821","mag":"3159986226"},"language":"en","primary_location":{"id":"doi:10.1109/isit45174.2021.9517821","is_oa":false,"landing_page_url":"https://doi.org/10.1109/isit45174.2021.9517821","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2021 IEEE International Symposium on Information Theory (ISIT)","raw_type":"proceedings-article"},"type":"preprint","indexed_in":["arxiv","crossref","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2107.06440","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5076785081","display_name":"Sundara Rajan Srinivasavaradhan","orcid":"https://orcid.org/0000-0003-2813-3166"},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sundara Rajan Srinivasavaradhan","raw_affiliation_strings":["University of California,Electrical and Computer Engineering,Los Angeles","University of California-Los Angeles"],"affiliations":[{"raw_affiliation_string":"University of California,Electrical and Computer Engineering,Los Angeles","institution_ids":["https://openalex.org/I161318765"]},{"raw_affiliation_string":"University of California-Los Angeles","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038687630","display_name":"Sivakanth Gopi","orcid":"https://orcid.org/0000-0001-9706-4171"},"institutions":[{"id":"https://openalex.org/I1290206253","display_name":"Microsoft (United States)","ror":"https://ror.org/00d0nc645","country_code":"US","type":"company","lineage":["https://openalex.org/I1290206253"]},{"id":"https://openalex.org/I4210164937","display_name":"Microsoft Research (United Kingdom)","ror":"https://ror.org/05k87vq12","country_code":"GB","type":"company","lineage":["https://openalex.org/I1290206253","https://openalex.org/I4210164937"]}],"countries":["GB","US"],"is_corresponding":false,"raw_author_name":"Sivakanth Gopi","raw_affiliation_strings":["Microsoft Research,Redmond,WA","(Microsoft)"],"affiliations":[{"raw_affiliation_string":"Microsoft Research,Redmond,WA","institution_ids":["https://openalex.org/I1290206253"]},{"raw_affiliation_string":"(Microsoft)","institution_ids":["https://openalex.org/I4210164937"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034044119","display_name":"Henry D. Pfister","orcid":"https://orcid.org/0000-0001-5521-4397"},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]},{"id":"https://openalex.org/I4210164937","display_name":"Microsoft Research (United Kingdom)","ror":"https://ror.org/05k87vq12","country_code":"GB","type":"company","lineage":["https://openalex.org/I1290206253","https://openalex.org/I4210164937"]}],"countries":["GB","US"],"is_corresponding":false,"raw_author_name":"Henry D. Pfister","raw_affiliation_strings":["Duke University,Electrical and Computer Engineering,Durham,NC","(Microsoft)"],"affiliations":[{"raw_affiliation_string":"Duke University,Electrical and Computer Engineering,Durham,NC","institution_ids":["https://openalex.org/I170897317"]},{"raw_affiliation_string":"(Microsoft)","institution_ids":["https://openalex.org/I4210164937"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046685409","display_name":"Sergey Yekhanin","orcid":null},"institutions":[{"id":"https://openalex.org/I1290206253","display_name":"Microsoft (United States)","ror":"https://ror.org/00d0nc645","country_code":"US","type":"company","lineage":["https://openalex.org/I1290206253"]},{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sergey Yekhanin","raw_affiliation_strings":["Microsoft Research,Redmond,WA","Duke University#TAB#"],"affiliations":[{"raw_affiliation_string":"Microsoft Research,Redmond,WA","institution_ids":["https://openalex.org/I1290206253"]},{"raw_affiliation_string":"Duke University#TAB#","institution_ids":["https://openalex.org/I170897317"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5076785081"],"corresponding_institution_ids":["https://openalex.org/I161318765"],"apc_list":null,"apc_paid":null,"fwci":0.0811,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.4272188,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":93},"biblio":{"volume":null,"issue":null,"first_page":"2453","last_page":"2458"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12029","display_name":"DNA and Biological Computing","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/T12029","display_name":"DNA and Biological Computing","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/T12162","display_name":"Cellular Automata and Applications","score":0.9972000122070312,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9969000220298767,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7390762567520142},{"id":"https://openalex.org/keywords/trellis","display_name":"Trellis (graph)","score":0.7026442289352417},{"id":"https://openalex.org/keywords/trace","display_name":"TRACE (psycholinguistics)","score":0.6439122557640076},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.6399824023246765},{"id":"https://openalex.org/keywords/decoding-methods","display_name":"Decoding methods","score":0.6338415145874023},{"id":"https://openalex.org/keywords/redundancy","display_name":"Redundancy (engineering)","score":0.59513920545578},{"id":"https://openalex.org/keywords/encoding","display_name":"Encoding (memory)","score":0.5441376566886902},{"id":"https://openalex.org/keywords/channel","display_name":"Channel (broadcasting)","score":0.49701836705207825},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.15041828155517578},{"id":"https://openalex.org/keywords/computer-network","display_name":"Computer network","score":0.09487873315811157}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7390762567520142},{"id":"https://openalex.org/C2781235587","wikidata":"https://www.wikidata.org/wiki/Q7838009","display_name":"Trellis (graph)","level":3,"score":0.7026442289352417},{"id":"https://openalex.org/C75291252","wikidata":"https://www.wikidata.org/wiki/Q1315756","display_name":"TRACE (psycholinguistics)","level":2,"score":0.6439122557640076},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.6399824023246765},{"id":"https://openalex.org/C57273362","wikidata":"https://www.wikidata.org/wiki/Q576722","display_name":"Decoding methods","level":2,"score":0.6338415145874023},{"id":"https://openalex.org/C152124472","wikidata":"https://www.wikidata.org/wiki/Q1204361","display_name":"Redundancy (engineering)","level":2,"score":0.59513920545578},{"id":"https://openalex.org/C125411270","wikidata":"https://www.wikidata.org/wiki/Q18653","display_name":"Encoding (memory)","level":2,"score":0.5441376566886902},{"id":"https://openalex.org/C127162648","wikidata":"https://www.wikidata.org/wiki/Q16858953","display_name":"Channel (broadcasting)","level":2,"score":0.49701836705207825},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.15041828155517578},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.09487873315811157},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1109/isit45174.2021.9517821","is_oa":false,"landing_page_url":"https://doi.org/10.1109/isit45174.2021.9517821","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2021 IEEE International Symposium on Information Theory (ISIT)","raw_type":"proceedings-article"},{"id":"pmh:oai:arXiv.org:2107.06440","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2107.06440","pdf_url":"https://arxiv.org/pdf/2107.06440","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},{"id":"mag:3159986226","is_oa":true,"landing_page_url":"https://arxiv.org/pdf/2107.06440v1","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"arXiv (Cornell University)","raw_type":null},{"id":"doi:10.48550/arxiv.2107.06440","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2107.06440","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2107.06440","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2107.06440","pdf_url":"https://arxiv.org/pdf/2107.06440","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3159986226.pdf","grobid_xml":"https://content.openalex.org/works/W3159986226.grobid-xml"},"referenced_works_count":59,"referenced_works":["https://openalex.org/W1518976047","https://openalex.org/W1562979145","https://openalex.org/W1946587648","https://openalex.org/W1968626661","https://openalex.org/W1974326986","https://openalex.org/W2025177415","https://openalex.org/W2025383314","https://openalex.org/W2045407304","https://openalex.org/W2063573129","https://openalex.org/W2114487425","https://openalex.org/W2121606987","https://openalex.org/W2127969627","https://openalex.org/W2137813581","https://openalex.org/W2139490030","https://openalex.org/W2151961505","https://openalex.org/W2163619651","https://openalex.org/W2165808853","https://openalex.org/W2167082268","https://openalex.org/W2170484108","https://openalex.org/W2564763601","https://openalex.org/W2565322834","https://openalex.org/W2615068531","https://openalex.org/W2753923014","https://openalex.org/W2788257106","https://openalex.org/W2791982652","https://openalex.org/W2845875391","https://openalex.org/W2951269465","https://openalex.org/W2955617048","https://openalex.org/W2962802724","https://openalex.org/W2963561675","https://openalex.org/W2976279718","https://openalex.org/W2987657883","https://openalex.org/W3015526058","https://openalex.org/W3015739952","https://openalex.org/W3018124914","https://openalex.org/W3028579427","https://openalex.org/W3029287700","https://openalex.org/W3080465559","https://openalex.org/W3085477517","https://openalex.org/W3093968171","https://openalex.org/W3097193862","https://openalex.org/W3111365375","https://openalex.org/W3128220280","https://openalex.org/W3131711615","https://openalex.org/W3158992927","https://openalex.org/W3161798670","https://openalex.org/W3175367689","https://openalex.org/W6656576250","https://openalex.org/W6666485203","https://openalex.org/W6744141380","https://openalex.org/W6763917341","https://openalex.org/W6766689395","https://openalex.org/W6766998900","https://openalex.org/W6768415740","https://openalex.org/W6772628738","https://openalex.org/W6784352541","https://openalex.org/W6787179994","https://openalex.org/W6795419849","https://openalex.org/W6800116375"],"related_works":["https://openalex.org/W3190296759","https://openalex.org/W3005617074","https://openalex.org/W2737590357","https://openalex.org/W1690308247","https://openalex.org/W2745045892","https://openalex.org/W1992518732","https://openalex.org/W1992342254","https://openalex.org/W2564215951","https://openalex.org/W3046595859","https://openalex.org/W3160240665","https://openalex.org/W3192493049","https://openalex.org/W1684692403","https://openalex.org/W2921653546","https://openalex.org/W2040204131","https://openalex.org/W2964751176","https://openalex.org/W3103649678","https://openalex.org/W2951396760","https://openalex.org/W2084516574","https://openalex.org/W1504909833","https://openalex.org/W2097508332"],"abstract_inverted_index":{"Sequencing":[0],"a":[1,85],"DNA":[2,11,60],"strand,":[3],"as":[4,63],"part":[5],"of":[6,25,96],"the":[7,26,37,59,94,111,129],"read":[8],"process":[9],"in":[10,44,93,123],"storage,":[12],"produces":[13],"multiple":[14],"noisy":[15],"copies":[16],"which":[17],"can":[18,35],"be":[19],"combined":[20],"to":[21,102],"produce":[22],"better":[23],"estimates":[24],"original":[27],"strand;":[28],"this":[29,48,55,124,137,143],"is":[30,49,91,141],"called":[31,50],"trace":[32,52,79],"reconstruction.":[33,53,80],"One":[34],"reduce":[36],"error":[38,112],"rate":[39,113],"further":[40],"by":[41,149],"introducing":[42],"redundancy":[43],"write":[45],"sequence":[46],"and":[47,68,73,98,117],"coded":[51,78],"In":[54],"paper,":[56],"we":[57],"model":[58],"storage":[61],"channel":[62,67],"an":[64],"insertion-deletion-substitution":[65],"(IDS)":[66],"design":[69],"both":[70,115],"encoding":[71],"schemes":[72],"low-complexity":[74],"decoding":[75],"algorithms":[76],"for":[77],"We":[81],"introduce":[82],"Trellis":[83],"BMA,":[84],"new":[86],"reconstruction":[87],"algorithm":[88],"whose":[89],"complexity":[90],"linear":[92],"number":[95],"traces,":[97],"compare":[99],"its":[100],"performance":[101,121],"previous":[103],"algorithms.":[104,155],"Our":[105,139],"results":[106],"show":[107],"that":[108,142],"it":[109],"reduces":[110],"on":[114,128],"simulated":[116],"experimental":[118],"data.":[119],"The":[120],"comparisons":[122,152],"paper":[125],"are":[126],"based":[127],"Clustered":[130],"Nanopore":[131],"Reads":[132],"Dataset":[133],"publicly":[134],"released":[135],"with":[136],"paper.":[138],"hope":[140],"dataset":[144],"will":[145],"enable":[146],"research":[147],"progress":[148],"allowing":[150],"objective":[151],"between":[153],"candidate":[154]},"counts_by_year":[{"year":2021,"cited_by_count":1}],"updated_date":"2026-03-14T06:41:57.775601","created_date":"2025-10-10T00:00:00"}
