{"id":"https://openalex.org/W3091333637","doi":"https://doi.org/10.1145/3410463.3414626","title":"Helix","display_name":"Helix","publication_year":2020,"publication_date":"2020-09-30","ids":{"openalex":"https://openalex.org/W3091333637","doi":"https://doi.org/10.1145/3410463.3414626","mag":"3091333637"},"language":"en","primary_location":{"id":"doi:10.1145/3410463.3414626","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3410463.3414626","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the ACM International Conference on Parallel Architectures and Compilation Techniques","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/A5006753786","display_name":"Qian Lou","orcid":"https://orcid.org/0000-0001-5462-2567"},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Qian Lou","raw_affiliation_strings":["Indiana University Bloomington, Bloomington, IN, USA"],"affiliations":[{"raw_affiliation_string":"Indiana University Bloomington, Bloomington, IN, USA","institution_ids":["https://openalex.org/I4210119109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066167699","display_name":"Sarath Chandra Janga","orcid":"https://orcid.org/0000-0001-7351-6268"},"institutions":[{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]},{"id":"https://openalex.org/I135191193","display_name":"University of Indianapolis","ror":"https://ror.org/052133d12","country_code":"US","type":"education","lineage":["https://openalex.org/I135191193"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sarath Chandra Janga","raw_affiliation_strings":["Indiana University - Purdue University Indianapolis, Indianapolis, IN, USA"],"affiliations":[{"raw_affiliation_string":"Indiana University - Purdue University Indianapolis, Indianapolis, IN, USA","institution_ids":["https://openalex.org/I135191193","https://openalex.org/I55769427"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103098320","display_name":"Lei Jiang","orcid":"https://orcid.org/0000-0003-4795-0284"},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lei Jiang","raw_affiliation_strings":["Indiana University Bloomington, Bloomington, IN, USA"],"affiliations":[{"raw_affiliation_string":"Indiana University Bloomington, Bloomington, IN, USA","institution_ids":["https://openalex.org/I4210119109"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5006753786"],"corresponding_institution_ids":["https://openalex.org/I4210119109"],"apc_list":null,"apc_paid":null,"fwci":0.9182,"has_fulltext":false,"cited_by_count":23,"citation_normalized_percentile":{"value":0.73523588,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":null,"issue":null,"first_page":"293","last_page":"304"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.9976999759674072,"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/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.9976999759674072,"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/T12808","display_name":"Ferroelectric and Negative Capacitance Devices","score":0.9962000250816345,"subfield":{"id":"https://openalex.org/subfields/2208","display_name":"Electrical and Electronic 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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9957000017166138,"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":0.7931237816810608},{"id":"https://openalex.org/keywords/bottleneck","display_name":"Bottleneck","score":0.7240030765533447},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.4987037181854248},{"id":"https://openalex.org/keywords/decoding-methods","display_name":"Decoding methods","score":0.45745861530303955},{"id":"https://openalex.org/keywords/quantization","display_name":"Quantization (signal processing)","score":0.43826085329055786},{"id":"https://openalex.org/keywords/overhead","display_name":"Overhead (engineering)","score":0.4147699177265167},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.36973080039024353},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.3401045501232147},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.1397741734981537},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.13121962547302246}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7931237816810608},{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.7240030765533447},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.4987037181854248},{"id":"https://openalex.org/C57273362","wikidata":"https://www.wikidata.org/wiki/Q576722","display_name":"Decoding methods","level":2,"score":0.45745861530303955},{"id":"https://openalex.org/C28855332","wikidata":"https://www.wikidata.org/wiki/Q198099","display_name":"Quantization (signal processing)","level":2,"score":0.43826085329055786},{"id":"https://openalex.org/C2779960059","wikidata":"https://www.wikidata.org/wiki/Q7113681","display_name":"Overhead (engineering)","level":2,"score":0.4147699177265167},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.36973080039024353},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.3401045501232147},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.1397741734981537},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.13121962547302246}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3410463.3414626","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3410463.3414626","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the ACM International Conference on Parallel Architectures and Compilation Techniques","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/2","display_name":"Zero hunger","score":0.5600000023841858}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W2010202670","https://openalex.org/W2127141656","https://openalex.org/W2317495605","https://openalex.org/W2330159693","https://openalex.org/W2331328369","https://openalex.org/W2742694477","https://openalex.org/W2782401175","https://openalex.org/W2791119250","https://openalex.org/W2890826549","https://openalex.org/W2907909057","https://openalex.org/W2913104037","https://openalex.org/W2949674408","https://openalex.org/W2979823675","https://openalex.org/W3004318991","https://openalex.org/W3005874416","https://openalex.org/W3006196114","https://openalex.org/W3102575390","https://openalex.org/W3104349737","https://openalex.org/W4229975054","https://openalex.org/W4232675554"],"related_works":["https://openalex.org/W2357461155","https://openalex.org/W2623483207","https://openalex.org/W2384129116","https://openalex.org/W2354251581","https://openalex.org/W3145924829","https://openalex.org/W2383932853","https://openalex.org/W2353647904","https://openalex.org/W3152267458","https://openalex.org/W2157013742","https://openalex.org/W2092715862"],"abstract_inverted_index":{"Nanopore":[0],"genome":[1],"sequencing":[2,48],"is":[3,52,128],"the":[4,66,75,92],"key":[5],"to":[6,24,32,54,64],"enabling":[7],"personalized":[8],"medicine,":[9],"global":[10],"food":[11],"security,":[12],"and":[13,58,141,154],"virus":[14],"surveillance.":[15],"The":[16,104],"state-of-the-art":[17],"base-callers":[18],"adopt":[19],"deep":[20],"neural":[21],"networks":[22],"(DNNs)":[23],"translate":[25],"electrical":[26],"signals":[27],"generated":[28],"by":[29,81,85,101,131],"nanopore":[30,47],"sequencers":[31],"digital":[33],"DNA":[34],"symbols.":[35],"A":[36],"DNN-based":[37],"base-caller":[38,57,80],"consumes":[39],"44.5%":[40],"of":[41,45,78,94,107,146],"total":[42,147],"execution":[43,148],"time":[44,149],"a":[46,56,60,79,151],"pipeline.":[49],"However,":[50],"it":[51,89],"difficult":[53],"quantize":[55],"build":[59],"power-efficient":[61],"processing-in-memory":[62],"(PIM)":[63],"run":[65],"quantized":[67,152],"base-caller.":[68],"Although":[69],"conventional":[70],"network":[71],"quantization":[72],"techniques":[73],"reduce":[74],"computing":[76],"overhead":[77],"replacing":[82],"floating-point":[83],"multiply-accumulations":[84],"cheaper":[86],"fixed-point":[87],"operations,":[88],"significantly":[90],"increases":[91],"number":[93],"systematic":[95],"errors":[96],"that":[97],"cannot":[98],"be":[99],"corrected":[100],"read":[102,142],"votes.":[103],"power":[105,126],"density":[106],"prior":[108],"nonvolatile":[109],"memory":[110,116],"(NVM)-based":[111],"PIMs":[112],"has":[113],"already":[114],"exceeded":[115],"thermal":[117],"tolerance":[118],"even":[119],"with":[120],"active":[121],"heat":[122],"sinks,":[123],"because":[124],"their":[125],"efficiency":[127],"severely":[129],"limited":[130],"analog-to-digital":[132],"converters":[133],"(ADC).":[134],"Finally,":[135],"Connectionist":[136],"Temporal":[137],"Classification":[138],"(CTC)":[139],"decoding":[140],"voting":[143],"cost":[144],"53.7%":[145],"in":[150],"base-caller,":[153],"thus":[155],"became":[156],"its":[157],"new":[158],"bottleneck.":[159]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":1}],"updated_date":"2026-03-06T13:50:29.536080","created_date":"2020-10-08T00:00:00"}