{"id":"https://openalex.org/W4225986528","doi":"https://doi.org/10.1186/s13015-022-00214-y","title":"Perplexity: evaluating transcript abundance estimation in the absence of ground truth","display_name":"Perplexity: evaluating transcript abundance estimation in the absence of ground truth","publication_year":2022,"publication_date":"2022-03-25","ids":{"openalex":"https://openalex.org/W4225986528","doi":"https://doi.org/10.1186/s13015-022-00214-y","pmid":"https://pubmed.ncbi.nlm.nih.gov/35331283"},"language":"en","primary_location":{"id":"doi:10.1186/s13015-022-00214-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-022-00214-y","pdf_url":"https://almob.biomedcentral.com/track/pdf/10.1186/s13015-022-00214-y","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://almob.biomedcentral.com/track/pdf/10.1186/s13015-022-00214-y","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001911878","display_name":"Jason Fan","orcid":"https://orcid.org/0000-0001-7617-4814"},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jason Fan","raw_affiliation_strings":["Center for Bioinformatics and Computational Biology, University of Maryland, College Park, USA. jasonfan@umd.edu","Center for Bioinformatics and Computational Biology, University of Maryland, College Park, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics and Computational Biology, University of Maryland, College Park, USA. jasonfan@umd.edu","institution_ids":["https://openalex.org/I66946132"]},{"raw_affiliation_string":"Center for Bioinformatics and Computational Biology, University of Maryland, College Park, USA","institution_ids":["https://openalex.org/I66946132"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021396179","display_name":"Spencer Skylar Chan","orcid":"https://orcid.org/0000-0001-7061-3695"},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Skylar Chan","raw_affiliation_strings":["Center for Bioinformatics and Computational Biology, University of Maryland, College Park, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics and Computational Biology, University of Maryland, College Park, USA","institution_ids":["https://openalex.org/I66946132"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014584023","display_name":"Rob Patro","orcid":"https://orcid.org/0000-0001-8463-1675"},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rob Patro","raw_affiliation_strings":["Center for Bioinformatics and Computational Biology, University of Maryland, College Park, USA. rob@cs.umd.edu","Center for Bioinformatics and Computational Biology, University of Maryland, College Park, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics and Computational Biology, University of Maryland, College Park, USA. rob@cs.umd.edu","institution_ids":["https://openalex.org/I66946132"]},{"raw_affiliation_string":"Center for Bioinformatics and Computational Biology, University of Maryland, College Park, USA","institution_ids":["https://openalex.org/I66946132"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5001911878"],"corresponding_institution_ids":["https://openalex.org/I66946132"],"apc_list":{"value":1490,"currency":"GBP","value_usd":1827},"apc_paid":{"value":1490,"currency":"GBP","value_usd":1827},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.03858688,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"17","issue":"1","first_page":"6","last_page":"6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.8349000215530396,"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":0.8349000215530396,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.07320000231266022,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.011699999682605267,"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/perplexity","display_name":"Perplexity","score":0.9344404935836792},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6720770001411438},{"id":"https://openalex.org/keywords/metric","display_name":"Metric (unit)","score":0.6112573146820068},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5964260101318359},{"id":"https://openalex.org/keywords/ground-truth","display_name":"Ground truth","score":0.5858734846115112},{"id":"https://openalex.org/keywords/abundance","display_name":"Abundance (ecology)","score":0.550184428691864},{"id":"https://openalex.org/keywords/model-selection","display_name":"Model selection","score":0.4341639578342438},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.344113826751709},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2500694990158081},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24088218808174133},{"id":"https://openalex.org/keywords/language-model","display_name":"Language model","score":0.14829719066619873},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.11623561382293701}],"concepts":[{"id":"https://openalex.org/C100279451","wikidata":"https://www.wikidata.org/wiki/Q372193","display_name":"Perplexity","level":3,"score":0.9344404935836792},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6720770001411438},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.6112573146820068},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5964260101318359},{"id":"https://openalex.org/C146849305","wikidata":"https://www.wikidata.org/wiki/Q370766","display_name":"Ground truth","level":2,"score":0.5858734846115112},{"id":"https://openalex.org/C77077793","wikidata":"https://www.wikidata.org/wiki/Q336019","display_name":"Abundance (ecology)","level":2,"score":0.550184428691864},{"id":"https://openalex.org/C93959086","wikidata":"https://www.wikidata.org/wiki/Q6888345","display_name":"Model selection","level":2,"score":0.4341639578342438},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.344113826751709},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2500694990158081},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24088218808174133},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.14829719066619873},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.11623561382293701},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.1186/s13015-022-00214-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-022-00214-y","pdf_url":"https://almob.biomedcentral.com/track/pdf/10.1186/s13015-022-00214-y","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},{"id":"pmid:35331283","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35331283","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":"Algorithms for molecular biology : AMB","raw_type":null},{"id":"pmh:oai:doaj.org/article:ddc5bc806d2d448f8708516c9cf8face","is_oa":false,"landing_page_url":"https://doaj.org/article/ddc5bc806d2d448f8708516c9cf8face","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms for Molecular Biology, Vol 17, Iss 1, Pp 1-23 (2022)","raw_type":"article"},{"id":"pmh:oai:drum.lib.umd.edu:1903/29069","is_oa":false,"landing_page_url":"http://hdl.handle.net/1903/29069","pdf_url":null,"source":{"id":"https://openalex.org/S4306401518","display_name":"University Libraries (University of Maryland)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I66946132","host_organization_name":"University of Maryland, College Park","host_organization_lineage":["https://openalex.org/I66946132"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8951746","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8951746","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms Mol Biol","raw_type":"Text"},{"id":"doi:10.13016/xfag-oldz","is_oa":true,"landing_page_url":"https://doi.org/10.13016/xfag-oldz","pdf_url":null,"source":{"id":"https://openalex.org/S4306402644","display_name":"Digital Repository at the University of Maryland (University of Maryland College Park)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I66946132","host_organization_name":"University of Maryland, College Park","host_organization_lineage":["https://openalex.org/I66946132"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1186/s13015-022-00214-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-022-00214-y","pdf_url":"https://almob.biomedcentral.com/track/pdf/10.1186/s13015-022-00214-y","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3146337093","display_name":"CSR: Medium: Approximate Membership Query Data Structures in Computational Biology and Storage","funder_award_id":"1763680","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3184792579","display_name":null,"funder_award_id":"CCF-1750472","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4624317431","display_name":null,"funder_award_id":"HG009937","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6262999909","display_name":null,"funder_award_id":"R01 HG009937","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6608149694","display_name":null,"funder_award_id":"1840340","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6624895376","display_name":null,"funder_award_id":"DGE-1840340","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6785428991","display_name":null,"funder_award_id":"CNS-1763680","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8288036582","display_name":null,"funder_award_id":"NIH R01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4225986528.pdf","grobid_xml":"https://content.openalex.org/works/W4225986528.grobid-xml"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W1847439710","https://openalex.org/W1987470886","https://openalex.org/W1987971958","https://openalex.org/W1990005915","https://openalex.org/W1990293955","https://openalex.org/W1999574084","https://openalex.org/W2008067936","https://openalex.org/W2009086942","https://openalex.org/W2010637767","https://openalex.org/W2022097310","https://openalex.org/W2045949302","https://openalex.org/W2064397275","https://openalex.org/W2097860373","https://openalex.org/W2098531465","https://openalex.org/W2100448568","https://openalex.org/W2112749286","https://openalex.org/W2112876600","https://openalex.org/W2126419817","https://openalex.org/W2129916363","https://openalex.org/W2134526812","https://openalex.org/W2138207763","https://openalex.org/W2152556446","https://openalex.org/W2152559563","https://openalex.org/W2170551349","https://openalex.org/W2197124664","https://openalex.org/W2235028661","https://openalex.org/W2409002067","https://openalex.org/W2474980444","https://openalex.org/W2555953877","https://openalex.org/W2592811885","https://openalex.org/W2734511552","https://openalex.org/W2897603717","https://openalex.org/W2940256315","https://openalex.org/W2964916138","https://openalex.org/W2970881455","https://openalex.org/W2972131171","https://openalex.org/W3043250694","https://openalex.org/W3122109253","https://openalex.org/W3165336786","https://openalex.org/W4206037526","https://openalex.org/W4210644165","https://openalex.org/W6639619044"],"related_works":["https://openalex.org/W2376415519","https://openalex.org/W4294769427","https://openalex.org/W1895908943","https://openalex.org/W4225667838","https://openalex.org/W1601381279","https://openalex.org/W4281893144","https://openalex.org/W2374747083","https://openalex.org/W4388254351","https://openalex.org/W4386270999","https://openalex.org/W2387906841"],"abstract_inverted_index":{"BACKGROUND:":[0],"There":[1],"has":[2],"been":[3,99],"rapid":[4],"development":[5],"of":[6,54,81,199,225],"probabilistic":[7],"models":[8,20,129],"and":[9,36,127,130,164,172,180,197],"inference":[10],"methods":[11,60],"for":[12,29,91,108,137,187,201,215],"transcript":[13,189,202,216],"abundance":[14,110,190,203,217],"estimation":[15,191,218],"from":[16,119],"RNA-seq":[17],"data.":[18],"These":[19],"aim":[21],"to":[22,27,38,48,77,124,134,141,210],"accurately":[23],"estimate":[24],"transcript-level":[25],"abundances,":[26],"account":[28,136],"different":[30],"biases":[31],"in":[32,41,69,95,222],"the":[33,55,70,79,120,132,148,195,208,223],"measurement":[34],"process,":[35],"even":[37],"assess":[39],"uncertainty":[40],"resulting":[42],"estimates":[43,56,111,146],"that":[44,182],"can":[45,184],"be":[46,185],"propagated":[47],"subsequent":[49],"analyses.":[50],"The":[51],"assumed":[52],"accuracy":[53],"inferred":[57,82],"by":[58],"such":[59],"underpin":[61],"gene":[62],"expression":[63,174],"based":[64],"analysis":[65],"routinely":[66],"carried":[67],"out":[68],"lab.":[71],"Although":[72],"hyperparameter":[73],"selection":[74,94,214],"is":[75,161,207],"known":[76],"affect":[78],"distributions":[80],"abundances":[83],"(e.g.":[84],"producing":[85],"smooth":[86],"versus":[87],"sparse":[88],"estimates),":[89],"strategies":[90],"performing":[92],"model":[93,213],"experimental":[96,144,220],"data":[97,221],"have":[98],"addressed":[100],"informally":[101],"at":[102],"best.":[103],"RESULTS:":[104],"We":[105,116],"derive":[106],"perplexity":[107,118,150,160,183,200],"evaluating":[109],"on":[112,219],"fragment":[113],"sets":[114],"directly.":[115],"adapt":[117],"analogous":[121],"metric":[122,133],"used":[123],"evaluate":[125],"language":[126],"topic":[128],"extend":[131],"carefully":[135],"corner":[138],"cases":[139],"unique":[140],"RNA-seq.":[142],"In":[143,157],"data,":[145,159],"with":[147,154,166],"best":[149,152],"also":[151],"correlate":[153],"qPCR":[155],"measurements.":[156],"simulated":[158],"well":[162],"behaved":[163],"concordant":[165],"genome-wide":[167],"measurements":[168],"against":[169],"ground":[170,226],"truth":[171],"differential":[173],"analysis.":[175],"Furthermore,":[176],"we":[177],"demonstrate":[178],"theoretically":[179],"experimentally":[181],"computed":[186],"arbitrary":[188],"models.":[192],"CONCLUSIONS:":[193],"Alongside":[194],"derivation":[196],"implementation":[198],"estimation,":[204],"our":[205],"study":[206],"first":[209],"make":[211],"possible":[212],"absence":[224],"truth.":[227]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
