{"id":"https://openalex.org/W3157373627","doi":"https://doi.org/10.1109/jbhi.2021.3094873","title":"Interpretable Classification of Bacterial Raman Spectra With Knockoff Wavelets","display_name":"Interpretable Classification of Bacterial Raman Spectra With Knockoff Wavelets","publication_year":2021,"publication_date":"2021-07-07","ids":{"openalex":"https://openalex.org/W3157373627","doi":"https://doi.org/10.1109/jbhi.2021.3094873","mag":"3157373627","pmid":"https://pubmed.ncbi.nlm.nih.gov/34232897"},"language":"en","primary_location":{"id":"doi:10.1109/jbhi.2021.3094873","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2021.3094873","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":["arxiv","crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2006.04937","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Charmaine Chia","orcid":null},"institutions":[{"id":"https://openalex.org/I4210099336","display_name":"Menlo School","ror":"https://ror.org/01240pn49","country_code":"US","type":"education","lineage":["https://openalex.org/I4210099336"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Charmaine Chia","raw_affiliation_strings":["Aether Biomachines, Menlo Park, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Aether Biomachines, Menlo Park, CA, USA","institution_ids":["https://openalex.org/I4210099336"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Matteo Sesia","orcid":"https://orcid.org/0000-0001-9046-907X"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matteo Sesia","raw_affiliation_strings":["Department of Data Sciences and Operations, University of Southern California, Los Angeles, CA, USA"],"raw_orcid":"https://orcid.org/0000-0001-9046-907X","affiliations":[{"raw_affiliation_string":"Department of Data Sciences and Operations, University of Southern California, Los Angeles, CA, USA","institution_ids":["https://openalex.org/I1174212"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Chi-Sing Ho","orcid":null},"institutions":[{"id":"https://openalex.org/I4210114883","display_name":"Tempus Labs (United States)","ror":"https://ror.org/01gbymr57","country_code":"US","type":"company","lineage":["https://openalex.org/I4210114883"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chi-Sing Ho","raw_affiliation_strings":["Tempus Labs, Redwood City, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tempus Labs, Redwood City, CA, USA","institution_ids":["https://openalex.org/I4210114883"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Stefanie S. Jeffrey","orcid":null},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stefanie S. Jeffrey","raw_affiliation_strings":["Department of Electrical Engineering, Stanford University, Stanford, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering, Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Jennifer Dionne","orcid":null},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jennifer Dionne","raw_affiliation_strings":["Department of Materials Science and Engineering, Stanford University, Stanford, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Materials Science and Engineering, Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Emmanuel J. Candes","orcid":null},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Emmanuel J. Candes","raw_affiliation_strings":["Department of Statistics, Stanford University, Stanford, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics, Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"last","author":{"id":null,"display_name":"Roger T. Howe","orcid":"https://orcid.org/0000-0002-5572-5194"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Roger T. Howe","raw_affiliation_strings":["Department of Electrical Engineering, Stanford University, Stanford, CA, USA"],"raw_orcid":"https://orcid.org/0000-0002-5572-5194","affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering, Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":2645,"currency":"USD","value_usd":2645},"apc_paid":null,"fwci":1.0557,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.81868208,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"26","issue":"2","first_page":"740","last_page":"748"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11324","display_name":"Spectroscopy Techniques in Biomedical and Chemical Research","score":0.9715999960899353,"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"}},"topics":[{"id":"https://openalex.org/T11324","display_name":"Spectroscopy Techniques in Biomedical and Chemical Research","score":0.9715999960899353,"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"}},{"id":"https://openalex.org/T10640","display_name":"Spectroscopy and Chemometric Analyses","score":0.0027000000700354576,"subfield":{"id":"https://openalex.org/subfields/1602","display_name":"Analytical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12167","display_name":"Bacterial Identification and Susceptibility Testing","score":0.0015999999595806003,"subfield":{"id":"https://openalex.org/subfields/1308","display_name":"Clinical Biochemistry"},"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/interpretability","display_name":"Interpretability","score":0.8989999890327454},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.7067000269889832},{"id":"https://openalex.org/keywords/wavelet","display_name":"Wavelet","score":0.6769999861717224},{"id":"https://openalex.org/keywords/feature-selection","display_name":"Feature selection","score":0.49540001153945923},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.4867999851703644},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.47859999537467957},{"id":"https://openalex.org/keywords/focus","display_name":"Focus (optics)","score":0.4636000096797943},{"id":"https://openalex.org/keywords/signal","display_name":"SIGNAL (programming language)","score":0.42829999327659607}],"concepts":[{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.8989999890327454},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.7791000008583069},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.7067000269889832},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6816999912261963},{"id":"https://openalex.org/C47432892","wikidata":"https://www.wikidata.org/wiki/Q831390","display_name":"Wavelet","level":2,"score":0.6769999861717224},{"id":"https://openalex.org/C148483581","wikidata":"https://www.wikidata.org/wiki/Q446488","display_name":"Feature selection","level":2,"score":0.49540001153945923},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.4867999851703644},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.47859999537467957},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.4636000096797943},{"id":"https://openalex.org/C2779843651","wikidata":"https://www.wikidata.org/wiki/Q7390335","display_name":"SIGNAL (programming language)","level":2,"score":0.42829999327659607},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4072999954223633},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3684000074863434},{"id":"https://openalex.org/C104267543","wikidata":"https://www.wikidata.org/wiki/Q208163","display_name":"Signal processing","level":3,"score":0.35749998688697815},{"id":"https://openalex.org/C196216189","wikidata":"https://www.wikidata.org/wiki/Q2867","display_name":"Wavelet transform","level":3,"score":0.35199999809265137},{"id":"https://openalex.org/C52622490","wikidata":"https://www.wikidata.org/wiki/Q1026626","display_name":"Feature extraction","level":2,"score":0.35109999775886536},{"id":"https://openalex.org/C67186912","wikidata":"https://www.wikidata.org/wiki/Q367664","display_name":"Data modeling","level":2,"score":0.3407000005245209},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.3239000141620636},{"id":"https://openalex.org/C93959086","wikidata":"https://www.wikidata.org/wiki/Q6888345","display_name":"Model selection","level":2,"score":0.2992999851703644},{"id":"https://openalex.org/C151956035","wikidata":"https://www.wikidata.org/wiki/Q1132755","display_name":"Logistic regression","level":2,"score":0.2791000008583069},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.2734000086784363},{"id":"https://openalex.org/C193244246","wikidata":"https://www.wikidata.org/wiki/Q5432696","display_name":"False discovery rate","level":3,"score":0.2572999894618988},{"id":"https://openalex.org/C110083411","wikidata":"https://www.wikidata.org/wiki/Q1744628","display_name":"Statistical classification","level":2,"score":0.2565000057220459},{"id":"https://openalex.org/C151406439","wikidata":"https://www.wikidata.org/wiki/Q186588","display_name":"Time series","level":2,"score":0.25119999051094055},{"id":"https://openalex.org/C114289077","wikidata":"https://www.wikidata.org/wiki/Q3284399","display_name":"Statistical model","level":2,"score":0.25029999017715454}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016015","descriptor_name":"Logistic Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016015","descriptor_name":"Logistic Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016015","descriptor_name":"Logistic Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1109/jbhi.2021.3094873","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2021.3094873","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"},{"id":"pmid:34232897","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34232897","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 journal of biomedical and health informatics","raw_type":"Journal Article"},{"id":"pmh:oai:arXiv.org:2006.04937","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2006.04937","pdf_url":"https://arxiv.org/pdf/2006.04937","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"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":null,"raw_type":"text"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2006.04937","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2006.04937","pdf_url":"https://arxiv.org/pdf/2006.04937","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"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":null,"raw_type":"text"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306164","display_name":"Simons Foundation","ror":"https://ror.org/01cmst727"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":42,"referenced_works":["https://openalex.org/W1976965124","https://openalex.org/W1996796871","https://openalex.org/W2006252838","https://openalex.org/W2029236612","https://openalex.org/W2069115302","https://openalex.org/W2109177042","https://openalex.org/W2110065044","https://openalex.org/W2115447612","https://openalex.org/W2119387367","https://openalex.org/W2135046866","https://openalex.org/W2162387923","https://openalex.org/W2167101736","https://openalex.org/W2485724554","https://openalex.org/W2551895583","https://openalex.org/W2561981131","https://openalex.org/W2782176193","https://openalex.org/W2792065904","https://openalex.org/W2807324057","https://openalex.org/W2901837190","https://openalex.org/W2905369320","https://openalex.org/W2910705748","https://openalex.org/W2911599113","https://openalex.org/W2922395038","https://openalex.org/W2947402981","https://openalex.org/W2952071070","https://openalex.org/W2963095307","https://openalex.org/W2963259533","https://openalex.org/W2963371845","https://openalex.org/W2968001089","https://openalex.org/W2969316698","https://openalex.org/W2982482221","https://openalex.org/W3010193979","https://openalex.org/W3138819813","https://openalex.org/W3161970055","https://openalex.org/W4241337469","https://openalex.org/W4289236186","https://openalex.org/W4294541781","https://openalex.org/W6680532216","https://openalex.org/W6682241100","https://openalex.org/W6734862562","https://openalex.org/W6753456638","https://openalex.org/W6754484873"],"related_works":[],"abstract_inverted_index":{"Deep":[0],"neural":[1,71],"networks":[2],"and":[3,21,54,77,89,102],"other":[4,119],"machine":[5],"learning":[6],"models":[7,31],"are":[8,100],"widely":[9],"applied":[10],"to":[11,68,96,118],"biomedical":[12],"signal":[13,122],"data":[14,53,110,123],"because":[15],"they":[16],"can":[17],"detect":[18],"complex":[19],"patterns":[20],"compute":[22],"accurate":[23],"predictions.":[24],"However,":[25],"the":[26,42,98,112],"difficulty":[27],"of":[28,44,70,121],"interpreting":[29],"such":[30],"is":[32,115],"a":[33,57,108],"limitation,":[34],"especially":[35],"for":[36,124],"applications":[37],"involving":[38],"high-stakes":[39],"decision,":[40],"including":[41],"identification":[43],"bacterial":[45],"infections.":[46],"This":[47],"paper":[48],"considers":[49],"fast":[50],"Raman":[51],"spectroscopy":[52],"demonstrates":[55],"that":[56,69],"logistic":[58],"regression":[59],"model":[60],"with":[61,85,94],"carefully":[62],"selected":[63],"features":[64,84],"achieves":[65],"accuracy":[66],"comparable":[67],"networks,":[72],"while":[73],"being":[74],"much":[75],"simpler":[76],"more":[78],"transparent.":[79],"Our":[80],"analysis":[81],"leverages":[82],"wavelet":[83],"intuitive":[86],"chemical":[87],"interpretations,":[88],"performs":[90],"controlled":[91],"variable":[92],"selection":[93],"knockoffs":[95],"ensure":[97],"predictors":[99],"relevant":[101],"non-redundant.":[103],"Although":[104],"we":[105],"focus":[106],"on":[107],"particular":[109],"set,":[111],"proposed":[113],"approach":[114],"broadly":[116],"applicable":[117],"types":[120],"which":[125],"interpretability":[126],"may":[127],"be":[128],"important.":[129]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2021-05-10T00:00:00"}
