{"id":"https://openalex.org/W3005333949","doi":"https://doi.org/10.1109/bibm47256.2019.8983240","title":"Fine Tuning Sparsity Penalties to Improve Structural Variant Detection","display_name":"Fine Tuning Sparsity Penalties to Improve Structural Variant Detection","publication_year":2019,"publication_date":"2019-11-01","ids":{"openalex":"https://openalex.org/W3005333949","doi":"https://doi.org/10.1109/bibm47256.2019.8983240","mag":"3005333949"},"language":"en","primary_location":{"id":"doi:10.1109/bibm47256.2019.8983240","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm47256.2019.8983240","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","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/A5100365893","display_name":"Xiaolong Chen","orcid":"https://orcid.org/0000-0002-9401-4299"},"institutions":[{"id":"https://openalex.org/I156087764","display_name":"University of California, Merced","ror":"https://ror.org/00d9ah105","country_code":"US","type":"education","lineage":["https://openalex.org/I156087764"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Xiaolong Chen","raw_affiliation_strings":["University of California, Merced,Department of Applied Mathematics,Merced,United States","Department of Applied Mathematics, University of California, Merced, Merced, United States"],"affiliations":[{"raw_affiliation_string":"University of California, Merced,Department of Applied Mathematics,Merced,United States","institution_ids":["https://openalex.org/I156087764"]},{"raw_affiliation_string":"Department of Applied Mathematics, University of California, Merced, Merced, United States","institution_ids":["https://openalex.org/I156087764"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007958404","display_name":"Hansell Perez","orcid":"https://orcid.org/0000-0002-9048-6686"},"institutions":[{"id":"https://openalex.org/I156087764","display_name":"University of California, Merced","ror":"https://ror.org/00d9ah105","country_code":"US","type":"education","lineage":["https://openalex.org/I156087764"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hansell Perez","raw_affiliation_strings":["University of California, Merced,Department of Applied Mathematics,Merced,United States","Department of Applied Mathematics, University of California, Merced, Merced, United States"],"affiliations":[{"raw_affiliation_string":"University of California, Merced,Department of Applied Mathematics,Merced,United States","institution_ids":["https://openalex.org/I156087764"]},{"raw_affiliation_string":"Department of Applied Mathematics, University of California, Merced, Merced, United States","institution_ids":["https://openalex.org/I156087764"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045718155","display_name":"Melissa Spence","orcid":null},"institutions":[{"id":"https://openalex.org/I156087764","display_name":"University of California, Merced","ror":"https://ror.org/00d9ah105","country_code":"US","type":"education","lineage":["https://openalex.org/I156087764"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Melissa Spence","raw_affiliation_strings":["University of California, Merced,Department of Applied Mathematics,Merced,United States","Department of Applied Mathematics, University of California, Merced, Merced, United States"],"affiliations":[{"raw_affiliation_string":"University of California, Merced,Department of Applied Mathematics,Merced,United States","institution_ids":["https://openalex.org/I156087764"]},{"raw_affiliation_string":"Department of Applied Mathematics, University of California, Merced, Merced, United States","institution_ids":["https://openalex.org/I156087764"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005703929","display_name":"Roummel F. Marcia","orcid":"https://orcid.org/0000-0001-6838-140X"},"institutions":[{"id":"https://openalex.org/I156087764","display_name":"University of California, Merced","ror":"https://ror.org/00d9ah105","country_code":"US","type":"education","lineage":["https://openalex.org/I156087764"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Roummel Marcia","raw_affiliation_strings":["University of California, Merced,Department of Applied Mathematics,Merced,United States","Department of Applied Mathematics, University of California, Merced, Merced, United States"],"affiliations":[{"raw_affiliation_string":"University of California, Merced,Department of Applied Mathematics,Merced,United States","institution_ids":["https://openalex.org/I156087764"]},{"raw_affiliation_string":"Department of Applied Mathematics, University of California, Merced, Merced, United States","institution_ids":["https://openalex.org/I156087764"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027970835","display_name":"Suzanne Sindi","orcid":"https://orcid.org/0000-0003-2742-4332"},"institutions":[{"id":"https://openalex.org/I156087764","display_name":"University of California, Merced","ror":"https://ror.org/00d9ah105","country_code":"US","type":"education","lineage":["https://openalex.org/I156087764"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Suzanne Sindi","raw_affiliation_strings":["University of California, Merced,Department of Applied Mathematics,Merced,United States","Department of Applied Mathematics, University of California, Merced, Merced, United States"],"affiliations":[{"raw_affiliation_string":"University of California, Merced,Department of Applied Mathematics,Merced,United States","institution_ids":["https://openalex.org/I156087764"]},{"raw_affiliation_string":"Department of Applied Mathematics, University of California, Merced, Merced, United States","institution_ids":["https://openalex.org/I156087764"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5100365893"],"corresponding_institution_ids":["https://openalex.org/I156087764"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.18882453,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1182","last_page":"1184"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9991000294685364,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T11642","display_name":"Genomics and Rare Diseases","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/robustness","display_name":"Robustness (evolution)","score":0.7943575382232666},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6500681638717651},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.611732006072998},{"id":"https://openalex.org/keywords/sensitivity","display_name":"Sensitivity (control systems)","score":0.524511456489563},{"id":"https://openalex.org/keywords/variation","display_name":"Variation (astronomy)","score":0.4573715031147003},{"id":"https://openalex.org/keywords/structural-variation","display_name":"Structural variation","score":0.4555432200431824},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.42109936475753784},{"id":"https://openalex.org/keywords/range","display_name":"Range (aeronautics)","score":0.41477084159851074},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.37045201659202576},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.36323320865631104},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3482288122177124},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.33163994550704956},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20185378193855286},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.17959389090538025},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.09708905220031738},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.08098715543746948}],"concepts":[{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.7943575382232666},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6500681638717651},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.611732006072998},{"id":"https://openalex.org/C21200559","wikidata":"https://www.wikidata.org/wiki/Q7451068","display_name":"Sensitivity (control systems)","level":2,"score":0.524511456489563},{"id":"https://openalex.org/C2778334786","wikidata":"https://www.wikidata.org/wiki/Q1586270","display_name":"Variation (astronomy)","level":2,"score":0.4573715031147003},{"id":"https://openalex.org/C151020129","wikidata":"https://www.wikidata.org/wiki/Q7625067","display_name":"Structural variation","level":4,"score":0.4555432200431824},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.42109936475753784},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.41477084159851074},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.37045201659202576},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.36323320865631104},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3482288122177124},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.33163994550704956},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20185378193855286},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17959389090538025},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.09708905220031738},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.08098715543746948},{"id":"https://openalex.org/C24326235","wikidata":"https://www.wikidata.org/wiki/Q126095","display_name":"Electronic engineering","level":1,"score":0.0},{"id":"https://openalex.org/C44870925","wikidata":"https://www.wikidata.org/wiki/Q37547","display_name":"Astrophysics","level":1,"score":0.0},{"id":"https://openalex.org/C146978453","wikidata":"https://www.wikidata.org/wiki/Q3798668","display_name":"Aerospace engineering","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm47256.2019.8983240","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm47256.2019.8983240","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":7,"referenced_works":["https://openalex.org/W2050892949","https://openalex.org/W2083870688","https://openalex.org/W2096791516","https://openalex.org/W2613868166","https://openalex.org/W2737819809","https://openalex.org/W2913878444","https://openalex.org/W3106237033"],"related_works":["https://openalex.org/W2386430105","https://openalex.org/W2356521405","https://openalex.org/W2038534795","https://openalex.org/W2384358604","https://openalex.org/W1567829292","https://openalex.org/W3001063351","https://openalex.org/W3196905815","https://openalex.org/W2351370765","https://openalex.org/W3133811809","https://openalex.org/W1967452726"],"abstract_inverted_index":{"Genomic":[0],"variation":[1,32],"shared":[2],"by":[3,106],"members":[4],"of":[5,31,45,69,77,90,103,111],"the":[6,67,82,88,101],"same":[7],"species":[8],"that":[9,55,114],"are":[10,16],"longer":[11],"than":[12],"a":[13,108],"single":[14],"nucleotide":[15],"commonly":[17],"called":[18],"structural":[19],"variants":[20],"(SVs).":[21],"Though":[22],"relatively":[23],"rare,":[24],"they":[25],"represent":[26],"an":[27],"increasingly":[28],"important":[29],"class":[30],"as":[33],"SVs":[34,51,73],"have":[35],"been":[36],"associated":[37],"with":[38],"diseases":[39],"and":[40,71],"susceptibility":[41],"to":[42,74,94,116],"some":[43],"types":[44],"cancer.":[46],"Computational":[47],"approaches":[48],"for":[49],"detecting":[50],"often":[52],"involve":[53],"parameters":[54,65],"describe":[56],"certain":[57],"relevant":[58],"biological":[59],"phenomena.":[60],"In":[61,81,97],"our":[62,91,104],"work,":[63],"such":[64],"relate":[66],"incidence":[68],"inherited":[70],"novel":[72],"probabilistic":[75],"models":[76],"observing":[78],"these":[79,95],"SVs.":[80],"work":[83],"presented":[84],"here,":[85],"we":[86,99],"investigate":[87],"sensitivity":[89],"computational":[92],"framework":[93],"parameters.":[96],"particular,":[98],"demonstrate":[100],"robustness":[102],"method":[105],"identifying":[107],"wide":[109],"range":[110],"parameter":[112],"values":[113],"lead":[115],"high-accuracy":[117],"SV":[118],"predictions":[119],"in":[120],"simulated":[121],"data.":[122]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}