{"id":"https://openalex.org/W2258133463","doi":"https://doi.org/10.1093/bioinformatics/btv648","title":"Shape component analysis: structure-preserving dimension reduction on biological shape spaces","display_name":"Shape component analysis: structure-preserving dimension reduction on biological shape spaces","publication_year":2015,"publication_date":"2015-11-04","ids":{"openalex":"https://openalex.org/W2258133463","doi":"https://doi.org/10.1093/bioinformatics/btv648","mag":"2258133463","pmid":"https://pubmed.ncbi.nlm.nih.gov/26543176"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv648","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv648","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/5/755/25588952/btv648.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/32/5/755/25588952/btv648.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5061960883","display_name":"Hao-Chih Lee","orcid":"https://orcid.org/0000-0002-1538-6175"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hao-Chih Lee","raw_affiliation_strings":["1 Department of Biomedical Engineering,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biomedical Engineering,","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101767579","display_name":"Tao Liao","orcid":"https://orcid.org/0000-0003-2534-4304"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Tao Liao","raw_affiliation_strings":["2 Department of Mechanical Engineering, and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"2 Department of Mechanical Engineering, and","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100402810","display_name":"Yongjie Zhang","orcid":"https://orcid.org/0000-0001-7436-9757"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yongjie Jessica Zhang","raw_affiliation_strings":["1 Department of Biomedical Engineering,","2 Department of Mechanical Engineering, and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biomedical Engineering,","institution_ids":[]},{"raw_affiliation_string":"2 Department of Mechanical Engineering, and","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021147939","display_name":"Ge Yang","orcid":"https://orcid.org/0000-0001-6176-3130"},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ge Yang","raw_affiliation_strings":["1 Department of Biomedical Engineering,","3 Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biomedical Engineering,","institution_ids":[]},{"raw_affiliation_string":"3 Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA","institution_ids":["https://openalex.org/I74973139"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5021147939"],"corresponding_institution_ids":["https://openalex.org/I74973139"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.9953,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.75947365,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"32","issue":"5","first_page":"755","last_page":"763"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12417","display_name":"Morphological variations and asymmetry","score":0.2718000113964081,"subfield":{"id":"https://openalex.org/subfields/2608","display_name":"Geometry and Topology"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T12417","display_name":"Morphological variations and asymmetry","score":0.2718000113964081,"subfield":{"id":"https://openalex.org/subfields/2608","display_name":"Geometry and Topology"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.18690000474452972,"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/T10052","display_name":"Medical Image Segmentation Techniques","score":0.07590000331401825,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"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":0.6872617602348328},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.6694055199623108},{"id":"https://openalex.org/keywords/dimensionality-reduction","display_name":"Dimensionality reduction","score":0.6393389701843262},{"id":"https://openalex.org/keywords/dimension","display_name":"Dimension (graph theory)","score":0.5943266153335571},{"id":"https://openalex.org/keywords/shape-analysis","display_name":"Shape analysis (program analysis)","score":0.5867027640342712},{"id":"https://openalex.org/keywords/matlab","display_name":"MATLAB","score":0.5585840344429016},{"id":"https://openalex.org/keywords/reduction","display_name":"Reduction (mathematics)","score":0.5545455813407898},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.5399982333183289},{"id":"https://openalex.org/keywords/dimensional-reduction","display_name":"Dimensional reduction","score":0.5129963755607605},{"id":"https://openalex.org/keywords/component","display_name":"Component (thermodynamics)","score":0.46412208676338196},{"id":"https://openalex.org/keywords/high-dimensional","display_name":"High dimensional","score":0.4284365773200989},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.38201266527175903},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.36420542001724243},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3583033084869385},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2288653552532196},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.19780680537223816},{"id":"https://openalex.org/keywords/static-analysis","display_name":"Static analysis","score":0.1253732144832611},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.12167197465896606},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.10380616784095764}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6872617602348328},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6694055199623108},{"id":"https://openalex.org/C70518039","wikidata":"https://www.wikidata.org/wiki/Q16000077","display_name":"Dimensionality reduction","level":2,"score":0.6393389701843262},{"id":"https://openalex.org/C33676613","wikidata":"https://www.wikidata.org/wiki/Q13415176","display_name":"Dimension (graph theory)","level":2,"score":0.5943266153335571},{"id":"https://openalex.org/C112604564","wikidata":"https://www.wikidata.org/wiki/Q7489226","display_name":"Shape analysis (program analysis)","level":3,"score":0.5867027640342712},{"id":"https://openalex.org/C2780365114","wikidata":"https://www.wikidata.org/wiki/Q169478","display_name":"MATLAB","level":2,"score":0.5585840344429016},{"id":"https://openalex.org/C111335779","wikidata":"https://www.wikidata.org/wiki/Q3454686","display_name":"Reduction (mathematics)","level":2,"score":0.5545455813407898},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.5399982333183289},{"id":"https://openalex.org/C2780091087","wikidata":"https://www.wikidata.org/wiki/Q3092131","display_name":"Dimensional reduction","level":2,"score":0.5129963755607605},{"id":"https://openalex.org/C168167062","wikidata":"https://www.wikidata.org/wiki/Q1117970","display_name":"Component (thermodynamics)","level":2,"score":0.46412208676338196},{"id":"https://openalex.org/C3019722297","wikidata":"https://www.wikidata.org/wiki/Q4440864","display_name":"High dimensional","level":2,"score":0.4284365773200989},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.38201266527175903},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.36420542001724243},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3583033084869385},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2288653552532196},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.19780680537223816},{"id":"https://openalex.org/C97686452","wikidata":"https://www.wikidata.org/wiki/Q7604153","display_name":"Static analysis","level":2,"score":0.1253732144832611},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.12167197465896606},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.10380616784095764},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C37914503","wikidata":"https://www.wikidata.org/wiki/Q156495","display_name":"Mathematical physics","level":1,"score":0.0},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btv648","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv648","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/5/755/25588952/btv648.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26543176","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26543176","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:32/5/755","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/5/755","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv648","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv648","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/5/755/25588952/btv648.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":36,"referenced_works":["https://openalex.org/W81377659","https://openalex.org/W327619053","https://openalex.org/W1536988231","https://openalex.org/W1561952261","https://openalex.org/W1571401318","https://openalex.org/W1964729837","https://openalex.org/W2001962164","https://openalex.org/W2008063578","https://openalex.org/W2024797763","https://openalex.org/W2030832812","https://openalex.org/W2031813546","https://openalex.org/W2034987376","https://openalex.org/W2051688318","https://openalex.org/W2067191022","https://openalex.org/W2069921584","https://openalex.org/W2073053696","https://openalex.org/W2090981496","https://openalex.org/W2095822427","https://openalex.org/W2097308346","https://openalex.org/W2102544846","https://openalex.org/W2112946416","https://openalex.org/W2116435022","https://openalex.org/W2125949583","https://openalex.org/W2135650997","https://openalex.org/W2146932984","https://openalex.org/W2158911079","https://openalex.org/W2162833336","https://openalex.org/W2164842737","https://openalex.org/W2496344256","https://openalex.org/W2798909945","https://openalex.org/W4254660365","https://openalex.org/W6633448084","https://openalex.org/W6641614933","https://openalex.org/W6650924355","https://openalex.org/W6669103462","https://openalex.org/W6684050148"],"related_works":["https://openalex.org/W4307320415","https://openalex.org/W4362029000","https://openalex.org/W2952130664","https://openalex.org/W2524653688","https://openalex.org/W2314120527","https://openalex.org/W2014591065","https://openalex.org/W2152214172","https://openalex.org/W3028241735","https://openalex.org/W1619196625","https://openalex.org/W4320801948"],"abstract_inverted_index":{"MOTIVATION:":[0],"Quantitative":[1],"shape":[2,43,51,71,95],"analysis":[3],"is":[4,83],"required":[5],"by":[6,104],"a":[7,60],"wide":[8],"range":[9],"of":[10,29,40,48,66,80,101,118,120,135],"biological":[11,30,50,70],"studies":[12,28],"across":[13],"diverse":[14],"scales,":[15],"ranging":[16],"from":[17],"molecules":[18],"to":[19,36],"cells":[20],"and":[21,26,32,46,68,123,130,149,155],"organisms.":[22],"In":[23],"particular,":[24],"high-throughput":[25],"systems-level":[27],"structures":[31],"functions":[33],"have":[34,58],"started":[35],"produce":[37],"large":[38],"volumes":[39],"complex":[41],"high-dimensional":[42,49],"data.":[44],"Analysis":[45],"understanding":[47],"data":[52,131],"require":[53],"dimension-reduction":[54],"techniques.":[55],"RESULTS:":[56],"We":[57,97],"developed":[59],"technique":[61,82,103],"for":[62,115,132],"non-linear":[63,108],"dimension":[64],"reduction":[65],"2D":[67],"3D":[69],"representations":[72],"on":[73,111,151],"their":[74],"Riemannian":[75,113],"spaces.":[76],"A":[77],"key":[78],"feature":[79],"this":[81,102,136],"that":[84],"it":[85,106],"preserves":[86],"distances":[87],"between":[88],"different":[89],"shapes":[90,119],"in":[91,147],"an":[92,99],"embedded":[93],"low-dimensional":[94],"space.":[96],"demonstrate":[98],"application":[100],"combining":[105],"with":[107],"mean-shift":[109],"clustering":[110,117],"the":[112],"spaces":[114],"unsupervised":[116],"cellular":[121],"organelles":[122],"proteins.":[124],"AVAILABILITY":[125],"AND":[126],"IMPLEMENTATION:":[127],"Source":[128],"code":[129],"reproducing":[133],"results":[134],"article":[137],"are":[138],"freely":[139],"available":[140],"at":[141],"https://github.com/ccdlcmu/shape_component_analysis_Matlab":[142],"The":[143],"implementation":[144],"was":[145],"made":[146],"MATLAB":[148],"supported":[150],"MS":[152],"Windows,":[153],"Linux":[154],"Mac":[156],"OS.":[157],"CONTACT:":[158],"geyang@andrew.cmu.edu.":[159]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":2}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}
