{"id":"https://openalex.org/W4389143060","doi":"https://doi.org/10.1137/22m1543082","title":"Quantifying Different Modeling Frameworks Using Topological Data Analysis: A Case Study with Zebrafish Patterns","display_name":"Quantifying Different Modeling Frameworks Using Topological Data Analysis: A Case Study with Zebrafish Patterns","publication_year":2023,"publication_date":"2023-11-29","ids":{"openalex":"https://openalex.org/W4389143060","doi":"https://doi.org/10.1137/22m1543082"},"language":"en","primary_location":{"id":"doi:10.1137/22m1543082","is_oa":false,"landing_page_url":"https://doi.org/10.1137/22m1543082","pdf_url":null,"source":{"id":"https://openalex.org/S161160597","display_name":"SIAM Journal on Applied Dynamical Systems","issn_l":"1536-0040","issn":["1536-0040"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320508","host_organization_name":"Society for Industrial and Applied Mathematics","host_organization_lineage":["https://openalex.org/P4310320508"],"host_organization_lineage_names":["Society for Industrial and Applied Mathematics"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"SIAM Journal on Applied Dynamical Systems","raw_type":"journal-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/A5067976852","display_name":"Electa Cleveland","orcid":"https://orcid.org/0009-0004-3231-6592"},"institutions":[{"id":"https://openalex.org/I27804330","display_name":"Brown University","ror":"https://ror.org/05gq02987","country_code":"US","type":"education","lineage":["https://openalex.org/I27804330"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Electa Cleveland","raw_affiliation_strings":["Division of Applied Mathematics, Brown University, Providence, RI 02912 USA"],"raw_orcid":"https://orcid.org/0009-0004-3231-6592","affiliations":[{"raw_affiliation_string":"Division of Applied Mathematics, Brown University, Providence, RI 02912 USA","institution_ids":["https://openalex.org/I27804330"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045707131","display_name":"Angela Y. Zhu","orcid":"https://orcid.org/0000-0002-3010-8464"},"institutions":[{"id":"https://openalex.org/I27804330","display_name":"Brown University","ror":"https://ror.org/05gq02987","country_code":"US","type":"education","lineage":["https://openalex.org/I27804330"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Angela Zhu","raw_affiliation_strings":["Division of Applied Mathematics, Brown University, Providence, RI 02912 USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Applied Mathematics, Brown University, Providence, RI 02912 USA","institution_ids":["https://openalex.org/I27804330"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024502637","display_name":"Bj\u00f6rn Sandstede","orcid":"https://orcid.org/0000-0002-5432-1235"},"institutions":[{"id":"https://openalex.org/I27804330","display_name":"Brown University","ror":"https://ror.org/05gq02987","country_code":"US","type":"education","lineage":["https://openalex.org/I27804330"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bj\u00f6rn Sandstede","raw_affiliation_strings":["Division of Applied Mathematics, Brown University, Providence, RI 02912 USA"],"raw_orcid":"https://orcid.org/0000-0002-5432-1235","affiliations":[{"raw_affiliation_string":"Division of Applied Mathematics, Brown University, Providence, RI 02912 USA","institution_ids":["https://openalex.org/I27804330"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021486216","display_name":"Alexandria Volkening","orcid":"https://orcid.org/0000-0003-3401-5094"},"institutions":[{"id":"https://openalex.org/I219193219","display_name":"Purdue University West Lafayette","ror":"https://ror.org/02dqehb95","country_code":"US","type":"education","lineage":["https://openalex.org/I219193219"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Alexandria Volkening","raw_affiliation_strings":["Department of Mathematics, Purdue University, West Lafayette, IN 47907 USA"],"raw_orcid":"https://orcid.org/0000-0003-3401-5094","affiliations":[{"raw_affiliation_string":"Department of Mathematics, Purdue University, West Lafayette, IN 47907 USA","institution_ids":["https://openalex.org/I219193219"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5021486216"],"corresponding_institution_ids":["https://openalex.org/I219193219"],"apc_list":null,"apc_paid":null,"fwci":0.8636,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.78143576,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"22","issue":"4","first_page":"3233","last_page":"3266"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12536","display_name":"Topological and Geometric Data Analysis","score":0.9988999962806702,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T12536","display_name":"Topological and Geometric Data Analysis","score":0.9988999962806702,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9871000051498413,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9751999974250793,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/cellular-automaton","display_name":"Cellular automaton","score":0.8065986633300781},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6972174644470215},{"id":"https://openalex.org/keywords/topological-data-analysis","display_name":"Topological data analysis","score":0.5431141257286072},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.523361325263977},{"id":"https://openalex.org/keywords/limiting","display_name":"Limiting","score":0.4699699282646179},{"id":"https://openalex.org/keywords/stochastic-cellular-automaton","display_name":"Stochastic cellular automaton","score":0.4461546540260315},{"id":"https://openalex.org/keywords/mathematical-model","display_name":"Mathematical model","score":0.4269089996814728},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3428117334842682},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3317890167236328},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3298100233078003},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.2569856643676758},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2273346483707428}],"concepts":[{"id":"https://openalex.org/C35527583","wikidata":"https://www.wikidata.org/wiki/Q189156","display_name":"Cellular automaton","level":2,"score":0.8065986633300781},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6972174644470215},{"id":"https://openalex.org/C2776477805","wikidata":"https://www.wikidata.org/wiki/Q4460773","display_name":"Topological data analysis","level":2,"score":0.5431141257286072},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.523361325263977},{"id":"https://openalex.org/C188198153","wikidata":"https://www.wikidata.org/wiki/Q1613840","display_name":"Limiting","level":2,"score":0.4699699282646179},{"id":"https://openalex.org/C192499940","wikidata":"https://www.wikidata.org/wiki/Q17022326","display_name":"Stochastic cellular automaton","level":3,"score":0.4461546540260315},{"id":"https://openalex.org/C76969082","wikidata":"https://www.wikidata.org/wiki/Q486902","display_name":"Mathematical model","level":2,"score":0.4269089996814728},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3428117334842682},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3317890167236328},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3298100233078003},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2569856643676758},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2273346483707428},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1137/22m1543082","is_oa":false,"landing_page_url":"https://doi.org/10.1137/22m1543082","pdf_url":null,"source":{"id":"https://openalex.org/S161160597","display_name":"SIAM Journal on Applied Dynamical Systems","issn_l":"1536-0040","issn":["1536-0040"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320508","host_organization_name":"Society for Industrial and Applied Mathematics","host_organization_lineage":["https://openalex.org/P4310320508"],"host_organization_lineage_names":["Society for Industrial and Applied Mathematics"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"SIAM Journal on Applied Dynamical Systems","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3240567085","display_name":null,"funder_award_id":"DMS-2106566","funder_id":"https://openalex.org/F4320337380","funder_display_name":"Division of Mathematical Sciences"},{"id":"https://openalex.org/G5156463252","display_name":null,"funder_award_id":"DMS-1714429","funder_id":"https://openalex.org/F4320337380","funder_display_name":"Division of Mathematical Sciences"},{"id":"https://openalex.org/G8344756968","display_name":null,"funder_award_id":"DMS-2038039","funder_id":"https://openalex.org/F4320337380","funder_display_name":"Division of Mathematical Sciences"}],"funders":[{"id":"https://openalex.org/F4320337380","display_name":"Division of Mathematical Sciences","ror":"https://ror.org/051fftw81"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":102,"referenced_works":["https://openalex.org/W256659003","https://openalex.org/W1494240806","https://openalex.org/W1495676205","https://openalex.org/W1596721197","https://openalex.org/W1753705553","https://openalex.org/W1966039196","https://openalex.org/W1977197164","https://openalex.org/W1977375303","https://openalex.org/W1978529094","https://openalex.org/W1979736337","https://openalex.org/W1980661496","https://openalex.org/W1987442025","https://openalex.org/W1990918775","https://openalex.org/W1991566301","https://openalex.org/W1993098627","https://openalex.org/W1994259922","https://openalex.org/W1995291300","https://openalex.org/W1996345822","https://openalex.org/W1997183853","https://openalex.org/W1997748595","https://openalex.org/W1999753634","https://openalex.org/W2002266200","https://openalex.org/W2003750019","https://openalex.org/W2017296776","https://openalex.org/W2020644315","https://openalex.org/W2026650969","https://openalex.org/W2027898140","https://openalex.org/W2038032147","https://openalex.org/W2041342850","https://openalex.org/W2042642964","https://openalex.org/W2047743211","https://openalex.org/W2056573049","https://openalex.org/W2060243607","https://openalex.org/W2064228121","https://openalex.org/W2064356142","https://openalex.org/W2065833332","https://openalex.org/W2070960656","https://openalex.org/W2075177658","https://openalex.org/W2078290150","https://openalex.org/W2080513987","https://openalex.org/W2084325983","https://openalex.org/W2087841994","https://openalex.org/W2089840306","https://openalex.org/W2099955171","https://openalex.org/W2113712276","https://openalex.org/W2115445832","https://openalex.org/W2116159413","https://openalex.org/W2117822539","https://openalex.org/W2118448270","https://openalex.org/W2123502357","https://openalex.org/W2126564632","https://openalex.org/W2129823023","https://openalex.org/W2142100384","https://openalex.org/W2143969246","https://openalex.org/W2151631165","https://openalex.org/W2159198630","https://openalex.org/W2159252299","https://openalex.org/W2159567538","https://openalex.org/W2163670870","https://openalex.org/W2190106403","https://openalex.org/W2296122684","https://openalex.org/W2406881686","https://openalex.org/W2531189335","https://openalex.org/W2587979287","https://openalex.org/W2623620232","https://openalex.org/W2725792925","https://openalex.org/W2751575385","https://openalex.org/W2774875815","https://openalex.org/W2796671865","https://openalex.org/W2811342017","https://openalex.org/W2885731571","https://openalex.org/W2900665823","https://openalex.org/W2902984213","https://openalex.org/W2920851774","https://openalex.org/W2951012718","https://openalex.org/W2951378914","https://openalex.org/W2963295400","https://openalex.org/W2964534207","https://openalex.org/W2967171209","https://openalex.org/W2973095164","https://openalex.org/W2978585646","https://openalex.org/W2995700079","https://openalex.org/W3008940045","https://openalex.org/W3014671498","https://openalex.org/W3023811636","https://openalex.org/W3037302061","https://openalex.org/W3037988805","https://openalex.org/W3090328960","https://openalex.org/W3098455240","https://openalex.org/W3099391356","https://openalex.org/W3100454378","https://openalex.org/W3106615546","https://openalex.org/W3110247023","https://openalex.org/W3112530233","https://openalex.org/W3118794388","https://openalex.org/W3123132565","https://openalex.org/W3136898777","https://openalex.org/W3141082020","https://openalex.org/W3160236045","https://openalex.org/W3213079817","https://openalex.org/W4233690291","https://openalex.org/W4281870735"],"related_works":["https://openalex.org/W4211227983","https://openalex.org/W4255696416","https://openalex.org/W2147358629","https://openalex.org/W2007974154","https://openalex.org/W1969391024","https://openalex.org/W3208503416","https://openalex.org/W2064715443","https://openalex.org/W2023344115","https://openalex.org/W2028377826","https://openalex.org/W2334514964"],"abstract_inverted_index":{".Mathematical":[0],"models":[1,20,45,50,73,132],"come":[2],"in":[3,101,138],"many":[4],"forms":[5],"across":[6],"biological":[7,136],"applications.":[8],"In":[9],"the":[10,80,107,134,154],"case":[11],"of":[12,133,156],"complex,":[13],"spatial":[14],"dynamics":[15],"and":[16,31,46,51,93,97,124,147,160,168],"pattern":[17,26,158],"formation,":[18,159],"stochastic":[19],"also":[21,67],"face":[22],"two":[23,130],"main":[24],"challenges:":[25],"data":[27,122,174],"are":[28,74],"largely":[29],"qualitative,":[30],"model":[32],"realizations":[33],"may":[34],"vary":[35],"significantly.":[36],"Together":[37],"these":[38],"issues":[39],"make":[40],"it":[41],"difficult":[42],"to":[43,59,79,109,127],"relate":[44,129,162],"empirical":[47],"data\u2014or":[48],"even":[49],"models\u2014limiting":[52],"how":[53,72],"different":[54,102,131],"approaches":[55,78],"can":[56],"be":[57],"combined":[58],"offer":[60],"new":[61],"insights":[62],"into":[63],"biology.":[64],"These":[65],"challenges":[66],"raise":[68],"mathematical":[69],"questions":[70,113],"about":[71],"related,":[75],"since":[76],"alternative":[77],"same":[81,135],"problem\u2014e.g.,":[82],"Cellular":[83],"Potts":[84],"models;":[85,88,92],"off-lattice,":[86],"agent-based":[87,167],"on-lattice,":[89],"cellular":[90,169],"automaton":[91,170],"continuum":[94],"approaches\u2014treat":[95],"uncertainty":[96],"implement":[98],"cell":[99],"behavior":[100],"ways.":[103],"To":[104,143],"help":[105],"open":[106],"door":[108],"future":[110],"work":[111,146],"on":[112,153],"like":[114],"these,":[115],"here":[116],"we":[117,151,161],"adapt":[118],"methods":[119],"from":[120,166],"topological":[121],"analysis":[123],"computational":[125],"geometry":[126],"quantitatively":[128],"process":[137],"a":[139],"fair,":[140],"comparable":[141],"way.":[142],"center":[144],"our":[145],"illustrate":[148],"concrete":[149],"challenges,":[150],"focus":[152],"example":[155],"zebrafish-skin":[157],"patterns":[163],"that":[164],"arise":[165],"models.Keywordsagent-based":[171],"modelcellular":[172],"automatontopological":[173],"analysisalpha-shapesvariabilityzebrafishpattern":[175],"formationMSC":[176],"codes92B0592C1570G6055N31":[177]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3}],"updated_date":"2026-07-13T07:31:44.756512","created_date":"2025-10-10T00:00:00"}