{"id":"https://openalex.org/W2153840021","doi":"https://doi.org/10.1093/bioinformatics/btt741","title":"SurpriseMe: an integrated tool for network community structure characterization using Surprise maximization","display_name":"SurpriseMe: an integrated tool for network community structure characterization using Surprise maximization","publication_year":2013,"publication_date":"2013-12-20","ids":{"openalex":"https://openalex.org/W2153840021","doi":"https://doi.org/10.1093/bioinformatics/btt741","mag":"2153840021","pmid":"https://pubmed.ncbi.nlm.nih.gov/24363381"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt741","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt741","pdf_url":null,"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":["arxiv","crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/1310.2357","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064451587","display_name":"Rodrigo Aldecoa","orcid":"https://orcid.org/0000-0002-8041-3416"},"institutions":[{"id":"https://openalex.org/I134820265","display_name":"Consejo Superior de Investigaciones Cient\u00edficas","ror":"https://ror.org/02gfc7t72","country_code":"ES","type":"government","lineage":["https://openalex.org/I134820265"]},{"id":"https://openalex.org/I4210148788","display_name":"Instituto de Biomedicina de Valencia","ror":"https://ror.org/05pq8vh42","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I4210148788"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Rodrigo Aldecoa","raw_affiliation_strings":["Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Cient\u00edficas (IBV-CSIC), Valencia 46010, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Cient\u00edficas (IBV-CSIC), Valencia 46010, Spain","institution_ids":["https://openalex.org/I134820265","https://openalex.org/I4210148788"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000994199","display_name":"Ignacio Mar\u0131\u0301n","orcid":"https://orcid.org/0000-0002-1315-8961"},"institutions":[{"id":"https://openalex.org/I134820265","display_name":"Consejo Superior de Investigaciones Cient\u00edficas","ror":"https://ror.org/02gfc7t72","country_code":"ES","type":"government","lineage":["https://openalex.org/I134820265"]},{"id":"https://openalex.org/I4210148788","display_name":"Instituto de Biomedicina de Valencia","ror":"https://ror.org/05pq8vh42","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I4210148788"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Ignacio Mar\u00edn","raw_affiliation_strings":["Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Cient\u00edficas (IBV-CSIC), Valencia 46010, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Cient\u00edficas (IBV-CSIC), Valencia 46010, Spain","institution_ids":["https://openalex.org/I134820265","https://openalex.org/I4210148788"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5000994199"],"corresponding_institution_ids":["https://openalex.org/I134820265","https://openalex.org/I4210148788"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":1.6472,"has_fulltext":false,"cited_by_count":22,"citation_normalized_percentile":{"value":0.84379688,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"30","issue":"7","first_page":"1041","last_page":"1042"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10064","display_name":"Complex Network Analysis Techniques","score":0.6312999725341797,"subfield":{"id":"https://openalex.org/subfields/3109","display_name":"Statistical and Nonlinear Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10064","display_name":"Complex Network Analysis Techniques","score":0.6312999725341797,"subfield":{"id":"https://openalex.org/subfields/3109","display_name":"Statistical and Nonlinear Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.2644999921321869,"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/T12292","display_name":"Graph Theory and Algorithms","score":0.011599999852478504,"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":0.8221163749694824},{"id":"https://openalex.org/keywords/perl","display_name":"Perl","score":0.80308997631073},{"id":"https://openalex.org/keywords/surprise","display_name":"Surprise","score":0.7080773711204529},{"id":"https://openalex.org/keywords/unix","display_name":"Unix","score":0.6831910014152527},{"id":"https://openalex.org/keywords/community-structure","display_name":"Community structure","score":0.4467572867870331},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.43159377574920654},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.4315170645713806},{"id":"https://openalex.org/keywords/maximization","display_name":"Maximization","score":0.42229267954826355},{"id":"https://openalex.org/keywords/complex-network","display_name":"Complex network","score":0.4211095869541168},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.38012391328811646},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.3564611077308655},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3395386338233948},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.2479771077632904},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.18146821856498718},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.17811235785484314},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.16800940036773682},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09481114149093628},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.08553531765937805}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8221163749694824},{"id":"https://openalex.org/C2777002779","wikidata":"https://www.wikidata.org/wiki/Q42478","display_name":"Perl","level":2,"score":0.80308997631073},{"id":"https://openalex.org/C2780343955","wikidata":"https://www.wikidata.org/wiki/Q333173","display_name":"Surprise","level":2,"score":0.7080773711204529},{"id":"https://openalex.org/C112968700","wikidata":"https://www.wikidata.org/wiki/Q11368","display_name":"Unix","level":3,"score":0.6831910014152527},{"id":"https://openalex.org/C133079900","wikidata":"https://www.wikidata.org/wiki/Q5155065","display_name":"Community structure","level":2,"score":0.4467572867870331},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.43159377574920654},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.4315170645713806},{"id":"https://openalex.org/C2776330181","wikidata":"https://www.wikidata.org/wiki/Q18358244","display_name":"Maximization","level":2,"score":0.42229267954826355},{"id":"https://openalex.org/C34947359","wikidata":"https://www.wikidata.org/wiki/Q665189","display_name":"Complex network","level":2,"score":0.4211095869541168},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.38012391328811646},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.3564611077308655},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3395386338233948},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.2479771077632904},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.18146821856498718},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.17811235785484314},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.16800940036773682},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09481114149093628},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.08553531765937805},{"id":"https://openalex.org/C77805123","wikidata":"https://www.wikidata.org/wiki/Q161272","display_name":"Social psychology","level":1,"score":0.0},{"id":"https://openalex.org/C175444787","wikidata":"https://www.wikidata.org/wiki/Q39072","display_name":"Microeconomics","level":1,"score":0.0},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","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":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","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":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btt741","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt741","pdf_url":null,"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:24363381","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24363381","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":"Journal Article"},{"id":"pmh:oai:arXiv.org:1310.2357","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1310.2357","pdf_url":"https://arxiv.org/pdf/1310.2357","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:1310.2357","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1310.2357","pdf_url":"https://arxiv.org/pdf/1310.2357","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":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W1486817521","https://openalex.org/W1971421925","https://openalex.org/W1978825280","https://openalex.org/W1999653836","https://openalex.org/W2005198909","https://openalex.org/W2019789576","https://openalex.org/W2022187699","https://openalex.org/W2025543856","https://openalex.org/W2029855260","https://openalex.org/W2033947830","https://openalex.org/W2041713562","https://openalex.org/W2095293504","https://openalex.org/W2098236822","https://openalex.org/W2120043163","https://openalex.org/W2132632499","https://openalex.org/W2133102806","https://openalex.org/W2138003801","https://openalex.org/W2138582694","https://openalex.org/W2140664585","https://openalex.org/W2157305458","https://openalex.org/W2160668429","https://openalex.org/W2163480486","https://openalex.org/W2164998314","https://openalex.org/W2327853194","https://openalex.org/W2569576787","https://openalex.org/W3099402906","https://openalex.org/W4254962106","https://openalex.org/W4312512934"],"related_works":["https://openalex.org/W2475789275","https://openalex.org/W2745097874","https://openalex.org/W2508823388","https://openalex.org/W2225951319","https://openalex.org/W645133142","https://openalex.org/W2992663142","https://openalex.org/W1538349749","https://openalex.org/W2099352317","https://openalex.org/W2034220069","https://openalex.org/W2006852656"],"abstract_inverted_index":{"SUMMARY:":[0],"Detecting":[1],"communities":[2,32,88],"and":[3,92,139,158,162,171,182],"densely":[4],"connected":[5],"groups":[6],"may":[7,121],"contribute":[8],"to":[9,61,97,127],"unravel":[10],"the":[11,15,52,57,63,75,78,82,87,119,186],"underlying":[12],"relationships":[13,76],"among":[14,77],"units":[16],"present":[17,46,89],"in":[18,90,156],"diverse":[19],"biological":[20],"networks":[21,124],"(e.g.":[22],"interactomes,":[23],"coexpression":[24],"networks,":[25,94],"ecological":[26],"networks).":[27],"We":[28,84],"recently":[29],"showed":[30],"that":[31,50,72,86],"can":[33,101],"be":[34,102],"precisely":[35],"characterized":[36],"by":[37,81],"maximizing":[38],"Surprise,":[39],"a":[40,48,143],"global":[41],"network":[42],"parameter.":[43],"Here,":[44],"we":[45],"SurpriseMe,":[47],"tool":[49,145],"integrates":[51],"outputs":[53],"of":[54,56,118,136],"seven":[55],"best":[58],"algorithms":[59,120],"available":[60,184],"estimate":[62],"maximum":[64],"Surprise":[65],"value.":[66],"SurpriseMe":[67,141,153],"also":[68],"generates":[69],"distance":[70],"matrices":[71],"allow":[73],"visualizing":[74],"solutions":[79],"generated":[80],"algorithms.":[83],"show":[85],"small-":[91],"medium-sized":[93],"with":[95,125],"up":[96,126],"10":[98],"000":[99,129],"nodes,":[100,130],"easily":[103],"characterized:":[104],"on":[105,164],"standard":[106,175],"PC":[107],"computers,":[108],"these":[109],"analyses":[110],"take":[111],"less":[112],"than":[113],"an":[114],"hour.":[115],"Also,":[116],"four":[117],"rapidly":[122],"analyze":[123],"100":[128],"given":[131],"enough":[132],"memory":[133],"resources.":[134],"Because":[135],"its":[137],"performance":[138],"simplicity,":[140],"is":[142,154,180],"reference":[144],"for":[146],"community":[147],"structure":[148],"characterization.":[149],"AVAILABILITY":[150],"AND":[151],"IMPLEMENTATION:":[152],"implemented":[155],"Perl":[157],"C/C++.":[159],"It":[160],"compiles":[161],"runs":[163],"any":[165],"UNIX-based":[166],"operating":[167],"system,":[168],"including":[169],"Linux":[170],"Mac":[172],"OS/X,":[173],"using":[174],"libraries.":[176],"The":[177],"source":[178],"code":[179],"freely":[181],"publicly":[183],"under":[185],"GPL":[187],"3.0":[188],"license":[189],"at":[190],"http://github.com/raldecoa/SurpriseMe/releases.":[191]},"counts_by_year":[{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":4}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}
