{"id":"https://openalex.org/W4385439373","doi":"https://doi.org/10.24963/kr.2023/2","title":"Revising Boolean Logical Models of Biological Regulatory Networks","display_name":"Revising Boolean Logical Models of Biological Regulatory Networks","publication_year":2023,"publication_date":"2023-07-31","ids":{"openalex":"https://openalex.org/W4385439373","doi":"https://doi.org/10.24963/kr.2023/2"},"language":"en","primary_location":{"id":"doi:10.24963/kr.2023/2","is_oa":true,"landing_page_url":"http://dx.doi.org/10.24963/kr.2023/2","pdf_url":"https://proceedings.kr.org/2023/2/kr2023-0002-aleixo-et-al.pdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the Twentieth International Conference on Principles of Knowledge Representation and Reasoning","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://proceedings.kr.org/2023/2/kr2023-0002-aleixo-et-al.pdf","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5065264366","display_name":"Frederico Aleixo","orcid":null},"institutions":[{"id":"https://openalex.org/I83558840","display_name":"Universidade Nova de Lisboa","ror":"https://ror.org/02xankh89","country_code":"PT","type":"education","lineage":["https://openalex.org/I83558840"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"Frederico Aleixo","raw_affiliation_strings":["NOVA LINCS, NOVA University Lisbon"],"affiliations":[{"raw_affiliation_string":"NOVA LINCS, NOVA University Lisbon","institution_ids":["https://openalex.org/I83558840"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086341479","display_name":"Matthias Knorr","orcid":"https://orcid.org/0000-0003-1826-1498"},"institutions":[{"id":"https://openalex.org/I83558840","display_name":"Universidade Nova de Lisboa","ror":"https://ror.org/02xankh89","country_code":"PT","type":"education","lineage":["https://openalex.org/I83558840"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Matthias Knorr","raw_affiliation_strings":["NOVA LINCS, NOVA University Lisbon"],"affiliations":[{"raw_affiliation_string":"NOVA LINCS, NOVA University Lisbon","institution_ids":["https://openalex.org/I83558840"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066466375","display_name":"Jo\u00e3o Leite","orcid":"https://orcid.org/0000-0001-6786-7360"},"institutions":[{"id":"https://openalex.org/I83558840","display_name":"Universidade Nova de Lisboa","ror":"https://ror.org/02xankh89","country_code":"PT","type":"education","lineage":["https://openalex.org/I83558840"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Jo\u00e3o Leite","raw_affiliation_strings":["NOVA LINCS, NOVA University Lisbon"],"affiliations":[{"raw_affiliation_string":"NOVA LINCS, NOVA University Lisbon","institution_ids":["https://openalex.org/I83558840"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5065264366"],"corresponding_institution_ids":["https://openalex.org/I83558840"],"apc_list":null,"apc_paid":null,"fwci":0.3136,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.63730032,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":95},"biblio":{"volume":null,"issue":null,"first_page":"12","last_page":"22"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998999834060669,"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"}},"topics":[{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998999834060669,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9970999956130981,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.993399977684021,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7234275937080383},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6467273831367493},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.5828813314437866},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.5556066632270813},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.535246729850769},{"id":"https://openalex.org/keywords/frame","display_name":"Frame (networking)","score":0.5190290212631226},{"id":"https://openalex.org/keywords/margin","display_name":"Margin (machine learning)","score":0.5185906887054443},{"id":"https://openalex.org/keywords/and-inverter-graph","display_name":"And-inverter graph","score":0.5021488666534424},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.4958404004573822},{"id":"https://openalex.org/keywords/boolean-network","display_name":"Boolean network","score":0.47759127616882324},{"id":"https://openalex.org/keywords/boolean-function","display_name":"Boolean function","score":0.4739156663417816},{"id":"https://openalex.org/keywords/logical-data-model","display_name":"Logical data model","score":0.4230264127254486},{"id":"https://openalex.org/keywords/boolean-model","display_name":"Boolean model","score":0.4135749936103821},{"id":"https://openalex.org/keywords/boolean-expression","display_name":"Boolean expression","score":0.38370805978775024},{"id":"https://openalex.org/keywords/data-modeling","display_name":"Data modeling","score":0.3041331171989441},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.2606998085975647},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.23981621861457825},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.17551791667938232},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.15678036212921143},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.11479854583740234},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10511207580566406},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09264644980430603},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08885359764099121}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7234275937080383},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6467273831367493},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.5828813314437866},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.5556066632270813},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.535246729850769},{"id":"https://openalex.org/C126042441","wikidata":"https://www.wikidata.org/wiki/Q1324888","display_name":"Frame (networking)","level":2,"score":0.5190290212631226},{"id":"https://openalex.org/C774472","wikidata":"https://www.wikidata.org/wiki/Q6760393","display_name":"Margin (machine learning)","level":2,"score":0.5185906887054443},{"id":"https://openalex.org/C196836630","wikidata":"https://www.wikidata.org/wiki/Q4753279","display_name":"And-inverter graph","level":4,"score":0.5021488666534424},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.4958404004573822},{"id":"https://openalex.org/C134444547","wikidata":"https://www.wikidata.org/wiki/Q585230","display_name":"Boolean network","level":3,"score":0.47759127616882324},{"id":"https://openalex.org/C187455244","wikidata":"https://www.wikidata.org/wiki/Q942353","display_name":"Boolean function","level":2,"score":0.4739156663417816},{"id":"https://openalex.org/C203702819","wikidata":"https://www.wikidata.org/wiki/Q17146953","display_name":"Logical data model","level":3,"score":0.4230264127254486},{"id":"https://openalex.org/C67499762","wikidata":"https://www.wikidata.org/wiki/Q4943358","display_name":"Boolean model","level":2,"score":0.4135749936103821},{"id":"https://openalex.org/C158465420","wikidata":"https://www.wikidata.org/wiki/Q1979515","display_name":"Boolean expression","level":3,"score":0.38370805978775024},{"id":"https://openalex.org/C67186912","wikidata":"https://www.wikidata.org/wiki/Q367664","display_name":"Data modeling","level":2,"score":0.3041331171989441},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2606998085975647},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.23981621861457825},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.17551791667938232},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.15678036212921143},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.11479854583740234},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10511207580566406},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09264644980430603},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08885359764099121},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.24963/kr.2023/2","is_oa":true,"landing_page_url":"http://dx.doi.org/10.24963/kr.2023/2","pdf_url":"https://proceedings.kr.org/2023/2/kr2023-0002-aleixo-et-al.pdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the Twentieth International Conference on Principles of Knowledge Representation and Reasoning","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.24963/kr.2023/2","is_oa":true,"landing_page_url":"http://dx.doi.org/10.24963/kr.2023/2","pdf_url":"https://proceedings.kr.org/2023/2/kr2023-0002-aleixo-et-al.pdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the Twentieth International Conference on Principles of Knowledge Representation and Reasoning","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3272457656","display_name":null,"funder_award_id":"UIDB/","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G4023552779","display_name":null,"funder_award_id":"NOVA LINCS (UIDB/04516/2020)","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G6348741101","display_name":null,"funder_award_id":"UIDB/04516/2020","funder_id":"https://openalex.org/F4320331406","funder_display_name":"NOVA Laboratory for Computer Science and Informatics"},{"id":"https://openalex.org/G769346256","display_name":null,"funder_award_id":"financial support","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G850683389","display_name":null,"funder_award_id":"UIDB/04516/202","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G8725369612","display_name":null,"funder_award_id":"UIDB/04516/2020","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"}],"funders":[{"id":"https://openalex.org/F4320331406","display_name":"NOVA Laboratory for Computer Science and Informatics","ror":null},{"id":"https://openalex.org/F4320334779","display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","ror":"https://ror.org/00snfqn58"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4385439373.pdf"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W203529317","https://openalex.org/W649201746","https://openalex.org/W1482498688","https://openalex.org/W1488563109","https://openalex.org/W1516806580","https://openalex.org/W1807981783","https://openalex.org/W1886819223","https://openalex.org/W1903938722","https://openalex.org/W1975274391","https://openalex.org/W2004073264","https://openalex.org/W2015401980","https://openalex.org/W2018519939","https://openalex.org/W2031369606","https://openalex.org/W2046538693","https://openalex.org/W2058221907","https://openalex.org/W2062029454","https://openalex.org/W2076935369","https://openalex.org/W2116137060","https://openalex.org/W2118449583","https://openalex.org/W2122902176","https://openalex.org/W2132935366","https://openalex.org/W2134487266","https://openalex.org/W2136559804","https://openalex.org/W2166214692","https://openalex.org/W2489066146","https://openalex.org/W2580749482","https://openalex.org/W2940498855","https://openalex.org/W2950638330","https://openalex.org/W2963234253","https://openalex.org/W2972484390","https://openalex.org/W2982415810","https://openalex.org/W2991335334","https://openalex.org/W2992094981","https://openalex.org/W3090482467","https://openalex.org/W3123035985","https://openalex.org/W4226521686","https://openalex.org/W6651482513","https://openalex.org/W6738388615","https://openalex.org/W7021090643"],"related_works":["https://openalex.org/W4243221174","https://openalex.org/W1830204300","https://openalex.org/W3201185782","https://openalex.org/W2995617542","https://openalex.org/W4231391991","https://openalex.org/W2024769762","https://openalex.org/W2952420532","https://openalex.org/W4291608200","https://openalex.org/W1966995004","https://openalex.org/W1997339100"],"abstract_inverted_index":{"Boolean":[0,144,181],"regulatory":[1,145],"networks":[2,38,104],"are":[3,106,152],"used":[4,176],"to":[5,91,102,118,148,165,177],"represent":[6],"complex":[7],"biological":[8,14],"processes,":[9,45],"modelling":[10],"the":[11,94,129,163,166],"interactions":[12],"of":[13,36,143,192],"compounds,":[15],"such":[16],"as":[17,46],"proteins":[18],"or":[19,105,127],"genes,":[20],"with":[21,25,154,196],"each":[22],"other":[23,26],"and":[24,32,52,56,68,89,93,160,195],"substances":[27],"in":[28,58,108,190],"a":[29,120,123,137,187,197],"cell.":[30],"Creating":[31],"maintaining":[33],"computational":[34],"models":[35,73,142,183],"these":[37],"is":[39,82,87],"crucial":[40],"for":[41,139],"comprehending":[42],"corresponding":[43],"cellular":[44],"they":[47,113],"allow":[48],"reproducing":[49],"known":[50],"behaviours":[51],"testing":[53],"new":[54,76],"hypotheses":[55],"predictions":[57],"silico.":[59],"In":[60,132],"this":[61,133],"context,":[62],"model":[63,80],"revision":[64,81,110],"focuses":[65],"on":[66,75],"validating":[67],"(if":[69],"necessary)":[70],"repairing":[71],"existing":[72,96],"based":[74],"experimental":[77,158],"data.":[78],"However,":[79],"commonly":[83],"performed":[84],"manually,":[85],"which":[86],"inefficient":[88],"prone":[90],"error,":[92],"few":[95],"automated":[97],"solutions":[98],"either":[99],"only":[100],"apply":[101],"simpler":[103],"limited":[107],"their":[109],"process,":[111],"since":[112],"may":[114],"not":[115],"be":[116,175],"able":[117,147],"produce":[119],"solution":[121,138,173,189],"within":[122],"reasonable":[124],"time":[125],"frame":[126],"miss":[128],"optimal":[130],"solution.":[131],"paper,":[134],"we":[135],"develop":[136],"revising":[140],"logical":[141,182],"networks,":[146],"find":[149],"repairs":[150],"that":[151,171],"consistent":[153],"provided,":[155],"possibly":[156],"incomplete":[157],"data,":[159],"minimal":[161],"w.r.t.":[162,200],"differences":[164],"original":[167],"network.":[168],"We":[169],"show":[170],"our":[172],"can":[174],"revise":[178],"different":[179],"real-world":[180],"very":[184],"efficiently,":[185],"surpassing":[186],"previous":[188],"terms":[191],"solved":[193],"instances":[194],"considerable":[198],"margin":[199],"processing":[201],"time.":[202]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1}],"updated_date":"2026-03-16T09:10:04.655348","created_date":"2025-10-10T00:00:00"}