{"id":"https://openalex.org/W2025508793","doi":"https://doi.org/10.1109/bibe.2007.4375669","title":"Quantitative and Probabilistic Modeling in Pathway Logic","display_name":"Quantitative and Probabilistic Modeling in Pathway Logic","publication_year":2007,"publication_date":"2007-10-01","ids":{"openalex":"https://openalex.org/W2025508793","doi":"https://doi.org/10.1109/bibe.2007.4375669","mag":"2025508793"},"language":"en","primary_location":{"id":"doi:10.1109/bibe.2007.4375669","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2007.4375669","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2007 IEEE 7th International Symposium on BioInformatics and BioEngineering","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/A5091718585","display_name":"Alessandro Abate","orcid":"https://orcid.org/0000-0002-5627-9093"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alessandro Abate","raw_affiliation_strings":["EECS Department, University of California Berkeley, USA","[University of California at Berkeley, Berkeley]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"EECS Department, University of California Berkeley, USA","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"[University of California at Berkeley, Berkeley]","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089870653","display_name":"Yu Bai","orcid":"https://orcid.org/0000-0001-7923-4376"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yu Bai","raw_affiliation_strings":["University of Stanford, USA","Biophysics Program, Stanford University, yubai@stanford.edu"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Stanford, USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Biophysics Program, Stanford University, yubai@stanford.edu","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028032477","display_name":"Nathalie Sznajder","orcid":"https://orcid.org/0000-0002-4199-2443"},"institutions":[{"id":"https://openalex.org/I29607241","display_name":"\u00c9cole Normale Sup\u00e9rieure - PSL","ror":"https://ror.org/05a0dhs15","country_code":"FR","type":"other","lineage":["https://openalex.org/I2746051580","https://openalex.org/I29607241"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Nathalie Sznajder","raw_affiliation_strings":["Ecole Normale Sup\u00e9rieur, France","\u00c9cole Normale Superi\u00e9ure, sznajder@lsv.ens-cachan.fr"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ecole Normale Sup\u00e9rieur, France","institution_ids":[]},{"raw_affiliation_string":"\u00c9cole Normale Superi\u00e9ure, sznajder@lsv.ens-cachan.fr","institution_ids":["https://openalex.org/I29607241"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090498111","display_name":"Carolyn Talcott","orcid":"https://orcid.org/0000-0003-2845-7144"},"institutions":[{"id":"https://openalex.org/I1298353152","display_name":"SRI International","ror":"https://ror.org/05s570m15","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1298353152"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Carolyn Talcott","raw_affiliation_strings":["CS Lab, SRI International, Inc., USA","CS Lab, SRI International, clt@csl.sri.com"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CS Lab, SRI International, Inc., USA","institution_ids":["https://openalex.org/I1298353152"]},{"raw_affiliation_string":"CS Lab, SRI International, clt@csl.sri.com","institution_ids":["https://openalex.org/I1298353152"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5086308451","display_name":"Ashish Tiwari","orcid":"https://orcid.org/0000-0002-5153-2686"},"institutions":[{"id":"https://openalex.org/I1298353152","display_name":"SRI International","ror":"https://ror.org/05s570m15","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1298353152"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ashish Tiwari","raw_affiliation_strings":["CS Lab, SRI International, Inc., USA","CS Lab, SRI International, tiwari@csl.sri.com"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CS Lab, SRI International, Inc., USA","institution_ids":["https://openalex.org/I1298353152"]},{"raw_affiliation_string":"CS Lab, SRI International, tiwari@csl.sri.com","institution_ids":["https://openalex.org/I1298353152"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.7994,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.70456523,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"6","issue":null,"first_page":"922","last_page":"929"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9965000152587891,"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":0.9965000152587891,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9905999898910522,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9868999719619751,"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/probabilistic-logic","display_name":"Probabilistic logic","score":0.7903214693069458},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6455064415931702},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5770906805992126},{"id":"https://openalex.org/keywords/theme","display_name":"Theme (computing)","score":0.5677107572555542},{"id":"https://openalex.org/keywords/signalling-pathways","display_name":"Signalling pathways","score":0.4168429970741272},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4113650918006897},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4064286947250366},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3733776807785034},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33635109663009644},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.16929033398628235},{"id":"https://openalex.org/keywords/signal-transduction","display_name":"Signal transduction","score":0.16184347867965698}],"concepts":[{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.7903214693069458},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6455064415931702},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5770906805992126},{"id":"https://openalex.org/C33566652","wikidata":"https://www.wikidata.org/wiki/Q1065927","display_name":"Theme (computing)","level":2,"score":0.5677107572555542},{"id":"https://openalex.org/C3018449070","wikidata":"https://www.wikidata.org/wiki/Q828130","display_name":"Signalling pathways","level":3,"score":0.4168429970741272},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4113650918006897},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4064286947250366},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3733776807785034},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33635109663009644},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.16929033398628235},{"id":"https://openalex.org/C62478195","wikidata":"https://www.wikidata.org/wiki/Q828130","display_name":"Signal transduction","level":2,"score":0.16184347867965698},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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":[],"locations_count":5,"locations":[{"id":"doi:10.1109/bibe.2007.4375669","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2007.4375669","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2007 IEEE 7th International Symposium on BioInformatics and BioEngineering","raw_type":"proceedings-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.135.1135","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.135.1135","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.csl.sri.com/~tiwari/papers/bibe07.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.712.2585","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.712.2585","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.dcsc.tudelft.nl/%7Eaabate/publications/Abate_etalBIBE07.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.93.6672","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.93.6672","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www-formal.stanford.edu/MT/07bibe.pdf","raw_type":"text"},{"id":"pmh:oai:berkeley.edu:13030-hb9v19p7g4","is_oa":false,"landing_page_url":"http://techreports.lib.berkeley.edu/accessPages/EECS-2006-180.html","pdf_url":null,"source":{"id":"https://openalex.org/S7407050879","display_name":"UC Berkeley","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":"technical reports"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":41,"referenced_works":["https://openalex.org/W151201039","https://openalex.org/W1487906584","https://openalex.org/W1566900355","https://openalex.org/W1576770735","https://openalex.org/W1859458367","https://openalex.org/W1964321121","https://openalex.org/W1976195354","https://openalex.org/W1999916184","https://openalex.org/W2001661334","https://openalex.org/W2002526701","https://openalex.org/W2007006124","https://openalex.org/W2012380912","https://openalex.org/W2025508793","https://openalex.org/W2041197407","https://openalex.org/W2042321087","https://openalex.org/W2066322491","https://openalex.org/W2078112275","https://openalex.org/W2078660746","https://openalex.org/W2081556416","https://openalex.org/W2104855667","https://openalex.org/W2105161851","https://openalex.org/W2106190666","https://openalex.org/W2110796675","https://openalex.org/W2118039525","https://openalex.org/W2132801975","https://openalex.org/W2152604899","https://openalex.org/W2155418451","https://openalex.org/W2157062252","https://openalex.org/W2160533336","https://openalex.org/W2887515392","https://openalex.org/W2985644547","https://openalex.org/W3147453326","https://openalex.org/W4249610466","https://openalex.org/W4285719527","https://openalex.org/W6606342648","https://openalex.org/W6633876618","https://openalex.org/W6653555429","https://openalex.org/W6656619912","https://openalex.org/W6663273948","https://openalex.org/W6671121592","https://openalex.org/W6675471491"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2358755282","https://openalex.org/W2625833328","https://openalex.org/W1497573972","https://openalex.org/W2071659383","https://openalex.org/W1846253165"],"abstract_inverted_index":{"This":[0],"paper":[1],"presents":[2],"a":[3,75],"study":[4],"of":[5,8,20,29,59],"possible":[6],"extensions":[7],"pathway":[9],"logic":[10],"to":[11,52,56],"represent":[12],"and":[13,17,48,55],"reason":[14],"about":[15],"semiquantitative":[16],"probabilistic":[18],"aspects":[19],"biological":[21],"processes.":[22],"The":[23],"underlying":[24],"theme":[25],"is":[26],"the":[27,64],"annotation":[28],"reaction":[30],"rules":[31],"with":[32],"affinity":[33],"information":[34],"that":[35],"can":[36],"be":[37],"used":[38,73],"in":[39,63,69],"different":[40,60],"simulation":[41],"strategies.":[42],"Several":[43],"such":[44],"strategies":[45],"were":[46],"implemented,":[47],"experiments":[49],"carried":[50],"out":[51],"test":[53,76],"feasibility,":[54],"compare":[57],"results":[58],"approaches.":[61],"Dimerization":[62],"ErbB":[65],"signalling":[66],"network,":[67],"important":[68],"cancer":[70],"biology,":[71],"was":[72],"as":[74],"case.":[77]},"counts_by_year":[{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
