{"id":"https://openalex.org/W4393968931","doi":"https://doi.org/10.46298/fi.13347","title":"Automated Inference of Graph Transformation Rules","display_name":"Automated Inference of Graph Transformation Rules","publication_year":2026,"publication_date":"2026-08-20","ids":{"openalex":"https://openalex.org/W4393968931","doi":"https://doi.org/10.46298/fi.13347"},"language":"en","primary_location":{"id":"doi:10.46298/fi.13347","is_oa":true,"landing_page_url":"https://doi.org/10.46298/fi.13347","pdf_url":"https://fi.episciences.org/18994/pdf","source":{"id":"https://openalex.org/S39012697","display_name":"Fundamenta Informaticae","issn_l":"0169-2968","issn":["0169-2968","1875-8681"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Fundamenta Informaticae","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref","datacite"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://fi.episciences.org/18994/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001028353","display_name":"Jakob L. Andersen","orcid":"https://orcid.org/0000-0002-4165-3732"},"institutions":[{"id":"https://openalex.org/I177969490","display_name":"University of Southern Denmark","ror":"https://ror.org/03yrrjy16","country_code":"DK","type":"education","lineage":["https://openalex.org/I177969490"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Jakob L. Andersen","raw_affiliation_strings":["Department of Mathematics and Computer Science , University of Southern Denmark ; Odense , Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Computer Science , University of Southern Denmark ; Odense , Denmark","institution_ids":["https://openalex.org/I177969490"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039225561","display_name":"Akbar Davoodi","orcid":"https://orcid.org/0000-0001-6403-5091"},"institutions":[{"id":"https://openalex.org/I177969490","display_name":"University of Southern Denmark","ror":"https://ror.org/03yrrjy16","country_code":"DK","type":"education","lineage":["https://openalex.org/I177969490"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Akbar Davoodi","raw_affiliation_strings":["Department of Mathematics and Computer Science , University of Southern Denmark ; Odense , Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Computer Science , University of Southern Denmark ; Odense , Denmark","institution_ids":["https://openalex.org/I177969490"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021765002","display_name":"Rolf Fagerberg","orcid":"https://orcid.org/0000-0003-1004-3314"},"institutions":[{"id":"https://openalex.org/I177969490","display_name":"University of Southern Denmark","ror":"https://ror.org/03yrrjy16","country_code":"DK","type":"education","lineage":["https://openalex.org/I177969490"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Rolf Fagerberg","raw_affiliation_strings":["Department of Mathematics and Computer Science , University of Southern Denmark ; Odense , Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Computer Science , University of Southern Denmark ; Odense , Denmark","institution_ids":["https://openalex.org/I177969490"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005564950","display_name":"Christoph Flamm","orcid":"https://orcid.org/0000-0001-5500-2415"},"institutions":[{"id":"https://openalex.org/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]},{"id":"https://openalex.org/I4210112966","display_name":"Instituto de F\u00edsica Te\u00f3rica","ror":"https://ror.org/022r8mj40","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I4210112966","https://openalex.org/I63634437"]}],"countries":["AT","ES"],"is_corresponding":false,"raw_author_name":"Christoph Flamm","raw_affiliation_strings":["Institute of Theoretical Chemistry , University of Vienna ; Vienna , Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Theoretical Chemistry , University of Vienna ; Vienna , Austria","institution_ids":["https://openalex.org/I129774422","https://openalex.org/I4210112966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067812040","display_name":"Walter Fontana","orcid":"https://orcid.org/0000-0003-4062-9957"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210155419","display_name":"Center for Systems Biology","ror":"https://ror.org/05r3dyn47","country_code":"US","type":"facility","lineage":["https://openalex.org/I136199984","https://openalex.org/I4210087915","https://openalex.org/I4210155419","https://openalex.org/I48633490"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Walter Fontana","raw_affiliation_strings":["Department of Systems Biology , Harvard Medical School ; Boston , Massachusetts , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Systems Biology , Harvard Medical School ; Boston , Massachusetts , USA","institution_ids":["https://openalex.org/I136199984","https://openalex.org/I4210155419"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016152929","display_name":"Juri Kol\u010d\u00e1k","orcid":"https://orcid.org/0000-0002-9407-9682"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Juri Kol\u010d\u00e1k","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042904279","display_name":"Christophe V. F. P. Laurent","orcid":"https://orcid.org/0000-0002-9112-6981"},"institutions":[{"id":"https://openalex.org/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]},{"id":"https://openalex.org/I177969490","display_name":"University of Southern Denmark","ror":"https://ror.org/03yrrjy16","country_code":"DK","type":"education","lineage":["https://openalex.org/I177969490"]},{"id":"https://openalex.org/I4210112966","display_name":"Instituto de F\u00edsica Te\u00f3rica","ror":"https://ror.org/022r8mj40","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I4210112966","https://openalex.org/I63634437"]}],"countries":["AT","DK","ES"],"is_corresponding":false,"raw_author_name":"Christophe V. F. P. Laurent","raw_affiliation_strings":["Department of Mathematics and Computer Science , University of Southern Denmark ; Odense , Denmark","Institute of Theoretical Chemistry , University of Vienna ; Vienna , Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Computer Science , University of Southern Denmark ; Odense , Denmark","institution_ids":["https://openalex.org/I177969490"]},{"raw_affiliation_string":"Institute of Theoretical Chemistry , University of Vienna ; Vienna , Austria","institution_ids":["https://openalex.org/I129774422","https://openalex.org/I4210112966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078883427","display_name":"Daniel Merkle","orcid":"https://orcid.org/0000-0001-7792-375X"},"institutions":[{"id":"https://openalex.org/I177969490","display_name":"University of Southern Denmark","ror":"https://ror.org/03yrrjy16","country_code":"DK","type":"education","lineage":["https://openalex.org/I177969490"]},{"id":"https://openalex.org/I20121455","display_name":"Bielefeld University","ror":"https://ror.org/02hpadn98","country_code":"DE","type":"education","lineage":["https://openalex.org/I20121455"]},{"id":"https://openalex.org/I203082224","display_name":"Hochschule Bielefeld","ror":"https://ror.org/00edvg943","country_code":"DE","type":"education","lineage":["https://openalex.org/I203082224"]}],"countries":["DE","DK"],"is_corresponding":false,"raw_author_name":"Daniel Merkle","raw_affiliation_strings":["Department of Mathematics and Computer Science , University of Southern Denmark ; Odense , Denmark","Faculty of Technology , Bielefeld University ; Bielefeld , Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Computer Science , University of Southern Denmark ; Odense , Denmark","institution_ids":["https://openalex.org/I177969490"]},{"raw_affiliation_string":"Faculty of Technology , Bielefeld University ; Bielefeld , Germany","institution_ids":["https://openalex.org/I20121455","https://openalex.org/I203082224"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021113778","display_name":"Nikolai N\u00f8jgaard","orcid":"https://orcid.org/0000-0002-7053-4716"},"institutions":[{"id":"https://openalex.org/I177969490","display_name":"University of Southern Denmark","ror":"https://ror.org/03yrrjy16","country_code":"DK","type":"education","lineage":["https://openalex.org/I177969490"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Nikolai N\u00f8jgaard","raw_affiliation_strings":["Department of Mathematics and Computer Science , University of Southern Denmark ; Odense , Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Computer Science , University of Southern Denmark ; Odense , Denmark","institution_ids":["https://openalex.org/I177969490"]}]}],"institutions":[],"countries_distinct_count":5,"institutions_distinct_count":7,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4150,"currency":"USD","value_usd":4150},"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.00265566,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"Volume 196, Issue 1","issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10215","display_name":"Semantic Web and Ontologies","score":0.994700014591217,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/T10215","display_name":"Semantic Web and Ontologies","score":0.994700014591217,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/T10538","display_name":"Data Mining Algorithms and Applications","score":0.9922000169754028,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"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/T12292","display_name":"Graph Theory and Algorithms","score":0.9894000291824341,"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/inference","display_name":"Inference","score":0.6999024152755737},{"id":"https://openalex.org/keywords/transformation","display_name":"Transformation (genetics)","score":0.6477790474891663},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6210113167762756},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5353029370307922},{"id":"https://openalex.org/keywords/graph-rewriting","display_name":"Graph rewriting","score":0.4746701717376709},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3593742847442627},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.35746851563453674},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.10222408175468445}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6999024152755737},{"id":"https://openalex.org/C204241405","wikidata":"https://www.wikidata.org/wiki/Q461499","display_name":"Transformation (genetics)","level":3,"score":0.6477790474891663},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6210113167762756},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5353029370307922},{"id":"https://openalex.org/C558772884","wikidata":"https://www.wikidata.org/wiki/Q1508564","display_name":"Graph rewriting","level":3,"score":0.4746701717376709},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3593742847442627},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.35746851563453674},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.10222408175468445},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.46298/fi.13347","is_oa":true,"landing_page_url":"https://doi.org/10.46298/fi.13347","pdf_url":"https://fi.episciences.org/18994/pdf","source":{"id":"https://openalex.org/S39012697","display_name":"Fundamenta Informaticae","issn_l":"0169-2968","issn":["0169-2968","1875-8681"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Fundamenta Informaticae","raw_type":"journal-article"},{"id":"pmh:oai:arXiv.org:2404.02692","is_oa":true,"landing_page_url":"https://arxiv.org/abs/2404.02692","pdf_url":"https://arxiv.org/pdf/2404.02692","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"},{"id":"doi:10.48550/arxiv.2404.02692","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2404.02692","pdf_url":null,"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":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"doi:10.46298/fi.13347","is_oa":true,"landing_page_url":"https://doi.org/10.46298/fi.13347","pdf_url":"https://fi.episciences.org/18994/pdf","source":{"id":"https://openalex.org/S39012697","display_name":"Fundamenta Informaticae","issn_l":"0169-2968","issn":["0169-2968","1875-8681"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Fundamenta Informaticae","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1032663478","display_name":null,"funder_award_id":"NNF19OC0057834","funder_id":"https://openalex.org/F4320325957","funder_display_name":"Novo Nordisk Fonden"},{"id":"https://openalex.org/G2942398999","display_name":null,"funder_award_id":"NNF21OC0066551","funder_id":"https://openalex.org/F4320322436","funder_display_name":"Novo Nordisk"},{"id":"https://openalex.org/G3843702472","display_name":null,"funder_award_id":"NNF21OC0066551","funder_id":"https://openalex.org/F4320325957","funder_display_name":"Novo Nordisk Fonden"},{"id":"https://openalex.org/G6894179864","display_name":null,"funder_award_id":"NNF19OC0057834","funder_id":"https://openalex.org/F4320322436","funder_display_name":"Novo Nordisk"}],"funders":[{"id":"https://openalex.org/F4320322436","display_name":"Novo Nordisk","ror":"https://ror.org/0435rc536"},{"id":"https://openalex.org/F4320325957","display_name":"Novo Nordisk Fonden","ror":"https://ror.org/04txyc737"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4393968931.pdf","grobid_xml":"https://content.openalex.org/works/W4393968931.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2140997306","https://openalex.org/W990257473","https://openalex.org/W1597906851","https://openalex.org/W179785347","https://openalex.org/W2275852252","https://openalex.org/W2031030123","https://openalex.org/W2348386261","https://openalex.org/W2787389163","https://openalex.org/W2087211823","https://openalex.org/W1933425755"],"abstract_inverted_index":{"The":[0,58,81,106,136],"explosion":[1,156],"of":[2,31,38,69,99,104,124,132,138,163,191],"data":[3],"available":[4],"in":[5,189],"life":[6],"sciences":[7],"is":[8,21,84,108,118,143],"fueling":[9],"an":[10],"increasing":[11],"demand":[12],"for":[13,24,172],"expressive":[14],"models":[15],"and":[16,46,76],"computational":[17],"methods.":[18],"Graph":[19],"transformation":[20,41,140],"a":[22,28,35,51,67,78,97,102,111,130,159,167],"model":[23,42,55,83,94,117,141],"dynamic":[25],"systems":[26],"with":[27],"large":[29],"variety":[30],"applications.":[32],"We":[33,152,178],"introduce":[34],"novel":[36],"method":[37,59],"the":[39,61,70,91,115,125,133,149,154,164],"graph":[40,139,192],"construction,":[43],"combining":[44],"generative":[45],"dynamical":[47,63],"viewpoints":[48],"to":[49,86,110,120,148,185],"give":[50],"fully":[52],"automated":[53],"data-driven":[54],"inference":[56,142],"method.":[57],"takes":[60],"input":[62,126,134],"properties,":[64],"given":[65],"as":[66,93],"\"snapshot\"":[68],"dynamics":[71],"encoded":[72],"by":[73,157],"explicit":[74],"transitions,":[75,127],"constructs":[77],"compatible":[79],"model.":[80],"obtained":[82],"guaranteed":[85],"be":[87],"minimal,":[88],"thus":[89,128],"framing":[90],"approach":[92],"compression":[95,107],"(from":[96],"set":[98,103,170],"transitions":[100],"into":[101,166],"rules).":[105],"permissive":[109],"lossy":[112],"case,":[113],"where":[114],"constructed":[116],"allowed":[119],"exhibit":[121],"behavior":[122],"outside":[123],"suggesting":[129],"completion":[131],"dynamics.":[135],"task":[137,165],"naturally":[144],"highly":[145,174],"challenging":[146],"due":[147],"combinatorics":[150],"involved.":[151],"tackle":[153],"exponential":[155],"proposing":[158],"heuristically":[160],"minimal":[161],"translation":[162],"well-established":[168],"problem,":[169],"cover,":[171],"which":[173],"optimized":[175],"solutions":[176],"exist.":[177],"further":[179],"showcase":[180],"how":[181],"our":[182],"results":[183],"relate":[184],"Kolmogorov":[186],"complexity":[187],"expressed":[188],"terms":[190],"transformation.":[193]},"counts_by_year":[],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}
