{"id":"https://openalex.org/W7110263358","doi":"https://doi.org/10.4230/lipics.sea.2025.26","title":"Mixed-Integer Optimization for Loopless Flux Distributions in Metabolic Networks","display_name":"Mixed-Integer Optimization for Loopless Flux Distributions in Metabolic Networks","publication_year":2025,"publication_date":"2025-01-01","ids":{"openalex":"https://openalex.org/W7110263358","doi":"https://doi.org/10.4230/lipics.sea.2025.26"},"language":"en","primary_location":{"id":"pmh:oai:HAL:hal-05432362v1","is_oa":true,"landing_page_url":"https://inria.hal.science/hal-05432362","pdf_url":"https://inria.hal.science/hal-05432362/document","source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"SEA 2025 - 23rd International Symposium on Experimental Algorithms, Jul 2025, Venice, Italy. &#x27E8;10.4230/LIPIcs.SEA.2025.26&#x27E9;","raw_type":"Conference papers"},"type":"article","indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://inria.hal.science/hal-05432362/document","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Troppens, Hannah","orcid":null},"institutions":[{"id":"https://openalex.org/I195893171","display_name":"Zuse Institute Berlin","ror":"https://ror.org/02eva5865","country_code":"DE","type":"facility","lineage":["https://openalex.org/I195893171"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Troppens, Hannah","raw_affiliation_strings":["ZIB - Zuse Institute Berlin (Konrad-Zuse-Zentrum f\u00fcr Informationstechnik Berlin (ZIB Takustra\u00dfe 7 D-14195 Berlin-Dahlem - Germany)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ZIB - Zuse Institute Berlin (Konrad-Zuse-Zentrum f\u00fcr Informationstechnik Berlin (ZIB Takustra\u00dfe 7 D-14195 Berlin-Dahlem - Germany)","institution_ids":[]}]},{"author_position":"middle","author":{"id":null,"display_name":"Besan\u00e7on, Mathieu","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210101348","display_name":"Centre Inria de l'Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/00n8d6z93","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1326498283","https://openalex.org/I4210101348"]},{"id":"https://openalex.org/I4210104430","display_name":"Laboratoire d'Informatique de Grenoble","ror":"https://ror.org/01c8rcg82","country_code":"FR","type":"facility","lineage":["https://openalex.org/I106785703","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I4210104430","https://openalex.org/I4210159245","https://openalex.org/I899635006","https://openalex.org/I899635006"]},{"id":"https://openalex.org/I899635006","display_name":"Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/02rx3b187","country_code":"FR","type":"education","lineage":["https://openalex.org/I899635006"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Besan\u00e7on, Mathieu","raw_affiliation_strings":["GHOST - Jeux, optimisation math\u00e9matique et syst\u00e8mes stochastiques (655 Av. de l'Europe, 38330 Montbonnot-Saint-Martin - France)","LIG - Laboratoire d'Informatique de Grenoble (UMR 5217 - Laboratoire LIG - B\u00e2timent IMAG - 700 avenue Centrale - Domaine Universitaire de Saint-Martin-d\u2019H\u00e8res \r\nAdresse postale : CS 40700 - 38058 Grenoble cedex 9\r\nT\u00e9l. : 04 57 42 14 00 - France)","POLARIS - Performance analysis and optimization of LARge Infrastructures and Systems (Laboratoire LIG - B\u00e2timent IMAG - 700 avenue Centrale, CS 40700 - 38058 Grenoble cedex 9 - France)","UGA - Universit\u00e9 Grenoble Alpes (Adresse CS 40700 - 38058 Grenoble cedex - France)","ZIB - Zuse Institute Berlin (Konrad-Zuse-Zentrum f\u00fcr Informationstechnik Berlin (ZIB Takustra\u00dfe 7 D-14195 Berlin-Dahlem - Germany)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"GHOST - Jeux, optimisation math\u00e9matique et syst\u00e8mes stochastiques (655 Av. de l'Europe, 38330 Montbonnot-Saint-Martin - France)","institution_ids":[]},{"raw_affiliation_string":"LIG - Laboratoire d'Informatique de Grenoble (UMR 5217 - Laboratoire LIG - B\u00e2timent IMAG - 700 avenue Centrale - Domaine Universitaire de Saint-Martin-d\u2019H\u00e8res \r\nAdresse postale : CS 40700 - 38058 Grenoble cedex 9\r\nT\u00e9l. : 04 57 42 14 00 - France)","institution_ids":[]},{"raw_affiliation_string":"POLARIS - Performance analysis and optimization of LARge Infrastructures and Systems (Laboratoire LIG - B\u00e2timent IMAG - 700 avenue Centrale, CS 40700 - 38058 Grenoble cedex 9 - France)","institution_ids":[]},{"raw_affiliation_string":"UGA - Universit\u00e9 Grenoble Alpes (Adresse CS 40700 - 38058 Grenoble cedex - France)","institution_ids":[]},{"raw_affiliation_string":"ZIB - Zuse Institute Berlin (Konrad-Zuse-Zentrum f\u00fcr Informationstechnik Berlin (ZIB Takustra\u00dfe 7 D-14195 Berlin-Dahlem - Germany)","institution_ids":[]}]},{"author_position":"middle","author":{"id":null,"display_name":"Wilken, St. Elmo","orcid":null},"institutions":[{"id":"https://openalex.org/I44260953","display_name":"Heinrich Heine University D\u00fcsseldorf","ror":"https://ror.org/024z2rq82","country_code":"DE","type":"education","lineage":["https://openalex.org/I44260953"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Wilken, St. Elmo","raw_affiliation_strings":["Heinrich Heine Universit\u00e4t D\u00fcsseldorf = Heinrich Heine University [D\u00fcsseldorf] (Universit\u00e4tsstr. 1\r\n40225 D\u00fcsseldorf - Germany)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Heinrich Heine Universit\u00e4t D\u00fcsseldorf = Heinrich Heine University [D\u00fcsseldorf] (Universit\u00e4tsstr. 1\r\n40225 D\u00fcsseldorf - Germany)","institution_ids":[]}]},{"author_position":"last","author":{"id":null,"display_name":"Pokutta, Sebastian","orcid":null},"institutions":[{"id":"https://openalex.org/I195893171","display_name":"Zuse Institute Berlin","ror":"https://ror.org/02eva5865","country_code":"DE","type":"facility","lineage":["https://openalex.org/I195893171"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Pokutta, Sebastian","raw_affiliation_strings":["TUB - Technical University of Berlin / Technische Universit\u00e4t Berlin (Stra\u00dfe des 17. Juni 135 10623 Berlin - Germany)","ZIB - Zuse Institute Berlin (Konrad-Zuse-Zentrum f\u00fcr Informationstechnik Berlin (ZIB Takustra\u00dfe 7 D-14195 Berlin-Dahlem - Germany)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"TUB - Technical University of Berlin / Technische Universit\u00e4t Berlin (Stra\u00dfe des 17. Juni 135 10623 Berlin - Germany)","institution_ids":[]},{"raw_affiliation_string":"ZIB - Zuse Institute Berlin (Konrad-Zuse-Zentrum f\u00fcr Informationstechnik Berlin (ZIB Takustra\u00dfe 7 D-14195 Berlin-Dahlem - Germany)","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.51620888,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9952999949455261,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9952999949455261,"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/T10791","display_name":"Advanced Control Systems Optimization","score":0.0008999999845400453,"subfield":{"id":"https://openalex.org/subfields/2207","display_name":"Control and Systems Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11053","display_name":"Process Optimization and Integration","score":0.000699999975040555,"subfield":{"id":"https://openalex.org/subfields/2207","display_name":"Control and Systems Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/flux-balance-analysis","display_name":"Flux balance analysis","score":0.8070999979972839},{"id":"https://openalex.org/keywords/flux","display_name":"Flux (metallurgy)","score":0.6527000069618225},{"id":"https://openalex.org/keywords/decomposition","display_name":"Decomposition","score":0.580299973487854},{"id":"https://openalex.org/keywords/optimization-problem","display_name":"Optimization problem","score":0.45579999685287476},{"id":"https://openalex.org/keywords/stability","display_name":"Stability (learning theory)","score":0.4043999910354614},{"id":"https://openalex.org/keywords/metabolic-network","display_name":"Metabolic network","score":0.3894999921321869},{"id":"https://openalex.org/keywords/cellular-metabolism","display_name":"Cellular metabolism","score":0.3695000112056732},{"id":"https://openalex.org/keywords/detailed-balance","display_name":"Detailed balance","score":0.3695000112056732}],"concepts":[{"id":"https://openalex.org/C167091322","wikidata":"https://www.wikidata.org/wiki/Q5463029","display_name":"Flux balance analysis","level":2,"score":0.8070999979972839},{"id":"https://openalex.org/C68709404","wikidata":"https://www.wikidata.org/wiki/Q1134475","display_name":"Flux (metallurgy)","level":2,"score":0.6527000069618225},{"id":"https://openalex.org/C124681953","wikidata":"https://www.wikidata.org/wiki/Q339062","display_name":"Decomposition","level":2,"score":0.580299973487854},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.47929999232292175},{"id":"https://openalex.org/C137836250","wikidata":"https://www.wikidata.org/wiki/Q984063","display_name":"Optimization problem","level":2,"score":0.45579999685287476},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.45100000500679016},{"id":"https://openalex.org/C112972136","wikidata":"https://www.wikidata.org/wiki/Q7595718","display_name":"Stability (learning theory)","level":2,"score":0.4043999910354614},{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.3894999921321869},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3765000104904175},{"id":"https://openalex.org/C28826006","wikidata":"https://www.wikidata.org/wiki/Q33521","display_name":"Applied mathematics","level":1,"score":0.37119999527931213},{"id":"https://openalex.org/C135694725","wikidata":"https://www.wikidata.org/wiki/Q1201087","display_name":"Detailed balance","level":2,"score":0.3695000112056732},{"id":"https://openalex.org/C2994212657","wikidata":"https://www.wikidata.org/wiki/Q1057","display_name":"Cellular metabolism","level":3,"score":0.3695000112056732},{"id":"https://openalex.org/C168031717","wikidata":"https://www.wikidata.org/wiki/Q1530280","display_name":"Balance (ability)","level":2,"score":0.3553999960422516},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.35249999165534973},{"id":"https://openalex.org/C2778258933","wikidata":"https://www.wikidata.org/wiki/Q16918986","display_name":"Decomposition method (queueing theory)","level":2,"score":0.3441999852657318},{"id":"https://openalex.org/C160941953","wikidata":"https://www.wikidata.org/wiki/Q6822342","display_name":"Metabolic flux analysis","level":3,"score":0.3111000061035156},{"id":"https://openalex.org/C2992708514","wikidata":"https://www.wikidata.org/wiki/Q48968323","display_name":"Quantitative biology","level":2,"score":0.30709999799728394},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.2955999970436096},{"id":"https://openalex.org/C207821765","wikidata":"https://www.wikidata.org/wiki/Q405372","display_name":"Instability","level":2,"score":0.29249998927116394},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.2809000015258789},{"id":"https://openalex.org/C76969082","wikidata":"https://www.wikidata.org/wiki/Q486902","display_name":"Mathematical model","level":2,"score":0.2802000045776367},{"id":"https://openalex.org/C137866125","wikidata":"https://www.wikidata.org/wiki/Q4299308","display_name":"Modelling biological systems","level":3,"score":0.2743000090122223},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.26409998536109924},{"id":"https://openalex.org/C2992768293","wikidata":"https://www.wikidata.org/wiki/Q623293","display_name":"Metabolic rate","level":2,"score":0.2522999942302704}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:HAL:hal-05432362v1","is_oa":true,"landing_page_url":"https://inria.hal.science/hal-05432362","pdf_url":"https://inria.hal.science/hal-05432362/document","source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"SEA 2025 - 23rd International Symposium on Experimental Algorithms, Jul 2025, Venice, Italy. &#x27E8;10.4230/LIPIcs.SEA.2025.26&#x27E9;","raw_type":"Conference papers"},{"id":"pmh:oai:drops-oai.dagstuhl.de:23264","is_oa":true,"landing_page_url":"https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2025.26","pdf_url":"https://drops.dagstuhl.de/storage/00lipics/lipics-vol338-sea2025/LIPIcs.SEA.2025.26/LIPIcs.SEA.2025.26.pdf","source":{"id":"https://openalex.org/S4377196569","display_name":"DROPS (Schloss Dagstuhl \u2013 Leibniz Center for Informatics)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2799853480","host_organization_name":"Schloss Dagstuhl \u2013 Leibniz Center for Informatics","host_organization_lineage":["https://openalex.org/I2799853480"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"publishedVersion"}],"best_oa_location":{"id":"pmh:oai:HAL:hal-05432362v1","is_oa":true,"landing_page_url":"https://inria.hal.science/hal-05432362","pdf_url":"https://inria.hal.science/hal-05432362/document","source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"SEA 2025 - 23rd International Symposium on Experimental Algorithms, Jul 2025, Venice, Italy. &#x27E8;10.4230/LIPIcs.SEA.2025.26&#x27E9;","raw_type":"Conference papers"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","score":0.40523964166641235,"display_name":"Partnerships for the goals"}],"awards":[{"id":"https://openalex.org/G4192406653","display_name":null,"funder_award_id":"05M20ZBM","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G8921868790","display_name":null,"funder_award_id":"05M14ZAM","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320324478","display_name":"Fondation Math\u00e9matique Jacques Hadamard","ror":"https://ror.org/0153me927"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7110263358.pdf","grobid_xml":"https://content.openalex.org/works/W7110263358.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Constraint-based":[0],"metabolic":[1],"models":[2,14,109],"can":[3],"be":[4],"used":[5],"to":[6,17,22,63,81,105,161],"investigate":[7],"the":[8,40,132,137,141,152,162],"intracellular":[9],"physiology":[10],"of":[11,42,114,125,140],"microorganisms.":[12],"These":[13],"couple":[15],"genes":[16],"reactions,":[18],"and":[19,102,116,127,155],"typically":[20],"seek":[21],"predict":[23,82],"metabolite":[24],"fluxes":[25],"that":[26,67,85,110],"optimize":[27],"some":[28],"biologically":[29],"important":[30],"metric.":[31],"Classical":[32],"techniques,":[33],"like":[34],"Flux":[35],"Balance":[36,77],"Analysis":[37,78],"(FBA),":[38],"formulate":[39],"metabolism":[41],"a":[43,93,99,159],"microbe":[44],"as":[45,98],"an":[46],"optimization":[47],"problem":[48],"where":[49],"growth":[50],"rate":[51],"is":[52,92,103,136],"maximized.":[53],"While":[54],"FBA":[55],"has":[56],"found":[57],"widespread":[58],"use,":[59],"it":[60],"often":[61,111],"leads":[62],"thermodynamically":[64],"infeasible":[65],"solutions":[66],"contain":[68,88,112],"internal":[69],"cycles":[70],"(loops).":[71],"To":[72],"address":[73],"this":[74,119],"shortcoming,":[75],"Loopless-Flux":[76],"(ll-FBA)":[79],"seeks":[80],"flux":[83],"distributions":[84],"do":[86],"not":[87],"these":[89],"loops.":[90],"ll-FBA":[91,126],"disjunctive":[94],"program,":[95,101],"usually":[96],"reformulated":[97],"mixed-integer":[100],"challenging":[104],"solve":[106,148],"for":[107],"biological":[108],"thousands":[113],"reactions":[115],"metabolites.":[117],"In":[118],"paper,":[120],"we":[121,146],"compare":[122],"various":[123],"reformulations":[124],"different":[128],"solution":[129],"approaches.":[130],"Overall,":[131],"combinatorial":[133,163],"Benders'":[134,164],"decomposition":[135],"most":[138,149],"promising":[139],"tested":[142],"approaches":[143],"with":[144],"which":[145],"could":[147],"instances.":[150],"However,":[151],"model":[153],"size":[154],"numerical":[156],"instability":[157],"pose":[158],"challenge":[160],"method.":[165]},"counts_by_year":[],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-12-08T00:00:00"}
