Learning Boolean logic models of signaling networks with ASP
- Autores
- Videla, Santiago; Guziolowski, Carito; Eduati, Federica; Thiele, Sven; Gebser, Martin; Nicolas, Jacques; Saez Rodriguez, Julio; Schaub, Torsten; Siegel, Anne
- Año de publicación
- 2015
- Idioma
- inglés
- Tipo de recurso
- artículo
- Estado
- versión publicada
- Descripción
- Boolean networks provide a simple yet powerful qualitative modeling approach in systems biology. However, manual identification of logic rules underlying the system being studied is in most cases out of reach. Therefore, automated inference of Boolean logical networks from experimental data is a fundamental question in this field. This paper addresses the problem consisting of learning from a prior knowledge network describing causal interactions and phosphorylation activities at a pseudo-steady state, Boolean logic models of immediate-early response in signaling transduction networks. The underlying optimization problem has been so far addressed through mathematical programming approaches and the use of dedicated genetic algorithms. In a recent work we have shown severe limitations of stochastic approaches in this domain and proposed to use Answer Set Programming (ASP), considering a simpler problem setting. Herein, we extend our previous work in order to consider more realistic biological conditions including numerical datasets, the presence of feedback-loops in the prior knowledge networkand the necessity of multi-objective optimization. In order to cope with such extensions, we propose several discretization schemes and elaborate upon our previous ASP encoding. Towards real-world biological data, we evaluate the performance of our approach over in siliconumerical datasets based on a real and large-scale prior knowledge network. The correctness of our encoding and discretization schemes are dealt with in Appendices A–B.
Fil: Videla, Santiago. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquimicas de Buenos Aires; Argentina. CNRS. UMR; Francia. Campus de Beaulieu. Dyliss project; Francia. Universität Potsdam; Alemania
Fil: Guziolowski, Carito. CNRS. École Centrale de Nantes; Francia
Fil: Eduati, Federica. European Bioinformatics Institute. European Molecular Biology Laboratory; Reino Unido
Fil: Thiele, Sven. CNRS. UMR; Francia. Campus de Beaulieu. Dyliss project; Francia
Fil: Gebser, Martin. Universität Potsdam; Alemania
Fil: Nicolas, Jacques. CNRS. UMR; Francia. Campus de Beaulieu. Dyliss project; Francia
Fil: Saez Rodriguez, Julio. European Bioinformatics Institute. European Molecular Biology Laboratory; Reino Unido
Fil: Schaub, Torsten. Universität Potsdam; Alemania
Fil: Siegel, Anne. CNRS. UMR; Francia. Campus de Beaulieu. Dyliss project; Francia - Materia
-
Answer Set Programming
Signaling Transduction Networks
Boolean Logic Models
Combinatorial Multi-Objective Optimization - Nivel de accesibilidad
- acceso abierto
- Condiciones de uso
- https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
- Repositorio
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/14203
Ver los metadatos del registro completo
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Learning Boolean logic models of signaling networks with ASPVidela, SantiagoGuziolowski, CaritoEduati, FedericaThiele, SvenGebser, MartinNicolas, JacquesSaez Rodriguez, JulioSchaub, TorstenSiegel, AnneAnswer Set ProgrammingSignaling Transduction NetworksBoolean Logic ModelsCombinatorial Multi-Objective Optimizationhttps://purl.org/becyt/ford/1.2https://purl.org/becyt/ford/1Boolean networks provide a simple yet powerful qualitative modeling approach in systems biology. However, manual identification of logic rules underlying the system being studied is in most cases out of reach. Therefore, automated inference of Boolean logical networks from experimental data is a fundamental question in this field. This paper addresses the problem consisting of learning from a prior knowledge network describing causal interactions and phosphorylation activities at a pseudo-steady state, Boolean logic models of immediate-early response in signaling transduction networks. The underlying optimization problem has been so far addressed through mathematical programming approaches and the use of dedicated genetic algorithms. In a recent work we have shown severe limitations of stochastic approaches in this domain and proposed to use Answer Set Programming (ASP), considering a simpler problem setting. Herein, we extend our previous work in order to consider more realistic biological conditions including numerical datasets, the presence of feedback-loops in the prior knowledge networkand the necessity of multi-objective optimization. In order to cope with such extensions, we propose several discretization schemes and elaborate upon our previous ASP encoding. Towards real-world biological data, we evaluate the performance of our approach over in siliconumerical datasets based on a real and large-scale prior knowledge network. The correctness of our encoding and discretization schemes are dealt with in Appendices A–B.Fil: Videla, Santiago. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquimicas de Buenos Aires; Argentina. CNRS. UMR; Francia. Campus de Beaulieu. Dyliss project; Francia. Universität Potsdam; AlemaniaFil: Guziolowski, Carito. CNRS. École Centrale de Nantes; FranciaFil: Eduati, Federica. European Bioinformatics Institute. European Molecular Biology Laboratory; Reino UnidoFil: Thiele, Sven. CNRS. UMR; Francia. Campus de Beaulieu. Dyliss project; FranciaFil: Gebser, Martin. Universität Potsdam; AlemaniaFil: Nicolas, Jacques. CNRS. UMR; Francia. Campus de Beaulieu. Dyliss project; FranciaFil: Saez Rodriguez, Julio. European Bioinformatics Institute. European Molecular Biology Laboratory; Reino UnidoFil: Schaub, Torsten. Universität Potsdam; AlemaniaFil: Siegel, Anne. CNRS. UMR; Francia. Campus de Beaulieu. Dyliss project; FranciaElsevier Science2015-09info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/14203Videla, Santiago; Guziolowski, Carito; Eduati, Federica; Thiele, Sven; Gebser, Martin; et al.; Learning Boolean logic models of signaling networks with ASP; Elsevier Science; Theoretical Computer Science; 599; 9-2015; 79-1010304-3975enginfo:eu-repo/semantics/altIdentifier/url/http://www.sciencedirect.com/science/article/pii/S0304397514004587info:eu-repo/semantics/altIdentifier/url/http://dx.doi.org/10.1016/j.tcs.2014.06.022info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-nd/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:12:35Zoai:ri.conicet.gov.ar:11336/14203instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 10:12:36.175CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse |
dc.title.none.fl_str_mv |
Learning Boolean logic models of signaling networks with ASP |
title |
Learning Boolean logic models of signaling networks with ASP |
spellingShingle |
Learning Boolean logic models of signaling networks with ASP Videla, Santiago Answer Set Programming Signaling Transduction Networks Boolean Logic Models Combinatorial Multi-Objective Optimization |
title_short |
Learning Boolean logic models of signaling networks with ASP |
title_full |
Learning Boolean logic models of signaling networks with ASP |
title_fullStr |
Learning Boolean logic models of signaling networks with ASP |
title_full_unstemmed |
Learning Boolean logic models of signaling networks with ASP |
title_sort |
Learning Boolean logic models of signaling networks with ASP |
dc.creator.none.fl_str_mv |
Videla, Santiago Guziolowski, Carito Eduati, Federica Thiele, Sven Gebser, Martin Nicolas, Jacques Saez Rodriguez, Julio Schaub, Torsten Siegel, Anne |
author |
Videla, Santiago |
author_facet |
Videla, Santiago Guziolowski, Carito Eduati, Federica Thiele, Sven Gebser, Martin Nicolas, Jacques Saez Rodriguez, Julio Schaub, Torsten Siegel, Anne |
author_role |
author |
author2 |
Guziolowski, Carito Eduati, Federica Thiele, Sven Gebser, Martin Nicolas, Jacques Saez Rodriguez, Julio Schaub, Torsten Siegel, Anne |
author2_role |
author author author author author author author author |
dc.subject.none.fl_str_mv |
Answer Set Programming Signaling Transduction Networks Boolean Logic Models Combinatorial Multi-Objective Optimization |
topic |
Answer Set Programming Signaling Transduction Networks Boolean Logic Models Combinatorial Multi-Objective Optimization |
purl_subject.fl_str_mv |
https://purl.org/becyt/ford/1.2 https://purl.org/becyt/ford/1 |
dc.description.none.fl_txt_mv |
Boolean networks provide a simple yet powerful qualitative modeling approach in systems biology. However, manual identification of logic rules underlying the system being studied is in most cases out of reach. Therefore, automated inference of Boolean logical networks from experimental data is a fundamental question in this field. This paper addresses the problem consisting of learning from a prior knowledge network describing causal interactions and phosphorylation activities at a pseudo-steady state, Boolean logic models of immediate-early response in signaling transduction networks. The underlying optimization problem has been so far addressed through mathematical programming approaches and the use of dedicated genetic algorithms. In a recent work we have shown severe limitations of stochastic approaches in this domain and proposed to use Answer Set Programming (ASP), considering a simpler problem setting. Herein, we extend our previous work in order to consider more realistic biological conditions including numerical datasets, the presence of feedback-loops in the prior knowledge networkand the necessity of multi-objective optimization. In order to cope with such extensions, we propose several discretization schemes and elaborate upon our previous ASP encoding. Towards real-world biological data, we evaluate the performance of our approach over in siliconumerical datasets based on a real and large-scale prior knowledge network. The correctness of our encoding and discretization schemes are dealt with in Appendices A–B. Fil: Videla, Santiago. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquimicas de Buenos Aires; Argentina. CNRS. UMR; Francia. Campus de Beaulieu. Dyliss project; Francia. Universität Potsdam; Alemania Fil: Guziolowski, Carito. CNRS. École Centrale de Nantes; Francia Fil: Eduati, Federica. European Bioinformatics Institute. European Molecular Biology Laboratory; Reino Unido Fil: Thiele, Sven. CNRS. UMR; Francia. Campus de Beaulieu. Dyliss project; Francia Fil: Gebser, Martin. Universität Potsdam; Alemania Fil: Nicolas, Jacques. CNRS. UMR; Francia. Campus de Beaulieu. Dyliss project; Francia Fil: Saez Rodriguez, Julio. European Bioinformatics Institute. European Molecular Biology Laboratory; Reino Unido Fil: Schaub, Torsten. Universität Potsdam; Alemania Fil: Siegel, Anne. CNRS. UMR; Francia. Campus de Beaulieu. Dyliss project; Francia |
description |
Boolean networks provide a simple yet powerful qualitative modeling approach in systems biology. However, manual identification of logic rules underlying the system being studied is in most cases out of reach. Therefore, automated inference of Boolean logical networks from experimental data is a fundamental question in this field. This paper addresses the problem consisting of learning from a prior knowledge network describing causal interactions and phosphorylation activities at a pseudo-steady state, Boolean logic models of immediate-early response in signaling transduction networks. The underlying optimization problem has been so far addressed through mathematical programming approaches and the use of dedicated genetic algorithms. In a recent work we have shown severe limitations of stochastic approaches in this domain and proposed to use Answer Set Programming (ASP), considering a simpler problem setting. Herein, we extend our previous work in order to consider more realistic biological conditions including numerical datasets, the presence of feedback-loops in the prior knowledge networkand the necessity of multi-objective optimization. In order to cope with such extensions, we propose several discretization schemes and elaborate upon our previous ASP encoding. Towards real-world biological data, we evaluate the performance of our approach over in siliconumerical datasets based on a real and large-scale prior knowledge network. The correctness of our encoding and discretization schemes are dealt with in Appendices A–B. |
publishDate |
2015 |
dc.date.none.fl_str_mv |
2015-09 |
dc.type.none.fl_str_mv |
info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://purl.org/coar/resource_type/c_6501 info:ar-repo/semantics/articulo |
format |
article |
status_str |
publishedVersion |
dc.identifier.none.fl_str_mv |
http://hdl.handle.net/11336/14203 Videla, Santiago; Guziolowski, Carito; Eduati, Federica; Thiele, Sven; Gebser, Martin; et al.; Learning Boolean logic models of signaling networks with ASP; Elsevier Science; Theoretical Computer Science; 599; 9-2015; 79-101 0304-3975 |
url |
http://hdl.handle.net/11336/14203 |
identifier_str_mv |
Videla, Santiago; Guziolowski, Carito; Eduati, Federica; Thiele, Sven; Gebser, Martin; et al.; Learning Boolean logic models of signaling networks with ASP; Elsevier Science; Theoretical Computer Science; 599; 9-2015; 79-101 0304-3975 |
dc.language.none.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
info:eu-repo/semantics/altIdentifier/url/http://www.sciencedirect.com/science/article/pii/S0304397514004587 info:eu-repo/semantics/altIdentifier/url/http://dx.doi.org/10.1016/j.tcs.2014.06.022 |
dc.rights.none.fl_str_mv |
info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by-nc-nd/2.5/ar/ |
eu_rights_str_mv |
openAccess |
rights_invalid_str_mv |
https://creativecommons.org/licenses/by-nc-nd/2.5/ar/ |
dc.format.none.fl_str_mv |
application/pdf application/pdf |
dc.publisher.none.fl_str_mv |
Elsevier Science |
publisher.none.fl_str_mv |
Elsevier Science |
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CONICET Digital (CONICET) |
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Consejo Nacional de Investigaciones Científicas y Técnicas |
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CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas |
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dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar |
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13.070432 |