AntNetAlign: A software package for network alignment

In this paper we introduce AntNetAlign, an open-source tool (written in C++) that implements an Ant Colony Optimization (ACO) for solving the Network Alignment (NA) problem, a well-known hard optimization problem with important applications in different areas, such as biology or social networks. Spe...

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Detalles Bibliográficos
Autores: Rodríguez i Corominas, Guillem, Blesa Aguilera, Maria Josep|||0000-0001-8246-9926, Blum, Christian
Tipo de recurso: artículo
Fecha de publicación:2023
País:España
Institución:Universitat Politècnica de Catalunya (UPC)
Repositorio:UPCommons. Portal del coneixement obert de la UPC
Idioma:inglés
OAI Identifier:oai:upcommons.upc.edu:2117/386762
Acceso en línea:https://hdl.handle.net/2117/386762
https://dx.doi.org/10.1016/j.simpa.2023.100476
Access Level:acceso abierto
Palabra clave:Combinatorial optimization
Ant algorithms
Network alignment
Open source software
Optimization
Ant colony optimization
Optimització combinatòria
Algorismes de les colònies de formigues
Àrees temàtiques de la UPC::Informàtica::Informàtica teòrica::Algorísmica i teoria de la complexitat
Àrees temàtiques de la UPC::Informàtica::Intel·ligència artificial
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spelling AntNetAlign: A software package for network alignmentRodríguez i Corominas, GuillemBlesa Aguilera, Maria Josep|||0000-0001-8246-9926Blum, ChristianCombinatorial optimizationAnt algorithmsNetwork alignmentOpen source softwareOptimizationAnt colony optimizationOptimització combinatòriaAlgorismes de les colònies de formiguesÀrees temàtiques de la UPC::Informàtica::Informàtica teòrica::Algorísmica i teoria de la complexitatÀrees temàtiques de la UPC::Informàtica::Intel·ligència artificialIn this paper we introduce AntNetAlign, an open-source tool (written in C++) that implements an Ant Colony Optimization (ACO) for solving the Network Alignment (NA) problem, a well-known hard optimization problem with important applications in different areas, such as biology or social networks. Specifically, given two input networks, the tool finds an alignment between them (i.e., a mapping between the respective nodes) that optimizes one out of the three main topological measures. Additionally, it can make use of user-defined pairwise similarities between nodes during its construction phase, allowing for the use of more application-dependent information in order to increase its performance. Results show that AntNetAlign outperforms other state-of-the-art algorithms in two out of the three aforementioned topological scores within a reasonable amount of time, and is able to achieve competitive results in the context of larger instances (Rodríguez Corominas et al., 2023). Furthermore, a new version of the algorithm, which makes use of Negative Learning, was able to further improve these results, specially in the EC score (Corominas et al., 2022).Guillem Rodríguez Corominas gets support from the Department of Research and Universities of the Government of Catalonia by means of an ESF-founded pre-doctoral grant of the Catalan Agency for Management of University and Research Grants (AGAUR, Catalonia, Spain), under ref. number 2022 FI_B 00903. Christian Blum was supported by two grants funded by MCIN/AEI/10.13039/501100011033: AEI, Spain PID2019-104156GB-I00, and TED2021-129319B-I00. Maria J. Blesa acknowledges support from AEI, Spain under grant PID-2020-112581GB-C21 (MOTION) and the Catalan Agency for Management of University and Research Grants (AGAUR , Catalonia, Spain), under grant 2021-SGR-01419 (ALBCOM).Peer ReviewedElsevier20232023-03-0120232023-04-27journal articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://hdl.handle.net/2117/386762https://dx.doi.org/10.1016/j.simpa.2023.100476reponame:UPCommons. Portal del coneixement obert de la UPCinstname:Universitat Politècnica de Catalunya (UPC)InglésengAgencia Estatal de Investigación http://doi.org/10.13039/501100011033 Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020 PID2020-112581GB-C21 MODELOS Y TECNICAS PARA EL PROCESAMIENTO DE INFORMACION A GRAN ESCALA -- BARCELONAopen accesshttp://purl.org/coar/access_right/c_abf2Attribution 4.0 Internationalhttp://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:upcommons.upc.edu:2117/3867622026-05-27T15:37:01Z
dc.title.none.fl_str_mv AntNetAlign: A software package for network alignment
title AntNetAlign: A software package for network alignment
spellingShingle AntNetAlign: A software package for network alignment
Rodríguez i Corominas, Guillem
Combinatorial optimization
Ant algorithms
Network alignment
Open source software
Optimization
Ant colony optimization
Optimització combinatòria
Algorismes de les colònies de formigues
Àrees temàtiques de la UPC::Informàtica::Informàtica teòrica::Algorísmica i teoria de la complexitat
Àrees temàtiques de la UPC::Informàtica::Intel·ligència artificial
title_short AntNetAlign: A software package for network alignment
title_full AntNetAlign: A software package for network alignment
title_fullStr AntNetAlign: A software package for network alignment
title_full_unstemmed AntNetAlign: A software package for network alignment
title_sort AntNetAlign: A software package for network alignment
dc.creator.none.fl_str_mv Rodríguez i Corominas, Guillem
Blesa Aguilera, Maria Josep|||0000-0001-8246-9926
Blum, Christian
author Rodríguez i Corominas, Guillem
author_facet Rodríguez i Corominas, Guillem
Blesa Aguilera, Maria Josep|||0000-0001-8246-9926
Blum, Christian
author_role author
author2 Blesa Aguilera, Maria Josep|||0000-0001-8246-9926
Blum, Christian
author2_role author
author
dc.subject.none.fl_str_mv Combinatorial optimization
Ant algorithms
Network alignment
Open source software
Optimization
Ant colony optimization
Optimització combinatòria
Algorismes de les colònies de formigues
Àrees temàtiques de la UPC::Informàtica::Informàtica teòrica::Algorísmica i teoria de la complexitat
Àrees temàtiques de la UPC::Informàtica::Intel·ligència artificial
topic Combinatorial optimization
Ant algorithms
Network alignment
Open source software
Optimization
Ant colony optimization
Optimització combinatòria
Algorismes de les colònies de formigues
Àrees temàtiques de la UPC::Informàtica::Informàtica teòrica::Algorísmica i teoria de la complexitat
Àrees temàtiques de la UPC::Informàtica::Intel·ligència artificial
description In this paper we introduce AntNetAlign, an open-source tool (written in C++) that implements an Ant Colony Optimization (ACO) for solving the Network Alignment (NA) problem, a well-known hard optimization problem with important applications in different areas, such as biology or social networks. Specifically, given two input networks, the tool finds an alignment between them (i.e., a mapping between the respective nodes) that optimizes one out of the three main topological measures. Additionally, it can make use of user-defined pairwise similarities between nodes during its construction phase, allowing for the use of more application-dependent information in order to increase its performance. Results show that AntNetAlign outperforms other state-of-the-art algorithms in two out of the three aforementioned topological scores within a reasonable amount of time, and is able to achieve competitive results in the context of larger instances (Rodríguez Corominas et al., 2023). Furthermore, a new version of the algorithm, which makes use of Negative Learning, was able to further improve these results, specially in the EC score (Corominas et al., 2022).
publishDate 2023
dc.date.none.fl_str_mv 2023
2023-03-01
2023
2023-04-27
dc.type.none.fl_str_mv journal article
http://purl.org/coar/resource_type/c_6501
VoR
http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://hdl.handle.net/2117/386762
https://dx.doi.org/10.1016/j.simpa.2023.100476
url https://hdl.handle.net/2117/386762
https://dx.doi.org/10.1016/j.simpa.2023.100476
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.relation.none.fl_str_mv Agencia Estatal de Investigación http://doi.org/10.13039/501100011033 Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020 PID2020-112581GB-C21 MODELOS Y TECNICAS PARA EL PROCESAMIENTO DE INFORMACION A GRAN ESCALA -- BARCELONA
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
Attribution 4.0 International
http://creativecommons.org/licenses/by/4.0/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
Attribution 4.0 International
http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Elsevier
publisher.none.fl_str_mv Elsevier
dc.source.none.fl_str_mv reponame:UPCommons. Portal del coneixement obert de la UPC
instname:Universitat Politècnica de Catalunya (UPC)
instname_str Universitat Politècnica de Catalunya (UPC)
reponame_str UPCommons. Portal del coneixement obert de la UPC
collection UPCommons. Portal del coneixement obert de la UPC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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