AntNetAlign: Ant colony optimization for network alignment
| Autor: | Guillem Rodríguez Corominas, Maria J. Blesa, Christian Blum |
|---|---|
| Přispěvatelé: | Universitat Politècnica de Catalunya. Departament de Ciències de la Computació, Universitat Politècnica de Catalunya. ALBCOM - Algorísmia, Bioinformàtica, Complexitat i Mètodes Formals, Ministerio de Ciencia e Innovación (España), Agència de Gestió d'Ajuts Universitaris i de Recerca, Blum, Christian [0000-0002-1736-3559], Blum, Christian |
| Jazyk: | angličtina |
| Rok vydání: | 2023 |
| Předmět: | |
| Zdroj: | Digital.CSIC. Repositorio Institucional del CSIC instname |
| Popis: | Network Alignment (NA) is a hard optimization problem with important applications such as, for example, the identification of orthologous relationships between different proteins and of phylogenetic relationships between species. Given two (or more) networks, the goal is to find an alignment between them, that is, a mapping between their respective nodes such that the topological and functional structure is well preserved. Although the problem has received great interest in recent years, there is still a need to unify the different trends that have emerged from diverse research areas. In this paper, we introduce AntNetAlign, an Ant Colony Optimization (ACO) approach for solving the problem. The proposed approach makes use of similarity information extracted from the input networks to guide the construction process. Combined with an improvement measure that depends on the current construction state, it is able to optimize any of the three main topological quality measures. We provide an extensive experimental evaluation using real-world Protein-Protein Interaction (PPI) networks. Results show that our method outperforms other state-of-the-art approaches in two out of three of the tested scores within a reasonable amount of time, specially in the important S3score. Moreover, it is able to obtain near-optimal results when aligning networks with themselves. Christian Blum and Guillem Rodríguez Corominas were funded by project CI-SUSTAIN of the Spanish Ministry of Science and Innovation (PID2019-104156GB-I00). Maria J. Blesa acknowledges support from AEI under grant PID-2020-112581GB-C21 (MOTION) and the Catalan Agency for Management of University and Research Grants (AGAUR) under grant 2017-SGR-786 (ALBCOM). |
| Databáze: | OpenAIRE |
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