Repository: Freie Universit├Ąt Berlin, Math Department

Parallel Exchange of Randomized SubGraphs for Optimization of Network Alignment: PERSONA

Tuncay, E. G. and Erdur, R. C. and Conrad, T. O. F. (2022) Parallel Exchange of Randomized SubGraphs for Optimization of Network Alignment: PERSONA. IEEE Transactions on Computational Biology and Bioinformatics . ISSN 1557-9964 (In Press)

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Official URL: https://doi.ieeecomputersociety.org/10.1109/TCBB.2...

Abstract

The aim of Network Alignment in Protein-Protein Interaction Networks is discovering functionally similar regions between compared organisms. One major compromise for solving a network alignment problem is the trade-off among multiple similarity objectives while applying an alignment strategy. An alignment may lose its biological relevance while favoring certain objectives upon others due to the actual relevance of unfavored objectives. One possible solution for solving this issue may be blending the stronger aspects of various alignment strategies until achieving mature solutions. This study proposes a parallel approach called PERSONA that allows aligners to share their partial solutions continuously while they progress. All these aligners pursue their particular heuristics as part of a particle swarm that searches for multi-objective solutions of the same alignment problem in a reactive actor environment. The actors use the stronger portion of a solution as a subgraph that they receive from leading or other actors and send their own stronger subgraphs back upon evaluation of those partial solutions. Moreover, the individual heuristics of each actor takes randomized parameter values at each cycle of parallel execution so that the problem search space can thoroughly be investigated. The results achieved with PERSONA are remarkably optimized and balanced for both topological and node similarity objectives.

Item Type:Article
Subjects:Mathematical and Computer Sciences
Divisions:Department of Mathematics and Computer Science > Institute of Mathematics
Department of Mathematics and Computer Science > Institute of Mathematics > Comp. Proteomics Group
ID Code:2454
Deposited By: Admin Administrator
Deposited On:20 Aug 2020 18:52
Last Modified:15 Feb 2023 10:17

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