Paper Info
Title
SUMONA: A supervised method for optimizing network alignment.
Abstract
This study focuses on improving the multi-objective memetic algorithm for protein-protein interaction (PPI) network alignment, Optimizing Network Aligner - OptNetAlign, via integration with other existing network alignment methods such as SPINAL, NETAL and HubAlign. The output of this algorithm is an elite set of aligned networks all of which are optimal with respect to multiple user-defined criteria. However, OptNetAlign is an unsupervised genetic algorithm that initiates its search with completely random solutions and it requires substantial running times to generate an elite set of solutions that have high scores with respect to the given criteria. In order to improve running time, the search space of the algorithm can be narrowed down by focusing on remarkably qualified alignments and trying to optimize the most desired criteria on a more limited set of solutions. The method presented in this study improves OptNetAlign in a supervised fashion by utilizing the alignment results of different network alignment algorithms with varying parameters that depend upon user preferences. Therefore, the user can prioritize certain objectives upon others and achieve better running time performance while optimizing the secondary objectives.
Year
DOI
Venue
2016
10.1016/j.compbiolchem.2016.03.003
Computational Biology and Chemistry
Keywords
Field
DocType
Network alignment,Genetic algorithms,Supervised optimization
Sequence alignment,Memetic algorithm,Data mining,Computer science,Network alignment,Artificial intelligence,Machine learning,Genetic algorithm
Journal
Volume
ISSN
Citations 
63
1476-9271
1
PageRank 
References 
Authors
0.35
0
2
Name
Order
Citations
PageRank
Erhun Giray Tuncay110.35
Tolga Can226816.39