3 research outputs found
Parallel Exchange of Randomized SubGraphs for Optimization of Network Alignment: PERSONA
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
Optimierung der globalen Netzwerkausrichtung in Protein-Protein-Interaktionsnetzwerken
Global Network Alignment in Protein-Protein Interaction Networks is an NP-complete
problem due to the contradicting nature of its biological and topological alignment objectives.
There have been several aligners developed focusing on various priorities and objectives of
the problem. However, none of these alignment heuristics provide exact solutions, despite
the fact that they achieve problem objectives up to a certain extent. For this reason, the
research question of uniting stronger aspects of dissimilar Network Alignment heuristics
is quite promising. In this thesis, it is aimed to improve the methods to scan the search
space of this problem by managing the simultaneous use of several heuristics and two novel
population-based meta-heuristic methods are proposed for this purpose.
The first one of these methods (SUMONA) is a supervised genetic algorithm approach
that is an extension to the computationally demanding multi-objective memetic algorithm
called OptNetAlign. This method intends to accelerate and guide the alignment process by
modifying the crossing-over mechanism of the genetic algorithm with inputs from other
aligners/heuristics while preventing premature convergence by randomizing the usage of
these inputs. The algorithm is based on a generic procedure that generates several alignments
with changing heuristics and input parameters, classifies the generated alignments, establishes
a randomized alignment selection mechanism from the classified alignments for cross-over
and finally adjusts global and local search parameters. It is possible to achieve better running
time performance, prioritize certain objectives upon others and also optimize the secondary
objectives with this method.
The second method (PERSONA) is a particle swarm inspired collaborative approach that
orchestrates several aligners to share their partial solutions continuously while they progress.
These aligners jointly constitute a particle swarm that searches for multi-objective solutions
of the alignment problem in a reactive actor environment. Within the swarm, the leading or
prominent actors send the stronger portion of their solution as a subgraph to other actors and
receive the stronger subgraphs of the counter party back upon evaluation of those partial
solutions. The individual alignment heuristics were also developed within the scope of the
same research and they were implemented based on alternatives such as seed-and-extend
approaches with various centrality and sequence seeds, cluster mapping approach and node
similarity prioritization. Both the population-based meta-heuristic tasks and the individual
heuristic tasks were implemented in a non-deterministic fashion in order to improve flexibility
and preventing to be trapped in locally optimal solutions. The results achieved with this
method are remarkably optimized and balanced for both topological and node similarity
objectives.Die âGlobale Netzwerkausrichtungâ in Protein-Protein-Interaktionsnetzwerken ist ein NP-
vollstĂ€ndiges Problem aufgrund der widersprĂŒchlichen Natur der biologischen und topol-
ogischen Ausrichtungsziele. Es wurden bereits mehrere Aligner entwickelt, die sich auf
verschiedene PrioritÀten und Ziele des Problems konzentrieren. Keine dieser Alignment-
Heuristiken liefert jedoch exakte Lösungen, obwohl sie die Problemziele bis zu einem
gewissen Grad erreichen. Aus diesem Grund ist die Forschungsfrage, wie man stÀrkere
Aspekte von unterschiedlichen Network Alignment Heuristiken vereinen kann, sehr vielver-
sprechend. In dieser Arbeit wird das Ziel verfolgt, die Methoden zum Durchsuchen des
Suchraumes dieses Problems zu verbessern, indem die gleichzeitige Verwendung mehrerer
Heuristiken verwaltet wird, und zu diesem Zweck werden zwei neuartige populationsbasierte
meta-heuristische Methoden vorgeschlagen.
Bei der ersten dieser Methoden (SUMONA) handelt es sich um einen ĂŒberwachten genetis-
chen Algorithmus, der eine Erweiterung des rechenintensiven memetischen Multi-Zielsetzung
algorithmus OptNetAlign darstellt. Diese Methode zielt darauf ab, den Ausrichtungsprozess
zu beschleunigen und zu leiten, indem der Crossing-Over-Mechanismus des genetischen
Algorithmus mit Eingaben von anderen Alignern/Heuristiken modifiziert wird. Der Algo-
rithmus basiert auf einer generischen Prozedur, die mehrere Alignments mit wechselnden
Heuristiken und Eingabeparametern generiert, die generierten Alignments klassifiziert, einen
randomisierten Alignment-Auswahlmechanismus aus den klassifizierten Alignments fĂŒr das
Cross-over etabliert und schlieĂlich globale und lokale Suchparameter anpasst. Mit dieser
Methode ist es möglich, eine bessere Laufzeitleistung zu erzielen, bestimmte Ziele gegenĂŒber
anderen zu priorisieren und auch die sekundÀren Ziele zu optimieren.
Die zweite Methode (PERSONA) ist ein von einem Partikelschwarm inspirierter kollabora-
tiver Ansatz, der mehrere Aligner so orchestriert, dass sie ihre Teillösungen kontinuierlich
austauschen, wÀhrend sie Fortschritte machen. Diese Aligner bilden gemeinsam einen
Partikelschwarm, der in einer reaktiven Akteur-Umgebung nach multiobjectiven Lösungen
fĂŒr das Alignment-Problem sucht. Innerhalb des Schwarms senden die fĂŒhrenden oder
prominenten Akteure den stÀrkeren Teil ihrer Lösung als Teilgraphen an andere Akteure und
erhalten nach Auswertung dieser Teillösungen die stÀrkeren Teilgraphen der Gegenpartei
zurĂŒck. Die individuellen Alignment-Heuristiken wurden ebenfalls im Rahmen dersel-
ben Forschung entwickelt und auf der Grundlage von Alternativen wie Seed-and-Extend-
AnsÀtzen mit verschiedenen ZentralitÀts- und Sequenz-Seeds, Cluster-Mapping-Ansatz und
KnotenÀhnlichkeitspriorisierung implementiert. Sowohl die populationsbasierten meta-
heuristischen Aufgaben als auch die individuellen heuristischen Aufgaben wurden in einer
nicht-deterministischen Weise implementiert, um die FlexibilitÀt zu verbessern und zu verhin-
dern, dass man in lokal optimalen Lösungen gefangen ist. Die mit dieser Methode erzielten
Ergebnisse sind sowohl fĂŒr topologische als auch fĂŒr KnotenĂ€hnlichkeitsziele bemerkenswert
optimiert und ausgewogen
SUMONA: A supervised method for optimizing network alignment
14th Asia Pacific Bioinformatics Conference (APBC) -- JAN 11-13, 2016 -- San Francisco, CAWOS: 000381837000006PubMed ID: 27177812This 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 varyingparameters 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. (C) 2016 Elsevier Ltd. All rights reserved