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An Evolutionary Algorithm for Improving the Quantity and Quality of the Detected Complexes from Protein Interaction Networks
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One of the recent significant but challenging research studies in computational biology and bioinformatics is to unveil protein complexes from protein-protein interaction networks (PPINs). However, the development of a reliable algorithm to detect more complexes with high quality is still ongoing in many studies. The main contribution of this paper is to improve the effectiveness of the well-known modularity density ( ) model when used as a single objective optimization function in the framework of the canonical evolutionary algorithm (EA). To this end, the design of the EA is modified with a gene ontology-based mutation operator, where the aim is to make a positive collaboration between the modularity density model and the proposed gene ontology-based mutation operator. The performance of the proposed EA to have a high quantity and quality of the detected complexes is assessed on two yeast PPINs and compared with two benchmarking gold complex sets. The reported results reveal the ability of modularity density to be more productive in detecting more complexes with high quality when teamed up with a gene ontology-based mutation operator.

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Publication Date
Mon Jan 01 2024
Journal Name
Ieee Access
An Evolutionary Algorithm With Heuristic Operator for Detecting Protein Complexes in Protein Interaction Networks With Negative Controls
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Publication Date
Thu Dec 05 2019
Journal Name
Advances In Intelligent Systems And Computing
An Enhanced Evolutionary Algorithm for Detecting Complexes in Protein Interaction Networks with Heuristic Biological Operator
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Publication Date
Sat Dec 01 2018
Journal Name
Applied Soft Computing
A new evolutionary algorithm with locally assisted heuristic for complex detection in protein interaction networks
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Publication Date
Sun Apr 30 2023
Journal Name
Iraqi Journal Of Science
An Evolutionary Algorithm with Gene Ontology-Aware Crossover Operator for Protein Complex Detection
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     Evolutionary algorithms (EAs), as global search methods, are proved to be more robust than their counterpart local heuristics for detecting protein complexes in protein-protein interaction (PPI) networks. Typically, the source of robustness of these EAs comes from their components and parameters. These components are solution representation, selection, crossover, and mutation. Unfortunately, almost all EA based complex detection methods suggested in the literature were designed with only canonical or traditional components. Further, topological structure of the protein network is the main information that is used in the design of almost all such components. The main contribution of this paper is to formulate a more robust E

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Publication Date
Thu Oct 31 2019
Journal Name
Journal Of Theoretical And Applied Information Technology
AN ENHANCED EVOLUTIONARY ALGORITHM WITH LOCAL HEURISTIC APPROACH FOR DETECTING COMMUNITY IN COMPLEX NETWORKS
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Publication Date
Sun Mar 01 2020
Journal Name
Computer Networks
An improved multi-objective evolutionary algorithm for detecting communities in complex networks with graphlet measure
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Publication Date
Sun Dec 01 2019
Journal Name
Applied Soft Computing
A new evolutionary multi-objective community mining algorithm for signed networks
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Publication Date
Mon Feb 01 2016
Journal Name
Swarm And Evolutionary Computation
Improving the performance of evolutionary multi-objective co-clustering models for community detection in complex social networks
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Publication Date
Thu Jul 01 2021
Journal Name
Journal Of Physics: Conference Series
An Evolutionary Algorithm for Task scheduling Problem in the Cloud-Fog environment
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Abstract<p>The rapid and enormous growth of the Internet of Things, as well as its widespread adoption, has resulted in the production of massive quantities of data that must be processed and sent to the cloud, but the delay in processing the data and the time it takes to send it to the cloud has resulted in the emergence of fog, a new generation of cloud in which the fog serves as an extension of cloud services at the edge of the network, reducing latency and traffic. The distribution of computational resources to minimize makespan and running costs is one of the disadvantages of fog computing. This paper provides a new approach for improving the task scheduling problem in a Cloud-Fog environme</p> ... Show More
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Publication Date
Thu Feb 09 2023
Journal Name
Artificial Intelligence Review
Community detection model for dynamic networks based on hidden Markov model and evolutionary algorithm
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Finding communities of connected individuals in complex networks is challenging, yet crucial for understanding different real-world societies and their interactions. Recently attention has turned to discover the dynamics of such communities. However, detecting accurate community structures that evolve over time adds additional challenges. Almost all the state-of-the-art algorithms are designed based on seemingly the same principle while treating the problem as a coupled optimization model to simultaneously identify community structures and their evolution over time. Unlike all these studies, the current work aims to individually consider this three measures, i.e. intra-community score, inter-community score, and evolution of community over

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