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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 EA with more biological consistency. For this purpose, a new crossover operator is suggested where biological information in terms of both gene semantic similarity and protein functional similarity is fed into its design. To reflect the heuristic roles of both semantic and functional similarities, this paper introduces two gene ontology (GO) aware crossover operators. These are direct annotation-aware and inherited annotation-aware crossover operators. The first strategy is handled with the direct gene ontology annotation of the proteins, while the second strategy is handled with the directed acyclic graph (DAG) of each gene ontology term in the gene product. To conduct our experiments, the proposed EAs with GO-aware crossover operators are compared against the state-of-the-art heuristic, canonical EAs with the traditional crossover operator, and GO-based EAs. Simulation results are evaluated in terms of recall, precision, and F measure at both complex level and protein level. The results prove that the new EA design encourages a more reliable treatment of exploration and exploitation and, thus, improves the detection ability for more accurate protein complex structures.

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Publication Date
Fri Apr 01 2022
Journal Name
Baghdad Science Journal
An Evolutionary Algorithm for Solving Academic Courses Timetable Scheduling Problem
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Scheduling Timetables for courses in the big departments in the universities is a very hard problem and is often be solved by many previous works although results are partially optimal. This work implements the principle of an evolutionary algorithm by using genetic theories to solve the timetabling problem to get a random and full optimal timetable with the ability to generate a multi-solution timetable for each stage in the collage. The major idea is to generate course timetables automatically while discovering the area of constraints to get an optimal and flexible schedule with no redundancy through the change of a viable course timetable. The main contribution in this work is indicated by increasing the flexibility of generating opti

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Publication Date
Wed Aug 30 2023
Journal Name
Iraqi Journal Of Science
Community Detection in Modular Complex Networks Using an Improved Particle Swarm Optimization Algorithm
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     Community detection is an important and interesting topic for better understanding and analyzing complex network structures. Detecting hidden partitions in complex networks is proven to be an NP-hard problem that may not be accurately resolved using traditional methods. So it is solved using evolutionary computation methods and modeled in the literature as an optimization problem.  In recent years, many researchers have directed their research efforts toward addressing the problem of community structure detection by developing different algorithms and making use of single-objective optimization methods. In this study, we have continued that research line by improving the Particle Swarm Optimization (PSO) algorithm using a

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Publication Date
Wed Aug 30 2023
Journal Name
Iraqi Journal Of Science
Community Detection in Modular Complex Networks Using an Improved Particle Swarm Optimization Algorithm
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     Community detection is an important and interesting topic for better understanding and analyzing complex network structures. Detecting hidden partitions in complex networks is proven to be an NP-hard problem that may not be accurately resolved using traditional methods. So it is solved using evolutionary computation methods and modeled in the literature as an optimization problem.  In recent years, many researchers have directed their research efforts toward addressing the problem of community structure detection by developing different algorithms and making use of single-objective optimization methods. In this study, we have continued that research line by improving the Particle Swarm Optimization (PSO) algorithm using a local

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Publication Date
Mon Oct 30 2023
Journal Name
Iraqi Journal Of Science
An Evolutionary-Based Mutation With Functional Annotation to Identify Protein Complexes Within PPI Networks
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     The research deals with an evolutionary-based mutation with functional annotation to identify protein complexes within PPI networks. An important field of research in computational biology is the difficult and fundamental challenge of revealing complexes in protein interaction networks. The complex detection models that have been developed to tackle challenges are mostly dependent on topological properties and rarely use the biological  properties of PPI networks. This research aims to push the evolutionary algorithm to its maximum by employing gene ontology (GO) to communicate across proteins based on biological information similarity for direct genes. The outcomes show that the suggested method can be utilized to improve the

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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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Publication Date
Thu Dec 01 2011
Journal Name
Swarm And Evolutionary Computation
Energy-aware evolutionary routing protocol for dynamic clustering of wireless sensor 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
Mon Aug 26 2019
Journal Name
Iraqi Journal Of Science
Heuristic Modularity for Complex Identification in Protein-Protein Interaction Networks
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     Due to the significant role in understanding cellular processes, the decomposition of Protein-Protein Interaction (PPI) networks into essential building blocks, or complexes, has received much attention for functional bioinformatics research in recent years. One of the well-known bi-clustering descriptors for identifying communities and complexes in complex networks, such as PPI networks, is modularity function.   The contribution of this paper is to introduce heuristic optimization models that can collaborate with the modularity function to improve its detection ability. The definitions of the formulated heuristics are based on nodes and different levels of their neighbor properties.  The modulari

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Publication Date
Wed Nov 17 2021
Journal Name
Periodicals Of Engineering And Natural Sciences (pen)
Pearson coefficient matrix for studying the correlation of community detection scores in multi-objective evolutionary algorithm
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