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Improving the Reliability of Evolutionary Algorithm for Complex Detection in Noisy Protein-Protein Interaction Networks
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Evolutionary algorithms are better than heuristic algorithms at finding protein complexes in protein-protein interaction networks (PPINs). Many of these algorithms depend on their standard frameworks, which are based on topology. Further, many of these algorithms have been exclusively examined on networks with only reliable interaction data. The main objective of this paper is to extend the design of the canonical and topological-based evolutionary algorithms suggested in the literature to cope with noisy PPINs. The design of the evolutionary algorithm is extended based on the functional domain of the proteins rather than on the topological domain of the PPIN. The gene ontology annotation in each molecular function, biological process, and cellular component is used to get the functional domain. The reliability of the proposed algorithm is examined against the algorithms proposed in the literature. To this end, a yeast protein-protein interaction dataset is used in the assessment of the final quality of the algorithms. To make fake negative controls of PPIs that are wrongly informed and are linked to the high-throughput interaction data, different noisy PPINs are created. The noisy PPINs are synthesized with a different and increasing percentage of misinformed PPIs. The results confirm the effectiveness of the extended evolutionary algorithm design to utilize the biological knowledge of the gene ontology. Feeding EA design with GO annotation data improves reliability and produces more accurate detection results than the counterpart algorithms.

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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
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
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
Tue Jan 30 2024
Journal Name
Iraqi Journal Of Science
Parallel Particle Swarm Optimization Algorithm for Identifying Complex Communities in Biological Networks
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    Identification of complex communities in biological networks is a critical and ongoing challenge since lots of network-related problems correspond to the subgraph isomorphism problem known in the literature as NP-hard. Several optimization algorithms have been dedicated and applied to solve this problem. The main challenge regarding the application of optimization algorithms, specifically to handle large-scale complex networks, is their relatively long execution time. Thus, this paper proposes a parallel extension of the PSO algorithm to detect communities in complex biological networks. The main contribution of this study is summarized in three- fold; Firstly, a modified PSO algorithm with a local search operator is proposed

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Publication Date
Tue Oct 01 2019
Journal Name
2019 International Conference On Electrical Engineering And Computer Science (icecos)
An Evolutionary Algorithm for Community Detection Using an Improved Mutation Operator
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Publication Date
Wed Jan 01 2020
Journal Name
International Journal Of Computational Intelligence Systems
Evolutionary Feature Optimization for Plant Leaf Disease Detection by Deep Neural Networks
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Publication Date
Sat Aug 25 2012
Journal Name
Wireless Personal Communications
Multi-Objective Evolutionary Algorithm Based on Decomposition for Energy Efficient Coverage in Wireless Sensor Networks
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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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Publication Date
Wed Dec 14 2016
Journal Name
Journal Of Baghdad College Of Dentistry
Detection of Granulocyte Chemotactic Protein 2 in Serum of Periodontitis Patients
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Background: Chronic periodontitis defined as “an infectious inflammatory disease within supporting tissues of the teeth, progressive attachment loss and bone loss". Aggressive periodontitis is rare which in most cases manifest themselves clinically during youth. It characterized by rapid rate of disease progression .Pro-inflammatory chemokines organized inflammatory responses. Granulocyte chemotactic protein 2 is involved in neutrophil gathering and movement. The purpose of the study is to detect serum of Granulocyte Chemotactic Protein 2 and correlate to periodontal condition in patients with chronic periodontitis, Aggressive periodontitis and Healthy Control subjects and measurement the count of neutrophils for the studied groups. S

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Publication Date
Wed May 17 2017
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
Comparative Study of Fucose, Protein, Protein Bound Fucose and Protein Bound Hexose in Sera of Hyperprolactinemia Human Female and Healthy Female
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This study was conducted in the specialized center of endocrinology and diabetic (AlKindy hospital from June 2004 to April 2005). Sera of 80 women (include 40 diagnosed Hyperprolactinemia (HPro) and 40 healthy women as control) were used to estimate some biochemical parameters which include prolactin (PRL),total fucose (TF), total protein (TP) and protein bound fucose (PBF), and protein bound hexose (PBHex),  also TP TF , TP PBF and TP PBHex   ratios. A significant elevation in TP and  PBHex, in sera of HPro patients compared to control was found while PBHex/TP ratio showed a slight non significant increase in sera of patients compared to control. On the other hand a significant decrease in TF, TF/TP and PBF/TP in ser

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