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Biological versus Topological Domains in Improving the Reliability of Evolutionary-Based Protein Complex Detection Algorithms
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     By definition, the detection of protein complexes that form protein-protein interaction networks (PPINs) is an NP-hard problem. Evolutionary algorithms (EAs), as global search methods, are proven in the literature to be more successful than greedy methods in detecting protein complexes. However, the design of most of these EA-based approaches relies on the topological information of the proteins in the PPIN. Biological information, as a key resource for molecular profiles, on the other hand, acquired a little interest in the design of the components in these EA-based methods. The main aim of this paper is to redesign two operators in the EA based on the functional domain rather than the graph topological domain. The perturbation mechanism of both crossover and mutation operators is designed based on the direct gene ontology annotations and Jaccard similarity coefficients for the proteins. The results on yeast Saccharomyces cerevisiae PPIN provide a useful perspective that the functional domain of the proteins, as compared with the topological domain, is more consistent with the true information reported in the Munich Information Center for Protein Sequence (MIPS) catalog. The evaluation at both complex and protein levels reveals that feeding the components of the EA with biological information will imply more accurate complex structures, whereas topological information may mislead the algorithm towards a faulty structure.

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Publication Date
Sat Dec 01 2018
Journal Name
Journal Of Theoretical And Applied Information Technology
Matching Algorithms for Intrusion Detection System based on DNA Encoding
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Pattern matching algorithms are usually used as detecting process in intrusion detection system. The efficiency of these algorithms is affected by the performance of the intrusion detection system which reflects the requirement of a new investigation in this field. Four matching algorithms and a combined of two algorithms, for intrusion detection system based on new DNA encoding, are applied for evaluation of their achievements. These algorithms are Brute-force algorithm, Boyer-Moore algorithm, Horspool algorithm, Knuth-Morris-Pratt algorithm, and the combined of Boyer-Moore algorithm and Knuth–Morris– Pratt algorithm. The performance of the proposed approach is calculated based on the executed time, where these algorithms are applied o

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Publication Date
Fri Feb 01 2019
Journal Name
Iraqi Journal Of Information & Communications Technology
Evaluation of DDoS attacks Detection in a New Intrusion Dataset Based on Classification Algorithms
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Intrusion detection system is an imperative role in increasing security and decreasing the harm of the computer security system and information system when using of network. It observes different events in a network or system to decide occurring an intrusion or not and it is used to make strategic decision, security purposes and analyzing directions. This paper describes host based intrusion detection system architecture for DDoS attack, which intelligently detects the intrusion periodically and dynamically by evaluating the intruder group respective to the present node with its neighbors. We analyze a dependable dataset named CICIDS 2017 that contains benign and DDoS attack network flows, which meets certifiable criteria and is ope

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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
Sun Aug 31 2025
Journal Name
International Journal Of Intelligent Engineering And Systems
Enhanced Evolutionary Algorithm for Dynamic Community Detection Using a Vulnerable Node Reassignment-based Mutation
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Recently, detecting dynamic patterns for growing communities in social networks have attracted significant attention. The objective of dynamic community detection is to analyze and identify clusters in complex networks that change over time. Different optimization algorithms, including both single-objective and multi-objective approaches, have been employed to address the challenge of dynamic community detection. Although current evolutionary algorithms for identifying community structure can traverse extensive areas of partition space, they often become stuck in local minima. In addition, limited studies have addressed this issue by integrating local search strategies with evolutionary algorithms for community identification. This paper in

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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 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
Fri Sep 30 2022
Journal Name
Industrial Engineering & Management Systems
Optimizing the Complex Systems Reliability Using Mixed Strategy in Ultra-fast Gas Turbine Protection System
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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
Mon Sep 30 2024
Journal Name
Iraqi Journal Of Science
Overlapping Structure Detection in Protein-Protein Interaction Networks Using a Modified Version of Particle Swarm Optimization
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In today's world, the science of bioinformatics is developing rapidly, especially with regard to the analysis and study of biological networks. Scientists have used various nature-inspired algorithms to find protein complexes in protein-protein interaction (PPI) networks. These networks help scientists guess the molecular function of unknown proteins and show how cells work regularly. It is very common in PPI networks for a protein to participate in multiple functions and belong to many complexes, and as a result, complexes may overlap in the PPI networks. However, developing an efficient and reliable method to address the problem of detecting overlapping protein complexes remains a challenge since it is considered a complex and har

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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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