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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 hard optimization problem. One of the main difficulties in identifying overlapping protein complexes is the accuracy of the partitioning results. In order to accurately identify the overlapping structure of protein complexes, this paper has proposed an overlapping complex detection algorithm termed OCDPSO-Net, which is based on PSO-Net (a well-known modified version of the particle swarm optimization algorithm). The framework of the OCDPSO-Net method consists of three main steps, including an initialization strategy, a movement strategy for each particle, and enhancing search ability in order to expand the solution space. The proposed algorithm has employed the partition density concept for measuring the partitioning quality in PPI network complexes and tried to optimize the value of this quantity by applying the line graph concept of the original graph representing the protein interaction network. The OCDPSO-Net algorithm is applied to a Collins PPI network and the obtained results are compared with different state-of-the-art algorithms in terms of precision ( ), recall ( ), and F-measure ( ). Experimental results confirm that the proposed algorithm has good clustering performance and has outperformed most of the existing recent overlapping algorithms. .

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Publication Date
Tue May 07 2024
Journal Name
Heliyon
Micro-shear bond strength of a novel resin-modified glass ionomer luting cement (eRMGIC) functionalized with organophosphorus monomer to different dental substrates
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Objectives: This study aims to assess and compare the micro-shear bond strength (μSBS) of a novel resin-modified glass-ionomer luting cement functionalized with a methacrylate co-monomer containing a phosphoric acid group, 30 wt% 2-(methacryloxy) ethyl phosphate (2-MEP), with different substrates (dentin, enamel, zirconia, and base metal alloy). This assessment is conducted in comparison with conventional resin-modified glass ionomer cement and self-adhesive resin cement. Materials and methods: In this in vitro study, ninety-six specimens were prepared and categorized into four groups: enamel (A), dentin (B), zirconia (C), and base metal alloys (D). Enamel (E) and dentin (D) specimens were obtained from 30 human maxillary first premolars e

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Publication Date
Thu Sep 26 2019
Journal Name
Processes
Fine-Tuning Meta-Heuristic Algorithm for Global Optimization
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This paper proposes a novel meta-heuristic optimization algorithm called the fine-tuning meta-heuristic algorithm (FTMA) for solving global optimization problems. In this algorithm, the solutions are fine-tuned using the fundamental steps in meta-heuristic optimization, namely, exploration, exploitation, and randomization, in such a way that if one step improves the solution, then it is unnecessary to execute the remaining steps. The performance of the proposed FTMA has been compared with that of five other optimization algorithms over ten benchmark test functions. Nine of them are well-known and already exist in the literature, while the tenth one is proposed by the authors and introduced in this article. One test trial was shown t

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Publication Date
Thu Mar 23 2023
Journal Name
Journal Of Applied Science And Engineering
Strong Fenchel Duality for Evenly Convex Optimization Problems
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Among a variety of approaches introduced in the literature to establish duality theory, Fenchel duality was of great importance in convex analysis and optimization. In this paper we establish some conditions to obtain classical strong Fenchel duality for evenly convex optimization problems defined in infinite dimensional spaces. The objective function of the primal problem is a family of (possible) infinite even convex functions. The strong duality conditions we present are based on the consideration of the epigraphs of the c-conjugate of the dual objective functions and the ε-c-subdifferential of the primal objective functions.

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Publication Date
Wed Sep 01 2021
Journal Name
Baghdad Science Journal
Optimum Median Filter Based on Crow Optimization Algorithm
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          A novel median filter based on crow optimization algorithms (OMF) is suggested to reduce the random salt and pepper noise and improve the quality of the RGB-colored and gray images. The fundamental idea of the approach is that first, the crow optimization algorithm detects noise pixels, and that replacing them with an optimum median value depending on a criterion of maximization fitness function. Finally, the standard measure peak signal-to-noise ratio (PSNR), Structural Similarity, absolute square error and mean square error have been used to test the performance of suggested filters (original and improved median filter) used to removed noise from images. It achieves the simulation based on MATLAB R2019b and the resul

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Publication Date
Sun Oct 29 2023
Journal Name
Journal Of Al-qadisiyah For Computer Science And Mathematics
Optimization Techniques for Human Multi-Biometric Recognition System
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Researchers are increasingly using multimodal biometrics to strengthen the security of biometric applications. In this study, a strong multimodal human identification model was developed to address the growing problem of spoofing attacks in biometric security systems. Through the use of metaheuristic optimization methods, such as the Genetic Algorithm(GA), Ant Colony Optimization(ACO), and Particle Swarm Optimization (PSO) for feature selection, this unique model incorporates three biometric modalities: face, iris, and fingerprint. Image pre-processing, feature extraction, critical image feature selection, and multibiometric recognition are the four main steps in the workflow of the system. To determine its performance, the model wa

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Publication Date
Mon Aug 01 2022
Journal Name
Bulletin Of Electrical Engineering And Informatics
Solid waste recycling and management cost optimization algorithm
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Solid waste is a major issue in today's world. Which can be a contributing factor to pollution and the spread of vector-borne diseases. Because of its complicated nonlinear processes, this problem is difficult to model and optimize using traditional methods. In this study, a mathematical model was developed to optimize the cost of solid waste recycling and management. In the optimization phase, the salp swarm algorithm (SSA) is utilized to determine the level of discarded solid waste and reclaimed solid waste. An optimization technique SSA is a new method of finding the ideal solution for a mathematical relationship based on leaders and followers. It takes a lot of random solutions, as well as their outward or inward fluctuations, t

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Publication Date
Thu Jun 16 2022
Journal Name
Periodicals Of Engineering And Natural Sciences (pen)
Optimization algorithms for transportation problems with stochastic demand
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The purpose of this paper is to solve the stochastic demand for the unbalanced transport problem using heuristic algorithms to obtain the optimum solution, by minimizing the costs of transporting the gasoline product for the Oil Products Distribution Company of the Iraqi Ministry of Oil. The most important conclusions that were reached are the results prove the possibility of solving the random transportation problem when the demand is uncertain by the stochastic programming model. The most obvious finding to emerge from this work is that the genetic algorithm was able to address the problems of unbalanced transport, And the possibility of applying the model approved by the oil products distribution company in the Iraqi Ministry of Oil to m

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Publication Date
Tue Dec 01 2009
Journal Name
Iraqi Journal Of Physics
Crystal Growth of High – Purity Bi2Se3 and Study of Crystal Structure
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The Bi2Se3 compound was synthesis by fusing initial compounds consisting of
extra pure elements in stoichiometric ratio from elements compound, charged inside
quartz ampoule. The crystal growth of Bi2Se3 carried out using Brighaman technique
process from melting f (Bi+Se ) at temperature of 810 ºC for about 48 hrs. Single crystal
of Bi2Se3 has been grown in direction (211) after slow cooling on account of heat
gradient to zone furnaces at cooling rate (1-3) C/hr. The structure study of the compound
was determined by x-ray diffraction technique, which it has bismuthinite structure and
orthorhombic unit cell with lattice parameters of a=10.2678 Å, b=11.2392 Å and
c=5.1737 Å

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Publication Date
Sat Dec 01 2012
Journal Name
Iraqi Journal Of Physics
Study of the electronic structure of indium gallium phosphide In0.5Ga0.5P nanocrystals
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The electronic structure of zinc blend indium gallium phosphide In0.5Ga0.5P nanocrystals which have dimension (2-2.8 nm) is investigated using the density functional theory coupled with large unit cell (LUC) for the different size core (8 ,16,54,64) atoms respectively. The investigated properties include total energy, energy gap, conduction band, valence band, cohesive energy, ionicity and density of state etc. as a function of core size and lattice constant. Results show the shape effect of increasing the core size and lattice constant on these electronic properties

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Publication Date
Sat Aug 01 2020
Journal Name
Iop Conference Series: Materials Science And Engineering
Probability Concepts of Transfer Load to the Foundation of Container Structure
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This paper presents stochastic analysis using the perturbation method to model the structure of a container to verify the distributions of probability of maximum and minimum axial forces reactions in piles. The proposed simulation of a container port terminal under 11 scenarios of load combinations was presented. The probability distributions for live loads are assigned according to the input parameters of simulation data. Part of the load itself is implicitly combined such as vertical live load which includes the weight of equipment and containers and wind load. The structural model was simulated in the software STAAD Pro., while the statistical analyses were performed with MATLAB. The results demonstrated that, the most significant extern

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