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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
Sat Jan 01 2022
Journal Name
Journal Of The Mechanical Behavior Of Materials
Time and finance optimization model for multiple construction projects using genetic algorithm
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Abstract<p>Construction contractors usually undertake multiple construction projects simultaneously. Such a situation involves sharing different types of resources, including monetary, equipment, and manpower, which may become a major challenge in many cases. In this study, the financial aspects of working on multiple projects at a time are addressed and investigated. The study considers dealing with financial shortages by proposing a multi-project scheduling optimization model for profit maximization, while minimizing the total project duration. Optimization genetic algorithm and finance-based scheduling are used to produce feasible schedules that balance the finance of activities at any time w</p> ... Show More
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Publication Date
Sun Jul 01 2012
Journal Name
Applied Soft Computing
A new evolutionary based routing protocol for clustered heterogeneous wireless sensor networks
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Publication Date
Wed Jan 01 2025
Journal Name
Iv. International Rimar Congress Of Pure, Applied Sciences
A New Intrusion Detection Approach Based on RNA Encoding and K-Means Clustering Algorithm Using KDD-Cup99 Dataset
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Intrusion detection systems (IDS) are useful tools that help security administrators in the developing task to secure the network and alert in any possible harmful event. IDS can be classified either as misuse or anomaly, depending on the detection methodology. Where Misuse IDS can recognize the known attack based on their signatures, the main disadvantage of these systems is that they cannot detect new attacks. At the same time, the anomaly IDS depends on normal behaviour, where the main advantage of this system is its ability to discover new attacks. On the other hand, the main drawback of anomaly IDS is high false alarm rate results. Therefore, a hybrid IDS is a combination of misuse and anomaly and acts as a solution to overcome the dis

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Publication Date
Wed Dec 01 2021
Journal Name
Open Biology
Structure and in silico simulations of a cold-active esterase reveals its prime cold-adaptation mechanism
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Here we determined the structure of a cold active family IV esterase (EstN7) cloned from Bacillus cohnii strain N1. EstN7 is a dimer with a classical α/β hydrolase fold. It has an acidic surface that is thought to play a role in cold-adaption by retaining solvation under changed water solvent entropy at lower temperatures. The conformation of the functionally important cap region is significantly different to EstN7's closest relatives, forming a bridge-like structure with reduced helical content providing greater access to the active site through more than one substrate access tunnel. However, dynamics do not appear to play a major role in cold adaption. Molecular dyn

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Publication Date
Thu Feb 01 2024
Journal Name
Baghdad Science Journal
A Novel Gravity ‎Optimization Algorithm for Extractive Arabic Text Summarization
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An automatic text summarization system mimics how humans summarize by picking the most ‎significant sentences in a source text. However, the complexities of the Arabic language have become ‎challenging to obtain information quickly and effectively. The main disadvantage of the ‎traditional approaches is that they are strictly constrained (especially for the Arabic language) by the ‎accuracy of sentence feature ‎functions, weighting schemes, ‎and similarity calculations. On the other hand, the meta-heuristic search approaches have a feature tha

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Publication Date
Wed Feb 01 2023
Journal Name
Baghdad Science Journal
Study the Nuclear Structure of Some Even-Even Ca Isotopes Using the Microscopic Theory
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The root-mean square-radius of proton, neutron, matter and charge radii, energy level, inelastic longitudinal form factors, reduced transition probability from the ground state to first-excited 2+ state of even-even isotopes, quadrupole moments, quadrupole deformation parameter, and the occupation numbers for some calcium isotopes for A=42,44,46,48,50 are computed using fp-model space and FPBM interaction. 40Ca nucleus is regarded as the inert core for all isotopes under this model space with valence nucleons are moving throughout the fp-shell model space involving 1f7/2, 2p3/2, 1f5/2, and 2p1/2 orbits. Model space is used to present calculations using FPBM intera

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Publication Date
Tue Aug 01 2023
Journal Name
Baghdad Science Journal
Reducing the Mutual Coupling of Cylindrical Circular Microstrip Antennas (CCMAs) Array Using EBG Structure
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A theoretical study to design a conformal microstrip antennas was introduced in this work. Conformal microstrip antennas define antennas which can be conformed to a certain shape or to any curved surface. It is used in high-speed trains, aircraft, defense and navigation systems, landing gear and various communications systems, as well as in body wearable. Conformal antennas have some advantages such as a wider-angle coverage compared to flat antennas and low radar cross-sectional (RCS) and they are suitable for using in Radome. The main disadvantage of these antennas is the narrow bandwidth. The FDTD method is extremely useful in simulating complicated structures because it allows for direct integration of Maxwell's equations depending o

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Publication Date
Sat Jan 01 2022
Journal Name
International Middle Eastern Simulation And Modelling Conference 2022, Mesm 2022,
MECHANICS OF COMPOSITE PLATE STRUCTURE REINFORCED WITH HYBRID NANO MATERIALS USING ARTIFICIAL NEURAL NETWORK
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Publication Date
Mon Feb 04 2019
Journal Name
Iraqi Journal Of Physics
Microscopic study of nuclear structure for some Si-isotopes using Skyrme-Hartree-Fock-method
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In this paper the nuclear structure of some of Si-isotopes namely, 28,32,36,40Si have been studied by calculating the static ground state properties of these isotopes such as charge, proton, neutron and mass densities together with their associated rms radii, neutron skin thicknesses, binding energies, and charge form factors. In performing these investigations, the Skyrme-Hartree-Fock method has been used with different parameterizations; SkM*, S1, S3, SkM, and SkX. The effects of these different parameterizations on the above mentioned properties of the selected isotopes have also been studied so as to specify which of these parameterizations achieves the best agreement between calculated and experimental data. It can be ded

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Publication Date
Sun Feb 10 2019
Journal Name
Iraqi Journal Of Physics
Nuclear structure study of some tin isotopes using the self-consistent mean field method
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Hartree-Fock calculations for even-even Tin isotopes using
Skyrme density dependent effective nucleon-nucleon interaction are
discussed systematically. Skyrme interaction and the general formula
for the mean energy of a spherical nucleus are described. The charge
and matter densities with their corresponding rms radii and the
nuclear skin for Sn isotopes are studied and compared with the
experimental data. The potential energy curves obtained with
inclusion of the pairing force between the like nucleons in Hartree-
Fock-Bogoliubov approach are also discussed.

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