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Topology-Based Modularity and Modularity Density for Detecting Protein Complexes: A Comparative Study

     Binary relations or interactions among bio-entities, such as proteins, set up the essential part of any living biological system. Protein-protein interactions are usually structured in a graph data structure called "protein-protein interaction networks" (PPINs). Analysis of PPINs into complexes tries to lay out the significant knowledge needed to answer many unresolved questions, including how cells are organized and how proteins work. However, complex detection problems fall under the category of non-deterministic polynomial-time hard (NP-Hard) problems due to their computational complexity. To accommodate such combinatorial explosions, evolutionary algorithms (EAs) are proven effective alternatives to heuristics in solving NP-hard problems. The main aim of this study is to make a close examination of the performance of the EAs where modularity and modularity density are selected as two different objective functions. Topology-based modularity and topology-based modularity density are designed to examine the detection ability of the EAs and to compare their performance. To conduct the experiments, two yeast Saccharomyces cerevisiae PPINs are used and evaluated under nine evaluation metrics. The results reveal the potential impact of the topology-based modularity density to outperform the counterpart modularity functions in almost all evaluation metrics. 

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Publication Date
Mon Feb 28 2022
Journal Name
International Journal Of Interactive Mobile Technologies (ijim)
Flying Ad hoc Networks (FANET): Performance Evaluation of Topology Based Routing Protocols

Flying Ad hoc Networks (FANETs) has developed as an innovative technology for access places without permanent infrastructure. This emerging form of networking is construct of flying nodes known as unmanned aerial vehicles (UAVs) that fly at a fast rate of speed, causing frequent changes in the network topology and connection failures. As a result, there is no dedicated FANET routing protocol that enables effective communication between these devices. The purpose of this paper is to evaluate the performance of the category of topology-based routing protocols in the FANET. In a surveillance system involving video traffic, four routing protocols with varying routing mechanisms were examined. Additionally, simulation experiments conduct

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Publication Date
Fri Feb 04 2022
Journal Name
Iraqi Journal Of Science
AHeuristic Strategy for Improving the Performance of Evolutionary Based Complex Detection in Protein-Protein Interaction Networks

One of the most interested problems that recently attracts many research investigations in Protein-protein interactions (PPI) networks is complex detection problem. Detecting natural divisions in such complex networks is proved to be extremely NP-hard problem wherein, recently, the field of Evolutionary Algorithms (EAs) reveals positive results. The contribution of this work is to introduce a heuristic operator, called protein-complex attraction and repulsion, which is especially tailored for the complex detection problem and to enable the EA to improve its detection ability. The proposed heuristic operator is designed to fine-grain the structure of a complex by dividing it into two more complexes, each being distinguished with a core pr

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Publication Date
Sat Jan 30 2021
Journal Name
Iraqi Journal Of Science
Signal Soft Sets for Atoms Modeling and Signal Soft Topology

In this paper we define a signal soft set as a mathematical tool to represent and study atoms, anti-atoms, electrons, anti-electrons, protons, and anti-protons, and generate a signal soft topology, with an example of signal soft topology on H2O.

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Publication Date
Sun Jun 07 2015
Journal Name
Baghdad Science Journal
A comparative study to determine the nature of the eye lens protein in the two types of birds Iraqi

The study showed significant differences between the average weight lens and the average amount protein in the lens between that Kestrel Falco tinnunculus L. and the Collared Dove Streptopelia decaocto F. , also the study electrical migration of lens proteins having one bundle of crystalline –? in Kestrel compared with three bundles in Collared Dove, two bundles of crystalline – ? in both , and crystalline – ? appeared as one bundle in both birds.

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Publication Date
Sat Dec 24 2022
Journal Name
Journal Of Legal Sciences
Legal System for Electoral Campaigns : A Comparative Study

Electoral campaigns are one of the stages of the electoral process, and it means the sum of the activities and activities carried out by the candidate or the political party within a period of time, usually one day or more before the polling date, according to the legislation. To vote for this candidate or party, and this process affects the results of the elections, whether parliamentary or presidential, because it targets the votes that lead the candidate or political party to a boost to the presidency of the state or the legislative authority, so that this right is not abused in promoting political ideas and visions, considering This is one of the branches of freedom of opinion and expression that is guaranteed by most constitutions.

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Publication Date
Mon Dec 25 2023
Journal Name
Journal Of Legal Sciences
Provisions for annulment in a reconciliation contract : A Comparative Study

First of all, The annulment raises scientific and practical problems that reflect its peculiarity, as it relates to how the judge faces the dispute in a case in which reconciliation between the litigants took place, and what can be attributed to the judge’s judgment in this regard, whether that estimate is related to the factual elements in the case or the objective elements and their approach With the circumstances surrounding the dispute, and considering the possibility of applying the provisions of annulment established in the general rules, which is not easy in all cases due to the special nature of annulment in the conciliation contract, it is necessary to clarify the role that the judge plays, and his use of his legal tools that

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Publication Date
Thu May 30 2024
Journal Name
Iraqi Journal Of Science
An Evolutionary Algorithm for Improving the Quantity and Quality of the Detected Complexes from Protein Interaction Networks

One of the recent significant but challenging research studies in computational biology and bioinformatics is to unveil protein complexes from protein-protein interaction networks (PPINs). However, the development of a reliable algorithm to detect more complexes with high quality is still ongoing in many studies. The main contribution of this paper is to improve the effectiveness of the well-known modularity density ( ) model when used as a single objective optimization function in the framework of the canonical evolutionary algorithm (EA). To this end, the design of the EA is modified with a gene ontology-based mutation operator, where the aim is to make a positive collaboration between the modularity density model and the proposed

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Publication Date
Tue Jan 25 2022
Journal Name
Iraqi Journal Of Science
A Modified Segmentation Approach for Real World Images Based on Edge Density Associated with Image Contrast Stretching

Segmentation of real world images considered as one of the most challenging tasks in the computer vision field due to several issues that associated with this kind of images such as high interference between object foreground and background, complicated objects and the pixels intensities of the object and background are almost similar in some cases. This research has introduced a modified adaptive segmentation process with image contrast stretching namely Gamma Stretching to improve the segmentation problem. The iterative segmentation process based on the proposed criteria has given the flexibility to the segmentation process in finding the suitable region of interest. As well as, the using of Gamma stretching will help in separating the

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Publication Date
Sun Jun 03 2012
Journal Name
Baghdad Science Journal
A Biochemical Study for Evaluation and Analysis of Serum Protein of Patients with Different Kidney Tumors

The amount of protein in the serum depends on the balance between the rate of its synthesis, and that of its catabolism or loss. Abnormal metabolism may result from nutritional deficiency, enzyme deficiency, abnormal secretion of hormones, or the actions of drugs and toxins. Renal cancer is the third most common malignancy of the genitourinary system, and accounts for 3% of adult malignancies globally. Total serum proteins were measured in malignant kidney tumor, benign kidney tumors, and non tumoral kidney diseases patient groups, as well as in healthy individuals. A significant decrease (p< 0.001) of total serum protein levels in patients with malignant kidney tumors when compared with those of benign tumors, non tumoral diseases, and hea

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Publication Date
Wed Sep 12 2018
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
A Comparison between Multi-Layer Perceptron and Radial Basis Function Networks in Detecting Humans Based on Object Shape

       Human detection represents a main problem of interest when using video based monitoring. In this paper, artificial neural networks, namely multilayer perceptron (MLP) and radial basis function (RBF) are used to detect humans among different objects in a sequence of frames (images) using classification approach. The classification used is based on the shape of the object instead of depending on the contents of the frame. Initially, background subtraction is depended to extract objects of interest from the frame, then statistical and geometric information are obtained from vertical and horizontal projections of the objects that are detected to stand for the shape of the object. Next to this step, two ty

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