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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
Sun Sep 04 2016
Journal Name
Baghdad Science Journal
The Importance and Interaction Indices of Bi-Capacities Based on Ternary-Element Sets
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Grabisch and Labreuche have recently proposed a generalization of capacities, called the bi-capacities. Recently, a new approach for studying bi-capacities through introducing a notion of ternary-element sets proposed by the author. In this paper, we propose many results such as bipolar Mobius transform, importance index, and interaction index of bi-capacities based on our approach.

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Publication Date
Wed Feb 01 2023
Journal Name
Journal Of Engineering
Double-Staged Syndrome Coding Scheme for Improving Information Transmission Security over the Wiretap Channel
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This paper presents a study of a syndrome coding scheme for different binary linear error correcting codes that refer to the code families such as BCH, BKLC, Golay, and Hamming. The study is implemented on Wyner’s wiretap channel model when the main channel is error-free and the eavesdropper channel is a binary symmetric channel with crossover error probability (0 < Pe ≤ 0.5) to show the security performance of error correcting codes while used in the single-staged syndrome coding scheme in terms of equivocation rate. Generally, these codes are not designed for secure information transmission, and they have low equivocation rates when they are used in the syndrome coding scheme. Therefore, to improve the transmiss

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Publication Date
Sun Jan 01 2023
Journal Name
Journal Of Oral Medicine And Oral Surgery
Reliability of two difficulty indexes in predicting the surgical extraction difficulty of impacted mandibular third molars
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Introduction: The aim of this study was to compare the reliability and the agreement of the Pederson and Pernambuco difficulty indexes in predicting the surgical extraction difficulty of the impacted mandibular third molars. Materials and methods: A prospective observational cohort study was conducted on 83 patients who had undergone surgical removal of impacted mandibular third molar. The difficulty of extraction was determined preoperatively according to the total scores obtained from the Pederson and Pernambuco difficulty indexes, the operative difficulty was determined by the surgical technique and the duration of extraction. The accuracy of prediction of the surgical difficulty and

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Publication Date
Tue Oct 27 2020
Journal Name
Proceedings Of The 2020 2nd International Conference On Sustainable Manufacturing, Materials And Technologies
The complex dynamic in three species food webmodel involving stage structure and cannibalism
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A three species food web model involving a stage structure and cannibalism in the top predator species is proposed and studied. It is assumed that the prey species growth logistically in the absence of predator and the predation process occurred according to theLotka-Volterra functional response. The existence, uniqueness and bounded-ness of the solution of the model are investigated. The local and global stability conditions of all possible equilibrium points are established.The persistence conditions of the model are also determined. The local bifurcation near each of the equilibrium points is analyzed. The global dynamics of the model is investigated numerically and compared with the obtained analytical results. It is observed that the p

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Publication Date
Tue Mar 30 2021
Journal Name
Journal Of Economics And Administrative Sciences
Using Iterative Reweighting Algorithm and Genetic Algorithm to Calculate The Estimation of The Parameters Of The Maximum Likelihood of The Skew Normal Distribution
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Excessive skewness which occurs sometimes in the data is represented as an obstacle against normal distribution. So, recent studies have witnessed activity in studying the skew-normal distribution (SND) that matches the skewness data which is regarded as a special case of the normal distribution with additional skewness parameter (α), which gives more flexibility to the normal distribution. When estimating the parameters of (SND), we face the problem of the non-linear equation and by using the method of Maximum Likelihood estimation (ML) their solutions will be inaccurate and unreliable. To solve this problem, two methods can be used that are: the genetic algorithm (GA) and the iterative reweighting algorithm (IR) based on the M

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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
Sun Jun 20 2021
Journal Name
Baghdad Science Journal
Multifactor Algorithm for Test Case Selection and Ordering
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Regression testing being expensive, requires optimization notion. Typically, the optimization of test cases results in selecting a reduced set or subset of test cases or prioritizing the test cases to detect potential faults at an earlier phase. Many former studies revealed the heuristic-dependent mechanism to attain optimality while reducing or prioritizing test cases. Nevertheless, those studies were deprived of systematic procedures to manage tied test cases issue. Moreover, evolutionary algorithms such as the genetic process often help in depleting test cases, together with a concurrent decrease in computational runtime. However, when examining the fault detection capacity along with other parameters, is required, the method falls sh

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Publication Date
Fri Apr 20 2012
Journal Name
International Journal Of Computer And Information Engineering
An Optimal Algorithm for HTML Page Building Process
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An Optimal Algorithm for HTML Page Building Process

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Publication Date
Thu Dec 01 2011
Journal Name
2011 Developments In E-systems Engineering
Enhanced Computation Time for Fast Block Matching Algorithm
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Publication Date
Fri Apr 01 2022
Journal Name
Symmetry
Fast Overlapping Block Processing Algorithm for Feature Extraction
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In many video and image processing applications, the frames are partitioned into blocks, which are extracted and processed sequentially. In this paper, we propose a fast algorithm for calculation of features of overlapping image blocks. We assume the features are projections of the block on separable 2D basis functions (usually orthogonal polynomials) where we benefit from the symmetry with respect to spatial variables. The main idea is based on a construction of auxiliary matrices that virtually extends the original image and makes it possible to avoid a time-consuming computation in loops. These matrices can be pre-calculated, stored and used repeatedly since they are independent of the image itself. We validated experimentally th

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