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Biological versus Topological Domains in Improving the Reliability of Evolutionary-Based Protein Complex Detection Algorithms

     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 Apr 30 2022
Journal Name
Iraqi Journal Of Science
The Complex Dynamics in a Food Chain Involving Different Functional Responses

      A food chain model in which the top predator growing logistically has been proposed and studied. Two types of Holling’s functional responses type IV and type II have been used in the first trophic level and second trophic level respectively, in addition to Leslie-Gower in the third level. The properties of the solution are discussed. Since the boundary dynamics are affecting the dynamical behavior of the whole dynamical system, the linearization technique is used to study the stability of the subsystem of the proposed model. The persistence conditions of the obtained subsystem of the food chain are established. Finally, the model is simulated numerically to understand the global dynamics of the food chain un

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Publication Date
Thu Apr 13 2017
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
On S*g--Open Sets In Topological Spaces

  In this paper, we introduce a new class of sets, namely , s*g--open sets and we show that the family of all s*g--open subsets of a topological space ) ,X(  from a topology on X which is finer than  . Also , we study the characterizations and basic properties of s*g-open sets and s*g--closed sets . Moreover, we use these sets to define and study a new class of functions, namely , s*g-  -continuous functions and s*g-  -irresolute functions in topological spaces . Some properties of these functions have been studied .

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Publication Date
Thu Dec 30 2021
Journal Name
Iraqi Journal Of Science
Neutrosophic Simply b-Open Set in Neutrosophic Topological Spaces

In this paper, we procure the notions of neutrosophic simply b-open set, neutrosophic simply b-open cover, and neutrosophic simply b-compactness via neutrosophic topological spaces. Then, we establish some remarks, propositions, and theorems on neutrosophic simply

b-compactness. Further, we furnish some counter examples where the result fails.

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Publication Date
Sat Jan 01 2022
Journal Name
1st Samarra International Conference For Pure And Applied Sciences (sicps2021): Sicps2021
Feeble Hausdorff spaces in alpha-topological spaces using graph

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Publication Date
Mon Feb 01 2016
Journal Name
International Journal Of Applied Mathematics & Statistical Sciences
Topological Structures Using Mixed Degree Systems in Graph Theory

This paper is concerned with introducing and studying the M-space by using the mixed degree systems which are the core concept in this paper. The necessary and sufficient condition for the equivalence of two reflexive M-spaces is super imposed. In addition, the m-derived graphs, m-open graphs, m-closed graphs, m-interior operators, m-closure operators and M-subspace are introduced. From an M-space, a unique supratopological space is introduced. Furthermore, the m-continuous (m-open and m-closed) functions are defined and the fundamental theorem of the m-continuity is provided. Finally, the m-homeomorphism is defined and some of its properties are investigated.

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Publication Date
Sun May 17 2020
Journal Name
Iraqi Journal Of Science
On Soft bc-Open Sets in Soft Topological Spaces

In this paper, we offer and study a novel type generalized soft-open sets in topological spaces, named soft Æ„c-open sets. Relationships of this set with other types of generalized soft-open sets are discussed, definitions of soft Æ„ , soft bc- closure and soft bc- interior are introduced, and its properties are investigated. Also, we introduce and explore several characterizations and properties of this type of sets.

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Publication Date
Wed Nov 13 2024
Journal Name
Aip Conference Proceedings
On Sδ.derived and Sδ.isolated sets in supra topological spaces

The topic of supra.topological.spaces considered one of the important topics because it is a generalization to topological.spaces. Many researchers have presented generalizations to supra open sets such as supra semi.open and supra pre.open sets and others. In this paper, the concept of δ∼open sets was employed and introduced in to the concept of supra topology and a new type of open set was extracted, which was named S∼δ∼open. Our research entails the utilization of this category of sets to form a new concepts in these spaces, namely S∼δ∼limit points and S∼δ∼derive points, and examining its relationship with S∼open and S∼reg∼open. Based on this class of sets, we have introduced other new concepts such as S∼isolate

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Publication Date
Tue Dec 15 2020
Journal Name
Al-academy
Acculturation and its Evolutionary Tendency in the Design of the Prayer Space Elements / Niche – A model: آلاء طالب كريم

The peculiarity of worship spaces in the Islamic architecture is evident by its symbolic connotations with doctrinal connections, thus the niche has a major status in that symbolic connotation, which transformed due to the cultural interaction from a rock on the wall directed towards Mecca into an element of integrated structural entity with performative and aesthetic characteristics. The spread of the Islamic religion contributed to subjecting it to a design acculturation process, thus the problem of the research was raised by the following question: has the evolutionary tendency of acculturation been able to effect a major transformation in the niche design? The research aims at identifying the design acculturation and its translation

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Publication Date
Sat Dec 31 2022
Journal Name
Mathematical Modelling Of Engineering Problems
Investigation of Energy Efficient Clustering Algorithms in WSNs: A Review

In recent years, Wireless Sensor Networks (WSNs) are attracting more attention in many fields as they are extensively used in a wide range of applications, such as environment monitoring, the Internet of Things, industrial operation control, electric distribution, and the oil industry. One of the major concerns in these networks is the limited energy sources. Clustering and routing algorithms represent one of the critical issues that directly contribute to power consumption in WSNs. Therefore, optimization techniques and routing protocols for such networks have to be studied and developed. This paper focuses on the most recent studies and algorithms that handle energy-efficiency clustering and routing in WSNs. In addition, the prime

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Publication Date
Tue Jul 01 2014
Journal Name
Computer Engineering And Intelligent Systems
Static Analysis Based Behavioral API for Malware Detection using Markov Chain

Researchers employ behavior based malware detection models that depend on API tracking and analyzing features to identify suspected PE applications. Those malware behavior models become more efficient than the signature based malware detection systems for detecting unknown malwares. This is because a simple polymorphic or metamorphic malware can defeat signature based detection systems easily. The growing number of computer malwares and the detection of malware have been the concern for security researchers for a large period of time. The use of logic formulae to model the malware behaviors is one of the most encouraging recent developments in malware research, which provides alternatives to classic virus detection methods. To address the l

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