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An Evolutionary Algorithm with Gene Ontology-Aware Crossover Operator for Protein Complex Detection

     Evolutionary algorithms (EAs), as global search methods, are proved to be more robust than their counterpart local heuristics for detecting protein complexes in protein-protein interaction (PPI) networks. Typically, the source of robustness of these EAs comes from their components and parameters. These components are solution representation, selection, crossover, and mutation. Unfortunately, almost all EA based complex detection methods suggested in the literature were designed with only canonical or traditional components. Further, topological structure of the protein network is the main information that is used in the design of almost all such components. The main contribution of this paper is to formulate a more robust EA with more biological consistency. For this purpose, a new crossover operator is suggested where biological information in terms of both gene semantic similarity and protein functional similarity is fed into its design. To reflect the heuristic roles of both semantic and functional similarities, this paper introduces two gene ontology (GO) aware crossover operators. These are direct annotation-aware and inherited annotation-aware crossover operators. The first strategy is handled with the direct gene ontology annotation of the proteins, while the second strategy is handled with the directed acyclic graph (DAG) of each gene ontology term in the gene product. To conduct our experiments, the proposed EAs with GO-aware crossover operators are compared against the state-of-the-art heuristic, canonical EAs with the traditional crossover operator, and GO-based EAs. Simulation results are evaluated in terms of recall, precision, and F measure at both complex level and protein level. The results prove that the new EA design encourages a more reliable treatment of exploration and exploitation and, thus, improves the detection ability for more accurate protein complex structures.

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Publication Date
Thu Jul 01 2021
Journal Name
Iraqi Journal Of Science
Meerkat Clan Algorithm for Solving N-Queen Problems

The swarm intelligence and evolutionary methods are commonly utilized by researchers in solving the difficult combinatorial and Non-Deterministic Polynomial (NP) problems. The N-Queen problem can be defined as a combinatorial problem that became intractable for the large ‘n’ values and, thereby, it is placed in the NP class of problems. In the present study, a solution is suggested for the N-Queen problem, on the basis of the Meerkat Clan Algorithm (MCA). The problem of n-Queen can be mainly defined as one of the generalized 8-Queen problem forms, for which the aim is placing 8 queens in a way that none of the queens has the ability of killing the others with the use of the standard moves of the chess queen. The Meerkat Clan environm

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Publication Date
Thu Sep 26 2019
Journal Name
Processes
Fine-Tuning Meta-Heuristic Algorithm for Global Optimization

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 Dec 01 2011
Journal Name
2011 Developments In E-systems Engineering
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Publication Date
Fri Apr 01 2022
Journal Name
Symmetry
Fast Overlapping Block Processing Algorithm for Feature Extraction

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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Publication Date
Thu Oct 01 2020
Journal Name
International Communications In Heat And Mass Transfer
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Publication Date
Thu Mar 09 2017
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
Synthesis, Spectroscopic and Adsorption Studies of Cobalt (II) Complex for a ligand β-enaminone Derived from

   This paper concerns is the preparation and characterization of a bidentate ligand [4-(5,5dimethyl-3-oxocyclohex-1-enylamino)-N-(5-methylisoxazol-3-yl) benzene sulfonamide].  The ligand was prepared from fusing of sulfamethoxazole and dimedone at (140) ºC for half hour.              The complex was prepared by refluxing the ligand with a bivalent cobalt ion using ethanol as a solvent. The prepared ligand and complex were identified using Spectroscopic methods. The proposed tetrahedral geometry around the metal ions studied were concluded from these measurements. Both molar ratio and continuous variation method were studied to determine metal to ligand ratio (M:L). The M to L ratio wa

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Publication Date
Sun Jul 01 1990
Journal Name
Bulletin Of The Iraq Natural History Museum (p-issn: 1017-8678 , E-issn: 2311-9799)
MEDIUM OPTIMIZATION FOR BIOMASS PRODUCTION AND PROTEIN CONTENT OF CANDIDA UTILES K50

Molasse medium containing different concentrations of (NH4)2 SO4, (NH4)3 PO4, urea, KCI, and P2O5 were compared with the medium used for commercial production of C. utilis in a factory south of Iraq. An efficient medium, which produced 19. 16% dry wt. and 5. 78% protein, was developed. The effect of adding various concentrations of micronutrients (FeSO4, 7T20, MnSO4. 7H20, ZnSO4. 7E20) was also studied. Results showed that FeSo4. 7H20 caused a noticeable increase in both dry wt. and protein content of the yeast.

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Publication Date
Wed Sep 07 2022
Journal Name
2022 Iraqi International Conference On Communication And Information Technologies (iiccit)
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Publication Date
Thu Oct 01 2020
Journal Name
Journal Of Herbal Medicine
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Publication Date
Thu Oct 01 2020
Journal Name
Journal Of Herbal Medicine
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