Search results for: Hany T. Alashwal

Authors: Nazar Zaki, Safaai Deris, Hany Alashwal

Abstract:

Detecting protein-protein interactions is a central problem in computational biology and aberrant such interactions may have implicated in a number of neurological disorders. As a result, the prediction of protein-protein interactions has recently received considerable attention from biologist around the globe. Computational tools that are capable of effectively identifying protein-protein interactions are much needed. In this paper, we propose a method to detect protein-protein interaction based on substring similarity measure. Two protein sequences may interact by the mean of the similarities of the substrings they contain. When applied on the currently available protein-protein interaction data for the yeast Saccharomyces cerevisiae, the proposed method delivered reasonable improvement over the existing ones.

Keywords: Protein-Protein Interaction, support vector machine, feature extraction, pairwise alignment, Smith-Waterman score.

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Authors: Hany Alashwal, Safaai Deris, Razib M. Othman

Abstract:

Predicting protein-protein interactions represent a key step in understanding proteins functions. This is due to the fact that proteins usually work in context of other proteins and rarely function alone. Machine learning techniques have been applied to predict protein-protein interactions. However, most of these techniques address this problem as a binary classification problem. Although it is easy to get a dataset of interacting proteins as positive examples, there are no experimentally confirmed non-interacting proteins to be considered as negative examples. Therefore, in this paper we solve this problem as a one-class classification problem using one-class support vector machines (SVM). Using only positive examples (interacting protein pairs) in training phase, the one-class SVM achieves accuracy of about 80%. These results imply that protein-protein interaction can be predicted using one-class classifier with comparable accuracy to the binary classifiers that use artificially constructed negative examples.

Keywords: Bioinformatics, Protein-protein interactions, One-Class Support Vector Machines

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Authors: Hany Alashwal, Safaai Deris, Razib M. Othman

Abstract:

The protein domain structure has been widely used as the most informative sequence feature to computationally predict protein-protein interactions. However, in a recent study, a research group has reported a very high accuracy of 94% using hydrophobicity feature. Therefore, in this study we compare and verify the usefulness of protein domain structure and hydrophobicity properties as the sequence features. Using the Support Vector Machines (SVM) as the learning system, our results indicate that both features achieved accuracy of nearly 80%. Furthermore, domains structure had receiver operating characteristic (ROC) score of 0.8480 with running time of 34 seconds, while hydrophobicity had ROC score of 0.8159 with running time of 20,571 seconds (5.7 hours). These results indicate that protein-protein interaction can be predicted from domain structure with reliable accuracy and acceptable running time.

Keywords: Bioinformatics, protein-protein interactions, support vector machines, protein features.

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Authors: Hany Alashwal, Safaai Deris, Razib M. Othman

Abstract:

Understanding proteins functions is a major goal in the post-genomic era. Proteins usually work in context of other proteins and rarely function alone. Therefore, it is highly relevant to study the interaction partners of a protein in order to understand its function. Machine learning techniques have been widely applied to predict protein-protein interactions. Kernel functions play an important role for a successful machine learning technique. Choosing the appropriate kernel function can lead to a better accuracy in a binary classifier such as the support vector machines. In this paper, we describe a Bayesian kernel for the support vector machine to predict protein-protein interactions. The use of Bayesian kernel can improve the classifier performance by incorporating the probability characteristic of the available experimental protein-protein interactions data that were compiled from different sources. In addition, the probabilistic output from the Bayesian kernel can assist biologists to conduct more research on the highly predicted interactions. The results show that the accuracy of the classifier has been improved using the Bayesian kernel compared to the standard SVM kernels. These results imply that protein-protein interaction can be predicted using Bayesian kernel with better accuracy compared to the standard SVM kernels.

Keywords: Bioinformatics, Protein-protein interactions, Bayesian Kernel, Support Vector Machines.

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Authors: Razib M. Othman, Safaai Deris, Rosli M. Illias, Hany T. Alashwal, Rohayanti Hassan, FarhanMohamed

Abstract:

The most important property of the Gene Ontology is the terms. These control vocabularies are defined to provide consistent descriptions of gene products that are shareable and computationally accessible by humans, software agent, or other machine-readable meta-data. Each term is associated with information such as definition, synonyms, database references, amino acid sequences, and relationships to other terms. This information has made the Gene Ontology broadly applied in microarray and proteomic analysis. However, the process of searching the terms is still carried out using traditional approach which is based on keyword matching. The weaknesses of this approach are: ignoring semantic relationships between terms, and highly depending on a specialist to find similar terms. Therefore, this study combines semantic similarity measure and genetic algorithm to perform a better retrieval process for searching semantically similar terms. The semantic similarity measure is used to compute similitude strength between two terms. Then, the genetic algorithm is employed to perform batch retrievals and to handle the situation of the large search space of the Gene Ontology graph. The computational results are presented to show the effectiveness of the proposed algorithm.

Keywords: Gene Ontology, Semantic similarity measure, Genetic algorithm, Ontology search

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Authors: Bakr Hashem Paumey Ahmed Alashwal

Abstract:

The urban transformation processes in its framework and its general significance became a fundamental and vital subject of consideration for both the developed and the developing societies. It has become important to regulate the architectural systems adopted by the city, to sustain the present development on one hand, and on the other hand, to facilitate its future growth. Thus, the study dealt with the phenomenon of urban transformation of the Mediterranean cities, and the city of Alexandria in particular, because of its significant historical and cultural legacy, its historical architecture and its contemporary urbanization. This article investigates the entirety of cities in the Mediterranean region through the analysis of the relationship between inflation and growth of these cities and the extent of the complexity of the city barriers. We hope to analyze not only the internal transformations, but the external relationships (both imperial and post-colonial) that have shaped Alexandria city growth from the nineteenth century until today.

Keywords: Urban Transformations, Mediterranean cities, Modern Era, Alexandria.

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Authors: Abdelrahman Elsehsah, Hany Madkour, Khalid Farah

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This article presents a 3-D modified non-linear elastic model in the strain space. The Helmholtz free energy function is introduced with the existence of a dissipation potential surface in the space of thermodynamic conjugate forces. The constitutive equation and the damage evolution were derived as well. The modified damage has been examined to model the nonlinear behavior of reinforced concrete (RC) slabs with an opening. A parametric study with RC was carried out to investigate the impact of different factors on the behavior of RC slabs. These factors are the opening area, the opening shape, the place of opening, and the thickness of the slabs. And the numerical results have been compared with the experimental data from literature. Finally, the model showed its ability to be applied to the structural analysis of RC slabs.

Keywords: 3-D numerical analysis, damage mechanics, RC slab with opening.

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Authors: Hany Osman, M. F. Baki

Abstract:

We address the balancing problem of transfer lines in this paper to find the optimal line balancing that minimizes the nonproductive time. We focus on the tool change time and face orientation change time both of which influence the makespane. We consider machine capacity limitations and technological constraints associated with the manufacturing process of auto cylinder heads. The problem is represented by a mixed integer programming model that aims at distributing the design features to workstations and sequencing the machining processes at a minimum non-productive time. The proposed model is solved by an algorithm established using linearization schemes and Benders- decomposition approach. The experiments show the efficiency of the algorithm in reaching the exact solution of small and medium problem instances at reasonable time.

Keywords: Transfer line balancing, Benders' decomposition, Linearization.

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Authors: Mahmoud Roushdi, Hany Mostafa, Khaled Kheireldin

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Sinai Peninsula and Suez Canal Corridor are promising and important economic regions in Egypt due to the unique location and development opportunities. Thus, the climate change impacts should be assessed over the mentioned area. Accordingly, this paper aims to assess the climate extreme indices in through the last 35 year over Sinai Peninsula and Suez Canal Corridor in addition to predict the climate extreme indices up to 2100. Present and future climate indices were analyzed with using different RCP scenarios 4.5 and 8.5 from 2010 until 2100 for Sinai Peninsula and Suez Canal Corridor. Furthermore, both CanESM and HadGEM2 global circulation models were used. The results indicate that the number of summer days is predicted to increase, on the other hand the frost days is predicted to decrease. Moreover, it is noted a slight positive trend for the percentile of wet and extremely days R95p and R99p for RCP4.5 and negative trend for RCP8.5.

Keywords: Climate change, extreme indices, RCP, Sinai Peninsula.

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Authors: Mona M. Salem, Khaled S. Al-Hagla, Hany M. Ayad

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The concept of urban metabolism has increasingly been employed in a diverse range of disciplines as a mean to analyze and theorize the city. Urban ecology has a particular focus on the implications of applying the metabolism concept to the urban realm. This approach has been developed by a few researchers, though it has rarely if ever been used in policy development for city planning. The aim of this research is to use ecologically informed urban planning interventions to increase the sustainability of urban metabolism; with special focus on land stock as a most important city resource by developing a system dynamic based DSS. This model identifies two critical management strategy variables for the Strategic Urban Plan Alexandria SUP 2032. As a result, this comprehensive and precise quantitative approach is needed to monitor, measure, evaluate and observe dynamic urban changes working as a decision support system (DSS) for policy making.

Keywords: Alexandria SUP 2032, DSS, ecology, land resource, LULCC, management, metabolism, model, scenarios, System dynamics, urban development.

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Authors: H. M. El-Zomor, M. Hany

Abstract:

Recycling of aluminum beverage cans is an important issue due to its economic and environmental effect. One of the significant factors in aluminum cans recycling process is the transportation cost from the landfill space. An automatic compression baler (ACB) machine has been designed and built to densify the aluminum beverage cans. It has been constructed using numerous fabricated components. Two types of control methodology have been introduced in this ACB machine to achieve its goal. The first is a semi-automatic system, and the second is a mechatronic system by using a Programmable Logic Control (PLC). The effect of single and double pre-compression for the beverage cans have been evaluated by using the PLC control. Comparisons have been performed between the two types of control methodologies by operating this ACB machine in different working conditions. The double pre-compression in PLC control proves that there is an enhancement in the ACB performance by 133% greater than the direct compression in the semi-automatic control. In addition, the percentage of the reduction ratio in volume reaches 77%, and the compaction ratio reaches about four times of the initial volume.

Keywords: Aluminum can recycling, Fully automatic machine, Hydraulic system control, Multi-compression.

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Authors: Hany Mahgoub

Abstract:

This paper presents a system for discovering association rules from collections of unstructured documents called EART (Extract Association Rules from Text). The EART system treats texts only not images or figures. EART discovers association rules amongst keywords labeling the collection of textual documents. The main characteristic of EART is that the system integrates XML technology (to transform unstructured documents into structured documents) with Information Retrieval scheme (TF-IDF) and Data Mining technique for association rules extraction. EART depends on word feature to extract association rules. It consists of four phases: structure phase, index phase, text mining phase and visualization phase. Our work depends on the analysis of the keywords in the extracted association rules through the co-occurrence of the keywords in one sentence in the original text and the existing of the keywords in one sentence without co-occurrence. Experiments applied on a collection of scientific documents selected from MEDLINE that are related to the outbreak of H5N1 avian influenza virus.

Keywords: Association rules, information retrieval, knowledgediscovery in text, text mining.

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Authors: Hany R. Ammar, Khalil A. Khalil, El-Sayed M. Sherif

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The current study investigated the influence of milling time and ball-to-powder (BPR) weight ratio on the microstructural constituents and mechanical properties of bulk nanocrystalline Al; Al-10%Cu; and Al-10%Cu-5%Ti alloys. Powder consolidation was carried out using a high frequency induction heat sintering where the processed metal powders were sintered into a dense and strong bulk material. The powders and the bulk samples were characterized using XRD and FEGSEM techniques. The mechanical properties were evaluated at various temperatures of 25°C, 100°C, 200°C, 300°C and 400°C to study the thermal stability of the processed alloys. The processed bulk nanocrystalline alloys displayed extremely high hardness values even at elevated temperatures. The Al-10%Cu-5%Ti alloy displayed the highest hardness values at room and elevated temperatures which are related to the presence of Ti-containing phases such as Al3Ti and AlCu2Ti. These phases are thermally stable and retain the high hardness values at elevated temperatures up to 400ºC.

Keywords: Nanocrystalline Aluminum Alloys, Mechanical Alloying, Sintering, Hardness, Thermal Stability.

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Authors: Sunitha Ramanujam, Hany El Yamany, Miriam A. M. Capretz

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Software reliability, defined as the probability of a software system or application functioning without failure or errors over a defined period of time, has been an important area of research for over three decades. Several research efforts aimed at developing models to improve reliability are currently underway. One of the most popular approaches to software reliability adopted by some of these research efforts involves the use of operational profiles to predict how software applications will be used. Operational profiles are a quantification of usage patterns for a software application. The research presented in this paper investigates an innovative multiagent framework for automatic creation and management of operational profiles for generic distributed systems after their release into the market. The architecture of the proposed Operational Profile MAS (Multi-Agent System) is presented along with detailed descriptions of the various models arrived at following the analysis and design phases of the proposed system. The operational profile in this paper is extended to comprise seven different profiles. Further, the criticality of operations is defined using a new composed metrics in order to organize the testing process as well as to decrease the time and cost involved in this process. A prototype implementation of the proposed MAS is included as proof-of-concept and the framework is considered as a step towards making distributed systems intelligent and self-managing.

Keywords: Software reliability, Software testing, Metrics, Distributed systems, Multi-agent systems

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Authors: Hany Mahgoub, Dietmar Rösner, Nabil Ismail, Fawzy Torkey

Abstract:

This paper describes text mining technique for automatically extracting association rules from collections of textual documents. The technique called, Extracting Association Rules from Text (EART). It depends on keyword features for discover association rules amongst keywords labeling the documents. In this work, the EART system ignores the order in which the words occur, but instead focusing on the words and their statistical distributions in documents. The main contributions of the technique are that it integrates XML technology with Information Retrieval scheme (TFIDF) (for keyword/feature selection that automatically selects the most discriminative keywords for use in association rules generation) and use Data Mining technique for association rules discovery. It consists of three phases: Text Preprocessing phase (transformation, filtration, stemming and indexing of the documents), Association Rule Mining (ARM) phase (applying our designed algorithm for Generating Association Rules based on Weighting scheme GARW) and Visualization phase (visualization of results). Experiments applied on WebPages news documents related to the outbreak of the bird flu disease. The extracted association rules contain important features and describe the informative news included in the documents collection. The performance of the EART system compared with another system that uses the Apriori algorithm throughout the execution time and evaluating extracted association rules.

Keywords: Text mining, data mining, association rule mining

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Authors: Mahmoud S. Ahmed, Hany A. Mohamed, Mohamed A. Omara, Mohamed F. Abdeen

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Experimental study of natural convection heat transfer inside smooth and rough surfaces of vertical and inclined equilateral triangular channels of different inclination angles with a uniformly heated surface are performed. The inclination angle is changed from 15º to 90º. Smooth and rough surface of average roughness (0.02mm) are used and their effect on the heat transfer characteristics are studied. The local and average heat transfer coefficients and Nusselt number are obtained for smooth and rough channels at different heat flux values, different inclination angles and different Rayleigh numbers (Ra) 6.48 × 105 ≤ Ra ≤ 4.78 × 106. The results show that the local Nusselt number decreases with increase of axial distance from the lower end of the triangular channel to a point near the upper end of channel, and then, it slightly increases. Higher values of local Nusselt number for rough channel along the axial distance compared with the smooth channel. The average Nusselt number of rough channel is higher than that of smooth channel by about 8.1% for inclined case at θ = 45o and 10% for vertical case. The results obtained are correlated using dimensionless groups for both rough and smooth surfaces of the inclined and vertical triangular channels.

Keywords: Natural heat transfer convection, constant heat flux, open channels, heat transfer.

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Authors: A. Abdullah, N. Faghih Mirzaei, S. Hany Haron

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Neighbourhood environment walkability on reported physical activity (PA) levels of students of Universiti Sains Malaysia (USM) in Malaysia. Compared with previous generations, today’s young people spend less time playing outdoors and have lower participation rates in PA. Research suggests that negative perceptions of neighbourhood walkability may be a potential barrier to adolescents’ PA. The sample consisted of 200 USM students (to 24 years old) who live outside of the main campus and engage in PA in sport halls and sport fields of USM. The data were analysed using the t-test, binary logistic regression, and discriminant analysis techniques. The present study found that youth PA was affected by neighbourhood environment walkability factors, including neighbourhood infrastructures, neighbourhood safety (crime), and recreation facilities, as well as street characteristics and neighbourhood design variables such as facades of sidewalks, roadside trees, green spaces, and aesthetics. The finding also illustrated that active students were influenced by street connectivity, neighbourhood infrastructures, recreation facilities, facades of sidewalks, and aesthetics, whereas students in the less active group were affected by access to destinations, neighbourhood safety (crime), and roadside trees and green spaces for their PAs. These results report which factors of built environments have more effect on youth PA and they message to the public to create more awareness about the benefits of PA on youth health.

Keywords: Fear of crime, neighbourhood built environment, physical activities, street characteristics design.

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