Search results for: bioinformatics framework

Authors: Sunitha Abburu, Golla Suresh Babu

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The issues that limit application interoperability is lack of common vocabulary, common structure, application domain knowledge ontology based semantic technology provides solutions that resolves application interoperability issues. Ontology is broadly used in diverse applications such as artificial intelligence, bioinformatics, biomedical, information integration, etc. Ontology can be used to interpret the knowledge of various domains. To reuse, enrich the available ontologies and reduce the duplication of ontologies of the same domain, there is a strong need to integrate the ontologies of the particular domain. The integrated ontology gives complete knowledge about the domain by sharing this comprehensive domain ontology among the groups. As per the literature survey there is no well-defined methodology to represent knowledge of a whole domain. The current research addresses a systematic methodology for knowledge representation using multiple sub-ontologies at different levels that addresses application interoperability and enables semantic information retrieval. The current method represents complete knowledge of a domain by importing concepts from multiple sub ontologies of same and relative domains that reduces ontology duplication, rework, implementation cost through ontology reusability.

Keywords: Knowledge acquisition, knowledge representation, knowledge transfer, ontologies, semantics.

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Authors: Abdulkadir Abu Lawal

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The study was carried out to establish the probability density function of some selected building construction projects of similar complexity delivered using Bill of Quantities (BQ) and Lump Sum (LS) forms of contract, and to draw a reliability scenario for each form of contract. 30 of such delivered projects are analyzed for each of the contract forms using Weibull Analysis, and their Weibull functions (α, and β) are determined based on their completion times. For the BQ form of contract delivered projects, α is calculated as 1.6737E20 and β as + 0.0115 and for the LS form, α is found to be 5.6556E03 and β is determined as + 0.4535. Using these values, respective probability density functions are calculated and plotted, as handy tool for risk analysis of future projects of similar characteristics. By input of variables from other projects, decision making processes can be made for a whole project or its components using EVM Analysis in project evaluation and review techniques. This framework, as a quantitative approach, depends on the assumption of normality in projects completion time, it can help greatly in determining the completion time probability for veritable projects using any of the contract forms under consideration. Projects aspects that are not amenable to measurement, on the other hand, can be analyzed using fuzzy sets and fuzzy logic. This scenario can be drawn for different types of building construction projects, and using different suitable forms of contract in projects delivery.

Keywords: Building construction, Projects, Forms of contract, Probability density function, Reliability scenario.

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Authors: Firas Mohamad Al-Sabek

Abstract:

The purpose of the paper is to examine the most critical and important factor which will affect the implementation of Total Quality Management (TQM) in the construction industry in the United Arab Emirates. It also examines the most effected Project outcome from implementing TQM. A framework was also proposed depending on the literature studies. The method used in this paper is a quantitative study. A survey with a sample of 60 respondents was created and distributed in a construction company in Abu Dhabi, which includes 15 questions to examine the most critical factor that will affect the implementation of TQM in addition to the most effected project outcome from implementing TQM. The survey showed that management commitment is the most important factor in implementing TQM in a construction company. Also it showed that Project cost is most effected outcome from the implementation of TQM. Management commitment is very important for implementing TQM in any company. If the management loose interest in quality then everyone in the organization will do so. The success of TQM will depend mostly on the top of the pyramid. Also cost is reduced and money is saved when the project team implement TQM. While if no quality measures are present within the team, the project will suffer a commercial failure. Based on literature, more factors can be examined and added to the model. In addition, more construction companies could be surveyed in order to obtain more accurate results. Also this study could be conducted outside the United Arab Emirates for further enchantment.

Keywords: Construction project, total quality management, management commitment, cost, theoretical framework.

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Authors: Wann-Ming Wey

Abstract:

The link between urban planning and design principles and the built environment of an urban renewal area is of interest to the field of urban studies. During the past decade, there has also been increasing interest in urban planning and design; this interest is motivated by the possibility that design policies associated with the built environment can be used to control, manage, and shape individual activity and behavior. However, direct assessments and design techniques of the links between how urban planning design policies influence individuals are still rare in the field. Recent research efforts in urban design have focused on the idea that land use and design policies can be used to increase the quality of design projects for an urban renewal area-s built environment. The development of appropriate design techniques for the built environment is an essential element of this research. Quality function deployment (QFD) is a powerful tool for improving alternative urban design and quality for urban renewal areas, and for procuring a citizen-driven quality system. In this research, we propose an integrated framework based on QFD and an Analytic Network Process (ANP) approach to determine the Alternative Technical Requirements (ATRs) to be considered in designing an urban renewal planning and design alternative. We also identify the research designs and methodologies that can be used to evaluate the performance of urban built environment projects. An application in an urban renewal built environment planning and design project evaluation is presented to illustrate the proposed framework.

Keywords: Analytic Network Process, Built Environment, Quality Function Deployment, Urban Design, Urban Renewal.

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Authors: Lukumba Phiri, Simon Tembo, Kumbuso Joshua Nyoni

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In Zambia, recent initiatives by various power operators like ZESCO, CEC, and consumers like the mines, to upgrade power systems into smart grids, target an even tighter integration with information technologies to enable the integration of renewable energy sources, local and bulk generation, and demand response. Thus, for the reliable operation of smart grids, its information infrastructure must be secure and reliable in the face of both failures and cyberattacks. Due to the nature of the systems, ICS/SCADA cybersecurity and governance face additional challenges compared to the corporate networks, and critical systems may be left exposed. There exist control frameworks internationally such as the NIST framework, however, they are generic and do not meet the domain-specific needs of the SCADA systems. Zambia is also lagging in cybersecurity awareness and adoption, and therefore there is a concern about securing ICS controlling key infrastructure critical to the Zambian economy as there are few known facts about the true posture. In this paper, we present a stochastic Edged-based Anomaly Detection for SCADA systems (SEADS) framework for threat modeling and risk assessment. SEADS enables the calculation of steady-steady probabilities that are further applied to establish metrics like system availability, maintainability, and reliability.

Keywords: Anomaly detection, SmartGrid, edge, maintainability, reliability, stochastic process.

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Authors: T. P. Athira, Gibin Chacko George

Abstract:

This paper proposes a dual tree complex wavelet transform (DT-CWT) based directional interpolation scheme for noisy images. The problems of denoising and interpolation are modelled as to estimate the noiseless and missing samples under the same framework of optimal estimation. Initially, DT-CWT is used to decompose an input low-resolution noisy image into low and high frequency subbands. The high-frequency subband images are interpolated by linear minimum mean square estimation (LMMSE) based interpolation, which preserves the edges of the interpolated images. For each noisy LR image sample, we compute multiple estimates of it along different directions and then fuse those directional estimates for a more accurate denoised LR image. The estimation parameters calculated in the denoising processing can be readily used to interpolate the missing samples. The inverse DT-CWT is applied on the denoised input and interpolated high frequency subband images to obtain the high resolution image. Compared with the conventional schemes that perform denoising and interpolation in tandem, the proposed DT-CWT based noisy image interpolation method can reduce many noise-caused interpolation artifacts and preserve well the image edge structures. The visual and quantitative results show that the proposed technique outperforms many of the existing denoising and interpolation methods.

Keywords: Dual-tree complex wavelet transform (DT-CWT), denoising, interpolation, optimal estimation, super resolution.

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Authors: A. Buruzs, M. F. Hatwágner, A. Torma, L. T. Kóczy

Abstract:

The development, operation and maintenance of Integrated Waste Management Systems (IWMS) affects essentially the sustainable concern of every region. The features of such systems have great influence on all of the components of sustainability. In order to reach the optimal way of processes, a comprehensive mapping of the variables affecting the future efficiency of the system is needed such as analysis of the interconnections among the components and modeling of their interactions. The planning of a IWMS is based fundamentally on technical and economical opportunities and the legal framework. Modeling the sustainability and operation effectiveness of a certain IWMS is not in the scope of the present research. The complexity of the systems and the large number of the variables require the utilization of a complex approach to model the outcomes and future risks. This complex method should be able to evaluate the logical framework of the factors composing the system and the interconnections between them. The authors of this paper studied the usability of the Fuzzy Cognitive Map (FCM) approach modeling the future operation of IWMS’s. The approach requires two input data set. One is the connection matrix containing all the factors affecting the system in focus with all the interconnections. The other input data set is the time series, a retrospective reconstruction of the weights and roles of the factors. This paper introduces a novel method to develop time series by content analysis.

Keywords: Content analysis, factors, integrated waste management system, time series.

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Authors: Achim Washington, Reece Clothier, Jose Silva

Abstract:

System Safety Regulations (SSR) are a central component to the airworthiness certification of Unmanned Aircraft Systems (UAS). There is significant debate on the setting of appropriate SSR for UAS. Putting this debate aside, the challenge lies in how to apply the system safety process to UAS, which lacks the data and operational heritage of conventionally piloted aircraft. The limited knowledge and lack of operational data result in uncertainty in the system safety assessment of UAS. This uncertainty can lead to incorrect compliance findings and the potential certification and operation of UAS that do not meet minimum safety performance requirements. The existing system safety assessment and compliance processes, as used for conventional piloted aviation, do not adequately account for the uncertainty, limiting the suitability of its application to UAS. This paper discusses the challenges of undertaking system safety assessments for UAS and presents current and envisaged research towards addressing these challenges. It aims to highlight the main advantages associated with adopting a risk based framework to the System Safety Performance Requirement (SSPR) compliance process that is capable of taking the uncertainty associated with each of the outputs of the system safety assessment process into consideration. Based on this study, it is made clear that developing a framework tailored to UAS, would allow for a more rational, transparent and systematic approach to decision making. This would reduce the need for conservative assumptions and take the risk posed by each UAS into consideration while determining its state of compliance to the SSR.

Keywords: Part 1309 regulations, unmanned aircraft systems, system safety, uncertainty.

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Authors: D. Sathan, A. Meetoo, R. K. Subramaniam

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Context awareness is a capability whereby mobile computing devices can sense their physical environment and adapt their behavior accordingly. The term context-awareness, in ubiquitous computing, was introduced by Schilit in 1994 and has become one of the most exciting concepts in early 21st-century computing, fueled by recent developments in pervasive computing (i.e. mobile and ubiquitous computing). These include computing devices worn by users, embedded devices, smart appliances, sensors surrounding users and a variety of wireless networking technologies. Context-aware applications use context information to adapt interfaces, tailor the set of application-relevant data, increase the precision of information retrieval, discover services, make the user interaction implicit, or build smart environments. For example: A context aware mobile phone will know that the user is currently in a meeting room, and reject any unimportant calls. One of the major challenges in providing users with context-aware services lies in continuously monitoring their contexts based on numerous sensors connected to the context aware system through wireless communication. A number of context aware frameworks based on sensors have been proposed, but many of them have neglected the fact that monitoring with sensors imposes heavy workloads on ubiquitous devices with limited computing power and battery. In this paper, we present CALEEF, a lightweight and energy efficient context aware framework for resource limited ubiquitous devices.

Keywords: Context-Aware, Energy-Efficient, Lightweight, Ubiquitous Devices.

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Authors: P. Pasomboon, P. Chumnanpuen, T. E-kobon

Abstract:

Hyaluronic acid (HA) consists of linear heteropolysaccharides repeat of D-glucuronic acid and N-acetyl-D-glucosamine. HA has various useful properties to maintain skin elasticity and moisture, reduce inflammation, and lubricate the movement of various body parts without causing immunogenic allergy. HA can be found in several animal tissues as well as in the capsule component of some bacteria including Pasteurella multocida. This study aimed to modify a genome-scale metabolic model of Escherichia coli using computational simulation and flux analysis methods to predict HA productivity under different carbon sources and nitrogen supplement by the addition of two enzymes (GLMU2 and HYAD) from P. multocida to improve the HA production under the specified amount of carbon sources and nitrogen supplements. Result revealed that threonine and aspartate supplement raised the HA production by 12.186%. Our analyses proposed the genome-scale metabolic model is useful for improving the HA production and narrows the number of conditions to be tested further.

Keywords: Pasteurella multocida, Escherichia coli, hyaluronic acid, genome-scale metabolic model, bioinformatics.

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Authors: A. Shukla, A. Tarsauliya, R. Tiwari, S. Sharma

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Cancer classification to their corresponding cohorts has been key area of research in bioinformatics aiming better prognosis of the disease. High dimensionality of gene data has been makes it a complex task and requires significance data identification technique in order to reducing the dimensionality and identification of significant information. In this paper, we have proposed a novel approach for classification of oral cancer into metastasis positive and negative patients. We have used significance analysis of microarrays (SAM) for identifying significant genes which constitutes gene signature. 3 different gene signatures were identified using SAM from 3 different combination of training datasets and their classification accuracy was calculated on corresponding testing datasets using k-Nearest Neighbour (kNN), Fuzzy C-Means Clustering (FCM), Support Vector Machine (SVM) and Backpropagation Neural Network (BPNN). A final gene signature of only 9 genes was obtained from above 3 individual gene signatures. 9 gene signature-s classification capability was compared using same classifiers on same testing datasets. Results obtained from experimentation shows that 9 gene signature classified all samples in testing dataset accurately while individual genes could not classify all accurately.

Keywords: Cancer, Gene Signature, SAM, Classification.

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Authors: Shatha Ghareeb, Rawaa Al-Jumeily, Thar Baker

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In Abu Dhabi, there are many different education curriculums where sector of private schools and quality assurance is supervising many private schools in Abu Dhabi for many nationalities. As there are many different education curriculums in Abu Dhabi to meet expats’ needs, there are different requirements for registration and success. In addition, there are different age groups for starting education in each curriculum. In fact, each curriculum has a different number of years, assessment techniques, reassessment rules, and exam boards. Currently, students that transfer curriculums are not being placed in the right year group due to different start and end dates of each academic year and their date of birth for each year group is different for each curriculum and as a result, we find students that are either younger or older for that year group which therefore creates gaps in their learning and performance. In addition, there is not a way of storing student data throughout their academic journey so that schools can track the student learning process. In this paper, we propose to develop a computational framework applicable in multicultural countries such as UAE in which multi-education systems are implemented. The ultimate goal is to use cloud and fog computing technology integrated with Artificial Intelligence techniques of Machine Learning to aid in a smooth transition when assigning students to their year groups, and provide leveling and differentiation information of students who relocate from a particular education curriculum to another, whilst also having the ability to store and access student data from anywhere throughout their academic journey.

Keywords: Admissions, algorithms, cloud computing, differentiation, fog computing, leveling, machine learning.

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Authors: Oluchukwu P. Obioma, Amarachi R. Dike

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Competition law promotes market competition by regulating anti-competitive conduct by undertakings. There is a need for a third party to regulate the market for efficiency and supervision, since, if the market is left unchecked, it may be skewed against the consumers and the economy. Competition law is geared towards the protection of consumers from economic exploitation. It is the duty of every rational government to optimally manage its economic system by employing the best regulatory practices over the market to ensure it functions effectively and efficiently. The Nigerian government has done this by enacting the Federal Competition and Consumer Protection Act, 2018 (FCCPA). This is a comprehensive legal framework with the objective of governing competition issues in Nigeria. Prior to its enactment, the competition law regime in Nigeria was grossly inadequate despite Nigeria being the biggest economy in Africa. This latest legislation has become a bold step in the right direction. This study will use the doctrinal methodology in analyzing the FCCPA, 2018 in order to discover the extent to which the Act will guard against anti-competitive practices and promote competitive markets for the benefit of the Nigerian economy and consumers. The study finds that although the FCCPA, 2018 provides for the regulation of competition in Nigeria, there is a need to effectively tackle the challenges to the implementation of the Act and the development of anti-trust jurisprudence in Nigeria. This study concludes that incisive implementation of competition law in Nigeria will help protect consumers and create a conducive environment for economic growth, development, and protection of consumers from obnoxious competition practices.

Keywords: Anti-competitive practices, competition law, competition regulation, consumer protection.

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Authors: Waralak Vongdoiwang Siricharoen

Abstract:

One of object oriented software developing problem is the difficulty of searching the appropriate and suitable objects for starting the system. In this work, ontologies appear in the part of supporting the object discovering in the initial of object oriented software developing. There are many researches try to demonstrate that there is a great potential between object model and ontologies. Constructing ontology from object model is called ontology engineering can be done; On the other hand, this research is aiming to support the idea of building object model from ontology is also promising and practical. Ontology classes are available online in any specific areas, which can be searched by semantic search engine. There are also many helping tools to do so; one of them which are used in this research is Protégé ontology editor and Visual Paradigm. To put them together give a great outcome. This research will be shown how it works efficiently with the real case study by using ontology classes in travel/tourism domain area. It needs to combine classes, properties, and relationships from more than two ontologies in order to generate the object model. In this paper presents a simple methodology framework which explains the process of discovering objects. The results show that this framework has great value while there is possible for expansion. Reusing of existing ontologies offers a much cheaper alternative than building new ones from scratch. More ontologies are becoming available on the web, and online ontologies libraries for storing and indexing ontologies are increasing in number and demand. Semantic and Ontologies search engines have also started to appear, to facilitate search and retrieval of online ontologies.

Keywords: Software Developing, Ontology, Ontology Library, Artificial Intelligent, Protégé, Object Model.

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Authors: Janet B. Badong-Badilla

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In Jesuit universities, laypersons, who come from the same or different faith backgrounds or traditions, are considered as collaborators in mission. The Jesuits themselves support the contributions of the lay partners in realizing the mission of the Society of Jesus and recognize the important role that they play in education. This study aims to investigate and generate particular notions and understandings of lived experiences of being a lay partner in Jesuit universities in the Philippines, particularly those involved in higher education. Using the qualitative approach as introduced by grounded theorist Barney Glaser, the lay partners’ concept of being a partner, as lived in higher education, is generated systematically from the data collected in the field primarily through in-depth interviews, field notes and observations. Glaser’s constant comparative method of analysis of data is used going through the phases of open coding, theoretical coding, and selective coding from memoing to theoretical sampling to sorting and then writing. In this study, Glaser’s grounded theory as a methodology will provide a substantial insight into and articulation of the layperson’s actual experience of being a partner of the Jesuits in education. Such articulation provides a phenomenological approach or framework to an understanding of the meaning and core characteristics of Jesuit-Lay partnership in Jesuit educational institution of higher learning in the country. This study is expected to provide a framework or model for lay partnership in academic institutions that have the same practice of having lay partners in mission.

Keywords: Grounded theory, Jesuit mission in higher education, lay partner, lived experience.

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Authors: Mohamad K. Hasan, Hameed Al-Qaheri

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Optimization plays an important role in most real world applications that support decision makers to take the right decision regarding the strategic directions and operations of the system they manage. Solutions for traffic management and traffic congestion problems are considered major problems that most decision making authorities for cities around the world are looking for. This review paper gives a full description of the traffic problem as part of the transportation planning process and present a view as a framework of urban transportation system analysis where the core of the system is a transportation network equilibrium model that is based on optimization techniques and that can also be used for evaluating an alternative solution or a combination of alternative solutions for the traffic congestion. Different transportation network equilibrium models are reviewed from the sequential approach to the multiclass combining trip generation, trip distribution, modal split, trip assignment and departure time model. A GIS-Based intelligent decision support system framework for urban transportation system analysis is suggested for implementation where the selection of optimized alternative solutions, single or packages, will be based on an intelligent agent rather than human being which would lead to reduction in time, cost and the elimination of the difficulty, by human being, for finding the best solution to the traffic congestion problem.

Keywords: Multiclass simultaneous transportation equilibrium models, transportation planning, urban transportation systems analysis, intelligent decision support system.

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Authors: Boon Yih Mah

Abstract:

Web-based Cognitive Writing Instruction (WeCWI) is a hybrid e-framework for the development of a web-based instruction (WBI), which contributes towards instructional design and language development. WeCWI divides its contribution in instructional design into macro and micro perspectives. In macro perspective, being a 21st century educator by disseminating knowledge and sharing ideas with the in-class and global learners is initiated. By leveraging the virtue of technology, WeCWI aims to transform an educator into an aggregator, curator, publisher, social networker and ultimately, a web-based instructor. Since the most notable contribution of integrating technology is being a tool of teaching as well as a stimulus for learning, WeCWI focuses on the use of contemporary web tools based on the multiple roles played by the 21st century educator. The micro perspective in instructional design draws attention to the pedagogical approaches focusing on three main aspects: reading, discussion, and writing. With the effective use of pedagogical approaches through free reading and enterprises, technology adds new dimensions and expands the boundaries of learning capacity. Lastly, WeCWI also imparts the fundamental theories and models for web-based instructors’ awareness such as interactionist theory, cognitive information processing (CIP) theory, computer-mediated communication (CMC), e-learning interactionalbased model, inquiry models, sensory mind model, and leaning styles model.

Keywords: WeCWI, instructional discovery, technological discovery, pedagogical discovery, theoretical discovery.

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Authors: Mohammed Sani Abdulai

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Ghana’s Public Financial Management reforms have been going on for some two decades now (1997/98 to 2017/18). Given this long period of reforms, Ghana in 2019 is putting together both a Public Financial Management (PFM) strategy and a Ghana Integrated Financial Management Information System (GIFMIS) strategy for the next 5-years (2020-2024). The primary aim of these dual strategies is assisting the country in moving beyond reforms to consolidation and sustainability. In this paper we, first, examined the evolution of Ghana’s PFM reforms. We, secondly, reviewed the legal and institutional reforms undertaken to strengthen the country’s key PFM institutions. Thirdly, we summarized the strengths and weaknesses identified by the 2018 Public Expenditure and Financial Accountability (PEFA) assessment of Ghana’s PFM system relating to its macro-fiscal framework, budget preparation and approval, budget execution, accounting and fiscal reporting as well as external scrutiny and audit. We, finally, considered what the country should be doing to achieve its intended goal of PFM consolidation and sustainability. Using a qualitative method of review and analysis of existing documents, we, through this paper, brought to the fore the lessons that could be learnt by other developing countries from Ghana’s PFM reforms experiences. These lessons included the need to: (a) undergird any PFM reform with a comprehensive PFM reform strategy; (b) undertake a legal and institutional reforms of the key PFM institutions; (c) assess the strengths and weaknesses of those reforms using PFM performance evaluation tools such as PEFA framework; and (d) move beyond reforms to consolidation and sustainability.

Keywords: Public financial management, public expenditure and financial accountability (PEFA), reforms, consolidation, sustainability.

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Authors: Sarabjeet Kaur Kochhar

Abstract:

With a surge of stream processing applications novel techniques are required for generation and analysis of association rules in streams. The traditional rule mining solutions cannot handle streams because they generally require multiple passes over the data and do not guarantee the results in a predictable, small time. Though researchers have been proposing algorithms for generation of rules from streams, there has not been much focus on their analysis. We propose Association rule profiling, a user centric process for analyzing association rules and attaching suitable profiles to them depending on their changing frequency behavior over a previous snapshot of time in a data stream. Association rule profiles provide insights into the changing nature of associations and can be used to characterize the associations. We discuss importance of characteristics such as predictability of linkages present in the data and propose metric to quantify it. We also show how association rule profiles can aid in generation of user specific, more understandable and actionable rules. The framework is implemented as SUPAR: System for Usercentric Profiling of Association Rules in streaming data. The proposed system offers following capabilities: i) Continuous monitoring of frequency of streaming item-sets and detection of significant changes therein for association rule profiling. ii) Computation of metrics for quantifying predictability of associations present in the data. iii) User-centric control of the characterization process: user can control the framework through a) constraint specification and b) non-interesting rule elimination.

Keywords: Data Streams, User subjectivity, Change detection, Association rule profiles, Predictability.

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Authors: Jindřiška Šedová

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In the past 20 years the economy of the Czech Republic has experienced substantial changes. In the 1990s the development was affected by the transformation which sought to establish the right conditions for privatization and creation of elementary market relations. In the last decade the characteristic elements such as private ownership and corresponding institutional framework have been strengthened. This development was marked by the accession of the Czech Republic to the EU. The Czech Republic is striving to reduce the difference between its level of economic development and the quality of institutional framework in comparison with other developed countries. The process of finding the adequate solutions has been hampered by the negative impact of the world financial crisis on the Czech Republic and the standard of living of its inhabitants. This contribution seeks to address the question of whether and to which extent the economic development of the transitive Czech economy is affected by the change in behaviour of households and their tendency to consumption, i.e. in the sense of reduction or increase in demand for goods and services. It aims to verify whether the increasing trend of household indebtedness and decreasing trend of saving pose a significant risk in the Czech Republic. At a general level the analysis aims to contribute to finding an answer to the question of whether the debt increase of Czech households is connected to the risk of "eating through" the borrowed money and whether Czech households risk falling into a debt trap. In addition to household indebtedness risks in the Czech Republic the analysis will focus on identification of specifics of the transformation phase of the Czech economy in comparison with the EU countries, or selected OECD countries.

Keywords: household indebtedness, household consumption, credits, financial literacy

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Authors: Ankit Agrawal, Ankush Mittal

Abstract:

A gene network gives the knowledge of the regulatory relationships among the genes. Each gene has its activators and inhibitors that regulate its expression positively and negatively respectively. Genes themselves are believed to act as activators and inhibitors of other genes. They can even activate one set of genes and inhibit another set. Identifying gene networks is one of the most crucial and challenging problems in Bioinformatics. Most work done so far either assumes that there is no time delay in gene regulation or there is a constant time delay. We here propose a Dynamic Time- Lagged Correlation Based Method (DTCBM) to learn the gene networks, which uses time-lagged correlation to find the potential gene interactions, and then uses a post-processing stage to remove false gene interactions to common parents, and finally uses dynamic correlation thresholds for each gene to construct the gene network. DTCBM finds correlation between gene expression signals shifted in time, and therefore takes into consideration the multi time delay relationships among the genes. The implementation of our method is done in MATLAB and experimental results on Saccharomyces cerevisiae gene expression data and comparison with other methods indicate that it has a better performance.

Keywords: Activators, correlation, dynamic time-lagged correlation based method, inhibitors, multi-time delay gene network.

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Authors: Amira Abbes Kheriji, Faouzi Bouani, Mekki Ksouri, Mohamed Ben Ahmed

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Model Predictive Control (MPC) is increasingly being proposed for real time applications and embedded systems. However comparing to PID controller, the implementation of the MPC in miniaturized devices like Field Programmable Gate Arrays (FPGA) and microcontrollers has historically been very small scale due to its complexity in implementation and its computation time requirement. At the same time, such embedded technologies have become an enabler for future manufacturing enterprises as well as a transformer of organizations and markets. Recently, advances in microelectronics and software allow such technique to be implemented in embedded systems. In this work, we take advantage of these recent advances in this area in the deployment of one of the most studied and applied control technique in the industrial engineering. In fact in this paper, we propose an efficient framework for implementation of Generalized Predictive Control (GPC) in the performed STM32 microcontroller. The STM32 keil starter kit based on a JTAG interface and the STM32 board was used to implement the proposed GPC firmware. Besides the GPC, the PID anti windup algorithm was also implemented using Keil development tools designed for ARM processor-based microcontroller devices and working with C/Cµ langage. A performances comparison study was done between both firmwares. This performances study show good execution speed and low computational burden. These results encourage to develop simple predictive algorithms to be programmed in industrial standard hardware. The main features of the proposed framework are illustrated through two examples and compared with the anti windup PID controller.

Keywords: Embedded systems, Model Predictive Control, microcontroller, Keil tool.

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Authors: Leong Lee, Cyriac Kandoth, Jennifer L. Leopold, Ronald L. Frank

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Protein 3D structure prediction has always been an important research area in bioinformatics. In particular, the prediction of secondary structure has been a well-studied research topic. Despite the recent breakthrough of combining multiple sequence alignment information and artificial intelligence algorithms to predict protein secondary structure, the Q3 accuracy of various computational prediction algorithms rarely has exceeded 75%. In a previous paper [1], this research team presented a rule-based method called RT-RICO (Relaxed Threshold Rule Induction from Coverings) to predict protein secondary structure. The average Q3 accuracy on the sample datasets using RT-RICO was 80.3%, an improvement over comparable computational methods. Although this demonstrated that RT-RICO might be a promising approach for predicting secondary structure, the algorithm-s computational complexity and program running time limited its use. Herein a parallelized implementation of a slightly modified RT-RICO approach is presented. This new version of the algorithm facilitated the testing of a much larger dataset of 396 protein domains [2]. Parallelized RTRICO achieved a Q3 score of 74.6%, which is higher than the consensus prediction accuracy of 72.9% that was achieved for the same test dataset by a combination of four secondary structure prediction methods [2].

Keywords: data mining, protein secondary structure prediction, parallelization.

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

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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: Yahia I. Mohamed, Ahmed I. Marzouk, Mohamed A. Yacout

Abstract:

Aim of this work was to study the genetic basis for oil accumulation in olive fruit via tracking DGAT2 (Diacylglycerol acyltransferase type-2) gene in three Egyptian Origen Olive cultivars namely Toffahi, Hamed and Maraki using molecular marker techniques and bioinformatics tools. Results illustrate that, firstly: specific genomic band of Maraki cultivars was identified as DGAT2 (Diacylglycerol acyltransferase type-2) and identical for this gene in Olea europaea with 100% of similarity. Secondly, differential genomic band of Maraki cultivars which produced from RAPD fingerprinting technique reflected predicted distinguished sequence which identified as DGAT2 (Diacylglycerol acyltransferase type-2) in Fragaria vesca subsp. Vesca with 76% of sequential similarity. Third and finally, specific genomic specific band of Hamed cultivars was identified as two fragments, 1- Olea europaea cultivar Koroneiki diacylglycerol acyltransferase type 2 mRNA, complete cds with two matches regions with 99% or 2- Predicted: Fragaria vesca subsp. vesca diacylglycerol O-acyltransferase 2-like (LOC101313050), mRNA with 86 % of similarity.

Keywords: Olea europaea, fingerprinting, Diacylglycerol acyltransferase type- 2 (DGAT2).

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Authors: Xiaocong Liu, Huazhen Wang, Ting He, Xiaozheng Li, Weihan Zhang, Jian Chen

Abstract:

The utilization of electronic medical record (EMR) data to establish the disease diagnosis model has become an important research content of biomedical informatics. Deep learning can automatically extract features from the massive data, which brings about breakthroughs in the study of EMR data. The challenge is that deep learning lacks semantic knowledge, which leads to impracticability in medical science. This research proposes a method of incorporating lexical-semantic knowledge from abundant entities into a convolutional neural network (CNN) framework for pediatric disease diagnosis. Firstly, medical terms are vectorized into Lexical Semantic Vectors (LSV), which are concatenated with the embedded word vectors of word2vec to enrich the feature representation. Secondly, the semantic distribution of medical terms serves as Semantic Decision Guide (SDG) for the optimization of deep learning models. The study evaluates the performance of LSV-SDG-CNN model on four kinds of Chinese EMR datasets. Additionally, CNN, LSV-CNN, and SDG-CNN are designed as baseline models for comparison. The experimental results show that LSV-SDG-CNN model outperforms baseline models on four kinds of Chinese EMR datasets. The best configuration of the model yielded an F1 score of 86.20%. The results clearly demonstrate that CNN has been effectively guided and optimized by lexical-semantic knowledge, and LSV-SDG-CNN model improves the disease classification accuracy with a clear margin.

Keywords: lexical semantics, feature representation, semantic decision, convolutional neural network, electronic medical record

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Authors: Yesubai Rubavathi Charles, Ravi Ramraj

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In order to retrieve images efficiently from a large database, a unique method integrating color and texture features using genetic programming has been proposed. Opponent color histogram which gives shadow, shade, and light intensity invariant property is employed in the proposed framework for extracting color features. For texture feature extraction, fast discrete curvelet transform which captures more orientation information at different scales is incorporated to represent curved like edges. The recent scenario in the issues of image retrieval is to reduce the semantic gap between user’s preference and low level features. To address this concern, genetic algorithm combined with relevance feedback is embedded to reduce semantic gap and retrieve user’s preference images. Extensive and comparative experiments have been conducted to evaluate proposed framework for content based image retrieval on two databases, i.e., COIL-100 and Corel-1000. Experimental results clearly show that the proposed system surpassed other existing systems in terms of precision and recall. The proposed work achieves highest performance with average precision of 88.2% on COIL-100 and 76.3% on Corel, the average recall of 69.9% on COIL and 76.3% on Corel. Thus, the experimental results confirm that the proposed content based image retrieval system architecture attains better solution for image retrieval.

Keywords: Content based image retrieval, Curvelet transform, Genetic algorithm, Opponent color histogram, Relevance feedback.

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Authors: Anthony Wachs, Guillaume Vinay, Gilles Ferrer, Jacques Kouakou, Calin Dan, Laurence Girolami

Abstract:

An original Direct Numerical Simulation (DNS) method to tackle the problem of particulate flows at moderate to high concentration and finite Reynolds number is presented. Our method is built on the framework established by Glowinski and his coworkers [1] in the sense that we use their Distributed Lagrange Multiplier/Fictitious Domain (DLM/FD) formulation and their operator-splitting idea but differs in the treatment of particle collisions. The novelty of our contribution relies on replacing the simple artificial repulsive force based collision model usually employed in the literature by an efficient Discrete Element Method (DEM) granular solver. The use of our DEM solver enables us to consider particles of arbitrary shape (at least convex) and to account for actual contacts, in the sense that particles actually touch each other, in contrast with the simple repulsive force based collision model. We recently upgraded our serial code, GRIFF 1 [2], to full MPI capabilities. Our new code, PeliGRIFF 2, is developed under the framework of the full MPI open source platform PELICANS [3]. The new MPI capabilities of PeliGRIFF open new perspectives in the study of particulate flows and significantly increase the number of particles that can be considered in a full DNS approach: O(100000) in 2D and O(10000) in 3D. Results on the 2D/3D sedimentation/fluidization of isometric polygonal/polyedral particles with collisions are presented.

Keywords: Particulate flow, distributed lagrange multiplier/fictitious domain method, discrete element method, polygonal shape, sedimentation, distributed computing, MPI

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Authors: Olayiwola M.O., Gbolagade A .W., Akinpelu F. O.

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In this work, we present a reliable framework to solve boundary value problems with particular significance in solid mechanics. These problems are used as mathematical models in deformation of beams. The algorithm rests mainly on a relatively new technique, the Variational Iteration Method. Some examples are given to confirm the efficiency and the accuracy of the method.

Keywords: Variational iteration method, boundary value problems, convergence, restricted variation.

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Authors: Raymond Xu, Ashley Hua, Andrew Wang, Yuru Lin

Abstract:

During COVID-19, the depression rate has increased dramatically. Young adults are most vulnerable to the mental health effects of the pandemic. Lower-income families have a higher ratio to be diagnosed with depression than the general population, but less access to clinics. This research aims to achieve early depression detection at low cost, large scale, and high accuracy with an interdisciplinary approach by incorporating clinical practices defined by American Psychiatric Association (APA) as well as multimodal AI framework. The proposed approach detected the nine depression symptoms with Natural Language Processing sentiment analysis and a symptom-based Lexicon uniquely designed for young adults. The experiments were conducted on the multimedia survey results from adolescents and young adults and unbiased Twitter communications. The result was further aggregated with the facial emotional cues analyzed by the Convolutional Neural Network on the multimedia survey videos. Five experiments each conducted on 10k data entries reached consistent results with an average accuracy of 88.31%, higher than the existing natural language analysis models. This approach can reach 300+ million daily active Twitter users and is highly accessible by low-income populations to promote early depression detection to raise awareness in adolescents and young adults and reveal complementary cues to assist clinical depression diagnosis.

Keywords: Artificial intelligence, depression detection, facial emotion recognition, natural language processing, mental disorder.

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