Search results for: Categorical data sequences

Authors: R. Blicha

Abstract:

High Peak to Average Power Ratio (PAPR) of the transmitted signal is a serious problem in multicarrier systems (MC), such as Orthogonal Frequency Division Multiplexing (OFDM), or in Multi-Carrier Code Division Multiple Access (MC-CDMA) systems, due to large number of subcarriers. This effect is possible reduce with some PAPR reduction techniques. Spreading sequences at the presence of Saleh and Rapp models of high power amplifier (HPA) have big influence on the behavior of system. In this paper we investigate the bit-error-rate (BER) performance of MC-CDMA systems. Basically we can see from simulations that the MC-CDMA system with Iterative algorithm can be providing significantly better results than the MC-CDMA system. The results of our analyses are verified via simulation.

Keywords: MC-CDMA, Iterative algorithm, PAPR, BER, Saleh, Rapp, Spreading Sequences.

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Authors: Sheikh Shams Azam, Manoj Raju, Venkatesh Pagidimarri, Vamsi Kasivajjala

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Over the past decade, there has been a steep rise in the data-driven analysis in major areas of medicine, such as clinical decision support system, survival analysis, patient similarity analysis, image analytics etc. Most of the data in the field are well-structured and available in numerical or categorical formats which can be used for experiments directly. But on the opposite end of the spectrum, there exists a wide expanse of data that is intractable for direct analysis owing to its unstructured nature which can be found in the form of discharge summaries, clinical notes, procedural notes which are in human written narrative format and neither have any relational model nor any standard grammatical structure. An important step in the utilization of these texts for such studies is to transform and process the data to retrieve structured information from the haystack of irrelevant data using information retrieval and data mining techniques. To address this problem, the authors present Q-Map in this paper, which is a simple yet robust system that can sift through massive datasets with unregulated formats to retrieve structured information aggressively and efficiently. It is backed by an effective mining technique which is based on a string matching algorithm that is indexed on curated knowledge sources, that is both fast and configurable. The authors also briefly examine its comparative performance with MetaMap, one of the most reputed tools for medical concepts retrieval and present the advantages the former displays over the latter.

Keywords: Information retrieval (IR), unified medical language system (UMLS), Syntax Based Analysis, natural language processing (NLP), medical informatics.

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Authors: Yuan-Jye Tseng, Fang-Yu Yu, Feng-Yi Huang

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A green design for assembly model is presented to integrate design evaluation and assembly and disassembly sequence planning by evaluating the three activities in one integrated model. For an assembled product, an assembly sequence planning model is required for assembling the product at the start of the product life cycle. A disassembly sequence planning model is needed for disassembling the product at the end. In a green product life cycle, it is important to plan how a product can be disassembled, reused, or recycled, before the product is actually assembled and produced. Given a product requirement, there may be several design alternative cases to design the same product. In the different design cases, the assembly and disassembly sequences for producing the product can be different. In this research, a new model is presented to concurrently evaluate the design and plan the assembly and disassembly sequences. First, the components are represented by using graph based models. Next, a particle swarm optimization (PSO) method with a new encoding scheme is developed. In the new PSO encoding scheme, a particle is represented by a position matrix defining an assembly sequence and a disassembly sequence. The assembly and disassembly sequences can be simultaneously planned with an objective of minimizing the total of assembly costs and disassembly costs. The test results show that the presented method is feasible and efficient for solving the integrated design evaluation and assembly and disassembly sequence planning problem. An example product is implemented and illustrated in this paper.

Keywords: green design, assembly and disassembly sequence planning, green design for assembly, particle swarm optimization.

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Authors: Jyh-Da Wei, Hsin-Chen Tsai

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This work presents a novel means of extracting fixedlength parameters from voice signals, such that words can be recognized in linear time. The power and the zero crossing rate are first calculated segment by segment from a voice signal; by doing so, two feature sequences are generated. We then construct an FIR system across these two sequences. The parameters of this FIR system, used as the input of a multilayer proceptron recognizer, can be derived by recursive LSE (least-square estimation), implying that the complexity of overall process is linear to the signal size. In the second part of this work, we introduce a weighting factor λ to emphasize recent input; therefore, we can further recognize continuous speech signals. Experiments employ the voice signals of numbers, from zero to nine, spoken in Mandarin Chinese. The proposed method is verified to recognize voice signals efficiently and accurately.

Keywords: Speech Recognition, FIR system, Recursive LSE, Multilayer Perceptron

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Authors: Erik Lilienblum, Robert Niese, Bernd Michaelis

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This paper proposes a novel stereo vision technique for top view book scanners which provide us with dense 3d point clouds of page surfaces. This is a precondition to dewarp bound volumes independent of 2d information on the page. Our method is based on algorithms, which normally require the projection of pattern sequences with structured light. We use image sequences of the moving stripe lighting of the top view scanner instead of an additional light projection. Thus the stereo vision setup is simplified without losing measurement accuracy. Furthermore we improve a surface model dewarping method through introducing a difference vector based on real measurements. Although our proposed method is hardly expensive neither in calculation time nor in hardware requirements we present good dewarping results even for difficult examples.

Keywords: stereo vision, 3d surface reconstruction, dewarpingdocuments, book scanner

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Authors: Hadi Seyedarabi, Ali Aghagolzadeh, Sohrab Khanmohammadi

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Face and facial expressions play essential roles in interpersonal communication. Most of the current works on the facial expression recognition attempt to recognize a small set of the prototypic expressions such as happy, surprise, anger, sad, disgust and fear. However the most of the human emotions are communicated by changes in one or two of discrete features. In this paper, we develop a facial expressions synthesis system, based on the facial characteristic points (FCP's) tracking in the frontal image sequences. Selected FCP's are automatically tracked using a crosscorrelation based optical flow. The proposed synthesis system uses a simple deformable facial features model with a few set of control points that can be tracked in original facial image sequences.

Keywords: Deformable face model, facial animation, facialcharacteristic points, optical flow.

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Authors: Jorge Maestre Vidal, Ana Lucila Sandoval Orozco, Luis Javier García Villalba

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With the increase in popularity of mobile devices, new and varied forms of malware have emerged. Consequently, the organizations for cyberdefense have echoed the need to deploy more effective defensive schemes adapted to the challenges posed by these recent monitoring environments. In order to contribute to their development, this paper presents a malware detection strategy for mobile devices based on sequence alignment algorithms. Unlike the previous proposals, only the system calls performed during the startup of applications are studied. In this way, it is possible to efficiently study in depth, the sequences of system calls executed by the applications just downloaded from app stores, and initialize them in a secure and isolated environment. As demonstrated in the performed experimentation, most of the analyzed malicious activities were successfully identified in their boot processes.

Keywords: Android, information security, intrusion detection systems, malware, mobile devices.

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Authors: Yasmeen A. S. Essawy, Khaled Nassar

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With the rapid increase of complexity in the building industry, professionals in the A/E/C industry were forced to adopt Building Information Modeling (BIM) in order to enhance the communication between the different project stakeholders throughout the project life cycle and create a semantic object-oriented building model that can support geometric-topological analysis of building elements during design and construction. This paper presents a model that extracts topological relationships and geometrical properties of building elements from an existing fully designed BIM, and maps this information into a directed acyclic Elemental Graph Data Model (EGDM). The model incorporates BIM-based search algorithms for automatic deduction of geometrical data and topological relationships for each building element type. Using graph search algorithms, such as Depth First Search (DFS) and topological sortings, all possible construction sequences can be generated and compared against production and construction rules to generate an optimized construction sequence and its associated schedule. The model is implemented in a C# platform.

Keywords: Building information modeling, elemental graph data model, geometric and topological data models, and graph theory.

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Authors: Mohammad N. Alanazi, David A. Gustafson

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In this article, we introduce a new approach for analyzing UML designs to detect the inconsistencies between multiple state diagrams and sequence diagrams. The Super State Analysis (SSA) identifies the inconsistencies in super states, single step transitions, and sequences. Because SSA considers multiple UML state diagrams, it discovers inconsistencies that cannot be discovered when considering only a single UML state diagram. We have introduced a transition set that captures relationship information that is not specifiable in UML diagrams. The SSA model uses the transition set to link transitions of multiple state diagrams together. The analysis generates three different sets automatically. These sets are compared to the provided sets to detect the inconsistencies. SSA identifies five types of inconsistencies: impossible super states, unreachable super states, illegal transitions, missing transitions, and illegal sequences.

Keywords: Modeling Languages, Object-Oriented Analysis, Sequence Diagrams, Software Models, State Diagrams, UML.

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Authors: Rao Fu, Jie Chen, Shutian Zeng, Yiping Zhuang, Agus Sudjianto

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Generative Adversarial Net (GAN) has proved to be a powerful machine learning tool in image data analysis and generation. In this paper, we propose to use Conditional Generative Adversarial Net (CGAN) to learn and simulate time series data. The conditions include both categorical and continuous variables with different auxiliary information. Our simulation studies show that CGAN has the capability to learn different types of normal and heavy-tailed distributions, as well as dependent structures of different time series. It also has the capability to generate conditional predictive distributions consistent with training data distributions. We also provide an in-depth discussion on the rationale behind GAN and the neural networks as hierarchical splines to establish a clear connection with existing statistical methods of distribution generation. In practice, CGAN has a wide range of applications in market risk and counterparty risk analysis: it can be applied to learn historical data and generate scenarios for the calculation of Value-at-Risk (VaR) and Expected Shortfall (ES), and it can also predict the movement of the market risk factors. We present a real data analysis including a backtesting to demonstrate that CGAN can outperform Historical Simulation (HS), a popular method in market risk analysis to calculate VaR. CGAN can also be applied in economic time series modeling and forecasting. In this regard, we have included an example of hypothetical shock analysis for economic models and the generation of potential CCAR scenarios by CGAN at the end of the paper.

Keywords: Conditional Generative Adversarial Net, market and credit risk management, neural network, time series.

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Authors: Feng-Yi Huang, Yuan-Jye Tseng

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In the traditional concept of product life cycle management, the activities of design, manufacturing, and assembly are performed in a sequential way. The drawback is that the considerations in design may contradict the considerations in manufacturing and assembly. The different designs of components can lead to different assembly sequences. Therefore, in some cases, a good design may result in a high cost in the downstream assembly activities. In this research, an integrated design evaluation and assembly sequence planning model is presented. Given a product requirement, there may be several design alternative cases to design the components for the same product. If a different design case is selected, the assembly sequence for constructing the product can be different. In this paper, first, the designed components are represented by using graph based models. The graph based models are transformed to assembly precedence constraints and assembly costs. A particle swarm optimization (PSO) approach is presented by encoding a particle using a position matrix defined by the design cases and the assembly sequences. The PSO algorithm simultaneously performs design evaluation and assembly sequence planning with an objective of minimizing the total assembly costs. As a result, the design cases and the assembly sequences can both be optimized. The main contribution lies in the new concept of integrated design evaluation and assembly sequence planning model and the new PSO solution method. The test results show that the presented method is feasible and efficient for solving the integrated design evaluation and assembly planning problem. In this paper, an example product is tested and illustrated.

Keywords: assembly sequence planning, design evaluation, design for assembly, particle swarm optimization

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Authors: Natarajan Vijayarangan, Prasanna S. Bidare

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Cryptography, Image watermarking and E-banking are filled with apparent oxymora and paradoxes. Random sequences are used as keys to encrypt information to be used as watermark during embedding the watermark and also to extract the watermark during detection. Also, the keys are very much utilized for 24x7x365 banking operations. Therefore a deterministic random sequence is very much useful for online applications. In order to obtain the same random sequence, we need to supply the same seed to the generator. Many researchers have used Deterministic Random Number Generators (DRNGs) for cryptographic applications and Pseudo Noise Random sequences (PNs) for watermarking. Even though, there are some weaknesses in PN due to attacks, the research community used it mostly in digital watermarking. On the other hand, DRNGs have not been widely used in online watermarking due to its computational complexity and non-robustness. Therefore, we have invented a new design of generating DRNG using Pi-series to make it useful for online Cryptographic, Digital watermarking and Banking applications.

Keywords: E-tokens, LFSR, non-linear, Pi series, pseudo random number.

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Authors: L. Rodriguez-Benitez, J. Moreno-Garcia, J.J. Castro-Schez, C. Solana, L. Jimenez

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In this paper the use of sequential machines for recognizing actions taken by the objects detected by a general tracking algorithm is proposed. The system may deal with the uncertainty inherent in medium-level vision data. For this purpose, fuzzification of input data is performed. Besides, this transformation allows to manage data independently of the tracking application selected and enables adding characteristics of the analyzed scenario. The representation of actions by means of an automaton and the generation of the input symbols for finite automaton depending on the object and action compared are described. The output of the comparison process between an object and an action is a numerical value that represents the membership of the object to the action. This value is computed depending on how similar the object and the action are. The work concludes with the application of the proposed technique to identify the behavior of vehicles in road traffic scenes.

Keywords: Approximate reasoning, finite state machines, video analysis.

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Authors: Razib M. Othman, Safaai Deris, Rosli M. Illias

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Gene Ontology terms have been actively used to annotate various protein sets. SWISS-PROT, TrEMBL, and InterPro are protein databases that are annotated according to the Gene Ontology terms. However, direct implementation of the Gene Ontology terms for annotation of anonymous protein sequences is not easy, especially for species not commonly represented in biological databases. UTMGO is developed as a tool that allows the user to quickly and easily search for a group of semantically related Gene Ontology terms. The applicability of the UTMGO is demonstrated by applying it to annotation of anonymous protein sequence. The extended UTMGO uses the Gene Ontology terms together with protein sequences associated with the terms to perform the annotation task. GOPET, GOtcha, GoFigure, and JAFA are used to compare the performance of the extended UTMGO.

Keywords: Anonymous protein sequence, Gene Ontology, Protein sequence annotation, Protein sequence alignment

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Authors: Rosalyn R. Porle, Ali Chekima, Farrah Wong, G. Sainarayanan

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Arms detection is one of the fundamental problems in human motion analysis application. The arms are considered as the most challenging body part to be detected since its pose and speed varies in image sequences. Moreover, the arms are usually occluded with other body parts such as the head and torso. In this paper, histogram-based skin colour segmentation is proposed to detect the arms in image sequences. Six different colour spaces namely RGB, rgb, HSI, TSL, SCT and CIELAB are evaluated to determine the best colour space for this segmentation procedure. The evaluation is divided into three categories, which are single colour component, colour without luminance and colour with luminance. The performance is measured using True Positive (TP) and True Negative (TN) on 250 images with manual ground truth. The best colour is selected based on the highest TN value followed by the highest TP value.

Keywords: image colour analysis, image motion analysis, skin, wavelet transform.

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Authors: Pedro Pablo González Pérez, Hiram I. Beltrán, Arturo Rojo-Domínguez, Máximo EduardoSánchez Gutiérrez

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Multi-agent system approach has proven to be an effective and appropriate abstraction level to construct whole models of a diversity of biological problems, integrating aspects which can be found both in "micro" and "macro" approaches when modeling this type of phenomena. Taking into account these considerations, this paper presents the important computational characteristics to be gathered into a novel bioinformatics framework built upon a multiagent architecture. The version of the tool presented herein allows studying and exploring complex problems belonging principally to structural biology, such as protein folding. The bioinformatics framework is used as a virtual laboratory to explore a minimalist model of protein folding as a test case. In order to show the laboratory concept of the platform as well as its flexibility and adaptability, we studied the folding of two particular sequences, one of 45-mer and another of 64-mer, both described by an HP model (only hydrophobic and polar residues) and coarse grained 2D-square lattice. According to the discussion section of this piece of work, these two sequences were chosen as breaking points towards the platform, in order to determine the tools to be created or improved in such a way to overcome the needs of a particular computation and analysis of a given tough sequence. The backwards philosophy herein is that the continuous studying of sequences provides itself important points to be added into the platform, to any time improve its efficiency, as is demonstrated herein.

Keywords: multi-agent systems, blackboard-based agent architecture, bioinformatics framework, virtual laboratory, protein folding.

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Authors: Mourad Moussa, Ali Douik, Hassani Messaoud

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In this paper, we present a comparative study between two computer vision systems for objects recognition and tracking, these algorithms describe two different approach based on regions constituted by a set of pixels which parameterized objects in shot sequences. For the image segmentation and objects detection, the FCM technique is used, the overlapping between cluster's distribution is minimized by the use of suitable color space (other that the RGB one). The first technique takes into account a priori probabilities governing the computation of various clusters to track objects. A Parzen kernel method is described and allows identifying the players in each frame, we also show the importance of standard deviation value research of the Gaussian probability density function. Region matching is carried out by an algorithm that operates on the Mahalanobis distance between region descriptors in two subsequent frames and uses singular value decomposition to compute a set of correspondences satisfying both the principle of proximity and the principle of exclusion.

Keywords: Image segmentation, objects tracking, Parzen window, singular value decomposition, target recognition.

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Authors: Parvaneh Shabanzadeh, Malik Hj Abu Hassan, Leong Wah June, Maryam Mohagheghtabar

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Clustering is one of an interesting data mining topics that can be applied in many fields. Recently, the problem of cluster analysis is formulated as a problem of nonsmooth, nonconvex optimization, and an algorithm for solving the cluster analysis problem based on nonsmooth optimization techniques is developed. This optimization problem has a number of characteristics that make it challenging: it has many local minimum, the optimization variables can be either continuous or categorical, and there are no exact analytical derivatives. In this study we show how to apply a particular class of optimization methods known as pattern search methods to address these challenges. These methods do not explicitly use derivatives, an important feature that has not been addressed in previous studies. Results of numerical experiments are presented which demonstrate the effectiveness of the proposed method.

Keywords: Clustering functions, Non-smooth Optimization, Nonconvex Optimization, Pattern Search Method.

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Authors: Michal Mardiak, Jaroslav Polec

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In this paper we proposed comparison of four content based objective metrics with results of subjective tests from 80 video sequences. We also include two objective metrics VQM and SSIM to our comparison to serve as “reference” objective metrics because their pros and cons have already been published. Each of the video sequence was preprocessed by the region recognition algorithm and then the particular objective video quality metric were calculated i.e. mutual information, angular distance, moment of angle and normalized cross-correlation measure. The Pearson coefficient was calculated to express metrics relationship to accuracy of the model and the Spearman rank order correlation coefficient to represent the metrics relationship to monotonicity. The results show that model with the mutual information as objective metric provides best result and it is suitable for evaluating quality of video sequences.

Keywords: Objective quality metrics, mutual information, region recognition, content based metrics

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Authors: V. Girondel, L. Bonnaud, A. Caplier, M. Rombaut

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This paper presents various classifiers results from a system that can automatically recognize four different static human body postures in video sequences. The considered postures are standing, sitting, squatting, and lying. The three classifiers considered are a naïve one and two based on the belief theory. The belief theory-based classifiers use either a classic or restricted plausibility criterion to make a decision after data fusion. The data come from the people 2D segmentation and from their face localization. Measurements consist in distances relative to a reference posture. The efficiency and the limits of the different classifiers on the recognition system are highlighted thanks to the analysis of a great number of results. This system allows real-time processing.

Keywords: Belief theory, classifiers comparison, data fusion, human motion analysis, real-time processing, static posture recognition.

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Authors: Nadezhda M. Usmanova, Nikolai V. Tomilin

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Mammalian genomes contain large number of retroelements (SINEs, LINEs and LTRs) which could affect expression of protein coding genes through associated transcription factor binding sites (TFBS). Activity of the retroelement-associated TFBS in many genes is confirmed experimentally but their global functional impact remains unclear. Human SINEs (Alu repeats) and mouse SINEs (B1 and B2 repeats) are known to be clustered in GCrich gene rich genome segments consistent with the view that they can contribute to regulation of gene expression. We have shown earlier that Alu are involved in formation of cis-regulatory modules (clusters of TFBS) in human promoters, and other authors reported that Alu located near promoter CpG islands have an increased frequency of CpG dinucleotides suggesting that these Alu are undermethylated. Human Alu and mouse B1/B2 elements have an internal bipartite promoter for RNA polymerase III containing conserved sequence motif called B-box which can bind basal transcription complex TFIIIC. It has been recently shown that TFIIIC binding to B-box leads to formation of a boundary which limits spread of repressive chromatin modifications in S. pombe. SINEassociated B-boxes may have similar function but conservation of TFIIIC binding sites in SINEs located near mammalian promoters has not been studied earlier. Here we analysed abundance and distribution of retroelements (SINEs, LINEs and LTRs) in annotated sequences of the Database of mammalian transcription start sites (DBTSS). Fractions of SINEs in human and mouse promoters are slightly lower than in all genome but >40% of human and mouse promoters contain Alu or B1/B2 elements within -1000 to +200 bp interval relative to transcription start site (TSS). Most of these SINEs is associated with distal segments of promoters (-1000 to -200 bp relative to TSS) indicating that their insertion at distances >200 bp upstream of TSS is tolerated during evolution. Distribution of SINEs in promoters correlates negatively with the distribution of CpG sequences. Using analysis of abundance of 12-mer motifs from the B1 and Alu consensus sequences in genome and DBTSS it has been confirmed that some subsegments of Alu and B1 elements are poorly conserved which depends in part on the presence of CpG dinucleotides. One of these CpG-containing subsegments in B1 elements overlaps with SINE-associated B-box and it shows better conservation in DBTSS compared to genomic sequences. It has been also studied conservation in DBTSS and genome of the B-box containing segments of old (AluJ, AluS) and young (AluY) Alu repeats and found that CpG sequence of the B-box of old Alu is better conserved in DBTSS than in genome. This indicates that Bbox- associated CpGs in promoters are better protected from methylation and mutation than B-box-associated CpGs in genomic SINEs. These results are consistent with the view that potential TFIIIC binding motifs in SINEs associated with human and mouse promoters may be functionally important. These motifs may protect promoters from repressive histone modifications which spread from adjacent sequences. This can potentially explain well known clustering of SINEs in GC-rich gene rich genome compartments and existence of unmethylated CpG islands.

Keywords: Retroelement, promoter, CpG island, DNAmethylation.

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Authors: Danilo López, Johana Hernández, Edwin Rivas

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The use of the Multilayer Perceptron Neural Networks (MLPNN) technique is presented to estimate the future state of use of a licensed channel by primary users (PUs); this will be useful at the spectral decision stage in cognitive radio networks (CRN) to determine approximately in which time instants of future may secondary users (SUs) opportunistically use the spectral bandwidth to send data through the primary wireless network. To validate the results, sequences of occupancy data of channel were generated by simulation. The results show that the prediction percentage is greater than 60% in some of the tests carried out.

Keywords: Cognitive radio, neural network, prediction, primary user.

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Authors: Mallikarjun B. Channappagoudar, Pallapa Venkataram

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As a node monitoring protocol, which is a part of network management, operates in distributed manner, conformance testing of such protocols is more tedious than testing a peer-to-peer protocol. Various works carried out to give the methodology to do conformance testing of distributed protocol. In this paper, we have presented a formal approach for conformance testing of a Node Monitoring Protocol, which uses both static and mobile agents, for MANETs. First, we use SDL to obtain MSCs, which represent the scenario descriptions by sequence diagrams, which in turn generate test sequences and test cases. Later, Testing and Test Control Notation Version-3 (TTCN-3) is used to execute test cases with respect to generated test sequences to know the conformance of protocol against the given specification. This approach shows, the effective conformance testing of the distributed protocols for the network with varying node density and complex behavior. Experimental results for the protocol scenario represent the effectiveness of the method used.

Keywords: Conformance Testing, FSM, Mobile agent, TTCN, Test sequence.

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Authors: T. Holden, G. Tremberger, Jr, E. Cheung, R. Subramaniam, R. Sullivan, N. Gadura, P. Schneider, P. Marchese, A. Flamholz, T. Cheung, D. Lieberman

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A nucleotide sequence can be expressed as a numerical sequence when each nucleotide is assigned its proton number. A resulting gene numerical sequence can be investigated for its fractal dimension in terms of evolution and chemical properties for comparative studies. We have investigated such nucleotide fluctuation in the 16S rRNA gene of archaea thermophiles. The studied archaea thermophiles were archaeoglobus fulgidus, methanothermobacter thermautotrophicus, methanocaldococcus jannaschii, pyrococcus horikoshii, and thermoplasma acidophilum. The studied five archaea-euryarchaeota thermophiles have fractal dimension values ranging from 1.93 to 1.97. Computer simulation shows that random sequences would have an average of about 2 with a standard deviation about 0.015. The fractal dimension was found to correlate (negative correlation) with the thermophile-s optimal growth temperature with R2 value of 0.90 (N =5). The inclusion of two aracheae-crenarchaeota thermophiles reduces the R2 value to 0.66 (N = 7). Further inclusion of two bacterial thermophiles reduces the R2 value to 0.50 (N =9). The fractal dimension is correlated (positive) to the sequence GC content with an R2 value of 0.89 for the five archaea-euryarchaeota thermophiles (and 0.74 for the entire set of N = 9), although computer simulation shows little correlation. The highest correlation (positive) was found to be between the fractal dimension and di-nucleotide Shannon entropy. However Shannon entropy and sequence GC content were observed to correlate with optimal growth temperature having an R2 of 0.8 (negative), and 0.88 (positive), respectively, for the entire set of 9 thermophiles; thus the correlation lacks species specificity. Together with another correlation study of bacterial radiation dosage with RecA repair gene sequence fractal dimension, it is postulated that fractal dimension analysis is a sensitive tool for studying the relationship between genotype and phenotype among closely related sequences.

Keywords: Fractal dimension, archaea thermophiles, Shannon entropy, GC content

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Authors: T. Kjosmoen, T. Ryen, T. Eftestøl

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In biological and biomedical research motif finding tools are important in locating regulatory elements in DNA sequences. There are many such motif finding tools available, which often yield position weight matrices and significance indicators. These indicators, p-values and E-values, describe the likelihood that a motif alignment is generated by the background process, and the expected number of occurrences of the motif in the data set, respectively. The various tools often estimate these indicators differently, making them not directly comparable. One approach for comparing motifs from different tools, is computing the E-value as the product of the p-value and the number of possible alignments in the data set. In this paper we explore the combinatorics of the motif alignment models OOPS, ZOOPS, and ANR, and propose a generic algorithm for computing the number of possible combinations accurately. We also show that using the wrong alignment model can give E-values that significantly diverge from their true values.

Keywords: Motif alignment, combinatorics, p-value, E-value, OOPS, ZOOPS, ANR.

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Authors: S. Makal, L. Ozyilmaz, S. Palavaroglu

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Gene, principal unit of inheritance, is an ordered sequence of nucleotides. The genes of eukaryotic organisms include alternating segments of exons and introns. The region of Deoxyribonucleic acid (DNA) within a gene containing instructions for coding a protein is called exon. On the other hand, non-coding regions called introns are another part of DNA that regulates gene expression by removing from the messenger Ribonucleic acid (RNA) in a splicing process. This paper proposes to determine splice junctions that are exon-intron boundaries by analyzing DNA sequences. A splice junction can be either exon-intron (EI) or intron exon (IE). Because of the popularity and compatibility of the artificial neural network (ANN) in genetic fields; various ANN models are applied in this research. Multi-layer Perceptron (MLP), Radial Basis Function (RBF) and Generalized Regression Neural Networks (GRNN) are used to analyze and detect the splice junctions of gene sequences. 10-fold cross validation is used to demonstrate the accuracy of networks. The real performances of these networks are found by applying Receiver Operating Characteristic (ROC) analysis.

Keywords: Gene, neural networks, ROC analysis, splice junctions.

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Authors: Mohamed A. Saleem

Abstract:

Using mostly seismic data, this study intends to show some examples of igneous intrusions found in some areas of the Sirt Basin and explore the period of their emplacement as well as the interrelationships between these sills. The study area is located in the south of the Zallah Trough, south-west Sirt basin, Libya. It is precisely between the longitudes 18.35ᵒ E and 19.35ᵒ E, and the latitudes 27.8ᵒ N and 28.0ᵒ N. Based on a variety of criteria that are usually used as marks on the igneous intrusions, 12 igneous intrusions (Sills), have been detected and analysed using 3D seismic data. One or more of the following were used as identification criteria: the high amplitude reflectors paired with abrupt reflector terminations, vertical offsets, or what is described as a dike-like connection, the violation, the saucer form, and the roughness. Because of their laying between the hosting layers, the majority of these intrusions are classified as sills. Another distinguishing feature is the intersection geometry link between some of these sills. Every single sill has given a name just to distinguish the sills from each other such as S-1, S-2, and … S-12. To avoid the repetition of description, the common characteristics and some statistics of these sills are shown in summary tables, while the specific characters that are not common and have been noticed for each sill are shown individually. The sills, S-1, S-2, and S-3, are approximately parallel to one other, with the shape of these sills being governed by the syncline structure of their host layers. The faults that dominated the strata (pre-upper Cretaceous strata) have a significant impact on the sills; they caused their discontinuity, while the upper layers have a shape of anticlines. S-1 and S-10 are the group's deepest and highest sills, respectively, with S-1 seated near the basement's top and S-10 extending into the sequence of the upper cretaceous. The dramatic escalation of sill S-4 can be seen in North-South profiles. The majority of the interpreted sills are influenced and impacted by a large number of normal faults that strike in various directions and propagate vertically from the surface to the basement's top. This indicates that the sediment sequences were existed before the sill’s intrusion, deposited, and that the younger faults occurred more recently. The pre-upper cretaceous unit is the current geological depth for the Sills S-1, S-2 … S-9, while Sills S-10, S-11, and S-12 are hosted by the Cretaceous unit. Over the sills S-1, S-2, and S-3, which are the deepest sills, the pre-upper cretaceous surface has a slightly forced folding, these forced folding is also noticed above the right and left tips of sill S-8 and S-6, respectively, while the absence of these marks on the above sequences of layers supports the idea that the aforementioned sills were emplaced during the early upper cretaceous period.

Keywords: Sirt Basin, Zallah Trough, igneous intrusions, seismic data.

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Authors: Tahani Aljohani, Jialin Yu, Alexandra. I. Cristea

Abstract:

The more an educational system knows about a learner, the more personalised interaction it can provide, which leads to better learning. However, asking a learner directly is potentially disruptive, and often ignored by learners. Especially in the booming realm of MOOC Massive Online Learning platforms, only a very low percentage of users disclose demographic information about themselves. Thus, in this paper, we aim to predict learners’ demographic characteristics, by proposing an approach using linguistically motivated Deep Learning Architectures for Learner Profiling, particularly targeting gender prediction on a FutureLearn MOOC platform. Additionally, we tackle here the difficult problem of predicting the gender of learners based on their comments only – which are often available across MOOCs. The most common current approaches to text classification use the Long Short-Term Memory (LSTM) model, considering sentences as sequences. However, human language also has structures. In this research, rather than considering sentences as plain sequences, we hypothesise that higher semantic - and syntactic level sentence processing based on linguistics will render a richer representation. We thus evaluate, the traditional LSTM versus other bleeding edge models, which take into account syntactic structure, such as tree-structured LSTM, Stack-augmented Parser-Interpreter Neural Network (SPINN) and the Structure-Aware Tag Augmented model (SATA). Additionally, we explore using different word-level encoding functions. We have implemented these methods on Our MOOC dataset, which is the most performant one comparing with a public dataset on sentiment analysis that is further used as a cross-examining for the models' results.

Keywords: Deep learning, data mining, gender predication, MOOCs.

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Authors: S. Dhahri, A. Zitouni, H. Chaouch, R. Tourki

Abstract:

This paper presents an adaptive motion estimator that can be dynamically reconfigured by the best algorithm depending on the variation of the video nature during the lifetime of an application under running. The 4 Step Search (4SS) and the Gradient Search (GS) algorithms are integrated in the estimator in order to be used in the case of rapid and slow video sequences respectively. The Full Search Block Matching (FSBM) algorithm has been also integrated in order to be used in the case of the video sequences which are not real time oriented. In order to efficiently reduce the computational cost while achieving better visual quality with low cost power, the proposed motion estimator is based on a Variable Block Size (VBS) scheme that uses only the 16x16, 16x8, 8x16 and 8x8 modes. Experimental results show that the adaptive motion estimator allows better results in term of Peak Signal to Noise Ratio (PSNR), computational cost, FPGA occupied area, and dissipated power relatively to the most popular variable block size schemes presented in the literature.

Keywords: H264, Configurable Motion Estimator, VariableBlock Size, PSNR, Dissipated power.

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Authors: Ihor Trots, Yuriy Tasinkevych, Andrzej Nowicki, Marcin Lewandowski

Abstract:

The paper presents the study of synthetic transmit aperture method applying the Golay coded transmission for medical ultrasound imaging. Longer coded excitation allows to increase the total energy of the transmitted signal without increasing the peak pressure. Signal-to-noise ratio and penetration depth are improved maintaining high ultrasound image resolution. In the work the 128-element linear transducer array with 0.3 mm inter-element spacing excited by one cycle and the 8 and 16-bit Golay coded sequences at nominal frequencies 4 MHz was used. Single element transmission aperture was used to generate a spherical wave covering the full image region and all the elements received the echo signals. The comparison of 2D ultrasound images of the wire phantom as well as of the tissue mimicking phantom is presented to demonstrate the benefits of the coded transmission. The results were obtained using the synthetic aperture algorithm with transmit and receive signals correction based on a single element directivity function.

Keywords: Golay coded sequences, radiation pattern, synthetic aperture, ultrasound imaging.

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