Search results for: sequence detection.

Authors: Nazar Zaki, Safaai Deris

Abstract:

The amount of the information being churned out by the field of biology has jumped manifold and now requires the extensive use of computer techniques for the management of this information. The predominance of biological information such as protein sequence similarity in the biological information sea is key information for detecting protein evolutionary relationship. Protein sequence similarity typically implies homology, which in turn may imply structural and functional similarities. In this work, we propose, a learning method for detecting remote protein homology. The proposed method uses a transformation that converts protein sequence into fixed-dimensional representative feature vectors. Each feature vector records the sensitivity of a protein sequence to a set of amino acids substrings generated from the protein sequences of interest. These features are then used in conjunction with support vector machines for the detection of the protein remote homology. The proposed method is tested and evaluated on two different benchmark protein datasets and it-s able to deliver improvements over most of the existing homology detection methods.

Keywords: Protein homology detection; support vectormachine; string kernel.

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Authors: A. A. Shafie, Fadhlan Hafiz, M. H. Ali

Abstract:

Motion detection is very important in image processing. One way of detecting motion is using optical flow. Optical flow cannot be computed locally, since only one independent measurement is available from the image sequence at a point, while the flow velocity has two components. A second constraint is needed. The method used for finding the optical flow in this project is assuming that the apparent velocity of the brightness pattern varies smoothly almost everywhere in the image. This technique is later used in developing software for motion detection which has the capability to carry out four types of motion detection. The motion detection software presented in this project also can highlight motion region, count motion level as well as counting object numbers. Many objects such as vehicles and human from video streams can be recognized by applying optical flow technique.

Keywords: Background modeling, Motion detection, Optical flow, Velocity smoothness constant, motion trajectories.

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Authors: M. F. Omar, R. A. Salam, R. Abdullah, N. A. Rashid

Abstract:

Proteins or genes that have similar sequences are likely to perform the same function. One of the most widely used techniques for sequence comparison is sequence alignment. Sequence alignment allows mismatches and insertion/deletion, which represents biological mutations. Sequence alignment is usually performed only on two sequences. Multiple sequence alignment, is a natural extension of two-sequence alignment. In multiple sequence alignment, the emphasis is to find optimal alignment for a group of sequences. Several applicable techniques were observed in this research, from traditional method such as dynamic programming to the extend of widely used stochastic optimization method such as Genetic Algorithms (GAs) and Simulated Annealing. A framework with combination of Genetic Algorithm and Simulated Annealing is presented to solve Multiple Sequence Alignment problem. The Genetic Algorithm phase will try to find new region of solution while Simulated Annealing can be considered as an alignment improver for any near optimal solution produced by GAs.

Keywords: Simulated annealing, genetic algorithm, sequence alignment, multiple sequence alignment.

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Authors: Oi Mean Foong, Tan Jung Low, Satrio Wibowo

Abstract:

Hand gesture is one of the typical methods used in sign language for non-verbal communication. It is most commonly used by people who have hearing or speech problems to communicate among themselves or with normal people. Various sign language systems have been developed by manufacturers around the globe but they are neither flexible nor cost-effective for the end users. This paper presents a system prototype that is able to automatically recognize sign language to help normal people to communicate more effectively with the hearing or speech impaired people. The Sign to Voice system prototype, S2V, was developed using Feed Forward Neural Network for two-sequence signs detection. Different sets of universal hand gestures were captured from video camera and utilized to train the neural network for classification purpose. The experimental results have shown that neural network has achieved satisfactory result for sign-to-voice translation.

Keywords: Hand gesture detection, neural network, signlanguage, sequence detection.

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Authors: M. Antonelli, G. Frosini, B. Lazzerini, F. Marcelloni

Abstract:

In this paper we describe a computer-aided diagnosis (CAD) system for automated detection of pulmonary nodules in computed-tomography (CT) images. After extracting the pulmonary parenchyma using a combination of image processing techniques, a region growing method is applied to detect nodules based on 3D geometric features. We applied the CAD system to CT scans collected in a screening program for lung cancer detection. Each scan consists of a sequence of about 300 slices stored in DICOM (Digital Imaging and Communications in Medicine) format. All malignant nodules were detected and a low false-positive detection rate was achieved.

Keywords: computer assisted diagnosis, medical imagesegmentation, shape recognition.

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Authors: Sallama Athab, Hala Bahjat

Abstract:

Detecting object in video sequence is a challenging mission for identifying, tracking moving objects. Background removal considered as a basic step in detected moving objects tasks. Dual static cameras placed in front and rear moving platform gathered information which is used to detect objects. Background change regarding with speed and direction moving platform, so moving objects distinguished become complicated. In this paper, we propose framework allows detection moving object with variety of speed and direction dynamically. Object detection technique built on two levels the first level apply background removal and edge detection to generate moving areas. The second level apply Moving Areas Filter (MAF) then calculate Correlation Score (CS) for adjusted moving area. Merging moving areas with closer CS and marked as moving object. Experiment result is prepared on real scene acquired by dual static cameras without overlap in sense. Results showing accuracy in detecting objects compared with optical flow and Mixture Module Gaussian (MMG), Accurate ratio produced to measure accurate detection moving object.

Keywords: Background Removal, Correlation, Mixture Module Gaussian, Moving Platform, Object Detection.

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Authors: G. Tamilpavai, C. Vishnuppriya

Abstract:

Studying DNA (deoxyribonucleic acid) sequence is useful in biological processes and it is applied in the fields such as diagnostic and forensic research. DNA is the hereditary information in human and almost all other organisms. It is passed to their generations. Earlier stage detection of defective DNA sequence may lead to many developments in the field of Bioinformatics. Nowadays various tedious techniques are used to identify defective DNA. The proposed work is to analyze and identify the cancer-causing DNA motif in a given sequence. Initially the human DNA sequence is separated as k-mers using k-mer separation rule. The separated k-mers are clustered using Self Organizing Map (SOM). Using Levenshtein distance measure, cancer associated DNA motif is identified from the k-mer clusters. Experimental results of this work indicate the presence or absence of cancer causing DNA motif. If the cancer associated DNA motif is found in DNA, it is declared as the cancer disease causing DNA sequence. Otherwise the input human DNA is declared as normal sequence. Finally, elapsed time is calculated for finding the presence of cancer causing DNA motif using clustering formation. It is compared with normal process of finding cancer causing DNA motif. Locating cancer associated motif is easier in cluster formation process than the other one. The proposed work will be an initiative aid for finding genetic disease related research.

Keywords: Bioinformatics, cancer motif, DNA, k-mers, Levenshtein distance, SOM.

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Authors: D. Ouahdi, R. Ladjeroud, I. Habi

Abstract:

The distance protection mainly the impedance relay which is considered as the main protection for transmission lines can be subjected to impedance measurement error which is, mainly, due to the fault resistance and to the power fluctuation. Thus, the impedance relay may not operate for a short circuit at the far end of the protected line (case of the under reach) or operates for a fault beyond its protected zone (case of overreach). In this paper, an approach to fault detection by a distance protection, which distinguishes between the faulty conditions and the effect of overload operation mode, has been developed. This approach is based on the symmetrical components; mainly the negative sequence, and it is taking into account both the effect of fault resistance and the overload situation which both have an effect upon the reliability of the protection in terms of dependability for the former and security for the latter.

Keywords: Distance Protection, Fault Detection, negative sequence, overload, Transmission line.

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Authors: Mubarak Saif Mohsen, Zurinahni Zainol, Rosalina Abdul Salam, Wahidah Husain

Abstract:

One of the major problems in genomic field is to perform sequence comparison on DNA and protein sequences. Executing sequence comparison on the DNA and protein data is a computationally intensive task. Sequence comparison is the basic step for all algorithms in protein sequences similarity. Parallel computing is an attractive solution to provide the computational power needed to speedup the lengthy process of the sequence comparison. Our main research is to enhance the protein sequence algorithm using dynamic programming method. In our approach, we parallelize the dynamic programming algorithm using multithreaded program to perform the sequence comparison and also developed a distributed protein database among many PCs using Remote Method Interface (RMI). As a result, we showed how different sizes of protein sequences data and computation of scoring matrix of these protein sequence on different number of processors affected the processing time and speed, as oppose to sequential processing.

Keywords: Protein sequence algorithm, dynamic programming algorithm, multithread

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Authors: Lenka Krulikovská, Jaroslav Polec

Abstract:

In this paper we present a modification to existed model of threshold for shot cut detection, which is able to adapt itself to the sequence statistics and operate in real time, because it use for calculation only previously evaluated frames. The efficiency of proposed modified adaptive threshold scheme was verified through extensive test experiment with several similarity metrics and achieved results were compared to the results reached by the original model. According to results proposed threshold scheme reached higher accuracy than existed original model.

Keywords: Abrupt cut, shot cut detection, adaptive threshold.

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Authors: Zine-Eddine Bouras, Abdelouaheb Talai

Abstract:

The need to merge software artifacts seems inherent to modern software development. Distribution of development over several teams and breaking tasks into smaller, more manageable pieces are an effective means to deal with the kind of complexity. In each case, the separately developed artifacts need to be assembled as efficiently as possible into a consistent whole in which the parts still function as described. In addition, earlier changes are introduced into the life cycle and easier is their management by designers. Interaction-based specifications such as UML sequence diagrams have been found effective in this regard. As a result, sequence diagrams can be used not only for capturing system behaviors but also for merging changes in order to create a new version. The objective of this paper is to suggest a new approach to deal with the problem of software merging at the level of sequence diagrams by using the concept of dependence analysis that captures, formally, all mapping, and differences between elements of sequence diagrams and serves as a key concept to create a new version of sequence diagram.

Keywords: System behaviors, sequence diagram merging, dependence analysis, sequence diagram slicing.

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Authors: Vidhu Mitha Goutham, Ruma Mukherjee

Abstract:

The low availability of well-trained, unlimited, dynamic-access models for specific languages makes it hard for corporate users to adopt quick translation techniques and incorporate them into product solutions. As translation tasks increasingly require a dynamic sequence learning curve; stable, cost-free opensource models are scarce. We survey and compare current translation techniques and propose a modified sequence to sequence model repurposed with attention techniques. Sequence learning using an encoder-decoder model is now paving the path for higher precision levels in translation. Using a Convolutional Neural Network (CNN) encoder and a Recurrent Neural Network (RNN) decoder background, we use Fairseq tools to produce an end-to-end bilingually trained Spanish-English machine translation model including source language detection. We acquire competitive results using a duo-lingo-corpus trained model to provide for prospective, ready-made plug-in use for compound sentences and document translations. Our model serves a decent system for large, organizational data translation needs. While acknowledging its shortcomings and future scope, it also identifies itself as a well-optimized deep neural network model and solution.

Keywords: Attention, encoder-decoder, Fairseq, Seq2Seq, Spanish, translation.

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Authors: N. Subramanian, C. Murugesan

Abstract:

The double difference sequence space I2 (M, of fuzzy numbers for both 1 < p < oo and 0 < p < 1, is introduced. Some general properties of this sequence space are studied. Some inclusion relations involving this sequence space are obtained.

Keywords: Orlicz function, solid space, metric space, completeness

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Authors: Qiu Chen, Feifei Lee, Koji Kotani, Tadahiro Ohmi

Abstract:

In this paper, we propose an efficient hierarchical DNA sequence search method to improve the search speed while the accuracy is being kept constant. For a given query DNA sequence, firstly, a fast local search method using histogram features is used as a filtering mechanism before scanning the sequences in the database. An overlapping processing is newly added to improve the robustness of the algorithm. A large number of DNA sequences with low similarity will be excluded for latter searching. The Smith-Waterman algorithm is then applied to each remainder sequences. Experimental results using GenBank sequence data show the proposed method combining histogram information and Smith-Waterman algorithm is more efficient for DNA sequence search.

Keywords: Fast search, DNA sequence, Histogram feature, Smith-Waterman algorithm, Local search

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Authors: Taeung Yoon, Youngpo Lee, Chonghan Song, Na Young Ha, Seokho Yoon

Abstract:

Ren et al. presented an efficient carrier frequency offset (CFO) estimation method for orthogonal frequency division multiplexing (OFDM), which has an estimation range as large as the bandwidth of the OFDM signal and achieves high accuracy without any constraint on the structure of the training sequence. However, its detection probability of the integer frequency offset (IFO) rapidly varies according to the fractional frequency offset (FFO) change. In this paper, we first analyze the Ren-s method and define two criteria suitable for detection of IFO. Then, we propose a novel method for the IFO estimation based on the maximum-likelihood (ML) principle and the detection criteria defined in this paper. The simulation results demonstrate that the proposed method outperforms the Ren-s method in terms of the IFO detection probability irrespective of a value of the FFO.

Keywords: Orthogonal frequency division multiplexing, integer frequency offset, estimation, training symbol

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Authors: Sing-Wu Liou, Yin-Fu Huang

Abstract:

For identifying the discriminative sequence features between exons and introns, a new paradigm, rescaled-range frameshift analysis (RRFA), was proposed. By RRFA, two new sequence features, the frameshift sensitivity (FS) and the accumulative penta-mer complexity (APC), were discovered which were further integrated into a new feature of larger scale, the persistency in anti-mutation (PAM). The feature-validation experiments were performed on six model organisms to test the power of discrimination. All the experimental results highly support that FS, APC and PAM were all distinguishing features between exons and introns. These identified new sequence features provide new insights into the sequence composition of genes and they have great potentials of forming a new basis for recognizing the exonintron boundaries in gene sequences.

Keywords: Exon-Intron Discrimination, Rescaled-Range Frameshift Analysis, Frameshift Sensitivity, Accumulative Sequence Complexity

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Authors: Mohamed Amine Ouddan, Hassane Essafi

Abstract:

Source code retrieval is of immense importance in the software engineering field. The complex tasks of retrieving and extracting information from source code documents is vital in the development cycle of the large software systems. The two main subtasks which result from these activities are code duplication prevention and plagiarism detection. In this paper, we propose a Mohamed Amine Ouddan, and Hassane Essafi source code retrieval system based on two-level fingerprint representation, respectively the structural and the semantic information within a source code. A sequence alignment technique is applied on these fingerprints in order to quantify the similarity between source code portions. The specific purpose of the system is to detect plagiarism and duplicated code between programs written in different programming languages belonging to the same class, such as C, Cµ, Java and CSharp. These four languages are supported by the actual version of the system which is designed such that it may be easily adapted for any programming language.

Keywords: Source code retrieval, plagiarism detection, clonedetection, sequence alignment.

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Authors: Shuzhen Yao, Fengjing Zhao, Jianwei He

Abstract:

The UML modeling of complex distributed systems often is a great challenge due to the large amount of parallel real-time operating components. In this paper the problems of verification of such systems are discussed. ECPN, an Extended Colored Petri Net is defined to formally describe state transitions of components and interactions among components. The relationship between sequence diagrams and Free Choice Petri Nets is investigated. Free Choice Petri Net theory helps verifying the liveness of sequence diagrams. By converting sequence diagrams to ECPNs and then comparing behaviors of sequence diagram ECPNs and statecharts, the consistency among models is analyzed. Finally, a verification process for an example model is demonstrated.

Keywords: Consistency, liveness, Petri Net, sequence diagram.

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Authors: Kolar Jan, Dvorak Vaclav

Abstract:

In this study, an optimization of supersonic air-to-air ejector is carried out by a recently developed single-objective genetic algorithm based on adaption of sequence of individuals. Adaptation of sequence is based on Shape-based distance of individuals and embedded micro-genetic algorithm. The optimal sequence found defines the succession of CFD-aimed objective calculation within each generation of regular micro-genetic algorithm. A spring-based deformation mutates the computational grid starting the initial individualvia adapted population in the optimized sequence. Selection of a generation initial individual is knowledge-based. A direct comparison of the newly defined and standard micro-genetic algorithm is carried out for supersonic air-to-air ejector. The only objective is to minimize the loose of total stagnation pressure in the ejector. The result is that sequence-adopted micro-genetic algorithm can provide comparative results to standard algorithm but in significantly lower number of overall CFD iteration steps.

Keywords: Grid deformation, Micro-genetic algorithm, shapebased sequence, supersonic ejector.

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Authors: Patsaraporn Somboonsak, Mud-Armeen Munlin

Abstract:

In April 2009, a new variant of Influenza A virus subtype H1N1 emerged in Mexico and spread all over the world. The influenza has three subtypes in human (H1N1, H1N2 and H3N2) Types B and C influenza tend to be associated with local or regional epidemics. Preliminary genetic characterization of the influenza viruses has identified them as swine influenza A (H1N1) viruses. Nucleotide sequence analysis of the Haemagglutinin (HA) and Neuraminidase (NA) are similar to each other and the majority of their genes of swine influenza viruses, two genes coding for the neuraminidase (NA) and matrix (M) proteins are similar to corresponding genes of swine influenza. Sequence similarity between the 2009 A (H1N1) virus and its nearest relatives indicates that its gene segments have been circulating undetected for an extended period. Nucleic acid sequence Maximum Likelihood (MCL) and DNA Empirical base frequencies, Phylogenetic relationship amongst the HA genes of H1N1 virus isolated in Genbank having high nucleotide sequence homology. In this paper we used 16 HA nucleotide sequences from NCBI for computing sequence relationships similarity of swine influenza A virus using the following method MCL the result is 28%, 36.64% for Optimal tree with the sum of branch length, 35.62% for Interior branch phylogeny Neighber – Join Tree, 1.85% for the overall transition/transversion, and 8.28% for Overall mean distance.

Keywords: Sequence DNA, Relationship of swine, Swineinfluenza, Sequence Similarity

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Authors: T. Balasubramanian, A. Pandiarani

Abstract:

In this paper we introduce some subspaces of fuzzy entire sequence space. Some general properties of these sequence spaces are discussed. Also some inclusion relation involving the spaces are obtained. Mathematics Subject Classification: 40A05, 40D25.

Keywords: Fuzzy Numbers, Entire sequences, completeness, Fuzzy entire sequences

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Authors: M. Heydari, S. A. Torabi

Abstract:

The problem of lot sizing, sequencing and scheduling multiple products in flow line production systems has been studied by several authors. Almost all of the researches in this area assumed that setup times and costs are sequence –independent even though sequence dependent setups are common in practice. In this paper we present a new mixed integer non linear program (MINLP) and a heuristic method to solve the problem in sequence dependent case. Furthermore, a genetic algorithm has been developed which applies this constructive heuristic to generate initial population. These two proposed solution methods are compared on randomly generated problems. Computational results show a clear superiority of our proposed GA for majority of the test problems.

Keywords: Economic lot scheduling problem, finite horizon, genetic algorithm, mixed zero-one nonlinear programming, sequence-dependent.

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Authors: Wei Zhang, Hong Yu, Xian-ping Zhao, Da-da Wang, Fei Xue

Abstract:

For lack of the visualization of the ultrasonic detection method of partial discharge (PD), the ultrasonic detection technology combined with the X-ray visual detection method (UXV) is proposed. The method can conduct qualitative analysis accurately and conduct reliable positioning diagnosis to the internal insulation defects of GIS, and while it could make up the blindness of the X-ray visual detection method and improve the detection rate. In this paper, an experimental model of GIS is used as the trial platform, a variety of insulation defects are set inside the GIS cavity. With the proposed method, the ultrasonic method is used to conduct the preliminary detection, and then the X-ray visual detection is used to locate and diagnose precisely. Therefore, the proposed UXV technology is feasible and practical.

Keywords: GIS, ultrasonic, visual detection, X-ray

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Authors: Yuka Kawakami, Tomoyuki Yokogawa, Hisashi Miyazaki, Sousuke Amasaki, Yoichiro Sato, Michiyoshi Hayase

Abstract:

In this paper, we proposed a method for detecting consistency violation between state machine diagrams and a sequence diagram defined in UML 2.0 using SMV. We extended a method expressing these diagrams defined in UML 1.0 with boolean formulas so that it can express a sequence diagram with combined fragments introduced in UML 2.0. This extension made it possible to represent three types of combined fragment: alternative, option and parallel. As a result of experiment, we confirmed that the proposed method could detect consistency violation correctly with SMV.

Keywords: UML, model checking, SMV, sequence diagram.

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Authors: M. Moosavi, H. Khatibzadeh

Abstract:

In this article, we study demiclosed and strongly quasi-nonexpansive of a sequence generated by the proximal point algorithm for a finite family of quasi-nonexpansive mappings in Hadamard spaces. Δ-convergence of iterations for the sequence of strongly quasi-nonexpansive mappings as well as the strong convergence of the Halpern type regularization of them to a common fixed point of sequence are also established. Our results generalize and improve several previously known results of the existing literature.

Keywords: Fixed point, Hadamard space, proximal point algorithm, quasi-nonexpansive sequence of mappings, resolvent.

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Authors: Yilun Shang

Abstract:

Let {Xi}i≥1 be a martingale difference sequence with Xi = Si - Si-1. Under some regularity conditions, we show that (X2 1+· · ·+X2N n)-1/2SNn is asymptotically normal, where {Ni}i≥1 is a sequence of positive integer-valued random variables tending to infinity. In a similar manner, a backward (or reverse) martingale central limit theorem with random indices is provided.

Keywords: central limit theorem, martingale difference sequence, backward martingale.

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Authors: M. V. A. Raju Bahubalendruni, Bibhuti Bhusan Biswal, B. B. V. L. Deepak

Abstract:

Achieving an appropriate assembly sequence needs deep verification for its physical feasibility. For this purpose, industrial engineers use several assembly predicates; namely, liaison, geometric feasibility, stability and mechanical feasibility. However, testing an assembly sequence for these predicates requires huge assembly information. Extracting such assembly information from an assembled product is a time consuming and highly skillful task with complex reasoning methods. In this paper, computer aided methods are proposed to extract all the necessary assembly information from computer aided design (CAD) environment in order to perform the assembly sequence planning efficiently. These methods use preliminary capabilities of three-dimensional solid modelling and assembly modelling methods used in CAD software considering equilibrium laws of physical bodies.

Keywords: Assembly automation, assembly attributes, assembly sequence generation, computer aided design.

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Authors: Manpreet Singh, Parminder Kaur Wadhwa, Surinder Kaur

Abstract:

The drug discovery process starts with protein identification because proteins are responsible for many functions required for maintenance of life. Protein identification further needs determination of protein function. Proposed method develops a classifier for human protein function prediction. The model uses decision tree for classification process. The protein function is predicted on the basis of matched sequence derived features per each protein function. The research work includes the development of a tool which determines sequence derived features by analyzing different parameters. The other sequence derived features are determined using various web based tools.

Keywords: Sequence Derived Features, decision tree.

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

Abstract:

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: Xiang Yu, Chuntao Feng, Lu Yang, Meiyang Song, Wenhao Zhou

Abstract:

The existing two-dimensional micro-Doppler features extraction ignores the correlation information between the spatial and temporal dimension features. For the range-Doppler map, the time dimension is introduced, and a frequency modulation continuous wave (FMCW) radar human fall detection algorithm based on time-varying range-Doppler features is proposed. Firstly, the range-Doppler sequence maps are generated from the echo signals of the continuous motion of the human body collected by the radar. Then the three-dimensional data cube composed of multiple frames of range-Doppler maps is input into the three-dimensional Convolutional Neural Network (3D CNN). The spatial and temporal features of time-varying range-Doppler are extracted by the convolution layer and pool layer at the same time. Finally, the extracted spatial and temporal features are input into the fully connected layer for classification. The experimental results show that the proposed fall detection algorithm has a detection accuracy of 95.66%.

Keywords: FMCW radar, fall detection, 3D CNN, time-varying range-Doppler features.

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