De Novo Assembly of Nucleotide Sequences in a Compressed Feature Space

Sequencing technologies allow for an in-depth analysis of biological species but the size of the generated datasets introduce a number of analytical challenges. Recently, we demonstrated the application of numerical sequence representations and data transformations for the alignment of short reads to a reference genome. Here, we expand out approach for de novo assembly of short reads. Our results demonstrate that highly compressed data can encapsulate the signal suffi- ciently to accurately assemble reads to big contigs or complete genomes

Map online system using internet-based image catalogue

Digital maps carry along its geodata information such as coordinate that is important in one particular topographic and thematic map. These geodatas are meaningful especially in military field. Since the maps carry along this information, its makes the size of the images is too big. The bigger size, the bigger storage is required to allocate the image file. It also can cause longer loading time. These conditions make it did not suitable to be applied in image catalogue approach via internet environment. With compression techniques, the image size can be reduced and the quality of the image is still guaranteed without much changes. This report is paying attention to one of the image compression technique using wavelet technology. Wavelet technology is much batter than any other image compression technique nowadays. As a result, the compressed images applied to a system called Map Online that used Internet-based Image Catalogue approach. This system allowed user to buy map online. User also can download the maps that had been bought besides using the searching the map. Map searching is based on several meaningful keywords. As a result, this system is expected to be used by Jabatan Ukur dan Pemetaan Malaysia (JUPEM) in order to make the organization vision is implemented

Compressive Mining: Fast and Optimal Data Mining in the Compressed Domain

Real-world data typically contain repeated and periodic patterns. This suggests that they can be effectively represented and compressed using only a few coefficients of an appropriate basis (e.g., Fourier, Wavelets, etc.). However, distance estimation when the data are represented using different sets of coefficients is still a largely unexplored area. This work studies the optimization problems related to obtaining the \emph{tightest} lower/upper bound on Euclidean distances when each data object is potentially compressed using a different set of orthonormal coefficients. Our technique leads to tighter distance estimates, which translates into more accurate search, learning and mining operations \textit{directly} in the compressed domain. We formulate the problem of estimating lower/upper distance bounds as an optimization problem. We establish the properties of optimal solutions, and leverage the theoretical analysis to develop a fast algorithm to obtain an \emph{exact} solution to the problem. The suggested solution provides the tightest estimation of the $L_2$-norm or the correlation. We show that typical data-analysis operations, such as k-NN search or k-Means clustering, can operate more accurately using the proposed compression and distance reconstruction technique. We compare it with many other prevalent compression and reconstruction techniques, including random projections and PCA-based techniques. We highlight a surprising result, namely that when the data are highly sparse in some basis, our technique may even outperform PCA-based compression. The contributions of this work are generic as our methodology is applicable to any sequential or high-dimensional data as well as to any orthogonal data transformation used for the underlying data compression scheme.Comment: 25 pages, 20 figures, accepted in VLD

The Utility of Data Transformation for Alignment, De Novo Assembly and Classification of Short Read Virus Sequences.

Advances in DNA sequencing technology are facilitating genomic analyses of unprecedented scope and scale, widening the gap between our abilities to generate and fully exploit biological sequence data. Comparable analytical challenges are encountered in other data-intensive fields involving sequential data, such as signal processing, in which dimensionality reduction (i.e., compression) methods are routinely used to lessen the computational burden of analyses. In this work, we explored the application of dimensionality reduction methods to numerically represent high-throughput sequence data for three important biological applications of virus sequence data: reference-based mapping, short sequence classification and de novo assembly. Leveraging highly compressed sequence transformations to accelerate sequence comparison, our approach yielded comparable accuracy to existing approaches, further demonstrating its suitability for sequences originating from diverse virus populations. We assessed the application of our methodology using both synthetic and real viral pathogen sequences. Our results show that the use of highly compressed sequence approximations can provide accurate results, with analytical performance retained and even enhanced through appropriate dimensionality reduction of sequence data

A Review of Fault Diagnosing Methods in Power Transmission Systems

Transient stability is important in power systems. Disturbances like faults need to be segregated to restore transient stability. A comprehensive review of fault diagnosing methods in the power transmission system is presented in this paper. Typically, voltage and current samples are deployed for analysis. Three tasks/topics; fault detection, classification, and location are presented separately to convey a more logical and comprehensive understanding of the concepts. Feature extractions, transformations with dimensionality reduction methods are discussed. Fault classification and location techniques largely use artificial intelligence (AI) and signal processing methods. After the discussion of overall methods and concepts, advancements and future aspects are discussed. Generalized strengths and weaknesses of different AI and machine learning-based algorithms are assessed. A comparison of different fault detection, classification, and location methods is also presented considering features, inputs, complexity, system used and results. This paper may serve as a guideline for the researchers to understand different methods and techniques in this field

FRESH – FRI-based single-image super-resolution algorithm

In this paper, we consider the problem of single image super-resolution and propose a novel algorithm that outperforms state-of-the-art methods without the need of learning patches pairs from external data sets. We achieve this by modeling images and, more precisely, lines of images as piecewise smooth functions and propose a resolution enhancement method for this type of functions. The method makes use of the theory of sampling signals with finite rate of innovation (FRI) and combines it with traditional linear reconstruction methods. We combine the two reconstructions by leveraging from the multi-resolution analysis in wavelet theory and show how an FRI reconstruction and a linear reconstruction can be fused using filter banks. We then apply this method along vertical, horizontal, and diagonal directions in an image to obtain a single-image super-resolution algorithm. We also propose a further improvement of the method based on learning from the errors of our super-resolution result at lower resolution levels. Simulation results show that our method outperforms state-of-the-art algorithms under different blurring kernels

Similarity Measures and Dimensionality Reduction Techniques for Time Series Data Mining

The chapter is organized as follows. Section 2 will introduce the similarity matching problem on time series. We will note the importance of the use of efficient data structures to perform search, and the choice of an adequate distance measure. Section 3 will show some of the most used distance measure for time series data mining. Section 4 will review the above mentioned dimensionality reduction techniques