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

Content-based image retrieval of museum images

Content-based image retrieval (CBIR) is becoming more and more important with the advance of multimedia and imaging technology. Among many retrieval features associated with CBIR, texture retrieval is one of the most difficult. This is mainly because no satisfactory quantitative definition of texture exists at this time, and also because of the complex nature of the texture itself. Another difficult problem in CBIR is query by low-quality images, which means attempts to retrieve images using a poor quality image as a query. Not many content-based retrieval systems have addressed the problem of query by low-quality images. Wavelet analysis is a relatively new and promising tool for signal and image analysis. Its time-scale representation provides both spatial and frequency information, thus giving extra information compared to other image representation schemes. This research aims to address some of the problems of query by texture and query by low quality images by exploiting all the advantages that wavelet analysis has to offer, particularly in the context of museum image collections. A novel query by low-quality images algorithm is presented as a solution to the problem of poor retrieval performance using conventional methods. In the query by texture problem, this thesis provides a comprehensive evaluation on wavelet-based texture method as well as comparison with other techniques. A novel automatic texture segmentation algorithm and an improved block oriented decomposition is proposed for use in query by texture. Finally all the proposed techniques are integrated in a content-based image retrieval application for museum image collections

Hybrid Information Retrieval Model For Web Images

The Bing Bang of the Internet in the early 90's increased dramatically the number of images being distributed and shared over the web. As a result, image information retrieval systems were developed to index and retrieve image files spread over the Internet. Most of these systems are keyword-based which search for images based on their textual metadata; and thus, they are imprecise as it is vague to describe an image with a human language. Besides, there exist the content-based image retrieval systems which search for images based on their visual information. However, content-based type systems are still immature and not that effective as they suffer from low retrieval recall/precision rate. This paper proposes a new hybrid image information retrieval model for indexing and retrieving web images published in HTML documents. The distinguishing mark of the proposed model is that it is based on both graphical content and textual metadata. The graphical content is denoted by color features and color histogram of the image; while textual metadata are denoted by the terms that surround the image in the HTML document, more particularly, the terms that appear in the tags p, h1, and h2, in addition to the terms that appear in the image's alt attribute, filename, and class-label. Moreover, this paper presents a new term weighting scheme called VTF-IDF short for Variable Term Frequency-Inverse Document Frequency which unlike traditional schemes, it exploits the HTML tag structure and assigns an extra bonus weight for terms that appear within certain particular HTML tags that are correlated to the semantics of the image. Experiments conducted to evaluate the proposed IR model showed a high retrieval precision rate that outpaced other current models.Comment: LACSC - Lebanese Association for Computational Sciences, http://www.lacsc.org/; International Journal of Computer Science & Emerging Technologies (IJCSET), Vol. 3, No. 1, February 201

Wavelets and Imaging Informatics: A Review of the Literature

AbstractModern medicine is a field that has been revolutionized by the emergence of computer and imaging technology. It is increasingly difficult, however, to manage the ever-growing enormous amount of medical imaging information available in digital formats. Numerous techniques have been developed to make the imaging information more easily accessible and to perform analysis automatically. Among these techniques, wavelet transforms have proven prominently useful not only for biomedical imaging but also for signal and image processing in general. Wavelet transforms decompose a signal into frequency bands, the width of which are determined by a dyadic scheme. This particular way of dividing frequency bands matches the statistical properties of most images very well. During the past decade, there has been active research in applying wavelets to various aspects of imaging informatics, including compression, enhancements, analysis, classification, and retrieval. This review represents a survey of the most significant practical and theoretical advances in the field of wavelet-based imaging informatics

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

Generic Subsequence Matching Framework: Modularity, Flexibility, Efficiency

Subsequence matching has appeared to be an ideal approach for solving many problems related to the fields of data mining and similarity retrieval. It has been shown that almost any data class (audio, image, biometrics, signals) is or can be represented by some kind of time series or string of symbols, which can be seen as an input for various subsequence matching approaches. The variety of data types, specific tasks and their partial or full solutions is so wide that the choice, implementation and parametrization of a suitable solution for a given task might be complicated and time-consuming; a possibly fruitful combination of fragments from different research areas may not be obvious nor easy to realize. The leading authors of this field also mention the implementation bias that makes difficult a proper comparison of competing approaches. Therefore we present a new generic Subsequence Matching Framework (SMF) that tries to overcome the aforementioned problems by a uniform frame that simplifies and speeds up the design, development and evaluation of subsequence matching related systems. We identify several relatively separate subtasks solved differently over the literature and SMF enables to combine them in straightforward manner achieving new quality and efficiency. This framework can be used in many application domains and its components can be reused effectively. Its strictly modular architecture and openness enables also involvement of efficient solutions from different fields, for instance efficient metric-based indexes. This is an extended version of a paper published on DEXA 2012.Comment: This is an extended version of a paper published on DEXA 201