A Reference-Free Lossless Compression Algorithm for DNA Sequences Using a Competitive Prediction of Two Classes of Weighted Models

The development of efficient data compressors for DNA sequences is crucial not only for reducing the storage and the bandwidth for transmission, but also for analysis purposes. In particular, the development of improved compression models directly influences the outcome of anthropological and biomedical compression-based methods. In this paper, we describe a new lossless compressor with improved compression capabilities for DNA sequences representing different domains and kingdoms. The reference-free method uses a competitive prediction model to estimate, for each symbol, the best class of models to be used before applying arithmetic encoding. There are two classes of models: weighted context models (including substitutional tolerant context models) and weighted stochastic repeat models. Both classes of models use specific sub-programs to handle inverted repeats efficiently. The results show that the proposed method attains a higher compression ratio than state-of-the-art approaches, on a balanced and diverse benchmark, using a competitive level of computational resources. An efficient implementation of the method is publicly available, under the GPLv3 license.Peer reviewe

Distributed Joint Source-Channel Coding in Wireless Sensor Networks

Considering the fact that sensors are energy-limited and the wireless channel conditions in wireless sensor networks, there is an urgent need for a low-complexity coding method with high compression ratio and noise-resisted features. This paper reviews the progress made in distributed joint source-channel coding which can address this issue. The main existing deployments, from the theory to practice, of distributed joint source-channel coding over the independent channels, the multiple access channels and the broadcast channels are introduced, respectively. To this end, we also present a practical scheme for compressing multiple correlated sources over the independent channels. The simulation results demonstrate the desired efficiency

Multiplicative Multiresolution Decomposition for Lossless Volumetric Medical Images Compression

With the emergence of medical imaging, the compression of volumetric medical images is essential. For this purpose, we propose a novel Multiplicative Multiresolution Decomposition (MMD) wavelet coding scheme for lossless compression of volumetric medical images. The MMD is used in speckle reduction technique but offers some proprieties which can be exploited in compression. Thus, as the wavelet transform the MMD provides a hierarchical representation and offers a possibility to realize lossless compression. We integrate in proposed scheme an inter slice filter based on wavelet transform and motion compensation to reduce data energy efficiently. We compare lossless results of classical wavelet coders such as 3D SPIHT and JP3D to the proposed scheme. This scheme incorporates MMD in lossless compression technique by applying MMD/wavelet or MMD transform to each slice, after inter slice filter is employed and the resulting sub-bands are coded by the 3D zero-tree algorithm SPIHT. Lossless experimental results show that the proposed scheme with the MMD can achieve lowest bit rates compared to 3D SPIHT and JP3D

Prediction and evaluation of zero order entropy changes in grammar-based codes

The change of zero order entropy is studied over different strategies of grammar production rule selection. The two major rules are distinguished: transformations leaving the message size intact and substitution functions changing the message size. Relations for zero order entropy changes were derived for both cases and conditions under which the entropy decreases were described. In this article, several different greedy strategies reducing zero order entropy, as well as message sizes are summarized, and the new strategy MinEnt is proposed. The resulting evolution of the zero order entropy is compared with a strategy of selecting the most frequent digram used in the Re-Pair algorithm.Web of Science195art. no. 22

A General Model for the Design of Efficient Sign-Coding Tools for Wavelet-Based Encoders

[EN] Traditionally, it has been assumed that the compression of the sign of wavelet coefficients is not worth the effort because they form a zero-mean process. However, several image encoders such as JPEG 2000 include sign-coding capabilities. In this paper, we analyze the convenience of including sign-coding techniques into wavelet-based image encoders and propose a methodology that allows the design of sign-prediction tools for whatever kind of wavelet-based encoder. The proposed methodology is based on the use of metaheuristic algorithms to find the best sign prediction with the most appropriate context distribution that maximizes the resulting sign-compression rate of a particular wavelet encoder. Following our proposal, we have designed and implemented a sign-coding module for the LTW wavelet encoder, to evaluate the benefits of the sign-coding tool provided by our proposed methodology. The experimental results show that sign compression can save up to 18.91% of bit-rate when enabling sign-coding capabilities. Also, we have observed two general behaviors when coding the sign of wavelet coefficients: (a) the best results are provided from moderate to high compression rates; and (b) the sign redundancy may be better exploited when working with high-textured images.This research was supported by the Spanish Ministry of Economy and Competitiveness under Grant RTI2018-098156-B-C54, co-financed by FEDER funds (MINECO/FEDER/UE).López-Granado, OM.; Martínez-Rach, MO.; Martí-Campoy, A.; Cruz-Chávez, MA.; Pérez Malumbres, M. (2020). A General Model for the Design of Efficient Sign-Coding Tools for Wavelet-Based Encoders. Electronics. 9(11):1-17. https://doi.org/10.3390/electronics9111899S117911Said, A., & Pearlman, W. A. (1996). A new, fast, and efficient image codec based on set partitioning in hierarchical trees. IEEE Transactions on Circuits and Systems for Video Technology, 6(3), 243-250. doi:10.1109/76.499834ISO/IEC 15444-1:2019. Information technology—JPEG 2000 Image Coding System—Part 1: Core Coding Systemhttps://www.iso.org/standard/78321.htmlTaubman, D. (2000). High performance scalable image compression with EBCOT. IEEE Transactions on Image Processing, 9(7), 1158-1170. doi:10.1109/83.847830Bilgin, A., Sementilli, P. J., & Marcellin, M. W. (1999). Progressive image coding using trellis coded quantization. IEEE Transactions on Image Processing, 8(11), 1638-1643. doi:10.1109/83.799891Oliver, J., & Malumbres, M. P. (2006). Low-Complexity Multiresolution Image Compression Using Wavelet Lower Trees. IEEE Transactions on Circuits and Systems for Video Technology, 16(11), 1437-1444. doi:10.1109/tcsvt.2006.883505Cho, Y., & Pearlman, W. A. (2007). Hierarchical Dynamic Range Coding of Wavelet Subbands for Fast and Efficient Image Decompression. IEEE Transactions on Image Processing, 16(8), 2005-2015. doi:10.1109/tip.2007.901247Deever, A. T., & Hemami, S. S. (2003). Efficient sign coding and estimation of zero-quantized coefficients in embedded wavelet image codecs. IEEE Transactions on Image Processing, 12(4), 420-430. doi:10.1109/tip.2003.811499Mallat, S., & Zhong, S. (1992). Characterization of signals from multiscale edges. IEEE Transactions on Pattern Analysis and Machine Intelligence, 14(7), 710-732. doi:10.1109/34.142909López-Granado, O., Galiano, V., Martí, A., Migallón, H., Martínez-Rach, M., Piñol, P., & Malumbres, M. P. (2013). Improving image compression through the use of evolutionary computing algorithms. Data Management and Security. doi:10.2495/data130041Kodak Lossless True Color Image Suitehttp://r0k.us/graphics/kodak/Rawzor—Lossless Compression Software for Camera Raw Imageshttp://imagecompression.info/test_images

Quantization and Compressive Sensing

Quantization is an essential step in digitizing signals, and, therefore, an indispensable component of any modern acquisition system. This book chapter explores the interaction of quantization and compressive sensing and examines practical quantization strategies for compressive acquisition systems. Specifically, we first provide a brief overview of quantization and examine fundamental performance bounds applicable to any quantization approach. Next, we consider several forms of scalar quantizers, namely uniform, non-uniform, and 1-bit. We provide performance bounds and fundamental analysis, as well as practical quantizer designs and reconstruction algorithms that account for quantization. Furthermore, we provide an overview of Sigma-Delta ($\Sigma\Delta$) quantization in the compressed sensing context, and also discuss implementation issues, recovery algorithms and performance bounds. As we demonstrate, proper accounting for quantization and careful quantizer design has significant impact in the performance of a compressive acquisition system.Comment: 35 pages, 20 figures, to appear in Springer book "Compressed Sensing and Its Applications", 201

Optimal Construction of Hierarchical Overlap Graphs

Genome assembly is a fundamental problem in Bioinformatics, where for a given set of overlapping substrings of a genome, the aim is to reconstruct the source genome. The classical approaches to solving this problem use assembly graphs, such as de Bruijn graphs or overlap graphs, which maintain partial information about such overlaps. For genome assembly algorithms, these graphs present a trade-off between overlap information stored and scalability. Thus, Hierarchical Overlap Graph (HOG) was proposed to overcome the limitations of both these approaches. For a given set P of n strings, the first algorithm to compute HOG was given by Cazaux and Rivals [IPL20] requiring O(||P||+n²) time using superlinear space, where ||P|| is the cumulative sum of the lengths of strings in P. This was improved by Park et al. [SPIRE20] to O(||P||log n) time and O(||P||) space using segment trees, and further to O(||P||(log n)/(log log n)) for the word RAM model. Both these results described an open problem to compute HOG in optimal O(||P||) time and space. In this paper, we achieve the desired optimal bounds by presenting a simple algorithm that does not use any complex data structures. At its core, our solution improves the classical result [IPL92] for a special case of the All Pairs Suffix Prefix (APSP) problem from O(||P||+n²) time to optimal O(||P||) time, which may be of independent interest.Peer reviewe