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

Fusion-Based Versatile Video Coding Intra Prediction Algorithm with Template Matching and Linear Prediction

The new generation video coding standard Versatile Video Coding (VVC) has adopted many novel technologies to improve compression performance, and consequently, remarkable results have been achieved. In practical applications, less data, in terms of bitrate, would reduce the burden of the sensors and improve their performance. Hence, to further enhance the intra compression performance of VVC, we propose a fusion-based intra prediction algorithm in this paper. Specifically, to better predict areas with similar texture information, we propose a fusion-based adaptive template matching method, which directly takes the error between reference and objective templates into account. Furthermore, to better utilize the correlation between reference pixels and the pixels to be predicted, we propose a fusion-based linear prediction method, which can compensate for the deficiency of single linear prediction. We implemented our algorithm on top of the VVC Test Model (VTM) 9.1. When compared with the VVC, our proposed fusion-based algorithm saves a bitrate of 0.89%, 0.84%, and 0.90% on average for the Y, Cb, and Cr components, respectively. In addition, when compared with some other existing works, our algorithm showed superior performance in bitrate savings

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

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

Saliency-Enabled Coding Unit Partitioning and Quantization Control for Versatile Video Coding

The latest video coding standard, versatile video coding (VVC), has greatly improved coding efficiency over its predecessor standard high efficiency video coding (HEVC), but at the expense of sharply increased complexity. In the context of perceptual video coding (PVC), the visual saliency model that utilizes the characteristics of the human visual system to improve coding efficiency has become a reliable method due to advances in computer performance and visual algorithms. In this paper, a novel VVC optimization scheme compliant PVC framework is proposed, which consists of fast coding unit (CU) partition algorithm and quantization control algorithm. Firstly, based on the visual saliency model, we proposed a fast CU division scheme, including the redetermination of the CU division depth by calculating Scharr operator and variance, as well as the executive decision for intra sub-partitions (ISP), to reduce the coding complexity. Secondly, a quantization control algorithm is proposed by adjusting the quantization parameter based on multi-level classification of saliency values at the CU level to reduce the bitrate. In comparison with the reference model, experimental results indicate that the proposed method can reduce about 47.19% computational complexity and achieve a bitrate saving of 3.68% on average. Meanwhile, the proposed algorithm has reasonable peak signal-to-noise ratio losses and nearly the same subjective perceptual quality

Subpath Queries on Compressed Graphs: A Survey

Text indexing is a classical algorithmic problem that has been studied for over four decades: given a text T, pre-process it off-line so that, later, we can quickly count and locate the occurrences of any string (the query pattern) in T in time proportional to the query’s length. The earliest optimal-time solution to the problem, the suffix tree, dates back to 1973 and requires up to two orders of magnitude more space than the plain text just to be stored. In the year 2000, two breakthrough works showed that efficient queries can be achieved without this space overhead: a fast index be stored in a space proportional to the text’s entropy. These contributions had an enormous impact in bioinformatics: today, virtually any DNA aligner employs compressed indexes. Recent trends considered more powerful compression schemes (dictionary compressors) and generalizations of the problem to labeled graphs: after all, texts can be viewed as labeled directed paths. In turn, since finite state automata can be considered as a particular case of labeled graphs, these findings created a bridge between the fields of compressed indexing and regular language theory, ultimately allowing to index regular languages and promising to shed new light on problems, such as regular expression matching. This survey is a gentle introduction to the main landmarks of the fascinating journey that took us from suffix trees to today’s compressed indexes for labeled graphs and regular languages

Reviewing and Discussing Graph Reduction in Edge Computing Context

Much effort has been devoted to transferring efficiently different machine-learning algorithms, and especially deep neural networks, to edge devices in order to fulfill, among others, real-time, storage and energy-consumption issues. The limited resources of edge devices and the necessity for energy saving to lengthen the durability of their batteries, has encouraged an interesting trend in reducing neural networks and graphs, while keeping their predictability almost untouched. In this work, an alternative to the latest techniques for finding these reductions in networks size is proposed, seeking to figure out a simplistic way to shrink networks while maintaining, as far as possible, their predictability testing on well-known datasets