Distribution des symboles finaux dans un arbre de recherche avec des sources de Markov

Lempel-Ziv'78 is one of the most popular data compression algorithm on words. Over the last decades we uncover its fascinating behavior and understand better many of its beautiful properties. Among others, in 1995 by settling the Ziv conjecture we proved that for memoryless source (i.e., when a sequence is generated by a source without memory) the number of LZ'78 phrases satisfies the Central Limit Theorem (CLT). Since then the quest commenced to extend it to Markov sources, however, despite several attempts this problem is still open. In this conference paper, we revisit the issue and focus on a much simpler, but not trivial problem that may lead to the resolution of the LZ'78 dilemma. We consider the associated Digital Search Tree (DST) version of the problem in which the DST is built over a fixed number of Markov generated sequences. In such a model we shall count the number of of the so called "tail symbol", that is, the symbol that follows the last inserted symbol. Our goal here is to analyze this new quantity under Markovian assumption since it plays crucial role in the analysis of the original LZ'78 problem. We establish the mean, the variance, and the central limit theorem for the number of tail symbols. We accomplish it by applying techniques of analytic combinatorics on words also known as analytic pattern matching

New analysis of the asymptotic behavior of the Lempel-Ziv compression algorithm

We give a new analysis and proof of the Normal limiting distribution of the number of phrases in the 1978 Lempel-Ziv compression algorithm on random sequences built from a memoriless source. This work is a follow-up of our last paper on this subject in 1995. The analysis stands on the asymptotic behavior of a DST obtained by the insertion of random sequences. Our proofs are augmented of new results on moment convergence, moderate and large deviations, redundancy analysis

On Prediction Using Variable Order Markov Models

This paper is concerned with algorithms for prediction of discrete sequences over a finite alphabet, using variable order Markov models. The class of such algorithms is large and in principle includes any lossless compression algorithm. We focus on six prominent prediction algorithms, including Context Tree Weighting (CTW), Prediction by Partial Match (PPM) and Probabilistic Suffix Trees (PSTs). We discuss the properties of these algorithms and compare their performance using real life sequences from three domains: proteins, English text and music pieces. The comparison is made with respect to prediction quality as measured by the average log-loss. We also compare classification algorithms based on these predictors with respect to a number of large protein classification tasks. Our results indicate that a "decomposed" CTW (a variant of the CTW algorithm) and PPM outperform all other algorithms in sequence prediction tasks. Somewhat surprisingly, a different algorithm, which is a modification of the Lempel-Ziv compression algorithm, significantly outperforms all algorithms on the protein classification problems

About Adaptive Coding on Countable Alphabets: Max-Stable Envelope Classes

In this paper, we study the problem of lossless universal source coding for stationary memoryless sources on countably infinite alphabets. This task is generally not achievable without restricting the class of sources over which universality is desired. Building on our prior work, we propose natural families of sources characterized by a common dominating envelope. We particularly emphasize the notion of adaptivity, which is the ability to perform as well as an oracle knowing the envelope, without actually knowing it. This is closely related to the notion of hierarchical universal source coding, but with the important difference that families of envelope classes are not discretely indexed and not necessarily nested. Our contribution is to extend the classes of envelopes over which adaptive universal source coding is possible, namely by including max-stable (heavy-tailed) envelopes which are excellent models in many applications, such as natural language modeling. We derive a minimax lower bound on the redundancy of any code on such envelope classes, including an oracle that knows the envelope. We then propose a constructive code that does not use knowledge of the envelope. The code is computationally efficient and is structured to use an {E}xpanding {T}hreshold for {A}uto-{C}ensoring, and we therefore dub it the \textsc{ETAC}-code. We prove that the \textsc{ETAC}-code achieves the lower bound on the minimax redundancy within a factor logarithmic in the sequence length, and can be therefore qualified as a near-adaptive code over families of heavy-tailed envelopes. For finite and light-tailed envelopes the penalty is even less, and the same code follows closely previous results that explicitly made the light-tailed assumption. Our technical results are founded on methods from regular variation theory and concentration of measure

Modeling, Predicting and Capturing Human Mobility

Realistic models of human mobility are critical for modern day applications, specifically for recommendation systems, resource planning and process optimization domains. Given the rapid proliferation of mobile devices equipped with Internet connectivity and GPS functionality today, aggregating large sums of individual geolocation data is feasible. The thesis focuses on methodologies to facilitate data-driven mobility modeling by drawing parallels between the inherent nature of mobility trajectories, statistical physics and information theory. On the applied side, the thesis contributions lie in leveraging the formulated mobility models to construct prediction workflows by adopting a privacy-by-design perspective. This enables end users to derive utility from location-based services while preserving their location privacy. Finally, the thesis presents several approaches to generate large-scale synthetic mobility datasets by applying machine learning approaches to facilitate experimental reproducibility

Efficient Storage of Genomic Sequences in High Performance Computing Systems

ABSTRACT: In this dissertation, we address the challenges of genomic data storage in high performance computing systems. In particular, we focus on developing a referential compression approach for Next Generation Sequence data stored in FASTQ format files. The amount of genomic data available for researchers to process has increased exponentially, bringing enormous challenges for its efficient storage and transmission. General-purpose compressors can only offer limited performance for genomic data, thus the need for specialized compression solutions. Two trends have emerged as alternatives to harness the particular properties of genomic data: non-referential and referential compression. Non-referential compressors offer higher compression rations than general purpose compressors, but still below of what a referential compressor could theoretically achieve. However, the effectiveness of referential compression depends on selecting a good reference and on having enough computing resources available. This thesis presents one of the first referential compressors for FASTQ files. We first present a comprehensive analytical and experimental evaluation of the most relevant tools for genomic raw data compression, which led us to identify the main needs and opportunities in this field. As a consequence, we propose a novel compression workflow that aims at improving the usability of referential compressors. Subsequently, we discuss the implementation and performance evaluation for the core of the proposed workflow: a referential compressor for reads in FASTQ format that combines local read-to-reference alignments with a specialized binary-encoding strategy. The compression algorithm, named UdeACompress, achieved very competitive compression ratios when compared to the best compressors in the current state of the art, while showing reasonable execution times and memory use. In particular, UdeACompress outperformed all competitors when compressing long reads, typical of the newest sequencing technologies. Finally, we study the main aspects of the data-level parallelism in the Intel AVX-512 architecture, in order to develop a parallel version of the UdeACompress algorithms to reduce the runtime. Through the use of SIMD programming, we managed to significantly accelerate the main bottleneck found in UdeACompress, the Suffix Array Construction