On Match Lengths, Zero Entropy and Large Deviations - with Application to Sliding Window Lempel-Ziv Algorithm

The Sliding Window Lempel-Ziv (SWLZ) algorithm that makes use of recurrence times and match lengths has been studied from various perspectives in information theory literature. In this paper, we undertake a finer study of these quantities under two different scenarios, i) \emph{zero entropy} sources that are characterized by strong long-term memory, and ii) the processes with weak memory as described through various mixing conditions. For zero entropy sources, a general statement on match length is obtained. It is used in the proof of almost sure optimality of Fixed Shift Variant of Lempel-Ziv (FSLZ) and SWLZ algorithms given in literature. Through an example of stationary and ergodic processes generated by an irrational rotation we establish that for a window of size $n_w$, a compression ratio given by $O(\frac{\log n_w}{{n_w}^a})$ where $a$ depends on $n_w$ and approaches 1 as $n_w \rightarrow \infty$, is obtained under the application of FSLZ and SWLZ algorithms. Also, we give a general expression for the compression ratio for a class of stationary and ergodic processes with zero entropy. Next, we extend the study of Ornstein and Weiss on the asymptotic behavior of the \emph{normalized} version of recurrence times and establish the \emph{large deviation property} (LDP) for a class of mixing processes. Also, an estimator of entropy based on recurrence times is proposed for which large deviation principle is proved for sources satisfying similar mixing conditions.Comment: accepted to appear in IEEE Transactions on Information Theor

Universal quantum information compression and degrees of prior knowledge

We describe a universal information compression scheme that compresses any pure quantum i.i.d. source asymptotically to its von Neumann entropy, with no prior knowledge of the structure of the source. We introduce a diagonalisation procedure that enables any classical compression algorithm to be utilised in a quantum context. Our scheme is then based on the corresponding quantum translation of the classical Lempel-Ziv algorithm. Our methods lead to a conceptually simple way of estimating the entropy of a source in terms of the measurement of an associated length parameter while maintaining high fidelity for long blocks. As a by-product we also estimate the eigenbasis of the source. Since our scheme is based on the Lempel-Ziv method, it can be applied also to target sequences that are not i.i.d.Comment: 17 pages, no figures. A preliminary version of this work was presented at EQIS '02, Tokyo, September 200

A Universal Scheme for Wyner–Ziv Coding of Discrete Sources

We consider the Wyner–Ziv (WZ) problem of lossy compression where the decompressor observes a noisy version of the source, whose statistics are unknown. A new family of WZ coding algorithms is proposed and their universal optimality is proven. Compression consists of sliding-window processing followed by Lempel–Ziv (LZ) compression, while the decompressor is based on a modification of the discrete universal denoiser (DUDE) algorithm to take advantage of side information. The new algorithms not only universally attain the fundamental limits, but also suggest a paradigm for practical WZ coding. The effectiveness of our approach is illustrated with experiments on binary images, and English text using a low complexity algorithm motivated by our class of universally optimal WZ codes

Lempel-Ziv Factorization May Be Harder Than Computing All Runs

The complexity of computing the Lempel-Ziv factorization and the set of all runs (= maximal repetitions) is studied in the decision tree model of computation over ordered alphabet. It is known that both these problems can be solved by RAM algorithms in $O(n\log\sigma)$ time, where $n$ is the length of the input string and $\sigma$ is the number of distinct letters in it. We prove an $\Omega(n\log\sigma)$ lower bound on the number of comparisons required to construct the Lempel-Ziv factorization and thereby conclude that a popular technique of computation of runs using the Lempel-Ziv factorization cannot achieve an $o(n\log\sigma)$ time bound. In contrast with this, we exhibit an $O(n)$ decision tree algorithm finding all runs in a string. Therefore, in the decision tree model the runs problem is easier than the Lempel-Ziv factorization. Thus we support the conjecture that there is a linear RAM algorithm finding all runs.Comment: 12 pages, 3 figures, submitte

RLZAP: Relative Lempel-Ziv with Adaptive Pointers

Relative Lempel-Ziv (RLZ) is a popular algorithm for compressing databases of genomes from individuals of the same species when fast random access is desired. With Kuruppu et al.'s (SPIRE 2010) original implementation, a reference genome is selected and then the other genomes are greedily parsed into phrases exactly matching substrings of the reference. Deorowicz and Grabowski (Bioinformatics, 2011) pointed out that letting each phrase end with a mismatch character usually gives better compression because many of the differences between individuals' genomes are single-nucleotide substitutions. Ferrada et al. (SPIRE 2014) then pointed out that also using relative pointers and run-length compressing them usually gives even better compression. In this paper we generalize Ferrada et al.'s idea to handle well also short insertions, deletions and multi-character substitutions. We show experimentally that our generalization achieves better compression than Ferrada et al.'s implementation with comparable random-access times

Reference Based Genome Compression

DNA sequencing technology has advanced to a point where storage is becoming the central bottleneck in the acquisition and mining of more data. Large amounts of data are vital for genomics research, and generic compression tools, while viable, cannot offer the same savings as approaches tuned to inherent biological properties. We propose an algorithm to compress a target genome given a known reference genome. The proposed algorithm first generates a mapping from the reference to the target genome, and then compresses this mapping with an entropy coder. As an illustration of the performance: applying our algorithm to James Watson's genome with hg18 as a reference, we are able to reduce the 2991 megabyte (MB) genome down to 6.99 MB, while Gzip compresses it to 834.8 MB.Comment: 5 pages; Submitted to the IEEE Information Theory Workshop (ITW) 201