On the Approximation Ratio of Lempel-Ziv Parsing

Shannon’s entropy is a clear lower bound for statistical compression. The situation is not so well understood for dictionary-based compression. A plausible lower bound is b, the least number of phrases of a general bidirectional parse of a text, where phrases can be copied from anywhere else in the text. Since computing b is NP-complete, a popular gold standard is z, the number of phrases in the Lempel-Ziv parse of the text, where phrases can be copied only from the left. While z can be computed in linear time, almost nothing has been known for decades about its approximation ratio with respect to b. In this paper we prove that z = O(b log(n/b)), where n is the text length. We also show that the bound is tight as a function of n, by exhibiting a string family where z = Ω(b log n). Our upper bound is obtained by building a run-length context-free grammar based on a locally consistent parsing of the text. Our lower bound is obtained by relating b with r, the number of equal-letter runs in the Burrows-Wheeler transform of the text. On our way, we prove other relevant bounds between compressibility measures

Bicriteria data compression

The advent of massive datasets (and the consequent design of high-performing distributed storage systems) have reignited the interest of the scientific and engineering community towards the design of lossless data compressors which achieve effective compression ratio and very efficient decompression speed. Lempel-Ziv's LZ77 algorithm is the de facto choice in this scenario because of its decompression speed and its flexibility in trading decompression speed versus compressed-space efficiency. Each of the existing implementations offers a trade-off between space occupancy and decompression speed, so software engineers have to content themselves by picking the one which comes closer to the requirements of the application in their hands. Starting from these premises, and for the first time in the literature, we address in this paper the problem of trading optimally, and in a principled way, the consumption of these two resources by introducing the Bicriteria LZ77-Parsing problem, which formalizes in a principled way what data-compressors have traditionally approached by means of heuristics. The goal is to determine an LZ77 parsing which minimizes the space occupancy in bits of the compressed file, provided that the decompression time is bounded by a fixed amount (or vice-versa). This way, the software engineer can set its space (or time) requirements and then derive the LZ77 parsing which optimizes the decompression speed (or the space occupancy, respectively). We solve this problem efficiently in O(n log^2 n) time and optimal linear space within a small, additive approximation, by proving and deploying some specific structural properties of the weighted graph derived from the possible LZ77-parsings of the input file. The preliminary set of experiments shows that our novel proposal dominates all the highly engineered competitors, hence offering a win-win situation in theory&practice

Lempel-Ziv-like Parsing in Small Space

Lempel-Ziv (LZ77 or, briefly, LZ) is one of the most effective and widely-used compressors for repetitive texts. However, the existing efficient methods computing the exact LZ parsing have to use linear or close to linear space to index the input text during the construction of the parsing, which is prohibitive for long inputs. An alternative is Relative Lempel-Ziv (RLZ), which indexes only a fixed reference sequence, whose size can be controlled. Deriving the reference sequence by sampling the text yields reasonable compression ratios for RLZ, but performance is not always competitive with that of LZ and depends heavily on the similarity of the reference to the text. In this paper we introduce ReLZ, a technique that uses RLZ as a preprocessor to approximate the LZ parsing using little memory. RLZ is first used to produce a sequence of phrases, and these are regarded as metasymbols that are input to LZ for a second-level parsing on a (most often) drastically shorter sequence. This parsing is finally translated into one on the original sequence. We analyze the new scheme and prove that, like LZ, it achieves the $k$th order empirical entropy compression $n H_k + o(n\log\sigma)$ with $k = o(\log_\sigma n)$, where $n$ is the input length and $\sigma$ is the alphabet size. In fact, we prove this entropy bound not only for ReLZ but for a wide class of LZ-like encodings. Then, we establish a lower bound on ReLZ approximation ratio showing that the number of phrases in it can be $\Omega(\log n)$ times larger than the number of phrases in LZ. Our experiments show that ReLZ is faster than existing alternatives to compute the (exact or approximate) LZ parsing, at the reasonable price of an approximation factor below $2.0$ in all tested scenarios, and sometimes below $1.05$, to the size of LZ.Comment: 21 pages, 6 figures, 2 table

Optimal-Time Text Indexing in BWT-runs Bounded Space

Indexing highly repetitive texts --- such as genomic databases, software repositories and versioned text collections --- has become an important problem since the turn of the millennium. A relevant compressibility measure for repetitive texts is $r$, the number of runs in their Burrows-Wheeler Transform (BWT). One of the earliest indexes for repetitive collections, the Run-Length FM-index, used $O(r)$ space and was able to efficiently count the number of occurrences of a pattern of length $m$ in the text (in loglogarithmic time per pattern symbol, with current techniques). However, it was unable to locate the positions of those occurrences efficiently within a space bounded in terms of $r$. Since then, a number of other indexes with space bounded by other measures of repetitiveness --- the number of phrases in the Lempel-Ziv parse, the size of the smallest grammar generating the text, the size of the smallest automaton recognizing the text factors --- have been proposed for efficiently locating, but not directly counting, the occurrences of a pattern. In this paper we close this long-standing problem, showing how to extend the Run-Length FM-index so that it can locate the $occ$ occurrences efficiently within $O(r)$ space (in loglogarithmic time each), and reaching optimal time $O(m+occ)$ within $O(r\log(n/r))$ space, on a RAM machine of $w=\Omega(\log n)$ bits. Within $O(r\log (n/r))$ space, our index can also count in optimal time $O(m)$. Raising the space to $O(r w\log_\sigma(n/r))$, we support count and locate in $O(m\log(\sigma)/w)$ and $O(m\log(\sigma)/w+occ)$ time, which is optimal in the packed setting and had not been obtained before in compressed space. We also describe a structure using $O(r\log(n/r))$ space that replaces the text and extracts any text substring of length $\ell$ in almost-optimal time $O(\log(n/r)+\ell\log(\sigma)/w)$. (...continues...

Real-time and distributed applications for dictionary-based data compression

The greedy approach to dictionary-based static text compression can be executed by a finite state machine. When it is applied in parallel to different blocks of data independently, there is no lack of robustness even on standard large scale distributed systems with input files of arbitrary size. Beyond standard large scale, a negative effect on the compression effectiveness is caused by the very small size of the data blocks. A robust approach for extreme distributed systems is presented in this paper, where this problem is fixed by overlapping adjacent blocks and preprocessing the neighborhoods of the boundaries. Moreover, we introduce the notion of pseudo-prefix dictionary, which allows optimal compression by means of a real-time semi-greedy procedure and a slight improvement on the compression ratio obtained by the distributed implementations

Universal Compressed Text Indexing

The rise of repetitive datasets has lately generated a lot of interest in compressed self-indexes based on dictionary compression, a rich and heterogeneous family that exploits text repetitions in different ways. For each such compression scheme, several different indexing solutions have been proposed in the last two decades. To date, the fastest indexes for repetitive texts are based on the run-length compressed Burrows-Wheeler transform and on the Compact Directed Acyclic Word Graph. The most space-efficient indexes, on the other hand, are based on the Lempel-Ziv parsing and on grammar compression. Indexes for more universal schemes such as collage systems and macro schemes have not yet been proposed. Very recently, Kempa and Prezza [STOC 2018] showed that all dictionary compressors can be interpreted as approximation algorithms for the smallest string attractor, that is, a set of text positions capturing all distinct substrings. Starting from this observation, in this paper we develop the first universal compressed self-index, that is, the first indexing data structure based on string attractors, which can therefore be built on top of any dictionary-compressed text representation. Let $\gamma$ be the size of a string attractor for a text of length $n$. Our index takes $O(\gamma\log(n/\gamma))$ words of space and supports locating the $occ$ occurrences of any pattern of length $m$ in $O(m\log n + occ\log^{\epsilon}n)$ time, for any constant $\epsilon>0$. This is, in particular, the first index for general macro schemes and collage systems. Our result shows that the relation between indexing and compression is much deeper than what was previously thought: the simple property standing at the core of all dictionary compressors is sufficient to support fast indexed queries.Comment: Fixed with reviewer's comment