New Algorithms and Lower Bounds for Sequential-Access Data Compression

This thesis concerns sequential-access data compression, i.e., by algorithms that read the input one or more times from beginning to end. In one chapter we consider adaptive prefix coding, for which we must read the input character by character, outputting each character's self-delimiting codeword before reading the next one. We show how to encode and decode each character in constant worst-case time while producing an encoding whose length is worst-case optimal. In another chapter we consider one-pass compression with memory bounded in terms of the alphabet size and context length, and prove a nearly tight tradeoff between the amount of memory we can use and the quality of the compression we can achieve. In a third chapter we consider compression in the read/write streams model, which allows us passes and memory both polylogarithmic in the size of the input. We first show how to achieve universal compression using only one pass over one stream. We then show that one stream is not sufficient for achieving good grammar-based compression. Finally, we show that two streams are necessary and sufficient for achieving entropy-only bounds.Comment: draft of PhD thesi

On vocabulary size of grammar-based codes

We discuss inequalities holding between the vocabulary size, i.e., the number of distinct nonterminal symbols in a grammar-based compression for a string, and the excess length of the respective universal code, i.e., the code-based analog of algorithmic mutual information. The aim is to strengthen inequalities which were discussed in a weaker form in linguistics but shed some light on redundancy of efficiently computable codes. The main contribution of the paper is a construction of universal grammar-based codes for which the excess lengths can be bounded easily.Comment: 5 pages, accepted to ISIT 2007 and correcte

Rank, select and access in grammar-compressed strings

Given a string $S$ of length $N$ on a fixed alphabet of $\sigma$ symbols, a grammar compressor produces a context-free grammar $G$ of size $n$ that generates $S$ and only $S$. In this paper we describe data structures to support the following operations on a grammar-compressed string: \mbox{rank}_c(S,i) (return the number of occurrences of symbol $c$ before position $i$ in $S$); \mbox{select}_c(S,i) (return the position of the $i$th occurrence of $c$ in $S$); and \mbox{access}(S,i,j) (return substring $S[i,j]$). For rank and select we describe data structures of size $O(n\sigma\log N)$ bits that support the two operations in $O(\log N)$ time. We propose another structure that uses $O(n\sigma\log (N/n)(\log N)^{1+\epsilon})$ bits and that supports the two queries in $O(\log N/\log\log N)$, where $\epsilon>0$ is an arbitrary constant. To our knowledge, we are the first to study the asymptotic complexity of rank and select in the grammar-compressed setting, and we provide a hardness result showing that significantly improving the bounds we achieve would imply a major breakthrough on a hard graph-theoretical problem. Our main result for access is a method that requires $O(n\log N)$ bits of space and $O(\log N+m/\log_\sigma N)$ time to extract $m=j-i+1$ consecutive symbols from $S$. Alternatively, we can achieve $O(\log N/\log\log N+m/\log_\sigma N)$ query time using $O(n\log (N/n)(\log N)^{1+\epsilon})$ bits of space. This matches a lower bound stated by Verbin and Yu for strings where $N$ is polynomially related to $n$.Comment: 16 page

Coding-theorem Like Behaviour and Emergence of the Universal Distribution from Resource-bounded Algorithmic Probability

Previously referred to as `miraculous' in the scientific literature because of its powerful properties and its wide application as optimal solution to the problem of induction/inference, (approximations to) Algorithmic Probability (AP) and the associated Universal Distribution are (or should be) of the greatest importance in science. Here we investigate the emergence, the rates of emergence and convergence, and the Coding-theorem like behaviour of AP in Turing-subuniversal models of computation. We investigate empirical distributions of computing models in the Chomsky hierarchy. We introduce measures of algorithmic probability and algorithmic complexity based upon resource-bounded computation, in contrast to previously thoroughly investigated distributions produced from the output distribution of Turing machines. This approach allows for numerical approximations to algorithmic (Kolmogorov-Chaitin) complexity-based estimations at each of the levels of a computational hierarchy. We demonstrate that all these estimations are correlated in rank and that they converge both in rank and values as a function of computational power, despite fundamental differences between computational models. In the context of natural processes that operate below the Turing universal level because of finite resources and physical degradation, the investigation of natural biases stemming from algorithmic rules may shed light on the distribution of outcomes. We show that up to 60\% of the simplicity/complexity bias in distributions produced even by the weakest of the computational models can be accounted for by Algorithmic Probability in its approximation to the Universal Distribution.Comment: 27 pages main text, 39 pages including supplement. Online complexity calculator: http://complexitycalculator.com

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...