A really simple approximation of smallest grammar

In this paper we present a really simple linear-time algorithm constructing a context-free grammar of size O(g log (N/g)) for the input string, where N is the size of the input string and g the size of the optimal grammar generating this string. The algorithm works for arbitrary size alphabets, but the running time is linear assuming that the alphabet Sigma of the input string can be identified with numbers from 1,ldots, N^c for some constant c. Algorithms with such an approximation guarantee and running time are known, however all of them were non-trivial and their analyses were involved. The here presented algorithm computes the LZ77 factorisation and transforms it in phases to a grammar. In each phase it maintains an LZ77-like factorisation of the word with at most l factors as well as additional O(l) letters, where l was the size of the original LZ77 factorisation. In one phase in a greedy way (by a left-to-right sweep and a help of the factorisation) we choose a set of pairs of consecutive letters to be replaced with new symbols, i.e. nonterminals of the constructed grammar. We choose at least 2/3 of the letters in the word and there are O(l) many different pairs among them. Hence there are O(log N) phases, each of them introduces O(l) nonterminals to a grammar. A more precise analysis yields a bound O(l log(N/l)). As l \leq g, this yields the desired bound O(g log(N/g)).Comment: Accepted for CPM 201

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

Rpair: Rescaling RePair with Rsync

Data compression is a powerful tool for managing massive but repetitive datasets, especially schemes such as grammar-based compression that support computation over the data without decompressing it. In the best case such a scheme takes a dataset so big that it must be stored on disk and shrinks it enough that it can be stored and processed in internal memory. Even then, however, the scheme is essentially useless unless it can be built on the original dataset reasonably quickly while keeping the dataset on disk. In this paper we show how we can preprocess such datasets with context-triggered piecewise hashing such that afterwards we can apply RePair and other grammar-based compressors more easily. We first give our algorithm, then show how a variant of it can be used to approximate the LZ77 parse, then leverage that to prove theoretical bounds on compression, and finally give experimental evidence that our approach is competitive in practice

One-dimensional staged self-assembly

17th International Conference, DNA 17, Pasadena, CA, USA, September 19-23, 2011. ProceedingsWe introduce the problem of staged self-assembly of one-dimensional nanostructures, which becomes interesting when the elements are labeled (e.g., representing functional units that must be placed at specific locations). In a restricted model in which each operation has a single terminal assembly, we prove that assembling a given string of labels with the fewest stages is equivalent, up to constant factors, to compressing the string to be uniquely derived from the smallest possible context-free grammar (a well-studied O(logn)-approximable problem). Without this restriction, we show that the optimal assembly can be substantially smaller than the optimal context-free grammar, by a factor of Ω √n/log n even for binary strings of length n. Fortunately, we can bound this separation in model power by a quadratic function in the number of distinct glues or tiles allowed in the assembly, which is typically small in practice

Accepted for CPM 2014

In this paper we present a really simple linear-time algorithm constructing a context-free grammar of size O(g log (N/g)) for the input string, where N is the size of the input string and g the size of the optimal grammar generating this string. The algorithm works for arbitrary size alphabets, but the running time is linear assuming that the alphabet Sigma of the input string can be identified with numbers from 1,ldots, N^c for some constant c. Algorithms with such an approximation guarantee and running time are known, however all of them were non-trivial and their analyses were involved. The here presented algorithm computes the LZ77 factorisation and transforms it in phases to a grammar. In each phase it maintains an LZ77-like factorisation of the word with at most l factors as well as additional O(l) letters, where l was the size of the original LZ77 factorisation. In one phase in a greedy way (by a left-to-right sweep and a help of the factorisation) we choose a set of pairs of consecutive letters to be replaced with new symbols, i.e. nonterminals of the constructed grammar. We choose at least 2/3 of the letters in the word and there are O(l) many different pairs among them. Hence there are O(log N) phases, each of them introduces O(l) nonterminals to a grammar. A more precise analysis yields a bound O(l log(N/l)). As l \leq g, this yields the desired bound O(g log(N/g))