Recompression: a simple and powerful technique for word equations

In this paper we present an application of a simple technique of local recompression, previously developed by the author in the context of compressed membership problems and compressed pattern matching, to word equations. The technique is based on local modification of variables (replacing X by aX or Xa) and iterative replacement of pairs of letters appearing in the equation by a `fresh' letter, which can be seen as a bottom-up compression of the solution of the given word equation, to be more specific, building an SLP (Straight-Line Programme) for the solution of the word equation. Using this technique we give a new, independent and self-contained proofs of most of the known results for word equations. To be more specific, the presented (nondeterministic) algorithm runs in O(n log n) space and in time polynomial in log N, where N is the size of the length-minimal solution of the word equation. The presented algorithm can be easily generalised to a generator of all solutions of the given word equation (without increasing the space usage). Furthermore, a further analysis of the algorithm yields a doubly exponential upper bound on the size of the length-minimal solution. The presented algorithm does not use exponential bound on the exponent of periodicity. Conversely, the analysis of the algorithm yields an independent proof of the exponential bound on exponent of periodicity. We believe that the presented algorithm, its idea and analysis are far simpler than all previously applied. Furthermore, thanks to it we can obtain a unified and simple approach to most of known results for word equations. As a small additional result we show that for O(1) variables (with arbitrary many appearances in the equation) word equations can be solved in linear space, i.e. they are context-sensitive.Comment: Submitted to a journal. Since previous version the proofs were simplified, overall presentation improve

Pattern matching in Lempel-Ziv compressed strings: fast, simple, and deterministic

Countless variants of the Lempel-Ziv compression are widely used in many real-life applications. This paper is concerned with a natural modification of the classical pattern matching problem inspired by the popularity of such compression methods: given an uncompressed pattern s[1..m] and a Lempel-Ziv representation of a string t[1..N], does s occur in t? Farach and Thorup gave a randomized O(nlog^2(N/n)+m) time solution for this problem, where n is the size of the compressed representation of t. We improve their result by developing a faster and fully deterministic O(nlog(N/n)+m) time algorithm with the same space complexity. Note that for highly compressible texts, log(N/n) might be of order n, so for such inputs the improvement is very significant. A (tiny) fragment of our method can be used to give an asymptotically optimal solution for the substring hashing problem considered by Farach and Muthukrishnan.Comment: submitte

One-variable word equations in linear time

In this paper we consider word equations with one variable (and arbitrary many appearances of it). A recent technique of recompression, which is applicable to general word equations, is shown to be suitable also in this case. While in general case it is non-deterministic, it determinises in case of one variable and the obtained running time is O(n + #_X log n), where #_X is the number of appearances of the variable in the equation. This matches the previously-best algorithm due to D\k{a}browski and Plandowski. Then, using a couple of heuristics as well as more detailed time analysis the running time is lowered to O(n) in RAM model. Unfortunately no new properties of solutions are shown.Comment: submitted to a journal, general overhaul over the previous versio

Repetition Detection in a Dynamic String

A string UU for a non-empty string U is called a square. Squares have been well-studied both from a combinatorial and an algorithmic perspective. In this paper, we are the first to consider the problem of maintaining a representation of the squares in a dynamic string S of length at most n. We present an algorithm that updates this representation in n^o(1) time. This representation allows us to report a longest square-substring of S in O(1) time and all square-substrings of S in O(output) time. We achieve this by introducing a novel tool - maintaining prefix-suffix matches of two dynamic strings. We extend the above result to address the problem of maintaining a representation of all runs (maximal repetitions) of the string. Runs are known to capture the periodic structure of a string, and, as an application, we show that our representation of runs allows us to efficiently answer periodicity queries for substrings of a dynamic string. These queries have proven useful in static pattern matching problems and our techniques have the potential of offering solutions to these problems in a dynamic text setting

Synchronization Strings: Codes for Insertions and Deletions Approaching the Singleton Bound

We introduce synchronization strings as a novel way of efficiently dealing with synchronization errors, i.e., insertions and deletions. Synchronization errors are strictly more general and much harder to deal with than commonly considered half-errors, i.e., symbol corruptions and erasures. For every $\epsilon >0$, synchronization strings allow to index a sequence with an $\epsilon^{-O(1)}$ size alphabet such that one can efficiently transform $k$ synchronization errors into $(1+\epsilon)k$ half-errors. This powerful new technique has many applications. In this paper, we focus on designing insdel codes, i.e., error correcting block codes (ECCs) for insertion deletion channels. While ECCs for both half-errors and synchronization errors have been intensely studied, the later has largely resisted progress. Indeed, it took until 1999 for the first insdel codes with constant rate, constant distance, and constant alphabet size to be constructed by Schulman and Zuckerman. Insdel codes for asymptotically large or small noise rates were given in 2016 by Guruswami et al. but these codes are still polynomially far from the optimal rate-distance tradeoff. This makes the understanding of insdel codes up to this work equivalent to what was known for regular ECCs after Forney introduced concatenated codes in his doctoral thesis 50 years ago. A direct application of our synchronization strings based indexing method gives a simple black-box construction which transforms any ECC into an equally efficient insdel code with a slightly larger alphabet size. This instantly transfers much of the highly developed understanding for regular ECCs over large constant alphabets into the realm of insdel codes. Most notably, we obtain efficient insdel codes which get arbitrarily close to the optimal rate-distance tradeoff given by the Singleton bound for the complete noise spectrum

Efficient Computation of Sequence Mappability

Sequence mappability is an important task in genome re-sequencing. In the $(k,m)$-mappability problem, for a given sequence $T$ of length $n$, our goal is to compute a table whose $i$th entry is the number of indices $j \ne i$ such that length-$m$ substrings of $T$ starting at positions $i$ and $j$ have at most $k$ mismatches. Previous works on this problem focused on heuristic approaches to compute a rough approximation of the result or on the case of $k=1$. We present several efficient algorithms for the general case of the problem. Our main result is an algorithm that works in $\mathcal{O}(n \min\{m^k,\log^{k+1} n\})$ time and $\mathcal{O}(n)$ space for $k=\mathcal{O}(1)$. It requires a carefu l adaptation of the technique of Cole et al.~[STOC 2004] to avoid multiple counting of pairs of substrings. We also show $\mathcal{O}(n^2)$-time algorithms to compute all results for a fixed $m$ and all $k=0,\ldots,m$ or a fixed $k$ and all $m=k,\ldots,n-1$. Finally we show that the $(k,m)$-mappability problem cannot be solved in strongly subquadratic time for $k,m = \Theta(\log n)$ unless the Strong Exponential Time Hypothesis fails.Comment: Accepted to SPIRE 201

Covering Problems for Partial Words and for Indeterminate Strings

We consider the problem of computing a shortest solid cover of an indeterminate string. An indeterminate string may contain non-solid symbols, each of which specifies a subset of the alphabet that could be present at the corresponding position. We also consider covering partial words, which are a special case of indeterminate strings where each non-solid symbol is a don't care symbol. We prove that indeterminate string covering problem and partial word covering problem are NP-complete for binary alphabet and show that both problems are fixed-parameter tractable with respect to $k$, the number of non-solid symbols. For the indeterminate string covering problem we obtain a $2^{O(k \log k)} + n k^{O(1)}$-time algorithm. For the partial word covering problem we obtain a $2^{O(\sqrt{k}\log k)} + nk^{O(1)}$-time algorithm. We prove that, unless the Exponential Time Hypothesis is false, no $2^{o(\sqrt{k})} n^{O(1)}$-time solution exists for either problem, which shows that our algorithm for this case is close to optimal. We also present an algorithm for both problems which is feasible in practice.Comment: full version (simplified and corrected); preliminary version appeared at ISAAC 2014; 14 pages, 4 figure