Quasiperiodicities in Fibonacci strings

We consider the problem of finding quasiperiodicities in a Fibonacci string. A factor u of a string y is a cover of y if every letter of y falls within some occurrence of u in y. A string v is a seed of y, if it is a cover of a superstring of y. A left seed of a string y is a prefix of y that it is a cover of a superstring of y. Similarly a right seed of a string y is a suffix of y that it is a cover of a superstring of y. In this paper, we present some interesting results regarding quasiperiodicities in Fibonacci strings, we identify all covers, left/right seeds and seeds of a Fibonacci string and all covers of a circular Fibonacci string.Comment: In Local Proceedings of "The 38th International Conference on Current Trends in Theory and Practice of Computer Science" (SOFSEM 2012

The 2-Attractor Problem is NP-Complete

A $k$-attractor is a combinatorial object unifying dictionary-based compression. It allows to compare the repetitiveness measures of different dictionary compressors such as Lempel-Ziv 77, the Burrows-Wheeler transform, straight line programs and macro schemes. For a string $T \in \Sigma^n$, the $k$-attractor is defined as a set of positions $\Gamma \subseteq [1,n]$, such that every distinct substring of length at most $k$ is covered by at least one of the selected positions. Thus, if a substring occurs multiple times in $T$, one position suffices to cover it. A 1-attractor is easily computed in linear time, while Kempa and Prezza [STOC 2018] have shown that for $k \geq 3$, it is NP-complete to compute the smallest $k$-attractor by a reduction from $k$-set cover. The main result of this paper answers the open question for the complexity of the 2-attractor problem, showing that the problem remains NP-complete. Kempa and Prezza's proof for $k \geq 3$ also reduces the 2-attractor problem to the 2-set cover problem, which is equivalent to edge cover, but that does not fully capture the complexity of the 2-attractor problem. For this reason, we extend edge cover by a color function on the edges, yielding the colorful edge cover problem. Any edge cover must then satisfy the additional constraint that each color is represented. This extension raises the complexity such that colorful edge cover becomes NP-complete while also more precisely modeling the 2-attractor problem. We obtain a reduction showing $k$-attractor to be NP-complete for any $k \geq 2$

An Information-Theoretic Analysis of Deduplication

Deduplication finds and removes long-range data duplicates. It is commonly used in cloud and enterprise server settings and has been successfully applied to primary, backup, and archival storage. Despite its practical importance as a source-coding technique, its analysis from the point of view of information theory is missing. This paper provides such an information-theoretic analysis of data deduplication. It introduces a new source model adapted to the deduplication setting. It formalizes the two standard fixed-length and variable-length deduplication schemes, and it introduces a novel multi-chunk deduplication scheme. It then provides an analysis of these three deduplication variants, emphasizing the importance of boundary synchronization between source blocks and deduplication chunks. In particular, under fairly mild assumptions, the proposed multi-chunk deduplication scheme is shown to be order optimal.Comment: 27 page

An Efficient Rank Based Approach for Closest String and Closest Substring

This paper aims to present a new genetic approach that uses rank distance for solving two known NP-hard problems, and to compare rank distance with other distance measures for strings. The two NP-hard problems we are trying to solve are closest string and closest substring. For each problem we build a genetic algorithm and we describe the genetic operations involved. Both genetic algorithms use a fitness function based on rank distance. We compare our algorithms with other genetic algorithms that use different distance measures, such as Hamming distance or Levenshtein distance, on real DNA sequences. Our experiments show that the genetic algorithms based on rank distance have the best results

Algorithms and Data Structures for Coding, Indexing, and Mining of Sequential Data

In recent years, the production of sequential data has been rapidly increasing. This requires solving challenging problems about how to represent information, how to retrieve information, and how to extract knowledge, from sequential data. These questions belong to the areas of coding, indexing, and mining, respectively. In this thesis, we investigate problems from those three areas. Coding refers to the way in which information is represented. Coding aims at generating optimal codes, that are codes having a minimum expected length. Codes can be generated for different purposes, from data compression to error detection/correction. The Lempel-Ziv 77 parsing produces an asymptotically optimal code in terms of compression. We study algorithms to efficiently decompress strings from the Lempel-Ziv 77 parsing, using memory proportional to the size of the parsing itself. We provide the first implementation of an algorithm by Bille et al., the only work we are aware of on this problem. We present a practical evaluation of this approach and several optimizations which improve the performance on all datasets we tested. Through the Ulam-R{'e}nyi game, it is possible to provide optimal adaptive error-correcting codes. The game consists of discovering an unknown $m$-bit number by asking membership questions the answers to which can be erroneous. Questions are formulated knowing the answers to all previous ones. We want to find an optimal strategy, i.e., a strategy that can identify any $m$-bit number using the theoretical minimum number of questions. We studied the case where questions are a union of up to a fixed number of intervals, and up to three answers can be erroneous. We first show that for any sufficiently large $m$, there exists a strategy to identify an initially unknown $m$-bit number which uses at most four intervals per question. We further refine our main tool to turn the above asymptotic result into a complete characterization of those instances of the Ulam-R{'e}nyi game that admit optimal strategies. Indexing refers to the way in which information is retrieved. An index for texts permits finding all occurrences of any substring, without traversing the whole text. Many applications require to look for approximate substrings. One of these is the problem of jumbled pattern matching, where two strings match if one is a permutation of the other. We study combinatorial aspects of prefix normal words, a class of binary words introduced in this context. These words can be used as indices for the Indexed Binary Jumbled Pattern Matching problem. We present a new recursive generation algorithm for prefix normal words that is competitive with the previous one but allows to list all prefix normal words sharing the same prefix. This sheds lights on novel insights that may help solving the problem of counting the number of prefix normal words of a given length. We then introduce infinite prefix normal words, and we show that one of the operations used by the algorithm, when repeatedly applied to extend a word, produces an infinite prefix normal word. This motivates the seeking for other operations that produce infinite prefix normal words. We found that one of these operations establishes a connection between prefix normal words and Sturmian words. We also explored the relationship between prefix normal words and Abelian complexity, as well as between prefix normal words and lexicographic order. Mining refers to the way in which information is converted into knowledge. The process of knowledge discovery covers several processing steps, including knowledge extraction. We analyze the problem of mining assertions for an embedded system from its simulation traces. This problem can be modeled as a pattern discovery problem on colored strings. We present two problems of pattern discovery on colored strings: patterns for one color only, or for all colors at the same time. We present two suffix tree-based algorithms. The first algorithm solves both the one color problem and the all colors problem. We then, introduce modifications which improve performance of the algorithm both on synthetic and on real data. We implemented and evaluated the proposed approaches, highlighting time trade-offs that can be obtained. A different way of knowledge extraction is based on the information-theoretic perspective of Pearl's model of causality. It has been postulated that the true causality direction between two phenomena A and B is related to the problem of finding the minimum entropy joint distribution between A and B. This problem is known to be NP-hard, and greedy algorithms have recently been proposed. We provide a novel analysis of one of the proposed heuristic showing that this algorithm guarantees an additive approximation of 1 bit. We then, provide a general criterion for guaranteeing an additive approximation factor of 1. This criterion may be of independent interest in other contexts where couplings are used

Safety in s-t Paths, Trails and Walks

Given a directed graph G and a pair of nodes s and t, an s-t bridge of G is an edge whose removal breaks all s-t paths of G (and thus appears in all s-t paths). Computing all s-t bridges of G is a basic graph problem, solvable in linear time. In this paper, we consider a natural generalisation of this problem, with the notion of “safety” from bioinformatics. We say that a walk W is safe with respect to a set W' of s-t walks, if W is a subwalk of all walks in W'. We start by considering the maximal safe walks when consists of: all s-t paths, all s-t trails, or all s-t walks of G. We show that the solutions for the first two problems immediately follow from finding all s-t bridges after incorporating simple characterisations. However, solving the third problem requires non-trivial techniques for incorporating its characterisation. In particular, we show that there exists a compact representation computable in linear time, that allows outputting all maximal safe walks in time linear in their length. Our solutions also directly extend to multigraphs, except for the second problem, which requires a more involved approach. We further generalise these problems, by assuming that safety is defined only with respect to a subset of visible edges. Here we prove a dichotomy between the s-t paths and s-t trails cases, and the s-t walks case: the former two are NP-hard, while the latter is solvable with the same complexity as when all edges are visible. We also show that the same complexity results hold for the analogous generalisations of s-t articulation points (nodes appearing in all s-t paths). We thus obtain the best possible results for natural “safety”-generalisations of these two fundamental graph problems. Moreover, our algorithms are simple and do not employ any complex data structures, making them ideal for use in practice.Peer reviewe

Towards a Definitive Compressibility Measure for Repetitive Sequences

Unlike in statistical compression, where Shannon's entropy is a definitive lower bound, no such clear measure exists for the compressibility of repetitive sequences. Since statistical entropy does not capture repetitiveness, ad-hoc measures like the size $z$ of the Lempel--Ziv parse are frequently used to estimate it. The size $b \le z$ of the smallest bidirectional macro scheme captures better what can be achieved via copy-paste processes, though it is NP-complete to compute and it is not monotonic upon symbol appends. Recently, a more principled measure, the size $\gamma$ of the smallest string \emph{attractor}, was introduced. The measure $\gamma \le b$ lower bounds all the previous relevant ones, yet length-$n$ strings can be represented and efficiently indexed within space $O(\gamma\log\frac{n}{\gamma})$, which also upper bounds most measures. While $\gamma$ is certainly a better measure of repetitiveness than $b$, it is also NP-complete to compute and not monotonic, and it is unknown if one can always represent a string in $o(\gamma\log n)$ space. In this paper, we study an even smaller measure, $\delta \le \gamma$, which can be computed in linear time, is monotonic, and allows encoding every string in $O(\delta\log\frac{n}{\delta})$ space because $z = O(\delta\log\frac{n}{\delta})$. We show that $\delta$ better captures the compressibility of repetitive strings. Concretely, we show that (1) $\delta$ can be strictly smaller than $\gamma$, by up to a logarithmic factor; (2) there are string families needing $\Omega(\delta\log\frac{n}{\delta})$ space to be encoded, so this space is optimal for every $n$ and $\delta$; (3) one can build run-length context-free grammars of size $O(\delta\log\frac{n}{\delta})$, whereas the smallest (non-run-length) grammar can be up to $\Theta(\log n/\log\log n)$ times larger; and (4) within $O(\delta\log\frac{n}{\delta})$ space we can not only..

In-Place Bijective Burrows-Wheeler Transforms

One of the most well-known variants of the Burrows-Wheeler transform (BWT) [Burrows and Wheeler, 1994] is the bijective BWT (BBWT) [Gil and Scott, arXiv 2012], which applies the extended BWT (EBWT) [Mantaci et al., TCS 2007] to the multiset of Lyndon factors of a given text. Since the EBWT is invertible, the BBWT is a bijective transform in the sense that the inverse image of the EBWT restores this multiset of Lyndon factors such that the original text can be obtained by sorting these factors in non-increasing order. In this paper, we present algorithms constructing or inverting the BBWT in-place using quadratic time. We also present conversions from the BBWT to the BWT, or vice versa, either (a) in-place using quadratic time, or (b) in the run-length compressed setting using ?(n lg r / lg lg r) time with ?(r lg n) bits of words, where r is the sum of character runs in the BWT and the BBWT