Practical lower and upper bounds for the Shortest Linear Superstring

Peer reviewe

Improving Table Compression with Combinatorial Optimization

We study the problem of compressing massive tables within the partition-training paradigm introduced by Buchsbaum et al. [SODA'00], in which a table is partitioned by an off-line training procedure into disjoint intervals of columns, each of which is compressed separately by a standard, on-line compressor like gzip. We provide a new theory that unifies previous experimental observations on partitioning and heuristic observations on column permutation, all of which are used to improve compression rates. Based on the theory, we devise the first on-line training algorithms for table compression, which can be applied to individual files, not just continuously operating sources; and also a new, off-line training algorithm, based on a link to the asymmetric traveling salesman problem, which improves on prior work by rearranging columns prior to partitioning. We demonstrate these results experimentally. On various test files, the on-line algorithms provide 35-55% improvement over gzip with negligible slowdown; the off-line reordering provides up to 20% further improvement over partitioning alone. We also show that a variation of the table compression problem is MAX-SNP hard.Comment: 22 pages, 2 figures, 5 tables, 23 references. Extended abstract appears in Proc. 13th ACM-SIAM SODA, pp. 213-222, 200

A Linear Time Algorithm for Constructing Hierarchical Overlap Graphs

The hierarchical overlap graph (HOG) is a graph that encodes overlaps from a given set P of n strings, as the overlap graph does. A best known algorithm constructs HOG in O(||P|| log n) time and O(||P||) space, where ||P|| is the sum of lengths of the strings in P. In this paper we present a new algorithm to construct HOG in O(||P||) time and space. Hence, the construction time and space of HOG are better than those of the overlap graph, which are O(||P|| + n^2).Comment: 8 pages, 2 figures, submitted to CPM 202

Superstrings with multiplicities

A superstring of a set of words P = s1, · · · , sp is a string that contains each word of P as substring. Given P, the well known Shortest Linear Superstring problem (SLS), asks for a shortest superstring of P. In a variant of SLS, called Multi-SLS, each word si comes with an integer m(i), its multiplicity, that sets a constraint on its number of occurrences, and the goal is to find a shortest superstring that contains at least m(i) occurrences of si. Multi-SLS generalizes SLS and is obviously as hard to solve, but it has been studied only in special cases (with words of length 2 or with a fixed number of words). The approximability of Multi-SLS in the general case remains open. Here, we study the approximability of Multi-SLS and that of the companion problem Multi-SCCS, which asks for a shortest cyclic cover instead of shortest superstring. First, we investigate the approximation of a greedy algorithm for maximizing the compression offered by a superstring or by a cyclic cover: the approximation ratio is 1/2 for Multi-SLS and 1 for Multi-SCCS. Then, we exhibit a linear time approximation algorithm, Concat-Greedy, and show it achieves a ratio of 4 regarding the superstring length. This demonstrates that for both measures Multi-SLS belongs to the class of APX problems. © 2018 Yoshifumi Sakai; licensed under Creative Commons License CC-BY.Peer reviewe

Information similarity metrics in information security and forensics

We study two information similarity measures, relative entropy and the similarity metric, and methods for estimating them. Relative entropy can be readily estimated with existing algorithms based on compression. The similarity metric, based on algorithmic complexity, proves to be more difficult to estimate due to the fact that algorithmic complexity itself is not computable. We again turn to compression for estimating the similarity metric. Previous studies rely on the compression ratio as an indicator for choosing compressors to estimate the similarity metric. This assumption, however, is fundamentally flawed. We propose a new method to benchmark compressors for estimating the similarity metric. To demonstrate its use, we propose to quantify the security of a stegosystem using the similarity metric. Unlike other measures of steganographic security, the similarity metric is not only a true distance metric, but it is also universal in the sense that it is asymptotically minimal among all computable metrics between two objects. Therefore, it accounts for all similarities between two objects. In contrast, relative entropy, a widely accepted steganographic security definition, only takes into consideration the statistical similarity between two random variables. As an application, we present a general method for benchmarking stegosystems. The method is general in the sense that it is not restricted to any covertext medium and therefore, can be applied to a wide range of stegosystems. For demonstration, we analyze several image stegosystems using the newly proposed similarity metric as the security metric. The results show the true security limits of stegosystems regardless of the chosen security metric or the existence of steganalysis detectors. In other words, this makes it possible to show that a stegosystem with a large similarity metric is inherently insecure, even if it has not yet been broken

String Covering: A Survey

The study of strings is an important combinatorial field that precedes the digital computer. Strings can be very long, trillions of letters, so it is important to find compact representations. Here we first survey various forms of one potential compaction methodology, the cover of a given string x, initially proposed in a simple form in 1990, but increasingly of interest as more sophisticated variants have been discovered. We then consider covering by a seed; that is, a cover of a superstring of x. We conclude with many proposals for research directions that could make significant contributions to string processing in future