A Recursive Method for Enumeration of Costas Arrays

In this paper, we propose a recursive method for finding Costas arrays that relies on a particular formation of Costas arrays from similar patterns of smaller size. By using such an idea, the proposed algorithm is able to dramatically reduce the computational burden (when compared to the exhaustive search), and at the same time, still can find all possible Costas arrays of given size. Similar to exhaustive search, the proposed method can be conveniently implemented in parallel computing. The efficiency of the method is discussed based on theoretical and numerical results

Linear-Time Superbubble Identification Algorithm for Genome Assembly

DNA sequencing is the process of determining the exact order of the nucleotide bases of an individual's genome in order to catalogue sequence variation and understand its biological implications. Whole-genome sequencing techniques produce masses of data in the form of short sequences known as reads. Assembling these reads into a whole genome constitutes a major algorithmic challenge. Most assembly algorithms utilize de Bruijn graphs constructed from reads for this purpose. A critical step of these algorithms is to detect typical motif structures in the graph caused by sequencing errors and genome repeats, and filter them out; one such complex subgraph class is a so-called superbubble. In this paper, we propose an O(n+m)-time algorithm to detect all superbubbles in a directed acyclic graph with n nodes and m (directed) edges, improving the best-known O(m log m)-time algorithm by Sung et al

String Synchronizing Sets: Sublinear-Time BWT Construction and Optimal LCE Data Structure

Burrows-Wheeler transform (BWT) is an invertible text transformation that, given a text $T$ of length $n$, permutes its symbols according to the lexicographic order of suffixes of $T$. BWT is one of the most heavily studied algorithms in data compression with numerous applications in indexing, sequence analysis, and bioinformatics. Its construction is a bottleneck in many scenarios, and settling the complexity of this task is one of the most important unsolved problems in sequence analysis that has remained open for 25 years. Given a binary string of length $n$, occupying $O(n/\log n)$ machine words, the BWT construction algorithm due to Hon et al. (SIAM J. Comput., 2009) runs in $O(n)$ time and $O(n/\log n)$ space. Recent advancements (Belazzougui, STOC 2014, and Munro et al., SODA 2017) focus on removing the alphabet-size dependency in the time complexity, but they still require $\Omega(n)$ time. In this paper, we propose the first algorithm that breaks the $O(n)$-time barrier for BWT construction. Given a binary string of length $n$, our procedure builds the Burrows-Wheeler transform in $O(n/\sqrt{\log n})$ time and $O(n/\log n)$ space. We complement this result with a conditional lower bound proving that any further progress in the time complexity of BWT construction would yield faster algorithms for the very well studied problem of counting inversions: it would improve the state-of-the-art $O(m\sqrt{\log m})$-time solution by Chan and P\v{a}tra\c{s}cu (SODA 2010). Our algorithm is based on a novel concept of string synchronizing sets, which is of independent interest. As one of the applications, we show that this technique lets us design a data structure of the optimal size $O(n/\log n)$ that answers Longest Common Extension queries (LCE queries) in $O(1)$ time and, furthermore, can be deterministically constructed in the optimal $O(n/\log n)$ time.Comment: Full version of a paper accepted to STOC 201

Wide-Sense Fingerprinting Codes and Honeycomb Arrays

Standard logo The logo should be reproduced in the primary colou Pantone 660c, on all publications printed in two or more colours. Refer to the ‘Branded merchandize’ sheet for guidelines on use on promotional items et The text, ‘University of London’, is set as a 50% transparency of white. Do not use a keyline see ‘Non standard background for exceptions. The College name has been specially drawn; please use the original digital artwork and do not try to re-set

Automatic modular abstractions for template numerical constraints

We propose a method for automatically generating abstract transformers for static analysis by abstract interpretation. The method focuses on linear constraints on programs operating on rational, real or floating-point variables and containing linear assignments and tests. In addition to loop-free code, the same method also applies for obtaining least fixed points as functions of the precondition, which permits the analysis of loops and recursive functions. Our algorithms are based on new quantifier elimination and symbolic manipulation techniques. Given the specification of an abstract domain, and a program block, our method automatically outputs an implementation of the corresponding abstract transformer. It is thus a form of program transformation. The motivation of our work is data-flow synchronous programming languages, used for building control-command embedded systems, but it also applies to imperative and functional programming