Related papers: An Elegant Algorithm for the Construction of Suffi…
We consider the problem of extracting a maximum-size reflected network in a linear program. This problem has been studied before and a state-of-the-art SGA heuristic with two variations have been proposed. In this paper we apply a new…
We consider the problem of constructing a sparse suffix tree (or suffix array) for $b$ suffixes of a given text $T$ of size $n$, using only $O(b)$ words of space during construction time. Breaking the naive bound of $\Omega(nb)$ time for…
The longest common prefix array is a very advantageous data structure that, combined with the suffix array and the Burrows-Wheeler transform, allows to efficiently compute some combinatorial properties of a string useful in several…
Packing several characters into one computer word is a simple and natural way to compress the representation of a string and to speed up its processing. Exploiting this idea, we propose an index for a packed string, based on a {\em sparse…
The paper investigates the computational problem of predicting RNA secondary structures. The general belief is that allowing pseudoknots makes the problem hard. Existing polynomial-time algorithms are heuristic algorithms with no…
The branching algorithm is a fundamental technique for designing fast exponential-time algorithms to solve combinatorial optimization problems exactly. It divides the entire solution space into independent search branches using…
The problem of Text Indexing is a fundamental algorithmic problem in which one wishes to preprocess a text in order to quickly locate pattern queries within the text. In the ever evolving world of dynamic and on-line data, there is also a…
Context: Detecting arrays are mathematical structures aimed at fault identification in combinatorial interaction testing. However, they cannot be directly applied to systems that have constraints among test parameters. Such constraints are…
We propose a novel algorithm for efficiently computing a sparse directed adjacency matrix from a group of time series following a causal graph process. Our solution is scalable for both dense and sparse graphs and automatically selects the…
In high-dimensional settings, Canonical Correlation Analysis (CCA) often fails, and existing sparse methods force an untenable choice between computational speed and statistical rigor. This work introduces a fast and provably consistent…
The suffix array is an efficient data structure for in-memory pattern search. Suffix arrays can also be used for external-memory pattern search, via two-level structures that use an internal index to identify the correct block of suffix…
The numerical study of physical problems often require integrating the dynamics of a large number of particles evolving according to a given set of equations. Particles are characterized by the information they are carrying such as an…
We give the first concise description of the fastest known suffix sorting algorithm in main memory, the DivSufSort by Yuta Mori. We then present an extension that also computes the LCP-array, which is competitive with the fastest known…
Adders are fundamental building blocks in modern digital systems, and their performance, power, and area (PPA) directly impact system efficiency. Contemporary adders typically use parallel-prefix architectures with established PPA…
We show how to build several data structures of central importance to string processing, taking as input the Burrows-Wheeler transform (BWT) and using small extra working space. Let $n$ be the text length and $\sigma$ be the alphabet size.…
We present an algorithm for regular expression parsing and submatch extraction based on tagged deterministic finite automata. The algorithm works with different disambiguation policies. We give detailed pseudocode for the algorithm,…
Sparse arrays with $N$-sensors can provide up to $O(N^2)$ degrees of freedom (DOF) by second-order cumulants. However, these sparse arrays like minimum-/low-redundancy arrays (MRAs/LRAs), nested arrays and coprime arrays can only provide…
We present the first linear time algorithm to construct the $2n$-bit version of the Lyndon array for a string of length $n$ using only $o(n)$ bits of working space. A simpler variant of this algorithm computes the plain ($n\lg n$-bit)…
We present a general framework that utilizes different efficient data structures to improve various sparsification problems involving an iterative process. We also provide insights and characterization for different iterative process, and…
Recently Kubica et al. (Inf. Process. Let., 2013) and Kim et al. (submitted to Theor. Comp. Sci.) introduced order-preserving pattern matching. In this problem we are looking for consecutive substrings of the text that have the same "shape"…