Related papers: On-the-Fly Array Initialization in Less Space
Motivated by challenges in pangenomic read alignment, we propose a generalization of Wheeler graphs that we call Wheeler maps. A Wheeler map stores a text $T[1..n]$ and an assignment of tags to the characters of $T$ such that we can…
Minimizers are sampling schemes with numerous applications in computational biology. Assuming a fixed alphabet of size $\sigma$, a minimizer is defined by two integers $k,w\ge2$ and a linear order $\rho$ on strings of length $k$ (also…
We consider the problem of indexing a string $t$ of length $n$ to report the occurrences of a query pattern $p$ containing $m$ characters and $j$ wildcards. Let $occ$ be the number of occurrences of $p$ in $t$, and $\sigma$ the size of the…
How hard is it to program $n$ robots to move about a long narrow aisle such that only $w$ of them can fit across the width of the aisle? In this paper, we answer that question by calculating the topological complexity of $\text{conf}(n,w)$,…
Work Stealing has been a very successful algorithm for scheduling parallel computations, and is known to achieve high performances even for computations exhibiting fine-grained parallelism. We present a variant of \ws\ that provably avoids…
Minimizer schemes, or just minimizers, are a very important computational primitive in sampling and sketching biological strings. Assuming a fixed alphabet of size $\sigma$, a minimizer is defined by two integers $k,w\ge2$ and a total order…
Let $P$ be a set of $m$ points in ${\mathbb R}^2$, let $\Sigma$ be a set of $n$ semi-algebraic sets of constant complexity in ${\mathbb R}^2$, let $(S,+)$ be a semigroup, and let $w: P \rightarrow S$ be a weight function on the points of…
Flash memory is a write-once medium in which reprogramming cells requires first erasing the block that contains them. The lifetime of the flash is a function of the number of block erasures and can be as small as several thousands. To…
Grammar based compression, where one replaces a long string by a small context-free grammar that generates the string, is a simple and powerful paradigm that captures many popular compression schemes. In this paper, we present a novel…
We introduce a novel multivariate approach for solving weighted parameterized problems. In our model, given an instance of size $n$ of a minimization (maximization) problem, and a parameter $W \geq 1$, we seek a solution of weight at most…
A data word is a sequence of pairs of a letter from a finite alphabet and an element from an infinite set, where the latter can only be compared for equality. Safety one-way alternating automata with one register on infinite data words are…
A string $w$ is said to be a minimal absent word (MAW) for a string $S$ if $w$ does not occur in $S$ and any proper substring of $w$ occurs in $S$. We focus on non-trivial MAWs which are of length at least 2. Finding such non-trivial MAWs…
We show how to build an alphabetic minimax tree for a sequence (W = w_1, >..., w_n) of real weights in (O (n d \log \log n)) time, where $d$ is the number of distinct integers (\lceil w_i \rceil). We apply this algorithm to building an…
We study an abstract optimization problem arising from biomolecular sequence analysis. For a sequence A of pairs (a_i,w_i) for i = 1,..,n and w_i>0, a segment A(i,j) is a consecutive subsequence of A starting with index i and ending with…
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…
A pattern $\alpha$ is a string of variables and terminal letters. We say that $\alpha$ matches a word $w$, consisting only of terminal letters, if $w$ can be obtained by replacing the variables of $\alpha$ by terminal words. The matching…
In order to generate prime implicants for a given cube (minterm), most of minimization methods increase the dimension of this cube by removing one literal from it at a time. But there are two problems of exponential complexity. One of them…
Covering arrays for words of length $t$ over a $d$ letter alphabet are $k \times n$ arrays with entries from the alphabet so that for each choice of $t$ columns, each of the $d^t$ $t$-letter words appears at least once among the rows of the…
Consider a variant of Tetris played on a board of width $w$ and infinite height, where the pieces are axis-aligned rectangles of arbitrary integer dimensions, the pieces can only be moved before letting them drop, and a row does not…
We show that the compressed suffix array and the compressed suffix tree of a string $T$ can be built in $O(n)$ deterministic time using $O(n\log\sigma)$ bits of space, where $n$ is the string length and $\sigma$ is the alphabet size.…