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In a \emph{weighted sequence}, for every position of the sequence and every letter of the alphabet a probability of occurrence of this letter at this position is specified. Weighted sequences are commonly used to represent imprecise or…
Pattern matching is a fundamental process in almost every scientific domain. The problem involves finding the positions of a given pattern (usually of short length) in a reference stream of data (usually of large length). The matching can…
Two strings $x$ and $y$ over $\Sigma \cup \Pi$ of equal length are said to \emph{parameterized match} (\emph{p-match}) if there is a renaming bijection $f:\Sigma \cup \Pi \rightarrow \Sigma \cup \Pi$ that is identity on $\Sigma$ and…
The problem of recovering a structured signal $\mathbf{x} \in \mathbb{C}^p$ from a set of dimensionality-reduced linear measurements $\mathbf{b} = \mathbf {A}\mathbf {x}$ arises in a variety of applications, such as medical imaging,…
It is well known that selecting a good Mixed Integer Programming (MIP) formulation is crucial for an effective solution with state-of-the art solvers. While best practices and guidelines for constructing good formulations abound, there is…
The {\em shortest common superstring} and the {\em shortest common supersequence} are two well studied problems having a wide range of applications. In this paper we consider both problems with resource constraints, denoted as the…
Motivated by the philosophy and phenomenal success of compressed sensing, the problem of reconstructing a matrix from a sampling of its entries has attracted much attention recently. Such a problem can be viewed as an information-theoretic…
Mixed-integer optimisation problems can be computationally challenging. Here, we introduce and analyse two efficient algorithms with a specific sequential design that are aimed at dealing with sampled problems within this class. At each…
We present an algorithm that, given an index $t$, produces the $t$-th (lexicographically ordered) answer of an MSO query over a string. The algorithm requires linear-time preprocessing, and builds a data structure that answers each of these…
We study the problem of learning a structured approximation (low-rank, sparse, banded, etc.) to an unknown matrix $A$ given access to matrix-vector product (matvec) queries of the form $x \rightarrow Ax$ and $x \rightarrow A^Tx$. This…
A dictionary is a database of standard vectors, so that other vectors / signals are expressed as linear combinations of dictionary vectors, and the task of learning a dictionary for a given data is to find a good dictionary so that the…
This paper is concerned with practical implementations of approximate string dictionaries that allow edit errors. In this problem, we have as input a dictionary $D$ of $d$ strings of total length $n$ over an alphabet of size $\sigma$. Given…
In this paper, we consider two versions of the Text Assembling problem. We are given a sequence of strings $s^1,\dots,s^n$ of total length $L$ that is a dictionary, and a string $t$ of length $m$ that is texts. The first version of the…
We study the cluster recovery problem in the semi-supervised active clustering framework. Given a finite set of input points, and an oracle revealing whether any two points lie in the same cluster, our goal is to recover all clusters…
There are efficient dynamic programming solutions to the computation of the Edit Distance from $S\in[1..\sigma]^n$ to $T\in[1..\sigma]^m$, for many natural subsets of edit operations, typically in time within $O(nm)$ in the worst-case over…
Countless variants of the Lempel-Ziv compression are widely used in many real-life applications. This paper is concerned with a natural modification of the classical pattern matching problem inspired by the popularity of such compression…
Given a static reference string $R$ and a source string $S$, a relative compression of $S$ with respect to $R$ is an encoding of $S$ as a sequence of references to substrings of $R$. Relative compression schemes are a classic model of…
To store and search genomic databases efficiently, researchers have recently started building compressed self-indexes based on grammars. In this paper we show how, given a straight-line program with $r$ rules for a string (S [1..n]) whose…
Let $\Sigma$ be an alphabet. For two strings $X$, $Y$, and a constrained string $P$ over the alphabet $\Sigma$, the constrained longest common subsequence and substring problem for two strings $X$ and $Y$ with respect to $P$ is to find a…
Let $S$ be a string of length $n$ over an alphabet $\Sigma$ and let $Q$ be a subset of $\Sigma$ of size $q \geq 2$. The 'co-occurrence problem' is to construct a compact data structure that supports the following query: given an integer $w$…