Related papers: The Tandem Duplication Distance is NP-hard
The edit distance problem is a classical fundamental problem in computer science in general, and in combinatorial pattern matching in particular. The standard dynamic programming solution for this problem computes the edit-distance between…
In genome rearrangements, the mutational event transposition swaps two adjacent blocks of genes in one chromosome. The Transposition Distance Problem (TDP) aims to find the minimum number of transpositions required to transform one…
High order networks are weighted hypergraphs col- lecting relationships between elements of tuples, not necessarily pairs. Valid metric distances between high order networks have been defined but they are difficult to compute when the…
The text-to-pattern Hamming distances problem asks to compute the Hamming distances between a given pattern of length $m$ and all length-$m$ substrings of a given text of length $n\ge m$. We focus on the $k$-mismatch version of the problem,…
Generalizations of plain strings have been proposed as a compact way to represent a collection of nearly identical sequences or to express uncertainty at specific text positions by enumerating all possibilities. While a plain string stores…
Thompson Sampling (TS) is one of the most effective algorithms for solving contextual multi-armed bandit problems. In this paper, we propose a new algorithm, called Neural Thompson Sampling, which adapts deep neural networks for both…
We consider large linear and nonlinear fixed point problems, and solution with proximal algorithms. We show that there is a close connection between two seemingly different types of methods from distinct fields: 1) Proximal iterations for…
The \textit{biharmonic distance} (BD) is a fundamental metric that measures the distance of two nodes in a graph. It has found applications in network coherence, machine learning, and computational graphics, among others. In spite of BD's…
Motivation: Thanks to the recent advances in structural biology, nowadays three-dimensional structures of various proteins are solved on a routine basis. A large portion of these contain structural repetitions or internal symmetries. To…
In this paper we consider the $p$-Norm Hamming Centroid problem which asks to determine whether some given binary strings have a centroid with a bound on the $p$-norm of its Hamming distances to the strings. Specifically, given a set of…
We consider the problem of performing a random walk in a distributed network. Given bandwidth constraints, the goal of the problem is to minimize the number of rounds required to obtain a random walk sample. Das Sarma et al. [PODC'10] show…
DNA synthesis is considered as one of the most expensive components in current DNA storage systems. In this paper, focusing on a common synthesis machine, which generates multiple DNA strands in parallel following a fixed supersequence,we…
This paper considers the problem of nonlinear dimensionality reduction. Unlike existing methods, such as LLE, ISOMAP, which attempt to unfold the true manifold in the low dimensional space, our algorithm tries to preserve the nonlinear…
The crossing number of a graph is the minimum number of edge crossings that a graph can have when drawn in the plane. Determining this number, known as the Crossing Number problem, is a celebrated problem in combinatorial optimization. It…
We study a combinatorial problem arising from microarrays synthesis. The synthesis is done by a light-directed chemical process. The objective is to minimize unintended illumination that may contaminate the quality of experiments.…
Suppose we are given an $n$-dimensional order-3 symmetric tensor $T \in (\mathbb{R}^n)^{\otimes 3}$ that is the sum of $r$ random rank-1 terms. The problem of recovering the rank-1 components is possible in principle when $r \lesssim n^2$…
Although real-world text datasets, such as DNA sequences, are far from being uniformly random, average-case string searching algorithms perform significantly better than worst-case ones in most applications of interest. In this paper, we…
$\newcommand{\Re}{\mathbb{R}}$We study the minWSPD problem of computing the minimum-size well-separated pairs decomposition of a set of points, and show constant approximation algorithms in low-dimensional Euclidean space and doubling…
The longest common extension problem is to preprocess a given string of length $n$ into a data structure that uses $S(n)$ bits on top of the input and answers in $T(n)$ time the queries $\mathit{LCE}(i,j)$ computing the length of the…
In the discrete Tempotron learning problem a neuron receives time varying inputs and for a set of such input sequences ($\mathcal S_-$ set) the neuron must be sub-threshold for all times while for some other sequences ($\mathcal S_+$ set)…