Related papers: The Tandem Duplication Distance is NP-hard
We study distributed algorithms for expected loss minimization where the datasets are large and have to be stored on different machines. Often we deal with minimizing the average of a set of convex functions where each function is the…
The problem of matching a query string to a directed graph, whose vertices are labeled by strings, has application in different fields, from data mining to computational biology. Several variants of the problem have been considered,…
We study bounded deviation of non-deterministic finite transducers under the Hamming distance: the bounded comparison problem asks, given two transducers and $k \in \mathbb{N}$, whether for every input the two transducers produce words at…
In this paper, we define the reoptimization variant of the closest substring problem (CSP) under sequence addition. We show that, even with the additional information we have about the problem instance, the problem of finding a closest…
This paper introduces the \emph{$d$-distance matching problem}, in which we are given a bipartite graph $G=(S,T;E)$ with $S=\{s_1,\dots,s_n\}$, a weight function on the edges and an integer $d\in\mathbb Z_+$. The goal is to find a maximum…
We address the problem of computing distances between rankings that take into account similarities between candidates. The need for evaluating such distances is governed by applications as diverse as rank aggregation, bioinformatics, social…
T-Duality is a poorly understood symmetry of the space-time fields of string theory that interchanges long and short distances. It is best understood in the context of toroidal compactification where, loosely speaking, radii of the torus…
Efficient learning and model compression algorithm for deep neural network (DNN) is a key workhorse behind the rise of deep learning (DL). In this work, we propose a message passing based Bayesian deep learning algorithm called EM-TDAMP to…
The use of target networks has been a popular and key component of recent deep Q-learning algorithms for reinforcement learning, yet little is known from the theory side. In this work, we introduce a new family of target-based temporal…
In this paper, we present and study the \emph{Hamming distance oracle problem}. In this problem, the task is to preprocess two strings $S$ and $T$ of lengths $n$ and $m$, respectively, to obtain a data-structure that is able to answer…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
The edit distance (a.k.a. the Levenshtein distance) between two strings is defined as the minimum number of insertions, deletions or substitutions of symbols needed to transform one string into another. The problem of computing the edit…
Imagine that unlabelled tokens are placed on the edges of a graph, such that no two tokens are placed on incident edges. A token can jump to another edge if the edges having tokens remain independent. We study the problem of determining the…
One of the basic tasks in bioinformatics is localizing a short subsequence $S$, read while sequencing, in a long reference sequence $R$, like the human geneome. A natural rapid approach would be finding a hash value for $S$ and compare it…
An RNA sequence is a string composed of four types of nucleotides, $A, C, G$, and $U$. The goal of the RNA folding problem is to find a maximum cardinality set of crossing-free pairs of the form $\{A,U\}$ or $\{C,G\}$ in a given RNA…
The coverage depth problem in DNA data storage is about computing the expected number of reads needed to recover all encoded strands. Given a generator matrix of a linear code, this quantity equals the expected number of randomly drawn…
The problem of similarity search is one of the main problems in computer science. This problem has many applications in text-retrieval, web search, computational biology, bioinformatics and others. Similarity between two data objects can be…
We address the problem of finding the minimal number of block interchanges (exchange of two intervals) required to transform a duplicated linear genome into a tandem duplicated linear genome. We provide a formula for the distance as well as…
An RNA molecule is structured on several layers. The primary and most obvious structure is its sequence of bases, i.e. a word over the alphabet {A,C,G,U}. The higher structure is a set of one-to-one base-pairings resulting in a…
The Traveling Salesman Problem (often called TSP) is a classic algorithmic problem in the field of computer science and operations research. It is an NP-Hard problem focused on optimization. TSP has several applications even in its purest…