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A standard format used for storing the output of high-throughput sequencing experiments is the FASTQ format. It comprises three main components: (i) headers, (ii) bases (nucleotide sequences), and (iii) quality scores. FASTQ files are…
Detecting all the strings that occur in a text more frequently or less frequently than expected according to an IID or a Markov model is a basic problem in string mining, yet current algorithms are based on data structures that are either…
In a dynamic retrieval system, documents must be ingested as they arrive, and be immediately findable by queries. Our purpose in this paper is to describe an index structure and processing regime that accommodates that requirement for…
In this paper we present a novel probabilistic sampling-based motion planning algorithm called the Fast Marching Tree algorithm (FMT*). The algorithm is specifically aimed at solving complex motion planning problems in high-dimensional…
The suffix tree is arguably the most fundamental data structure on strings: introduced by Weiner (SWAT 1973) and McCreight (JACM 1976), it allows solving a myriad of computational problems on strings in linear time. Motivated by its large…
The kinetics of a variety of transport-controlled processes can be reduced to the problem of determining the mean time needed to arrive at a given location for the first time, the so called mean first passage time (MFPT) problem. The…
Long-term location tracking, where trajectory compression is commonly used, has gained high interest for many applications in transport, ecology, and wearable computing. However, state-of-the-art compression methods involve high space-time…
Given a string of length $n$ that is composed of $r$ runs of letters from the alphabet $\{0,1,\ldots,\sigma{-}1\}$ such that $2 \le \sigma \le r$, we describe a data structure that, provided $r \le n / \log^{\omega(1)} n$, stores the string…
We present a succinct data structure for permutation graphs, and their superclass of circular permutation graphs, i.e., data structures using optimal space up to lower order terms. Unlike concurrent work on circle graphs (Acan et al. 2022),…
We investigate the limits of one of the fundamental ideas in data structures: fractional cascading. This is an important data structure technique to speed up repeated searches for the same key in multiple lists and it has numerous…
Mantaci et al. [TCS 2007] defined the eBWT to extend the definition of the BWT to a collection of strings, however, since this introduction, it has been used more generally to describe any BWT of a collection of strings and the fundamental…
A superpermutation is a sequence that contains every permutation of $n$ distinct symbols as a contiguous substring. For instance, a valid example for three symbols is a sequence that contains all six permutations. This paper introduces a…
In the dynamic range mode problem, we are given a sequence $a$ of length bounded by $N$ and asked to support element insertion, deletion, and queries for the most frequent element of a contiguous subsequence of $a$. In this work, we devise…
Given an integer array $A[1..n]$, the Range Minimum Query problem (RMQ) asks to preprocess $A$ into a data structure, supporting RMQ queries: given $a,b\in [1,n]$, return the index $i\in[a,b]$ that minimizes $A[i]$, i.e.,…
The Burrows-Wheeler transform (BWT) is used by the bzip2 family of compressors. In this paper, we present a hardware architecture that implements an inplace algorithm to compute the BWT. Our design does not have explicit storage for the…
Trapped-ion quantum computers based on segmented traps rely on shuttling operations to establish long-range connectivity between sub-registers. Qubit routing dynamically reconfigures qubit positions so that all qubits involved in a gate…
Long flows contribute huge volumes of traffic over inter-datacenter WAN. The Flow Completion Time (FCT) is a vital network performance metric that affects the running time of distributed applications and the users' quality of experience.…
The Burrows-Wheeler Transform (BWT) of a string is an invertible permutation of the string, which can be used for data compression and compact indexes for string pattern matching. Ganguly et al. [SODA, 2017] introduced the parameterized BWT…
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…
The retrieval problem is the problem of associating data with keys in a set. Formally, the data structure must store a function f: U ->{0,1}^r that has specified values on the elements of a given set S, a subset of U, |S|=n, but may have…