Related papers: Hamming Distance Oracle

The most fundamental problem considered in algorithms for text processing is pattern matching: given a pattern $p$ of length $m$ and a text $t$ of length $n$, does $p$ occur in $t$? Multiple versions of this basic question have been…

In this work, we consider the problem of pattern matching under the dynamic time warping (DTW) distance motivated by potential applications in the analysis of biological data produced by the third generation sequencing. To measure the DTW…

Binary embedding is a nonlinear dimension reduction methodology where high dimensional data are embedded into the Hamming cube while preserving the structure of the original space. Specifically, for an arbitrary $N$ distinct points in…

Protein structures can be encoded into binary sequences, these are used to define a Hamming distance in conformational space: the distance between two different molecular conformations is the number of different bits in their sequences.…

The Cartesian tree of a sequence captures the relative order of the sequence's elements. In recent years, Cartesian tree matching has attracted considerable attention, particularly due to its applications in time series analysis. Consider a…

Given a set of strings over a specified alphabet, identifying a median or consensus string that minimizes the total distance to all input strings is a fundamental data aggregation problem. When the Hamming distance is considered as the…

For a text given in advance, the substring minimal suffix queries ask to determine the lexicographically minimal non-empty suffix of a substring specified by the location of its occurrence in the text. We develop a data structure answering…

In this work, we revisit the fundamental and well-studied problem of approximate pattern matching under edit distance. Given an integer $k$, a pattern $P$ of length $m$, and a text $T$ of length $n \ge m$, the task is to find substrings of…

Encoding data structures store enough information to answer the queries they are meant to support but not enough to recover their underlying datasets. In this paper we give the first encoding data structure for the challenging problem of…

We study the fundamental problem of approximating the edit distance of two strings. After an extensive line of research led to the development of a constant-factor approximation algorithm in almost-linear time, recent years have witnessed a…

The \emph{longest common extension} (\emph{LCE}) problem is to preprocess a given string $w$ of length $n$ so that the length of the longest common prefix between suffixes of $w$ that start at any two given positions is answered quickly. In…

In the k-mappability problem, we are given a string x of length n and integers m and k, and we are asked to count, for each length-m factor y of x, the number of other factors of length m of x that are at Hamming distance at most k from y.…

We study the $c$-approximate near neighbor problem under the continuous Fr\'echet distance: Given a set of $n$ polygonal curves with $m$ vertices, a radius $\delta > 0$, and a parameter $k \leq m$, we want to preprocess the curves into a…

Let $S_1, S_2 \in \Sigma^*$ strings, we say that $S_1$ {\em jumble match} $S_2$ if they are permutations of each other. Given a text $T$ of size $N$ and a string $S \in \Sigma^*$, the problem of \emph{Jumbled Pattern Matching} (JPM) is to…

The $\mathsf{HYBRID}$ model was introduced as a means for theoretical study of distributed networks that use various communication modes. Conceptually, it is a synchronous message passing model with a local communication mode, where in each…

We address the problem of designing a sublinear-time spectral clustering oracle for graphs that exhibit strong clusterability. Such graphs contain $k$ latent clusters, each characterized by a large inner conductance (at least $\varphi$) and…

We present a dual fault-tolerant distance oracle for undirected and unweighted graphs. Given a set $F$ of two edges, as well as a source node $s$ and a destination node $t$, our oracle returns the length of the shortest path from $s$ to $t$…

We show how, given a straight-line program with $g$ rules for a binary string $B$ of length $n$, in $O(g^{2 / 3} n^{4 / 3})$ time we can build a linear-space index such that, given $m$ and $c$, in O(1) time we can determine whether there is…

We prove that, up to subpolynomial or polylogarithmic factors, there is no tradeoff between preprocessing time, query time, and size of exact distance oracles for planar graphs. Namely, we show how given an $n$-vertex weighted directed…

We define sequence patterns of length $n$ and level $\ell$ to be equivalence classes of sequences that have $n$ elements from the set of $\ell$ integer symbols $\{1,2,\ldots,\ell\}$ with no restriction on repetition, where the equivalence…