Related papers: Streaming Algorithms For Computing Edit Distance W…
We study approximation algorithms for the following three string measures that are widely used in practice: edit distance (ED), longest common subsequence (LCS), and longest increasing sequence (LIS). All three problems can be solved…
The dynamic time warping (DTW) is a widely-used method that allows us to efficiently compare two time series that can vary in speed. Given two strings $A$ and $B$ of respective lengths $m$ and $n$, there is a fundamental dynamic programming…
We study sketching and streaming algorithms for the Longest Common Subsequence problem (LCS) on strings of small alphabet size $|\Sigma|$. For the problem of deciding whether the LCS of strings $x,y$ has length at least $L$, we obtain a…
We study streaming algorithms for two fundamental geometric problems: computing the cost of a Minimum Spanning Tree (MST) of an $n$-point set $X \subset \{1,2,\dots,\Delta\}^d$, and computing the Earth Mover Distance (EMD) between two…
We study the classic Text-to-Pattern Hamming Distances problem: given a pattern $P$ of length $m$ and a text $T$ of length $n$, both over a polynomial-size alphabet, compute the Hamming distance between $P$ and $T[i\, .\, . \, i+m-1]$ for…
Dot plots are a standard method for local comparison of biological sequences. In a dot plot, a substring to substring distance is computed for all pairs of fixed-size windows in the input strings. Commonly, the Hamming distance is used…
We study the $k$-connectivity augmentation problem ($k$-CAP) in the single-pass streaming model. Given a $(k-1)$-edge connected graph $G=(V,E)$ that is stored in memory, and a stream of weighted edges $L$ with weights in $\{0,1,\dots,W\}$,…
Determining whether an unordered collection of overlapping substrings (called shingles) can be uniquely decoded into a consistent string is a problem that lies within the foundation of a broad assortment of disciplines ranging from…
The problem of computing the edit-distance between a string and a finite automaton arises in a variety of applications in computational biology, text processing, and speech recognition. This paper presents linear-space algorithms for…
In this paper, we propose a novel framework that converts streaming algorithms for monotone submodular maximization into streaming algorithms for non-monotone submodular maximization. This reduction readily leads to the currently tightest…
Kondo et al. (DS 2014) proposed methods for computing distances between unordered rooted trees by transforming an instance of the distance computing problem into an instance of the integer programming problem. They showed that the tree edit…
We show that the edit distance between two strings of length $n$ can be computed within a factor of $f(\epsilon)$ in $n^{1+\epsilon}$ time as long as the edit distance is at least $n^{1-\delta}$ for some $\delta(\epsilon) > 0$.
In the $k$-cut problem, we are given an edge-weighted graph $G$ and an integer $k$, and have to remove a set of edges with minimum total weight so that $G$ has at least $k$ connected components. The current best algorithms are an…
We present parameterized streaming algorithms for the graph matching problem in both the dynamic and the insert-only models. For the dynamic streaming model, we present a one-pass algorithm that, with high probability, computes a…
A streaming algorithm to compute the spectral proper orthogonal decomposition (SPOD) of stationary random processes is presented. As new data becomes available, an incremental update of the truncated eigenbasis of the estimated…
We study the problem of solving semidefinite programs (SDP) in the streaming model. Specifically, $m$ constraint matrices and a target matrix $C$, all of size $n\times n$ together with a vector $b\in \mathbb{R}^m$ are streamed to us…
Given an LZW/LZ78 compressed text, we want to find an approximate occurrence of a given pattern of length m. The goal is to achieve time complexity depending on the size n of the compressed representation of the text instead of its length.…
Real-time streaming communication requires a high quality of service despite contending with packet loss. Streaming codes are a class of codes best suited for this setting. A key challenge for streaming codes is that they operate in an…
In recent years, the problem of computing the frequencies of the induced $k$-vertex subgraphs of a graph, or \emph{$k$-graphlets}, has become central. One approach for this problem is to sample $k$-graphlets randomly. Classic algorithms for…
The substring edit error is the operation of replacing a substring $u$ of $x$ with another string $v$, where the lengths of $u$ and $v$ are bounded by a given constant $k$. It encompasses localized insertions, deletions, and substitutions…