Related papers: Longest Alignment with Edits in Data Streams
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…
As an essential operation in data cleaning, the similarity join has attracted considerable attention from the database community. In this paper, we study string similarity joins with edit-distance constraints, which find similar string…
Motivated by applications in computer vision and databases, we introduce and study the Simultaneous Nearest Neighbor Search (SNN) problem. Given a set of data points, the goal of SNN is to design a data structure that, given a collection of…
We revisit the complexity of one of the most basic problems in pattern matching. In the k-mismatch problem we must compute the Hamming distance between a pattern of length m and every m-length substring of a text of length n, as long as…
We study the problem of estimating the maximum matching size in graphs whose edges are revealed in a streaming manner. We consider both insertion-only streams and dynamic streams and present new upper and lower bound results for both…
Histograms, i.e., piece-wise constant approximations, are a popular tool used to represent data distributions. Traditionally, the difference between the histogram and the underlying distribution (i.e., the approximation error) is measured…
Given two strings $A[1..n]$ and $B[1..m]$, and a set of operations allowed to edit the strings, the edit distance between $A$ and $B$ is the minimum number of operations required to transform $A$ into $B$. Sequentially, a standard Dynamic…
We study fully dynamic algorithms for maximum matching. This is a well-studied problem, known to admit several update-time/approximation trade-offs. For instance, it is known how to maintain a 1/2-approximate matching in $\log^{O(1)} n$…
Computing the edit distance of two strings is one of the most basic problems in computer science and combinatorial optimization. Tree edit distance is a natural generalization of edit distance in which the task is to compute a measure of…
Motivated by the imminent growth of massive, highly redundant genomic databases, we study the problem of compressing a string database while simultaneously supporting fast random access, substring extraction and pattern matching to the…
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…
The problem of estimating the pth moment F_p (p nonnegative and real) in data streams is as follows. There is a vector x which starts at 0, and many updates of the form x_i <-- x_i + v come sequentially in a stream. The algorithm also…
We study streaming algorithms for Correlation Clustering. Given a graph as an arbitrary-order stream of edges, with each edge labeled as positive or negative, the goal is to partition the vertices into disjoint clusters, such that the…
Link Streams were proposed a few years ago as a model of temporal networks. We seek to understand the topological and temporal nature of those objects through efficiently computing the distances, latencies and lengths of shortest fastest…
We initiate the study of sub-linear sketching and streaming techniques for estimating the output size of common dictionary compressors such as Lempel-Ziv '77, the run-length Burrows-Wheeler transform, and grammar compression. To this end,…
We show how to compute the edit distance between two strings of length n up to a factor of 2^{\~O(sqrt(log n))} in n^(1+o(1)) time. This is the first sub-polynomial approximation algorithm for this problem that runs in near-linear time,…
Given a text $T$ of length $n$ and a pattern $P$ of length $m$, the string matching problem is a task to find all occurrences of $P$ in $T$. In this study, we propose an algorithm that solves this problem in $O((n + m)q)$ time considering…
Let two static sequences of strings $P$ and $S$, representing prefix and suffix conditions respectively, be given as input for preprocessing. For the query, let two positive integers $k_1$ and $k_2$ be given, as well as a string $T$ given…
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…
Given a set of $k$ strings $I$, their longest common subsequence (LCS) is the string with the maximum length that is a subset of all the strings in $I$. A data-structure for this problem preprocesses $I$ into a data-structure such that the…