Related papers: Computing alignment plots efficiently
The classical pattern matching asks for locating all occurrences of one string, called the pattern, in another, called the text, where a string is simply a sequence of characters. Due to the potential practical applications, it is desirable…
We use exponential start time clustering to design faster and more work-efficient parallel graph algorithms involving distances. Previous algorithms usually rely on graph decomposition routines with strict restrictions on the diameters of…
Conformance checking techniques let us find out to what degree a process model and real execution data correspond to each other. In recent years, alignments have proven extremely useful in calculating conformance statistics. Most techniques…
We study here the so called subsequence pattern matching also known as hidden pattern matching in which one searches for a given pattern $w$ of length $m$ as a subsequence in a random text of length $n$. The quantity of interest is the…
The normalized edit distance is one of the distances derived from the edit distance. It is useful in some applications because it takes into account the lengths of the two strings compared. The normalized edit distance is not defined in…
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…
Dynamic time warping distance (DTW) is a widely used distance measure between time series. The best known algorithms for computing DTW run in near quadratic time, and conditional lower bounds prohibit the existence of significantly faster…
We consider the problem of computing distance between a pattern of length $n$ and all $n$-length subwords of a text in the streaming model. In the streaming setting, only the Hamming distance ($L_0$) has been studied. It is known that…
Randomized parallel algorithms for many fundamental problems achieve optimal linear work in expectation, but upgrading this guarantee to hold with high probability (whp) remains a recurring theoretical challenge. In this paper, we address…
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…
The Word Movers Distance (WMD) measures the semantic dissimilarity between two text documents by computing the cost of optimally moving all words of a source/query document to the most similar words of a target document. Computing WMD…
Given a pattern of length $m$ and a text of length $n$, the goal in $k$-mismatch pattern matching is to compute, for every $m$-substring of the text, the exact Hamming distance to the pattern or report that it exceeds $k$. This can be…
We study the influence of a graph parameter called modular-width on the time complexity for optimally solving well-known polynomial problems such as Maximum Matching, Triangle Counting, and Maximum $s$-$t$ Vertex-Capacitated Flow. The…
In this paper we revisit the classical regular expression matching problem, namely, given a regular expression $R$ and a string $Q$, decide if $Q$ matches one of the strings specified by $R$. Let $m$ and $n$ be the length of $R$ and $Q$,…
We consider a class of pattern matching problems where a normalising transformation is applied at every alignment. Normalised pattern matching plays a key role in fields as diverse as image processing and musical information processing…
Here we study the complexity of string problems as a function of the size of a program that generates input. We consider straight-line programs (SLP), since all algorithms on SLP-generated strings could be applied to processing…
This paper presents a new approach to statistical similarity assessment based on sequence alignment. The algorithm performs mutual matching of two random sequences by successively searching for common elements and by applying sequence…
We propose a new method for shape recognition and retrieval based on dynamic programming. Our approach uses the dynamic programming algorithm to compute the optimal score and to find the optimal alignment between two strings. First, each…
In this article we consider the graph alignment problem from the perspective of high-dimensional statistics: we aim to estimate an unknown permutation $\pi^*$ from the observation of two correlated random adjacency matrices $A_1$, $A_2$. We…
Pattern matching is a fundamental process in almost every scientific domain. The problem involves finding the positions of a given pattern (usually of short length) in a reference stream of data (usually of large length). The matching can…