Related papers: A New String Edit Distance and Applications
Mixture interpretation is a central challenge in forensic science, where evidence often contains contributions from multiple sources. In the context of DNA analysis, biological samples recovered from crime scenes may include genetic…
We present new algorithms for the problem of multiple string matching of gapped patterns, where a gapped pattern is a sequence of strings such that there is a gap of fixed length between each two consecutive strings. The problem has…
The theory of sequences, supported by many SMT solvers, can model program data types including bounded arrays and lists. Sequences are parameterized by the element data type and provide operations such as accessing elements, concatenation,…
One approach to matching texts from asymmetrical domains is projecting the input sequences into a common semantic space as feature vectors upon which the matching function can be readily defined and learned. In real-world matching…
The Swap-Insert Correction distance from a string $S$ of length $n$ to another string $L$ of length $m\geq n$ on the alphabet $[1..d]$ is the minimum number of insertions, and swaps of pairs of adjacent symbols, converting $S$ into $L$.…
Writing, as an omnipresent form of human communication, permeates nearly every aspect of contemporary life. Consequently, inaccuracies or errors in written communication can lead to profound consequences, ranging from financial losses to…
In the trace reconstruction problem, one observes the output of passing a binary string $s \in \{0,1\}^n$ through a deletion channel $T$ times and wishes to recover $s$ from the resulting $T$ "traces." Most of the literature has focused on…
Phylogenomics, even more so than traditional phylogenetics, needs to represent the uncertainty in evolutionary trees due to systematic error. Here we illustrate the analysis of genome-scale alignments of yeast, using robust measures of the…
The Fr\'echet distance is a computational mainstay for comparing polygonal curves. The Fr\'echet distance under translation, which is a translation invariant version, considers the similarity of two curves independent of their location in…
A (tandem) duplication of length $ k $ is an insertion of an exact copy of a substring of length $ k $ next to its original position. This and related types of impairments are of relevance in modeling communication in the presence of…
Political scientists often find themselves tracking amendments to political texts. As different actors weigh in, texts change as they are drafted and redrafted, reflecting political preferences and power. This study provides a novel…
The Weisfeiler-Lehman (WL) test is a widely used algorithm in graph machine learning, including graph kernels, graph metrics, and graph neural networks. However, it focuses only on the consistency of the graph, which means that it is unable…
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…
We study the problem of edit similarity joins, where given a set of strings and a threshold value $K$, we want to output all pairs of strings whose edit distances are at most $K$. Edit similarity join is a fundamental problem in data…
Although several self-indexes for highly repetitive text collections exist, developing an index and search algorithm with editing operations remains a challenge. Edit distance with moves (EDM) is a string-to-string distance measure that…
Given a set of sequences, the distance between pairs of them helps us to find their similarity and derive structural relationship amongst them. For genomic sequences such measures make it possible to construct the evolution tree of…
We study the classical approximate string matching problem, that is, given strings $P$ and $Q$ and an error threshold $k$, find all ending positions of substrings of $Q$ whose edit distance to $P$ is at most $k$. Let $P$ and $Q$ have…
In this paper we present $LCSk$++: a new metric for measuring the similarity of long strings, and provide an algorithm for its efficient computation. With ever increasing size of strings occuring in practice, e.g. large genomes of plants…
Various approaches to alignment-free sequence comparison are based on the length of exact or inexact word matches between two input sequences. Haubold {\em et al.} (2009) showed how the average number of substitutions between two DNA…
In this paper, we present a new approach dedicated to correcting the spelling errors of the Arabic language. This approach corrects typographical errors like inserting, deleting, and permutation. Our method is inspired from the Levenshtein…