Related papers: Computing Covers under Substring Consistent Equiva…
This paper introduces a new similarity measure, the covering similarity, that we formally define for evaluating the similarity between a symbolic sequence and a set of symbolic sequences. A pair-wise similarity can also be directly derived…
Given a pair of strings, the problems of computing their Longest Common Subsequence and Edit Distance have been extensively studied for decades. For exact algorithms, LCS and Edit Distance (with character insertions and deletions) are…
The nature of the alignment with gaps corresponding to a longest common subsequence (LCS) of two independent iid random sequences drawn from a finite alphabet is investigated. It is shown that such an optimal alignment typically matches…
A $k$-matching cover of a graph $G$ is a union of $k$ matchings of $G$ which covers $V(G)$. A matching cover of $G$ is optimal if it consists of the fewest matchings of $G$. In this paper, we present an algorithm for finding an optimal…
Longest Common Subsequence ($LCS$) deals with the problem of measuring similarity of two strings. While this problem has been analyzed for decades, the recent interest stems from a practical observation that considering single characters is…
An $(n,R)$-covering sequence is a cyclic sequence whose consecutive $n$-tuples form a code of length $n$ and covering radius $R$. Using several construction methods improvements of the upper bounds on the length of such sequences for $n…
In the classic longest common substring (LCS) problem, we are given two strings $S$ and $T$, each of length at most $n$, over an alphabet of size $\sigma$, and we are asked to find a longest string occurring as a fragment of both $S$ and…
One of the most fundamental method for comparing two given strings $A$ and $B$ is the longest common subsequence (LCS), where the task is to find (the length) of an LCS of $A$ and $B$. In this paper, we deal with the STR-IC-LCS problem…
The Longest Common Subsequence (LCS) of two strings is a fundamental string similarity measure with a classical dynamic programming solution taking quadratic time. Despite significant efforts, little progress was made in improving the…
The Nearest subspace classifier (NSS) finds an estimation of the underlying subspace within each class and assigns data points to the class that corresponds to its nearest subspace. This paper mainly studies how well NSS can be generalized…
The problem of approximate string matching is important in many different areas such as computational biology, text processing and pattern recognition. A great effort has been made to design efficient algorithms addressing several variants…
The study of strings is an important combinatorial field that precedes the digital computer. Strings can be very long, trillions of letters, so it is important to find compact representations. Here we first survey various forms of one…
Kernel methods are powerful tools in machine learning. They have to be computationally efficient. In this paper, we present a novel Geometric-based approach to compute efficiently the string subsequence kernel (SSK). Our main idea is that…
We revisit the problem of finding shortest unique substring (SUS) proposed recently by [6]. We propose an optimal $O(n)$ time and space algorithm that can find an SUS for every location of a string of size $n$. Our algorithm significantly…
The Average Common Substring (ACS) is a popular alignment-free distance measure for phylogeny reconstruction. The ACS can be computed in O(n) space and time, where n=x+y is the input size. The compressed string matching is the study of…
The classic string indexing problem is to preprocess a string $S$ into a compact data structure that supports efficient subsequent pattern matching queries, that is, given a pattern string $P$, report all occurrences of $P$ within $S$. In…
We consider string matching with variable length gaps. Given a string $T$ and a pattern $P$ consisting of strings separated by variable length gaps (arbitrary strings of length in a specified range), the problem is to find all ending…
The longest square subsequence (LSS) problem consists of computing a longest subsequence of a given string $S$ that is a square, i.e., a longest subsequence of form $XX$ appearing in $S$. It is known that an LSS of a string $S$ of length…
This note provides very simple, efficient algorithms for computing the number of distinct longest common subsequences of two input strings and for computing the number of LCS embeddings.
The Longest Common Subsequence (LCS) problem is a fundamental problem of sequence comparison. A natural approximation to this problem is a model in which every pairs of letters of two ``sequences'' are matched independently of the other…