Related papers: Fast computation of approximate weak common interv…
Motivated by the study of genome rearrangements, the NP-hard Minimum Common String Partition problems asks, given two strings, to split both strings into an identical set of blocks. We consider an extension of this problem to unbalanced…
A string matching -- and more generally, sequence matching -- algorithm is presented that has a linear worst-case computing time bound, a low worst-case bound on the number of comparisons (2n), and sublinear average-case behavior that is…
Given an elementary chain of vertex set V, seen as a labelling of V by the set {1, ...,n=|V|}, and another discrete structure over $V$, say a graph G, the problem of common intervals is to compute the induced subgraphs G[I], such that $I$…
Common intervals have been defined as a modelisation of gene clusters in genomes represented either as permutations or as sequences. Whereas optimal algorithms for finding common intervals in permutations exist even for an arbitrary number…
We propose efficient algorithms for enumerating maximal common subsequences (MCSs) of two strings. Efficiency of the algorithms are estimated by the preprocessing-time, space, and delay-time complexities. One algorithm prepares a…
String matching is the problem of finding all the substrings of a text which match a given pattern. It is one of the most investigated problems in computer science, mainly due to its very diverse applications in several fields. Recently,…
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…
Common intervals of K permutations over the same set of n elements were firstly investigated by T. Uno and M.Yagiura (Algorithmica, 26:290:309, 2000), who proposed an efficient algorithm to find common intervals when K=2. Several particular…
Given a pattern string $P$ of length $n$ and a query string $T$ of length $m$, where the characters of $P$ and $T$ are drawn from an alphabet of size $\Delta$, the {\em exact string matching} problem consists of finding all occurrences of…
The problem of computing functions of values at the nodes in a network in a totally distributed manner, where nodes do not have unique identities and make decisions based only on local information, has applications in sensor, peer-to-peer,…
For a given set of intervals on the real line, we consider the problem of ordering the intervals with the goal of minimizing an objective function that depends on the exposed interval pieces (that is, the pieces that are not covered by…
We study the problem of estimating the covariance matrix of a high-dimensional distribution when a small constant fraction of the samples can be arbitrarily corrupted. Recent work gave the first polynomial time algorithms for this problem…
Searching for all occurrences of a pattern in a text is a fundamental problem in computer science with applications in many other fields, like natural language processing, information retrieval and computational biology. Sampled string…
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…
We study the complexity of the problem of searching for a set of patterns that separate two given sets of strings. This problem has applications in a wide variety of areas, most notably in data mining, computational biology, and in…
Consider two independent random strings having same length and taking values uniformly in a common finite alphabet. We study the order of the variance of the length of the longest common subsequences (LCS) of these strings when long blocks,…
Finding the longest common subsequence in $k$-length substrings (LCS$k$) is a recently proposed problem motivated by computational biology. This is a generalization of the well-known LCS problem in which matching symbols from two sequences…
We say a string has a cadence if a certain character is repeated at regular intervals, possibly with intervening occurrences of that character. We call the cadence anchored if the first interval must be the same length as the others. We…
In multicenter biomedical research, integrating data from multiple decentralized sites provides more robust and generalizable findings due to its larger sample size and the ability to account for the between-site heterogeneity. However,…
We consider the problem of computing a shortest solid cover of an indeterminate string. An indeterminate string may contain non-solid symbols, each of which specifies a subset of the alphabet that could be present at the corresponding…