Related papers: Efficient algorithms for enumerating maximal commo…
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…
We develop algorithms for inner approximating the cone of positive semidefinite matrices via linear programming and second order cone programming. Starting with an initial linear algebraic approximation suggested recently by Ahmadi and…
The notion of the cover is a generalization of a period of a string, and there are linear time algorithms for finding the shortest cover. The seed is a more complicated generalization of periodicity, it is a cover of a superstring of a…
A set of vertices in a graph forms a potential maximal clique if there exists a minimal chordal completion in which it is a maximal clique. Potential maximal cliques were first introduced as a key tool to obtain an efficient, though…
The performance of anytime algorithms can be improved by simultaneously solving several instances of algorithm-problem pairs. These pairs may include different instances of a problem (such as starting from a different initial state),…
A simple yet efficient computational algorithm for computing the continuous optimal experimental design for linear models is proposed. An alternative proof the monotonic convergence for $D$-optimal criterion on continuous design spaces are…
In ongoing work to define a principled method for syntenic block discovery and structuring, work based on homology-derived constraints and a generalization of common intervals, we faced a fundamental computational problem: how to determine…
The longest common subsequence (LCS) is a fundamental problem in string processing which has numerous algorithmic studies, extensions, and applications. A sequence $u_1, \ldots, u_f$ of $f$ strings s said to be an ($f$-)segmentation of a…
In the Shortest Common Superstring problem (SCS), one needs to find the shortest superstring for a set of strings. While SCS is NP-hard and MAX-SNP-hard, the Greedy Algorithm "choose two strings with the largest overlap; merge them; repeat"…
One way to speed up the algorithm configuration task is to use short runs instead of long runs as much as possible, but without discarding the configurations that eventually do well on the long runs. We consider the problem of selecting the…
The binary string matching problem consists in finding all the occurrences of a pattern in a text where both strings are built on a binary alphabet. This is an interesting problem in computer science, since binary data are omnipresent in…
We propose a very fast approximate Markov Chain Monte Carlo (MCMC) sampling framework that is applicable to a large class of sparse Bayesian inference problems, where the computational cost per iteration in several models is of order…
A longest common extension (LCE) query on a string computes the length of the longest common suffix or prefix at two given positions. A dynamic LCE algorithm maintains a data structure that allows efficient LCE queries on a string that can…
We study dense packings of a large number of congruent non-overlapping circles inside a square by looking for configurations which maximize the packing density, defined as the ratio between the area occupied by the disks and the area of the…
Given the vast reservoirs of data stored worldwide, efficient mining of data from a large information store has emerged as a great challenge. Many databases like that of intrusion detection systems, web-click records, player statistics,…
Bipartite graphs are a prevalent modeling tool for real-world networks, capturing interactions between vertices of two different types. Within this framework, bicliques emerge as crucial structures when studying dense subgraphs: they are…
We consider the problem of identifying tandem scattered subsequences within a string. Our algorithm identifies a longest subsequence which occurs twice without overlap in a string. This algorithm is based on the Hunt-Szymanski algorithm,…
Sequence classification algorithms, such as SVM, require a definition of distance (similarity) measure between two sequences. A commonly used notion of similarity is the number of matches between $k$-mers ($k$-length subsequences) in the…
In the Shortest Common Superstring (SCS) problem, one is given a collection of strings, and needs to find a shortest string containing each of them as a substring. SCS admits $2\frac{11}{23}$-approximation in polynomial time (Mucha,…
The time complexity of data clustering has been viewed as fundamentally quadratic, slowing with the number of data items, as each item is compared for similarity to preceding items. Clustering of large data sets has been infeasible without…