Related papers: Efficient Seeds Computation Revisited
We apply the concept of subset seeds proposed in [1] to similarity search in protein sequences. The main question studied is the design of efficient seed alphabets to construct seeds with optimal sensitivity/selectivity trade-offs. We…
The (non-uniform) sparsest cut problem is the following graph-partitioning problem: given a "supply" graph, and demands on pairs of vertices, delete some subset of supply edges to minimize the ratio of the supply edges cut to the total…
String matching is the problem of finding all the occurrences of a pattern in a text. We propose improved versions of the fast family of string matching algorithms based on hashing $q$-grams. The improvement consists of considering minimal…
Longest common substring (LCS), longest palindrome substring (LPS), and Ulam distance (UL) are three fundamental string problems that can be classically solved in near linear time. In this work, we present sublinear time quantum algorithms…
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…
The problem of finding the shortest path in a graph G(V, E) has been widely studied. However, in many applications it is necessary to compute an arbitrary number of them, k. Even though the problem has raised a lot of interest from…
The edit distance between two rooted ordered trees with $n$ nodes labeled from an alphabet~$\Sigma$ is the minimum cost of transforming one tree into the other by a sequence of elementary operations consisting of deleting and relabeling…
We give an algorithm for finding the arboricity of a weighted, undirected graph, defined as the minimum number of spanning forests that cover all edges of the graph, in $\sqrt{n} m^{1+o(1)}$ time. This improves on the previous best bound of…
We consider problems that can be formulated as a task of finding an optimal triangulation of a graph w.r.t. some notion of optimality. We present algorithms parameterized by the size of a minimum edge clique cover ($cc$) to such problems.…
Best subset selection in linear regression is well known to be nonconvex and computationally challenging to solve, as the number of possible subsets grows rapidly with increasing dimensionality of the problem. As a result, finding the…
We study the densest subgraph problem and its NP-hard densest at-most-$k$ subgraph variant through the lens of learning-augmented algorithms. We show that, given a reasonably accurate predictor that estimates whether a node belongs to the…
Positive linear programs (LP), also known as packing and covering linear programs, are an important class of problems that bridges computer science, operations research, and optimization. Despite the consistent efforts on this problem, all…
The minimum degree algorithm is one of the most widely-used heuristics for reducing the cost of solving large sparse systems of linear equations. It has been studied for nearly half a century and has a rich history of bridging techniques…
Linear diagrams are an effective way to visualize set-based data by representing elements as columns and sets as rows with one or more horizontal line segments, whose vertical overlaps with other rows indicate set intersections and their…
The worst-case fastest known algorithm for the Set Cover problem on universes with $n$ elements still essentially is the simple $O^*(2^n)$-time dynamic programming algorithm, and no non-trivial consequences of an $O^*(1.01^n)$-time…
Covering problems are classical computational problems concerning whether a certain combinatorial structure 'covers' another. For example, the minimum vertex covering problem aims to find the smallest set of vertices in a graph so that each…
The closest string problem is an NP-hard problem, whose task is to find a string that minimizes maximum Hamming distance to a given set of strings. This can be reduced to an integer program (IP). However, to date, there exists no known…
Motivated by computing duplication patterns in sequences, a new fundamental problem called the longest subsequence-repeated subsequence (LSRS) is proposed. Given a sequence $S$ of length $n$, a letter-repeated subsequence is a subsequence…
Consider the classical Min-Sum Set Cover problem: We are given a universe $\mathcal{U}$ of $n$ elements and a collection $\mathcal{S}$ of $k$ subsets of $\mathcal{U}$. Moreover, a cost function is associated with each set. The goal is to…
As a research field of stream ciphers, the pursuit of a balance of security and practicality is the focus. The conditions for security usually have to satisfy at least high period and high linear complexity. Because the feedforward…