Related papers: On the Optimisation of the GSACA Suffix Array Cons…

We consider the problem of finding repetitive structures and inherent patterns in a given string $\s{s}$ of length $n$ over a finite totally ordered alphabet. A border $\s{u}$ of a string $\s{s}$ is both a prefix and a suffix of $\s{s}$…

Suffix trees and suffix arrays are two of the most widely used data structures for text indexing. Each uses linear space and can be constructed in linear time for polynomially sized alphabets. However, when it comes to answering queries…

We consider a sliding window $W$ over a stream of characters from some alphabet of constant size. The user wants to perform deterministic substring matching on the current sliding window content and obtain positions of the matches. We…

Density-based clustering has found numerous applications across various domains. The Density-Based Spatial Clustering of Applications with Noise (DBSCAN) algorithm is capable of finding clusters of varied shapes that are not linearly…

We propose and analyze a new stochastic gradient method, which we call Stochastic Unbiased Curvature-aided Gradient (SUCAG), for finite sum optimization problems. SUCAG constitutes an unbiased total gradient tracking technique that uses…

We present several results about position heaps, a relatively new alternative to suffix trees and suffix arrays. First, we show that, if we limit the maximum length of patterns to be sought, then we can also limit the height of the heap and…

This study presents a novel deterministic optimization algorithm based on a special variant of the Linear Congruential Generator (LCG). While conventional algorithms generally operate within the search space, the introduced technique…

Differentiable neural architecture search methods became popular in recent years, mainly due to their low search costs and flexibility in designing the search space. However, these methods suffer the difficulty in optimizing network, so…

In 2017, a research paper compared 18 Time Series Classification (TSC) algorithms on 85 datasets from the University of California, Riverside (UCR) archive. This study, commonly referred to as a `bake off', identified that only nine…

Existing decentralized algorithms usually require knowledge of problem parameters for updating local iterates. For example, the hyperparameters (such as learning rate) usually require the knowledge of Lipschitz constant of the global…

The suffix tree is arguably the most fundamental data structure on strings: introduced by Weiner (SWAT 1973) and McCreight (JACM 1976), it allows solving a myriad of computational problems on strings in linear time. Motivated by its large…

In this paper, we propose a StochAstic Recursive grAdient algoritHm (SARAH), as well as its practical variant SARAH+, as a novel approach to the finite-sum minimization problems. Different from the vanilla SGD and other modern stochastic…

We solve the problem of finding interspersed maximal repeats using a suffix array construction. As it is well known, all the functionality of suffix trees can be handled by suffix arrays, gaining practicality. Our solution improves the…

Clustering algorithms are fundamental tools across many fields, with density-based methods offering particular advantages in identifying arbitrarily shaped clusters and handling noise. However, their effectiveness is often limited by the…

This paper presents an efficient method to perform Structured Matrix Approximation by Separation and Hierarchy (SMASH), when the original dense matrix is associated with a kernel function. Given points in a domain, a tree structure is first…

Lexicographical sorting is a fundamental problem with applications to contingency tables, databases, Bayesian networks, and more. A standard method to lexicographically sort general data is to iteratively use a stable sort -- a sort which…

Spaced seeds are important tools for similarity search in bioinformatics, and using several seeds together often significantly improves their performance. With existing approaches, however, for each seed we keep a separate linear-size data…

DBSCAN is a very classic algorithm for data clus- tering, which is widely used in many fields. However, with the data scale growing much more bigger than before, the traditional serial algorithm can not meet the performance requirement.…

After an apparent hiatus of roughly 30 years, we revisit a seemingly neglected subject in the theory of (one-dimensional) cellular automata: sublinear-time computation. The model considered is that of ACAs, which are language acceptors…

We consider the large sum of DC (Difference of Convex) functions minimization problem which appear in several different areas, especially in stochastic optimization and machine learning. Two DCA (DC Algorithm) based algorithms are proposed:…