Related papers: Fast Iteration of Spaced k-mers

One of the applications of center-based clustering algorithms such as K-Means is partitioning data points into K clusters. In some examples, the feature space relates to the underlying problem we are trying to solve, and sometimes we can…

Transforming an input sequence into its constituent k-mers is a fundamental operation in computational genomics. To reduce storage costs associated with k-mer datasets, we introduce and formally analyze MCTR, a novel two-stage algorithm for…

We devise and explore an iterative optimization procedure for controlling particle populations in particle-in-cell (PIC) codes via merging and splitting of computational macro-particles. Our approach, is to compute an optimal representation…

A popular approach to sentence compression is to formulate the task as a constrained optimization problem and solve it with integer linear programming (ILP) tools. Unfortunately, dependence on ILP may make the compressor prohibitively slow,…

Metagenomics characterizes the taxonomic diversity of microbial communities by sequencing DNA directly from an environmental sample. One of the main challenges in metagenomics data analysis is the binning step, where each sequenced read is…

Classification is at the core of data-driven prediction and decision-making, representing a fundamental task in supervised machine learning. Recently, several quantum machine learning algorithms that use quantum kernels as a measure of…

Coresets are among the most popular paradigms for summarizing data. In particular, there exist many high performance coresets for clustering problems such as $k$-means in both theory and practice. Curiously, there exists no work on…

The utility of DNA sequence substrings (k-mers) in alignment-free phylogenetic classification, including that of bacteria and viruses, is increasingly recognized. However, its biological basis eludes many twenty-first century practitioners.…

Owing to the inherently dynamic and complex characteristics of cardiac magnetic resonance (CMR) imaging, high-quality and diverse k-space data are rarely available in practice, which in turn hampers robust reconstruction of dynamic cardiac…

A buffer k-d tree is a k-d tree variant for massively-parallel nearest neighbor search. While providing valuable speed-ups on modern many-core devices in case both a large number of reference and query points are given, buffer k-d trees are…

The scanning time for a fully sampled MRI can be undesirably lengthy. Compressed sensing has been developed to minimize image artifacts in accelerated scans, but the required iterative reconstruction is computationally complex and difficult…

$\renewcommand{\Re}{{\rm I\!\hspace{-0.025em} R}} \newcommand{\eps}{{\varepsilon}} \newcommand{\Coreset}{{\mathcal{S}}} $ In this paper, we show the existence of small coresets for the problems of computing $k$-median and $k$-means…

K-means is a popular clustering method used in data mining area. To work with large datasets, researchers propose PKMeans, which is a parallel k-means on MapReduce. However, the existing k-means parallelization methods including PKMeans…

Motivation: High throughput DNA sequencing (HTS) technologies generate an excessive number of small DNA segments -- called short reads -- that cause significant computational burden. To analyze the entire genome, each of the billions of…

We survey permutation-based methods for approximate k-nearest neighbor search. In these methods, every data point is represented by a ranked list of pivots sorted by the distance to this point. Such ranked lists are called permutations. The…

Quantum machine learning, though in its initial stage, has demonstrated its potential to speed up some of the costly machine learning calculations when compared to the existing classical approaches. Among the challenging subroutines,…

Low-field magnetic resonance imaging (MRI) provides affordable access to diagnostic imaging but suffers from prolonged acquisition and limited image quality. Accelerated imaging can be achieved with k-space undersampling, while…

Objective: Spike sorting is a fundamental step in analysing extracellular recordings, enabling the isolation of single-neuron activity. However, it remains a challenging problem because extracellular traces mix overlapping spikes from…

Recently, it has been observed that when representations are learnt in a way that encourages sparsity, improved performance is obtained on classification tasks. These methods involve combinations of activation functions, sampling steps and…

In this work, we propose a framework to store and manage spatial data, which includes new efficient algorithms to perform operations accepting as input a raster dataset and a vector dataset. More concretely, we present algorithms for…