Related papers: SPRISS: Approximating Frequent $k$-mers by Samplin…

Purpose: A fast data-driven optimization approach, named bias-accelerated subset selection (BASS), is proposed for learning efficacious sampling patterns (SPs) with the purpose of reducing scan time in large-dimensional parallel MRI.…

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,…

$k$-means++ \cite{arthur2007k} is a widely used clustering algorithm that is easy to implement, has nice theoretical guarantees and strong empirical performance. Despite its wide adoption, $k$-means++ sometimes suffers from being slow on…

Efficient Maximum Inner Product Search (MIPS) is an important task that has a wide applicability in recommendation systems and classification with a large number of classes. Solutions based on locality-sensitive hashing (LSH) as well as…

Consistent sampling is a technique for specifying, in small space, a subset $S$ of a potentially large universe $U$ such that the elements in $S$ satisfy a suitably chosen sampling condition. Given a subset $\mathcal{I}\subseteq U$ it…

Data selection is essential for training deep learning models. An effective data sampler assigns proper sampling probability for training data and helps the model converge to a good local minimum with high performance. Previous studies in…

$k$-subset sampling is ubiquitous in machine learning, enabling regularization and interpretability through sparsity. The challenge lies in rendering $k$-subset sampling amenable to end-to-end learning. This has typically involved relaxing…

Pairwise alignment of DNA sequencing data is a ubiquitous task in bioinformatics and typically represents a heavy computational burden. State-of-the-art approaches to speed up this task use hashing to identify short segments (k-mers) that…

Sub-sequence splitting (SSS) has been demonstrated as an effective approach to mitigate data sparsity in sequential recommendation (SR) by splitting a raw user interaction sequence into multiple sub-sequences. Previous studies have…

Background: High-throughput proteomics techniques, such as mass spectrometry (MS)-based approaches, produce very high-dimensional data-sets. In a clinical setting one is often interested in how mass spectra differ between patients of…

This paper describes a new asynchronous algorithm and implementation for the problem of k-mer counting (KC), which concerns quantifying the frequency of length k substrings in a DNA sequence. This operation is common to many computational…

Frequent pattern mining is a flagship problem in data mining. In its most basic form, it asks for the set of substrings of a given string $S$ of length $n$ that occur at least $\tau$ times in $S$, for some integer $\tau\in[1,n]$. We…

Existing systems dealing with the increasing volume of data series cannot guarantee interactive response times, even for fundamental tasks such as similarity search. Therefore, it is necessary to develop analytic approaches that support…

Clustering, a fundamental activity in unsupervised learning, is notoriously difficult when the feature space is high-dimensional. Fortunately, in many realistic scenarios, only a handful of features are relevant in distinguishing clusters.…

We propose sequenced-replacement sampling (SRS) for training deep neural networks. The basic idea is to assign a fixed sequence index to each sample in the dataset. Once a mini-batch is randomly drawn in each training iteration, we refill…

Selecting a small set of representatives from a large database is important in many applications such as multi-criteria decision making, web search, and recommendation. The $k$-regret minimizing set ($k$-RMS) problem was recently proposed…

Motivation: Seed filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to identify genomic variants of the donor. Read mappers 1) quickly…

For single-cell or metagenomic sequencing projects, it is necessary to sequence with a very high mean coverage in order to make sure that all parts of the sample DNA get covered by the reads produced. This leads to huge datasets with lots…

Sparse Subspace Clustering (SSC) has been used extensively for subspace identification tasks due to its theoretical guarantees and relative ease of implementation. However SSC has quadratic computation and memory requirements with respect…

Most kernel-based methods, such as kernel or Gaussian process regression, kernel PCA, ICA, or $k$-means clustering, do not scale to large datasets, because constructing and storing the kernel matrix $\mathbf{K}_n$ requires at least…