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In the past few years powerful generalizations to the Euclidean k-means problem have been made, such as Bregman clustering [7], co-clustering (i.e., simultaneous clustering of rows and columns of an input matrix) [9,18], and tensor…

String Kernel (SK) techniques, especially those using gapped $k$-mers as features (gk), have obtained great success in classifying sequences like DNA, protein, and text. However, the state-of-the-art gk-SK runs extremely slow when we…

$k$-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…

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…

Among ensemble clustering methods, Evidence Accumulation Clustering is one of the simplest technics. In this approach, a co-association (CA) matrix representing the co-clustering frequency is built and then clustered to extract consensus…

Background: With the fast development of next generation sequencing technologies, increasing numbers of genomes are being de novo sequenced and assembled. However, most are in fragmental and incomplete draft status, and thus it is often…

k-means is one of the most influential and utilized machine learning algorithms. Its computation limits the performance and scalability of many statistical analysis and machine learning tasks. We rethink and optimize k-means in terms of…

In the trace reconstruction problem, one attempts to reconstruct a fixed but unknown string $x$ of length $n$ from a given number of traces $\tilde{x}$ drawn iid from the application of a noisy process (such as the deletion channel) to $x$.…

We devise coresets for kernel $k$-Means with a general kernel, and use them to obtain new, more efficient, algorithms. Kernel $k$-Means has superior clustering capability compared to classical $k$-Means, particularly when clusters are…

This paper develops a memory-efficient approach for Sequential Pattern Mining (SPM), a fundamental topic in knowledge discovery that faces a well-known memory bottleneck for large data sets. Our methodology involves a novel hybrid trie data…

In longitudinal data analysis, observation points of repeated measurements over time often vary among subjects except in well-designed experimental studies. Additionally, measurements for each subject are typically obtained at only a few…

Huge memory consumption has been a major bottleneck for deploying high-throughput large language models in real-world applications. In addition to the large number of parameters, the key-value (KV) cache for the attention mechanism in the…

The $k$-means algorithm (Lloyd's algorithm) is a widely used method for clustering unlabeled data. A key bottleneck of the $k$-means algorithm is that each iteration requires time linear in the number of data points, which can be expensive…

This paper introduces kernel continual learning, a simple but effective variant of continual learning that leverages the non-parametric nature of kernel methods to tackle catastrophic forgetting. We deploy an episodic memory unit that…

We describe $k$-MLE, a fast and efficient local search algorithm for learning finite statistical mixtures of exponential families such as Gaussian mixture models. Mixture models are traditionally learned using the expectation-maximization…

Educators evaluate student knowledge using knowledge component (KC) models that map assessment questions to KCs. Still, designing KC models for large question banks remains an insurmountable challenge for instructors who need to analyze…

Many computational factors limit broader deployment of large language models. In this paper, we focus on a memory bottleneck imposed by the key-value (KV) cache, a computational shortcut that requires storing previous KV pairs during…

Scientific workflow management systems enable the reproducible execution of data analysis pipelines on cluster infrastructures managed by resource managers such as Kubernetes, Slurm, or HTCondor. These resource managers require resource…

Clustering data is a popular feature in the field of unsupervised machine learning. Most algorithms aim to find the best method to extract consistent clusters of data, but very few of them intend to cluster data that share the same…

Input pipelines, which ingest and transform input data, are an essential part of training Machine Learning (ML) models. However, it is challenging to implement efficient input pipelines, as it requires reasoning about parallelism,…