Related papers: kruX: Matrix-based non-parametric eQTL discovery
Recently-developed genotype imputation methods are a powerful tool for detecting untyped genetic variants that affect disease susceptibility in genetic association studies. However, existing imputation methods require individual-level…
The $k$-dimensional Weisfeiler-Leman algorithm ($k$-WL) is a very useful combinatorial tool in graph isomorphism testing. We address the applicability of $k$-WL to recognition of graph properties. Let $G$ be an input graph with $n$…
This paper develops and analyzes a new algorithm for QR decomposition with column pivoting (QRCP) of rectangular matrices with many more rows than columns. The algorithm carefully combines methods from randomized numerical linear algebra to…
The K-means algorithm is among the most commonly used data clustering methods. However, the regular K-means can only be applied in the input space and it is applicable when clusters are linearly separable. The kernel K-means, which extends…
Neutral atom platforms are analogue quantum simulators that offer the possibility to map graphs onto a 2D qubit register using programmable Rubidium atoms arrays, whose valence electrons' energy state is used as qubits, using optical…
$k$ Nearest Neighbors ($k$NN) is one of the most widely used supervised learning algorithms to classify Gaussian distributed data, but it does not achieve good results when it is applied to nonlinear manifold distributed data, especially…
In this abstract paper, we introduce a new kernel learning method by a nonparametric density estimator. The estimator consists of a group of k-centroids clusterings. Each clustering randomly selects data points with randomly selected…
We investigate a novel non-parametric regression-based clustering algorithm for longitudinal data analysis. Combining natural cubic splines with Gaussian mixture models (GMM), the algorithm can produce smooth cluster means that describe the…
Testing the existence of a quantitative trait locus (QTL) effect is an important task in QTL mapping studies. Most studies concentrate on the case where the phenotype distributions of different QTL groups follow normal distributions with…
Probabilistic Structured Queries (PSQ) is a cross-language information retrieval (CLIR) method that uses translation probabilities statistically derived from aligned corpora. PSQ is a strong baseline for efficient CLIR using sparse…
Clustering methods are a valuable tool for the identification of patterns in high dimensional data with applications in many scientific problems. However, quantifying uncertainty in clustering is a challenging problem, particularly when…
Kernel-based multi-marker tests for survival outcomes use primarily the Cox model to adjust for covariates. The proportional hazards assumption made by the Cox model could be unrealistic, especially in the long-term follow-up. We develop a…
Clinical randomized controlled trials (RCTs) collect hundreds of measurements spanning various metric types (e.g., laboratory tests, cognitive/motor assessments, etc.) across 100s-1000s of subjects to evaluate the effect of a treatment, but…
This paper studies two potential modifications of XTrace (Epperly et al., SIMAX 45(1):1-23, 2024), a randomized algorithm for estimating the trace of a matrix. The first is a variance reduction step that averages the output of XTrace over…
Graph Representation Learning (GRL) has emerged as a cornerstone technique for analysing complex, networked data across diverse domains, including biological systems, social networks, and data analysis. Traditional GRL methods often…
This paper introduces hybrid LU-QR al- gorithms for solving dense linear systems of the form Ax = b. Throughout a matrix factorization, these al- gorithms dynamically alternate LU with local pivoting and QR elimination steps, based upon…
Commonly-used clustering algorithms usually find ellipsoidal, spherical or other regular-structured clusters, but are more challenged when the underlying groups lack formal structure or definition. Syncytial clustering is the name that we…
In pharmacogenomic studies, biomedical researchers commonly analyze the association between genotype and biological response by using the Kruskal--Wallis test or one-way analysis of variance (ANOVA) after logarithmic transformation of the…
Background: The development, optimization and validation of protein modeling methods require efficient tools for structural comparison. Frequently, a large number of models need to be compared with the target native structure. The main…
The identification of disease-gene associations is instrumental in understanding the mechanisms of diseases and developing novel treatments. Besides identifying genes from RNA-Seq datasets, it is often necessary to identify gene clusters…