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We present `latentcor`, an R package for correlation estimation from data with mixed variable types. Mixed variables types, including continuous, binary, ordinal, zero-inflated, or truncated data are routinely collected in many areas of…
Multisource data has spurred the development of advanced clustering algorithms, such as multi-view clustering, which critically relies on constructing similarity matrices. Traditional algorithms typically generate these matrices from sample…
Emerging artificial intelligence (AI) and machine learning (ML) workloads present new challenges of managing the collective communication used in distributed training across hundreds or even thousands of GPUs. This paper presents STrack, a…
We describe the \proglang{R} package \pkg{glmmrBase} and an extension \pkg{glmmrOptim}. \pkg{glmmrBase} provides a flexible approach to specifying, fitting, and analysing generalised linear mixed models. We use an object-orientated class…
Conducting research often involves managing multiple disconnected tools for survey design, data collection, response analysis, and report generation, leading to inefficiencies, increased error risks, and challenges in ensuring…
This article describes SimEngine, an open-source R package for structuring, maintaining, running, and debugging statistical simulations on both local and cluster-based computing environments. Several R packages exist for structuring…
The study of animal diets and the proportional contribution that different foods make to their diets is an important task in ecology. Stable Isotope Mixing Models (SIMMs) are an important tool for studying an animal's diet and understanding…
Large Language Models (LLMs) have shown promising results on various language and vision tasks. Recently, there has been growing interest in applying LLMs to graph-based tasks, particularly on Text-Attributed Graphs (TAGs). However, most…
Diverse computing paradigms have emerged to meet the growing needs for intelligent energy-efficient systems. The Margin Propagation (MP) framework, being one such initiative in the analog computing domain, stands out due to its scalability…
Nested data structures arise when observations are grouped into distinct units, such as patients within hospitals or students within schools. Accounting for this hierarchical organization is essential for valid inference, as ignoring it can…
Trojanized software packages used in software supply chain attacks constitute an emerging threat. Unfortunately, there is still a lack of scalable approaches that allow automated and timely detection of malicious software packages and thus…
In this paper we present GeoThinneR, an R package for efficient and flexible spatial thinning of species occurrence data. Spatial thinning is a widely used preprocessing step in species distribution modeling (SDM) that can help reduce…
We introduce an \verb|R| package, called \verb|MPS|, for computing the probability density function, computing the cumulative distribution function, computing the quantile function, simulating random variables, and estimating the parameters…
Spectral clustering has been one of the widely used methods for community detection in networks. However, large-scale networks bring computational challenges to the eigenvalue decomposition therein. In this paper, we study the spectral…
Numerous machine learning (ML) models employed in protein function and structure prediction depend on evolutionary information, which is captured through multiple-sequence alignments (MSA) or position-specific scoring matrices (PSSM) as…
We introduce a novel self-supervised deep clustering approach tailored for unstructured data without requiring prior knowledge of the number of clusters, termed Adaptive Self-supervised Robust Clustering (ASRC). In particular, ASRC…
Sparse subspace clustering (SSC) is one of the current state-of-the-art methods for partitioning data points into the union of subspaces, with strong theoretical guarantees. However, it is not practical for large data sets as it requires…
A genome read data set can be quickly and efficiently remapped from one reference to another similar reference (e.g., between two reference versions or two similar species) using a variety of tools, e.g., the commonly-used CrossMap tool.…
Crossover designs are widely applied in medicine, agriculture, and other biological sciences, yet their analysis remains challenging due to longitudinal observations within each unit and the presence of carry-over effects. Despite their…
The OSTSC package is a powerful oversampling approach for classifying univariant, but multinomial time series data in R. This article provides a brief overview of the oversampling methodology implemented by the package. A tutorial of the…