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Paul D. McNicholas

Paul D. McNicholas contributes to research discovery and scholarly infrastructure.

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Published work

6 published item(s)

preprint2026arXiv

Classification Fields: Arbitrarily Fine Recursive Hierarchical Clustering From Few Examples

Classical clustering methods usually return either a finite partition of the observed data or a finite dendrogram over it. This finite-sample view is inadequate when the hierarchy of interest is a recursive geometric object with fine-scale refinements that continue beyond the levels directly observed. We introduce classification fields: infinite-depth hierarchical cluster structures on $\mathbb{R}^d$ generated by a local parent-to-child refinement rule. A classification field generator maps each parent centre to an ordered, bounded, and separated tuple of child residuals. Together with a root and a scale factor, this rule recursively generates cluster centres, Voronoi cells, and a metric DAG encoding the hierarchy. Given only a finite prefix of such a hierarchy, we learn a classification field predictor that approximates the generator and can be rolled out to unseen depths. We prove exponential truncation convergence in the completed cell metric and ReLU realizability with width $O(\varepsilon^{-γ})$ and depth $\widetilde O(\varepsilon^{-3γ/2})$, where $γ=\log K/(-\log s)$, up to finite-window aspect-ratio factors. The approximation holds at the level of the induced compact metric structures, measured in the completed cell-metric Hausdorff distance. Experimental validation on matched CFG-generated hierarchies, IFS fractals, and image-induced recursive clustering hierarchies shows that learned predictors preserve ordered child slots, unordered geometry, and hierarchy-level path metrics under recursive rollout. These results support the claim that finite hierarchical observations can reveal local refinement rules capable of generating substantially deeper classification fields.

preprint2022arXiv

Finite mixtures of matrix-variate Poisson-log normal distributions for three-way count data

Three-way data structures, characterized by three entities, the units, the variables and the occasions, are frequent in biological studies. In RNA sequencing, three-way data structures are obtained when high-throughput transcriptome sequencing data are collected for $n$ genes across $p$ conditions at $r$ occasions. Matrix variate distributions offer a natural way to model three-way data and mixtures of matrix variate distributions can be used to cluster three-way data. Clustering of gene expression data is carried out as means of discovering gene co-expression networks. In this work, a mixture of matrix variate Poisson-log normal distributions is proposed for clustering read counts from RNA sequencing. By considering the matrix variate structure, full information on the conditions and occasions of the RNA sequencing dataset is simultaneously considered, and the number of covariance parameters to be estimated is reduced. We propose three different frameworks for parameter estimation: a Markov chain Monte Carlo based approach, a variational Gaussian approximation based approach, and a hybrid approach. Various information criteria are used for model selection. The models are applied to both real and simulated data, and we demonstrate that the proposed approaches can recover the underlying cluster structure in both cases. In simulation studies where the true model parameters are known, our proposed approach shows good parameter recovery.

preprint2020arXiv

An Evolutionary Algorithm with Crossover and Mutation for Model-Based Clustering

An evolutionary algorithm (EA) is developed as an alternative to the EM algorithm for parameter estimation in model-based clustering. This EA facilitates a different search of the fitness landscape, i.e., the likelihood surface, utilizing both crossover and mutation. Furthermore, this EA represents an efficient approach to "hard" model-based clustering and so it can be viewed as a sort of generalization of the k-means algorithm, which is itself equivalent to a restricted Gaussian mixture model. The EA is illustrated on several datasets, and its performance is compared to other hard clustering approaches and model-based clustering via the EM algorithm.

preprint2020arXiv

Clustering Discrete-Valued Time Series

There is a need for the development of models that are able to account for discreteness in data, along with its time series properties and correlation. Our focus falls on INteger-valued AutoRegressive (INAR) type models. The INAR type models can be used in conjunction with existing model-based clustering techniques to cluster discrete-valued time series data. With the use of a finite mixture model, several existing techniques such as the selection of the number of clusters, estimation using expectation-maximization and model selection are applicable. The proposed model is then demonstrated on real data to illustrate its clustering applications.

preprint2020arXiv

Detecting British Columbia Coastal Rainfall Patterns by Clustering Gaussian Processes

Functional data analysis is a statistical framework where data are assumed to follow some functional form. This method of analysis is commonly applied to time series data, where time, measured continuously or in discrete intervals, serves as the location for a function's value. Gaussian processes are a generalization of the multivariate normal distribution to function space and, in this paper, they are used to shed light on coastal rainfall patterns in British Columbia (BC). Specifically, this work addressed the question over how one should carry out an exploratory cluster analysis for the BC, or any similar, coastal rainfall data. An approach is developed for clustering multiple processes observed on a comparable interval, based on how similar their underlying covariance kernel is. This approach provides interesting insights into the BC data, and these insights can be framed in terms of El Niño and La Niña; however, the result is not simply one cluster representing El Niño years and another for La Niña years. From one perspective, the results show that clustering annual rainfall can potentially be used to identify extreme weather patterns.

preprint2020arXiv

Mixtures of Contaminated Matrix Variate Normal Distributions

Analysis of three-way data is becoming ever more prevalent in the literature, especially in the area of clustering and classification. Real data, including real three-way data, are often contaminated by potential outlying observations. Their detection, as well as the development of robust models insensitive to their presence, is particularly important for this type of data because of the practical issues concerning their effective visualization. Herein, the contaminated matrix variate normal distribution is discussed and then utilized in the mixture model paradigm for clustering. One key advantage of the proposed model is the ability to automatically detect potential outlying matrices by computing their \textit{a posteriori} probability to be a "good" or "bad" point. Such detection is currently unavailable using existing matrix variate methods. An expectation conditional maximization algorithm is used for parameter estimation, and both simulated and real data are used for illustration.