Subzero matrix completion for sparse data analysis: large-scale learning of latent low-rank structure

We investigate when a sparse nonnegative matrix can be recovered from a real-valued matrix of much lower rank by zeroing out its negative elements. The potential for such decompositions suggests a mathematical connection between sparsity and rank; we analyze a number of sparse matrices with this latent low-rank structure and use them to illustrate the geometric origins of this connection. Previous algorithms have discovered these decompositions via an alternating minimization over the factors of a low-rank matrix, but to do so, they have also needed to compute and store another matrix, neither sparse nor low-rank, that is the size of their product. We develop a stochastic, alternating least-squares algorithm that operates on smaller blocks of this dense matrix and scales as a result to much larger problems. We also show how to further accelerate this algorithm with sparse optimizations and customized CUDA kernels. As one example, we use the algorithm to analyze the sparse matrix of synaptic weights for the recently published $\textit{Drosphilia}$ connectome. The nonzero elements of this matrix, with 139,255 rows and columns, record the number of synapses between cells in the nervous system of a female fruit fly. Despite a slowly decaying spectrum of singular values, this matrix exhibits a latent low-rank structure that is predictive of cell categories across multiple levels of specificity.

Goodness-of-Fit Tests and Calibration Machine-Learning Algorithms for Logistic Regression with Sparse Data

Assessing the goodness-of-fit of a logistic regression model is a critical prerequisite before the model is used for inference. However, goodness-of-fit (GOF) tests such as the chi-square and deviance tests often give invalid results when the data are "sparse" -- a common issue with continuous predictors like age or weight, where the asymptotic distributional assumptions are not satisfied. This thesis studies classical GOF tests for binary logistic regression under both grouped and sparse data, comparing about 30 statistical tests and machine-learning calibration algorithms. These span the classical chi-square and Hosmer-Lemeshow variants, standardized Pearson statistics, covariate-space partitioning, smoothing-based methods, and contemporary calibration machine-learning and bootstrap procedures. At a fixed size, the GiViTI calibration test (2016), McCullagh (1989), Osius-Rojek (1992), le Cessie (1995) and Stute-Zhu (2002) proved empirically powerful, balancing correct identification of bad models (high empirical power) against not raising false alarms on good models (correct empirical Type I error). Relying on formal methods alone is insufficient: visual diagnostics such as calibration plots are a vital exploratory step for detecting model deficiencies that formal tests often overlook. An application to real data (the Low Birth Weight dataset) shows that many of these tests fail to give valid conclusions when exposed to the complexities of actual datasets. The main conclusion is that model assessment requires a combination of several powerful statistical tests alongside careful visual inspection of model calibration.

Bayesian Poisson-Randomized Gamma Tensor Factorization with Application to International Trade Flows

We study sparse semi-continuous tensor data with excess zeros, heavy right tails, and slice-specific dispersion. Such features arise naturally in monetary-valued multi-way data, such as international trade, where most exporter--importer--product--year cells are zero while positive values are continuous and highly variable. To model these data, we propose a Bayesian hierarchical tensor factorization model that places a low-rank CP structure on a latent Poisson rate tensor and couples it with a conditional Gamma model for positive outcomes, with rate parameters that can vary across slices within a mode. The model therefore separates the occurrence and magnitude of positive observations while borrowing strength across all tensor dimensions through a shared low-rank latent structure. To scale posterior inference to large arrays, we develop a hybrid variational--Monte Carlo algorithm that combines efficient coordinate ascent updates with a partially collapsed augmented-data sampler. Applied to approximately 60 million trade flows, the method surfaces multiway dependence across exporters, importers, products, and years that is difficult to recover from gravity-type or pairwise network analyses, which do not jointly model the product and temporal dimensions.

KG-SoftMAP: Soft Knowledge-Graph Priors for Bayesian Network Structure Learning from Sparse Discrete Data

Learning Bayesian network (BN) structure from sparse discrete data is hard: when each instance records only a few variables, most variable pairs lack the joint observations needed for reliable scoring, and data-only methods recover little structure. Imperfect domain knowledge, expressible as a weighted directed knowledge graph (KG), is often available. We propose KG-SoftMAP, which encodes such a KG as a soft, confidence-weighted, data-overridable edge prior and maximizes a MAP objective combining the BDeu score with a logit-form prior; the KG may be expert-curated or LLM-extracted. On controlled synthetic benchmarks, the only setting with ground-truth DAGs, KG-SoftMAP recovers partial directed structure at $ρ=0.05$ (DF1 $0.14$ to $0.29$, versus near-zero baselines) and substantially more once $ρ\geq0.2$ (DF1 $0.46$ to $0.96$), when paired with an informative but imperfect KG; recovery degrades gracefully as KG quality drops. On real sparse educational data, which has no ground-truth DAG, we evaluate deployment-facing measures only: prediction, calibration, and KG-consistency. The learned BN is best read as a diagnostic model: on SAF it trails logistic regression by $0.03$ F1_FAIL while providing KG-consistent edges, calibrated joint probabilities, and inference from arbitrary observed concept subsets; when no meaningful KG exists, discriminative logistic regression is preferable.