Persistent Nonnegative Matrix Factorization via Multi-Scale Graph Regularization

Separable nonnegative matrix factorization (SNMF) has been widely used for low-rank representation and clustering of nonnegative data, owing to its ability to produce part-based and interpretable decompositions. In particular, SNMF is closely related to graph clustering and community detection. To enhance sparsity and identifiability of the learned factors, we propose an $\ell_1^p/\ell_2$-regularized SNMF model based on a powered ratio-of-norms regularizer. The resulting formulation is nonconvex and nonsmooth, which poses significant challenges for optimization. To address this, we develop efficient algorithms based on the difference-of-convex function algorithm (DCA) and the alternating direction method of multipliers (ADMM). The proposed methods decompose the original problem into tractable subproblems, leveraging closed-form proximal operators associated with the powered norm terms. We establish descent and limiting criticality properties for the DCA scheme and convergence under standard assumptions for the ADMM scheme. Extensive numerical experiments on synthetic datasets and hand gesture classification tasks demonstrate that the proposed approach achieves competitive or improved performance in anchor identification and classification accuracy compared with existing SNMF methods, while maintaining competitive computational efficiency.

We investigate the learning of interpretable bases in non-negative matrix factorisation (NMF) by regularising the topology of the learned basis functions. Our approach is motivated by the observation that many data modalities can be viewed as non-negative functions on a structured domain, where the quality of a basis is intrinsically linked to its topology. However, naive methods for incorporating the topology of the support are often hindered by discreteness and threshold dependence, rendering them unsuitable for continuous optimisation. We address these challenges by employing persistent homology as a stable, threshold-free topological quantifier and by designing topological scores that integrate into the NMF objective as regularisers. The resulting framework encompasses spatially coherent image components, periodic time-series structures, and clique-like graph signals within a unified modelling language.

Dimensionality reduction (DR) involves two longstanding trade-offs. First, preserving local neighborhoods can come at the cost of global structure. Neighbor embedding methods such as t-SNE and UMAP prioritize local similarity preservation but do not explicitly constrain global organization, whereas standard spectral methods such as Laplacian Eigenmaps capture smooth, coarse-scale graph structure but offer limited flexibility to depict finer local structure. Second, the flexibility of nonlinear DR methods often comes at the cost of analytical transparency. Many methods do not explicitly reveal how high-dimensional structure produces patterns in the embedding. We introduce SDMP (Spectral Decomposition for Multiscale Projection), a nonlinear DR framework built on an explicit spectral decomposition. In this formulation, each embedding dimension is expressed as a weighted combination of Laplacian eigenvectors derived from a neighborhood graph, with the weights learned via a UMAP-style cross-entropy objective. By progressively expanding the spectral subspace to capture increasingly fine graph structure, SDMP produces a sequence of embeddings, making the evolving balance between global organization and local detail explicit, controllable, and inspectable. The explicit decomposition also reveals which spectral scales shape the overall embedding and how individual eigenvectors influence point positions. Quantitative evaluations on synthetic, image, and single-cell data show competitive local and global structure preservation, while case studies illustrate how the decomposition supports interpretation of clusters and developmental trajectories across spectral scales.