Spatial transcriptomics (ST) enables genome-wide gene expression profiling while preserving tissue architecture, but its cost and limited scalability remain major bottlenecks. This has motivated models that predict spatial expression directly from routine histology. Despite promising results, most existing approaches operate at the gene level without leveraging established transcriptomic modeling practices and rely on heterogeneous gene selection strategies, which complicates fair comparison across methods. We propose to reformulate morphology-to-transcriptomics prediction as conditional generation in transcriptional program space, thereby exploiting coordinated transcriptional variation instead of predicting genes independently. Using consensus non-negative matrix factorization (cNMF), we extract a low-dimensional set of transcriptional programs capturing coordinated expression variation in the training data, and train a conditional diffusion model to generate program activations from histology. This formulation exploits coordinated transcriptional variation and substantially lowers the dimensionality of the conditional generative task.
Symmetric non-negative matrix factorization (SymNMF) recovers latent group structure from a dependence matrix, but its dense, quadratic-memory objective has confined prior work to moderate sizes. We present a large-scale GPU study of seven algorithm families (over 30 configurations) on absolute Pearson correlation and tail pairwise dependence matrices from Extreme Value Theory, two proxies for empirical risk-factor estimation on large portfolios. A trace-identity reformulation eliminates all $n \times n$ intermediates, so a single GPU reaches $n \approx 10^5$ and multi-node distribution scales to $n = 10^6$ and beyond. Under a two-phase protocol, eleven methods converge at moderate scale; six remain efficient enough at $n = 10^5$ (five AdaGrad-family plus ADMM), and five AdaGrad-family methods still converge at $n = 10^6$: AdaGrad, RMSprop, and three we introduce (Piecewise AdaGrad, Row-Stochastic SVRG, Block-SVRG AdaptGrow). At $n = 10^6$ the fastest solver tracks the matrix spectrum: Block-SVRG AdaptGrow wins on the flat, ill-conditioned tail-dependence spectrum, where its lower per-iteration cost decides a long factorization, and full-batch AdaGrad wins on the dominant-low-rank correlation spectrum, where the run is short. We also benchmark spherical K-means as a hard-label baseline: cheaper when angular cluster structure is present, yet provably degenerate once the matrix collapses toward a single common factor, where the soft factorization remains necessary.
Autoencoder-based anomalous sound detection is attractive for machine condition monitoring because it can be trained using only normal recordings and yields an interpretable anomaly score from reconstruction error. Most prior work uses spectrogram autoencoders, but reconstructing detailed time--frequency patterns is sensitive to noise and transients, and models can reconstruct some anomalous inputs well, weakening normal--anomaly separation. We propose MemNMF, a constrained reconstruction method that operates on the Linear Predictive Coding spectrum, a compact estimate of the spectral envelope. MemNMF initializes a memory module from an NMF dictionary learned on normal LPC spectra and reconstructs each input as an attention-weighted combination of prototypical normal spectral patterns. Experiments on MIMII and DCASE 2020 Task 2 across multiple machine types and operating conditions show that LPC-spectrum inputs improve a standard autoencoder baseline and that MemNMF yields further gains, with especially strong robustness under noisy, non-stationary settings.
Non--negative matrix factorization (NMF) has become an established dimensionality reduction technique for extracting latent structures from non--negative data and has found widespread applications in fields such as bioinformatics, text mining, image analysis, and recommender systems. As the popularity of NMF has increased, numerous \textit{R} packages implementing different optimization strategies and computational frameworks have been developed. Despite their widespread availability, comprehensive evaluations of these implementations under real--world data conditions remain limited. Consequently, researchers often lack objective guidance when selecting an appropriate package for practical applications. This study introduces a new \textit{R} package for NMF and offers asystematic performance comparison with two widely available \textit{R} packages for NMF analysis. Rather than relying on simulated datasets, the evaluation is conducted using real--world data to better reflect the complexity, heterogeneity, and noise characteristics encountered in practical analytical settings. The packages are assessed using a consistent experimental framework, with emphasis on computational efficiency, convergence behavior, reconstruction accuracy, memory utilization, and the stability of the resulting matrix factorization.
The deep nonnegative matrix factorization (DNMF) technique is proposed to address the low interpretability of deep learning-based methods in extracting multilayer features from synthetic aperture radar (SAR) target samples. However, existing DNMF methods employ a layer-by-layer decomposition strategy, which is prone to causing error accumulation and local optimum, thereby hindering a consistent improvement in recognition accuracy as the number of layer increases. In this paper, a robust multilayer feature extraction method, termed generalized deep non-negative matrix factorization (G-DNMF), is proposed to address the above challenges in SAR automatic target recognition (ATR). The G-DNMF aims global optimality and derives the update rules for each parameter using lagrangian multiplier method. The new update formula indicates that both the DNMF method based on the encoding matrix and the mixing matrix are special cases of the proposed method, theoretically demonstrating the universality of proposed method. In general, the proposed method discards the layer-by-layer decomposition strategy, thereby effectively mitigating the risk of local optima and eliminating error accumulation, leading to a significant improvement in DNMF's multi-layer feature extraction capability. The experimental results, by presenting the feature images extracted from each layer by G-DNMF and the reconstructed original images, verified the proposed method's pure additive understanding of multi-layer features and demonstrated its interpretability. The experimental results based on MSTAR and OpenSARship datasets show that G-DNMF outperforms existing DNMF algorithms and their derivatives in terms of stability and recognition performance.
Matias de Jong van Lier, Shizuo Kaji, Keunsu Kimcs.LG cs.CG math.AT
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.
Continuous-time event data, in which entities emit instantaneous events over time, arises naturally across many domains such as neuroscience, seismology, and social networks. Non-negative matrix factorization (NMF) is a natural tool to uncover interpretable structure in such data, but it has so far only been applied after binning or smoothing the entity-level counting measures. This preprocessing step comes with the risk of erasing entity-level heterogeneities and fine-grained temporal features. In this paper, we introduce EventNMF, a continuous-time non-negative factorization model that operates directly on event times: each entity's events are modeled as a Poisson process whose intensity factorizes through a non-negative B-spline basis, and a simple estimation procedure recovers interpretable temporal templates shared across entities. The resulting method is mathematically principled, easy to implement, and computationally efficient. We further show that standard binned-count approaches arise as the special case of degree-zero splines, explore bias-variance tradeoffs and compare against existing methods on a synthetic latent factor model, and demonstrate the effectiveness of EventNMF on several real-world applications.