Theory of Speciation Transitions in Diffusion Models with General Class Structure

Diffusion Models generate data by reversing a stochastic diffusion process, progressively transforming noise into structured samples drawn from a target distribution. Recent theoretical work has shown that this backward dynamics can undergo sharp qualitative transitions, known as speciation transitions, during which trajectories become dynamically committed to data classes. Existing theoretical analyses, however, are limited to settings where classes are identifiable through first moments, such as mixtures of Gaussians with well-separated means. In this work, we develop a general theory of speciation in diffusion models that applies to arbitrary target distributions admitting well-defined classes. We formalize the notion of class structure through Bayes classification and characterize speciation times in terms of free-entropy difference between classes. This criterion recovers known results in previously studied Gaussian-mixture models, while extending to situations in which classes are not distinguishable by first moments and may instead differ through higher-order or collective features. Our framework also accommodates multiple classes and predicts the existence of successive speciation times associated with increasingly fine-grained class commitment. We illustrate the theory on two analytically tractable examples: mixtures of one-dimensional Ising models at different temperatures and mixtures of zero-mean Gaussians with distinct covariance structures. In the Ising case, we obtain explicit expressions for speciation times by mapping the problem onto a random-field Ising model and solving it via the replica method. Our results provide a unified and broadly applicable description of speciation transitions in diffusion-based generative models.

Geometry-Preserving Neural Architectures on Manifolds with Boundary

Preserving geometric structure is important in learning. We propose a unified class of geometry-aware architectures that interleave geometric updates between layers, where both projection layers and intrinsic exponential map updates arise as discretizations of projected dynamical systems on manifolds (with or without boundary). Within this framework, we establish universal approximation results for constrained neural ODEs. We also analyze architectures that enforce geometry only at the output, proving a separate universal approximation property that enables direct comparison to interleaved designs. When the constraint set is unknown, we learn projections via small-time heat-kernel limits, showing diffusion/flow-matching can be used as data-based projections. Experiments on dynamics over S^2 and SO(3), and diffusion on S^{d-1}-valued features demonstrate exact feasibility for analytic updates and strong performance for learned projections

SSNAPS: Audio-Visual Separation of Speech and Background Noise with Diffusion Inverse Sampling

This paper addresses the challenge of audio-visual single-microphone speech separation and enhancement in the presence of real-world environmental noise. Our approach is based on generative inverse sampling, where we model clean speech and ambient noise with dedicated diffusion priors and jointly leverage them to recover all underlying sources. To achieve this, we reformulate a recent inverse sampler to match our setting. We evaluate on mixtures of 1, 2, and 3 speakers with noise and show that, despite being entirely unsupervised, our method consistently outperforms leading supervised baselines in \ac{WER} across all conditions. We further extend our framework to handle off-screen speaker separation. Moreover, the high fidelity of the separated noise component makes it suitable for downstream acoustic scene detection. Demo page: https://ssnapsicml.github.io/ssnapsicml2026/

Training-free score-based diffusion for parameter-dependent stochastic dynamical systems

Simulating parameter-dependent stochastic differential equations (SDEs) presents significant computational challenges, as separate high-fidelity simulations are typically required for each parameter value of interest. Despite the success of machine learning methods in learning SDE dynamics, existing approaches either require expensive neural network training for score function estimation or lack the ability to handle continuous parameter dependence. We present a training-free conditional diffusion model framework for learning stochastic flow maps of parameter-dependent SDEs, where both drift and diffusion coefficients depend on physical parameters. The key technical innovation is a joint kernel-weighted Monte Carlo estimator that approximates the conditional score function using trajectory data sampled at discrete parameter values, enabling interpolation across both state space and the continuous parameter domain. Once trained, the resulting generative model produces sample trajectories for any parameter value within the training range without retraining, significantly accelerating parameter studies, uncertainty quantification, and real-time filtering applications. The performance of the proposed approach is demonstrated via three numerical examples of increasing complexity, showing accurate approximation of conditional distributions across varying parameter values.

PIMPC-GNN: Physics-Informed Multi-Phase Consensus Learning for Enhancing Imbalanced Node Classification in Graph Neural Networks

Graph neural networks (GNNs) often struggle in class-imbalanced settings, where minority classes are under-represented and predictions are biased toward majorities. We propose \textbf{PIMPC-GNN}, a physics-informed multi-phase consensus framework for imbalanced node classification. Our method integrates three complementary dynamics: (i) thermodynamic diffusion, which spreads minority labels to capture long-range dependencies, (ii) Kuramoto synchronisation, which aligns minority nodes through oscillatory consensus, and (iii) spectral embedding, which separates classes via structural regularisation. These perspectives are combined through class-adaptive ensemble weighting and trained with an imbalance-aware loss that couples balanced cross-entropy with physics-based constraints. Across five benchmark datasets and imbalance ratios from 5-100, PIMPC-GNN outperforms 16 state-of-the-art baselines, achieving notable gains in minority-class recall (up to +12.7\%) and balanced accuracy (up to +8.3\%). Beyond empirical improvements, the framework also provides interpretable insights into consensus dynamics in graph learning. The code is available at \texttt{https://github.com/afofanah/PIMPC-GNN}.

Diffusion-Driven Inter-Outer Surface Separation for Point Clouds with Open Boundaries

We propose a diffusion-based algorithm for separating the inter and outer layer surfaces from double-layered point clouds, particularly those exhibiting the "double surface artifact" caused by truncation in Truncated Signed Distance Function (TSDF) fusion during indoor or medical 3D reconstruction. This artifact arises from asymmetric truncation thresholds, leading to erroneous inter and outer shells in the fused volume, which our method addresses by extracting the true inter layer to mitigate challenges like overlapping surfaces and disordered normals. We focus on point clouds with \emph{open boundaries} (i.e., sampled surfaces with topological openings/holes through which particles may escape), rather than point clouds with \emph{missing surface regions} where no samples exist. Our approach enables robust processing of both watertight and open-boundary models, achieving extraction of the inter layer from 20,000 inter and 20,000 outer points in approximately 10 seconds. This solution is particularly effective for applications requiring accurate surface representations, such as indoor scene modeling and medical imaging, where double-layered point clouds are prevalent, and it accommodates both closed (watertight) and open-boundary surface geometries. Our goal is \emph{post-hoc} inter/outer shell separation as a lightweight module after TSDF fusion; we do not aim to replace full variational or learning-based reconstruction pipelines.

hSNMF: Hybrid Spatially Regularized NMF for Image-Derived Spatial Transcriptomics

High-resolution spatial transcriptomics platforms, such as Xenium, generate single-cell images that capture both molecular and spatial context, but their extremely high dimensionality poses major challenges for representation learning and clustering. In this study, we analyze data from the Xenium platform, which captures high-resolution images of tumor microarray (TMA) tissues and converts them into cell-by-gene matrices suitable for computational analysis. We benchmark and extend nonnegative matrix factorization (NMF) for spatial transcriptomics by introducing two spatially regularized variants. First, we propose Spatial NMF (SNMF), a lightweight baseline that enforces local spatial smoothness by diffusing each cell's NMF factor vector over its spatial neighborhood. Second, we introduce Hybrid Spatial NMF (hSNMF), which performs spatially regularized NMF followed by Leiden clustering on a hybrid adjacency that integrates spatial proximity (via a contact-radius graph) and transcriptomic similarity through a tunable mixing parameter alpha. Evaluated on a cholangiocarcinoma dataset, SNMF and hSNMF achieve markedly improved spatial compactness (CHAOS < 0.004, Moran's I > 0.96), greater cluster separability (Silhouette > 0.12, DBI < 1.8), and higher biological coherence (CMC and enrichment) compared to other spatial baselines. Availability and implementation: https://github.com/ishtyaqmahmud/hSNMF

Manifold-Constrained Energy-Based Transition Models for Offline Reinforcement Learning

Model-based offline reinforcement learning is brittle under distribution shift: policy improvement drives rollouts into state--action regions weakly supported by the dataset, where compounding model error yields severe value overestimation. We propose Manifold-Constrained Energy-based Transition Models (MC-ETM), which train conditional energy-based transition models using a manifold projection--diffusion negative sampler. MC-ETM learns a latent manifold of next states and generates near-manifold hard negatives by perturbing latent codes and running Langevin dynamics in latent space with the learned conditional energy, sharpening the energy landscape around the dataset support and improving sensitivity to subtle out-of-distribution deviations. For policy optimization, the learned energy provides a single reliability signal: rollouts are truncated when the minimum energy over sampled next states exceeds a threshold, and Bellman backups are stabilized via pessimistic penalties based on Q-value-level dispersion across energy-guided samples. We formalize MC-ETM through a hybrid pessimistic MDP formulation and derive a conservative performance bound separating in-support evaluation error from truncation risk. Empirically, MC-ETM improves multi-step dynamics fidelity and yields higher normalized returns on standard offline control benchmarks, particularly under irregular dynamics and sparse data coverage.

Scale-Cascaded Diffusion Models for Super-Resolution in Medical Imaging

Diffusion models have been increasingly used as strong generative priors for solving inverse problems such as super-resolution in medical imaging. However, these approaches typically utilize a diffusion prior trained at a single scale, ignoring the hierarchical scale structure of image data. In this work, we propose to decompose images into Laplacian pyramid scales and train separate diffusion priors for each frequency band. We then develop an algorithm to perform super-resolution that utilizes these priors to progressively refine reconstructions across different scales. Evaluated on brain, knee, and prostate MRI data, our approach both improves perceptual quality over baselines and reduces inference time through smaller coarse-scale networks. Our framework unifies multiscale reconstruction and diffusion priors for medical image super-resolution.

Multimodal Scientific Learning Beyond Diffusions and Flows

Scientific machine learning (SciML) increasingly requires models that capture multimodal conditional uncertainty arising from ill-posed inverse problems, multistability, and chaotic dynamics. While recent work has favored highly expressive implicit generative models such as diffusion and flow-based methods, these approaches are often data-hungry, computationally costly, and misaligned with the structured solution spaces frequently found in scientific problems. We demonstrate that Mixture Density Networks (MDNs) provide a principled yet largely overlooked alternative for multimodal uncertainty quantification in SciML. As explicit parametric density estimators, MDNs impose an inductive bias tailored to low-dimensional, multimodal physics, enabling direct global allocation of probability mass across distinct solution branches. This structure delivers strong data efficiency, allowing reliable recovery of separated modes in regimes where scientific data is scarce. We formalize these insights through a unified probabilistic framework contrasting explicit and implicit distribution networks, and demonstrate empirically that MDNs achieve superior generalization, interpretability, and sample efficiency across a range of inverse, multistable, and chaotic scientific regression tasks.