In DM, kernels play an important role for capturing the nonlinear relationship of data.

Diffusion distance is a spectral method for measuring distance among nodes on graph considering global data structure. In this work, we propose a spec-diff-net for computing diffusion distance on graph based on approximate spectral decomposition. The network is a differentiable deep architecture consisting of feature extraction and diffusion distance modules for computing diffusion distance on image by end-to-end training. We design low resolution kernel matching loss and high resolution segment matching loss to enforce the network's output to be consistent with human-labeled image segments. To compute high-resolution diffusion distance or segmentation mask, we design an up-sampling strategy by feature-attentional interpolation which can be learned when training spec-diff-net. With the learned diffusion distance, we propose a hierarchical image segmentation method outperforming previous segmentation methods. Moreover, a weakly supervised semantic segmentation network is designed using diffusion distance and achieved promising results on PASCAL VOC 2012 segmentation dataset.

Persistent homology is a popular computational tool for analyzing the topology of point clouds, such as the presence of loops or voids. However, many real-world datasets with low intrinsic dimensionality reside in an ambient space of much higher dimensionality. We show that in this case traditional persistent homology becomes very sensitive to noise and fails to detect the correct topology. The same holds true for existing refinements of persistent homology. As a remedy, we find that spectral distances on the k-nearest-neighbor graph of the data, such as diffusion distance and effective resistance, allow to detect the correct topology even in the presence of high-dimensional noise. Moreover, we derive a novel closed-form formula for effective resistance, and describe its relation to diffusion distances. Finally, we apply these methods to high-dimensional single-cell RNA-sequencing data and show that spectral distances allow robust detection of cell cycle loops.

This paper introduces a comprehensive unified framework for constructing multi-view diffusion geometries through intertwined multi-view diffusion trajectories (MDTs), a class of inhomogeneous diffusion processes that iteratively combine the random walk operators of multiple data views. Each MDT defines a trajectory-dependent diffusion operator with a clear probabilistic and geometric interpretation, capturing over time the interplay between data views. Our formulation encompasses existing multi-view diffusion models, while providing new degrees of freedom for view interaction and fusion. We establish theoretical properties under mild assumptions, including ergodicity of both the point-wise operator and the process in itself. We also derive MDT-based diffusion distances, and associated embeddings via singular value decompositions. Finally, we propose various strategies for learning MDT operators within the defined operator space, guided by internal quality measures. Beyond enabling flexible model design, MDTs also offer a neutral baseline for evaluating diffusion-based approaches through comparison with randomly selected MDTs. Experiments show the practical impact of the MDT operators in a manifold learning and data clustering context.

Message passing neural networks (MPNNs) have emerged as go-to models for learning on graph-structured data in the past decade. Despite their effectiveness, most of such models still incur severe issues such as over-smoothing and -correlation, due to their underlying objective of minimizing the Dirichlet energy and the derived neighborhood aggregation operations. In this paper, we propose the DDSM, a new MPNN model built on an optimization framework that includes the stress majorization and orthogonal regularization for overcoming the above issues. Further, we introduce the diffusion distances for nodes into the framework to guide the new message passing operations and develop efficient algorithms for distance approximations, both backed by rigorous theoretical analyses. Our comprehensive experiments showcase that DDSM consistently and considerably outperforms 15 strong baselines on both homophilic and heterophilic graphs.

Moreover, we derive a novel closed-form formula for effective resistance, and describe its relation to diffusion distances.

The network is a differentiable deep architecture consisting of feature extraction and diffusion distance modules for computing diffusion distance on image by end-to-end training. We design low resolution kernel matching loss and high resolution segment matching loss to enforce the network's output to be consistent with human-labeled image segments.

Markov state trajectories, where the transition kernel has a small intrinsic rank. In the spirit of diffusion map, we propose an efficient method for learning a low-dimensional state embedding and capturing the process's dynamics.