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We present a new method for learning Soft Random Geometric Graphs (SRGGs), drawn in probabilistic metric spaces, with the connection function of the graph defined as the marginal posterior probability of an edge random variable, given the…

Kernel-based non-linear dimensionality reduction methods, such as Local Linear Embedding (LLE) and Laplacian Eigenmaps, rely heavily upon pairwise distances or similarity scores, with which one can construct and study a weighted graph…

We consider the problem of learning distance-based Graph Convolutional Networks (GCNs) for relational data. Specifically, we first embed the original graph into the Euclidean space $\mathbb{R}^m$ using a relational density estimation…

In this paper, we present GGSD, a novel graph generative model based on 1) the spectral decomposition of the graph Laplacian matrix and 2) a diffusion process. Specifically, we propose to use a denoising model to sample eigenvectors and…

Machine learning for molecules holds great potential for efficiently exploring the vast chemical space and thus streamlining the drug discovery process by facilitating the design of new therapeutic molecules. Deep generative models have…

Learning and reasoning about 3D molecular structures with varying size is an emerging and important challenge in machine learning and especially in drug discovery. Equivariant Graph Neural Networks (GNNs) can simultaneously leverage the…

We view molecular optimization as a graph-to-graph translation problem. The goal is to learn to map from one molecular graph to another with better properties based on an available corpus of paired molecules. Since molecules can be…

The graphical structure of Probabilistic Graphical Models (PGMs) encodes the conditional independence (CI) relations that hold in the modeled distribution. Graph algorithms, such as d-separation, use this structure to infer additional…

Graph Neural Networks (GNNs) have emerged as the de facto standard for modeling graph data, with attention mechanisms and transformers significantly enhancing their performance on graph-based tasks. Despite these advancements, the…

Diffusion models are central to generative modeling and have been adapted to graphs by diffusing adjacency matrix representations. The challenge of having up to $n!$ such representations for graphs with $n$ nodes is only partially mitigated…

This work introduces NetDiff, an expressive graph denoising diffusion probabilistic architecture that generates wireless ad hoc network link topologies. Such networks, with directional antennas, can achieve unmatched performance when the…

This paper explores the application diffusion maps as graph shift operators in understanding the underlying geometry of graph signals. The study evaluates the improvements in graph learning when using diffusion map generated filters to the…

The concern of overconfident mis-predictions under distributional shift demands extensive reliability research on Graph Neural Networks used in critical tasks in drug discovery. Here we first introduce CardioTox, a real-world benchmark on…

The geometry of three-dimensional (3D) graphs, consisting of nodes and edges, plays a crucial role in many important applications. An excellent example is molecular graphs, whose geometry influences important properties of a molecule…

We propose the Lanczos network (LanczosNet), which uses the Lanczos algorithm to construct low rank approximations of the graph Laplacian for graph convolution. Relying on the tridiagonal decomposition of the Lanczos algorithm, we not only…

The geometry of a graph is encoded in dynamical processes on the graph. Many graph neural network (GNN) architectures are inspired by such dynamical systems, typically based on the graph Laplacian. Here, we introduce Dirac--Bianconi GNNs…

Learning node representations is a fundamental problem in graph machine learning. While existing embedding methods effectively preserve local similarity measures, they often fail to capture global functions like graph distances. Inspired by…

Simplicial complexes can be viewed as high dimensional generalizations of graphs that explicitly encode multi-way ordered relations between vertices at different resolutions, all at once. This concept is central towards detection of higher…

Graph partitioning (GP), a.k.a. community detection, is a classic problem that divides nodes of a graph into densely-connected blocks. From a perspective of graph signal processing, we find that graph Laplacian with a negative correction…

Predicting drug side-effects before they occur is a key task in keeping the number of drug-related hospitalizations low and to improve drug discovery processes. Automatic predictors of side-effects generally are not able to process the…