Simplicial complexes provide a powerful framework for modeling high-order interactions in structured data, making them particularly suitable for applications such as trajectory prediction and mesh processing. However, existing simplicial neural networks (SNNs), whether convolutional or attention-based, rely primarily on discrete filtering techniques, which can be restrictive. In contrast, partial differential equations (PDEs) on simplicial complexes offer a principled approach to capture continuous dynamics in such structures. In this work, we introduce COntinuous SiMplicial neural netwOrkS (COSMOS), a novel SNN architecture derived from PDEs on simplicial complexes. We provide theoretical and experimental justifications of COSMOS's stability under simplicial perturbations. Furthermore, we investigate the over-smoothing phenomenon, a common issue in geometric deep learning, demonstrating that COSMOS offers better control over this effect than discrete SNNs. Our experiments on real-world datasets of ocean trajectory prediction and regression on partial deformable shapes demonstrate that COSMOS achieves competitive performance compared to state-of-the-art SNNs in complex and noisy environments.

Graph generation is fundamental in diverse scientific applications, due to its ability to reveal the underlying distribution of complex data, and eventually generate new, realistic data points. Despite the success of diffusion models in this domain, those face limitations in sampling efficiency and flexibility, stemming from the tight coupling between the training and sampling stages. To address this, we propose DeFoG, a novel framework using discrete flow matching for graph generation. DeFoG employs a flow-based approach that features an efficient linear interpolation noising process and a flexible denoising process based on a continuous-time Markov chain formulation. We leverage an expressive graph transformer and ensure desirable node permutation properties to respect graph symmetry. Crucially, our framework enables a disentangled design of the training and sampling stages, enabling more effective and efficient optimization of model performance. We navigate this design space by introducing several algorithmic improvements that boost the model performance, consistently surpassing existing diffusion models. We also theoretically demonstrate that, for general discrete data, discrete flow models can faithfully replicate the ground truth distribution - a result that naturally extends to graph data and reinforces DeFoG's foundations. Extensive experiments show that DeFoG achieves state-of-the-art results on synthetic and molecular datasets, improving both training and sampling efficiency over diffusion models, and excels in conditional generation on a digital pathology dataset.

Graph-based representation approaches have been proven to be successful in the analysis of biomedical data, due to their capability of capturing intricate dependencies between biological entities, such as the spatial organization of different cell types in a tumor tissue. However, to further enhance our understanding of the underlying governing biological mechanisms, it is important to accurately capture the actual distributions of such complex data. Graph-based deep generative models are specifically tailored to accomplish that. In this work, we leverage state-of-the-art graph-based diffusion models to generate biologically meaningful cell-graphs. In particular, we show that the adopted graph diffusion model is able to accurately learn the distribution of cells in terms of their tertiary lymphoid structures (TLS) content, a well-established biomarker for evaluating the cancer progression in oncology research. Additionally, we further illustrate the utility of the learned generative models for data augmentation in a TLS classification task. To the best of our knowledge, this is the first work that leverages the power of graph diffusion models in generating meaningful biological cell structures.

In order to perform network analysis tasks, representations that capture the most relevant information in the graph structure are needed. However, existing methods do not learn representations that can be interpreted in a straightforward way and that are robust to perturbations to the graph structure. In this work, we address these two limitations by proposing node2coords, a representation learning algorithm for graphs, which learns simultaneously a low-dimensional space and coordinates for the nodes in that space. The patterns that span the low dimensional space reveal the graph's most important structural information. The coordinates of the nodes reveal the proximity of their local structure to the graph structural patterns. In order to measure this proximity by taking into account the underlying graph, we propose to use Wasserstein distances. We introduce an autoencoder that employs a linear layer in the encoder and a novel Wasserstein barycentric layer at the decoder. Node connectivity descriptors, that capture the local structure of the nodes, are passed through the encoder to learn the small set of graph structural patterns. In the decoder, the node connectivity descriptors are reconstructed as Wasserstein barycenters of the graph structural patterns. The optimal weights for the barycenter representation of a node's connectivity descriptor correspond to the coordinates of that node in the low-dimensional space. Experimental results demonstrate that the representations learned with node2coords are interpretable, lead to node embeddings that are stable to perturbations of the graph structure and achieve competitive or superior results compared to state-of-the-art methods in node classification.

The effective representation, processing, analysis, and visualization of large-scale structured data, especially those related to complex domains such as networks and graphs, are one of the key questions in modern machine learning. Graph signal processing (GSP), a vibrant branch of signal processing models and algorithms that aims at handling data supported on graphs, opens new paths of research to address this challenge. In this article, we review a few important contributions made by GSP concepts and tools, such as graph filters and transforms, to the development of novel machine learning algorithms. In particular, our discussion focuses on the following three aspects: exploiting data structure and relational priors, improving data and computational efficiency, and enhancing model interpretability. Furthermore, we provide new perspectives on future development of GSP techniques that may serve as a bridge between applied mathematics and signal processing on one side, and machine learning and network science on the other. Cross-fertilization across these different disciplines may help unlock the numerous challenges of complex data analysis in the modern age.

Structure inference is an important task for network data processing and analysis in data science. In recent years, quite a few approaches have been developed to learn the graph structure underlying a set of observations captured in a data space. Although real world data is often acquired in settings where relationships are influenced by a priori known rules, this domain knowledge is still not well exploited in structure inference problems. In this paper, we identify the structure of signals defined in a data space whose inner relationships are encoded by multi-layer graphs. We aim at properly exploiting the information originating from each layer to infer the global structure underlying the signals. We thus present a novel method for combining the multiple graphs into a global graph using mask matrices, which are estimated through an optimization problem that accommodates the multi-layer graph information and a signal representation model. The proposed mask combination method also estimates the contribution of each graph layer in the structure of signals. The experiments conducted both on synthetic and real world data suggest that integrating the multi-layer graph representation of the data in the structure inference framework enhances the learning procedure considerably by adapting to the quality and the quantity of the input data

While the prevalence of Autism Spectrum Disorder (ASD) is increasing, research towards the definition of a common etiology is still ongoing. In this regard, modern machine learning and network science pave the way for a better understanding of the pathology and the development of diagnosis aid systems. At the same time, the culture of data sharing heads favorably in that direction, with the availability of large datasets such as the Autism Brain Imaging Data Exchange (ABIDE) one. The present work addresses the classification of neurotypical and ASD subjects by combining knowledge about both the anatomy and the functional activity of the brain. In particular, we model the brain structure as a graph, and the time-varying resting-state functional MRI (rs-fMRI) signals as values that live on the nodes of that graph. We then borrow tools from the emerging field of Graph Signal Processing (GSP) to build features related to the frequency content of these signals. In order to make these features highly discriminative, we apply an extension of the Fukunaga-Koontz transform. Finally, we use these new markers to train a decision tree, an interpretable classification scheme, which results in a final diagnosis aid model. Interestingly, the resulting decision tree outperforms state-of-the-art methods on the ABIDE dataset. Moreover, the analysis of the predictive markers reveals the influence of the frontal and temporal lobes in the diagnosis of the disorder, which is in line with previous findings in the literature of neuroscience. Our results indicate that exploiting jointly structural and functional information of the brain can reveal important information about the complexity of the neuropathology.

The construction of a meaningful graph topology plays a crucial role in the effective representation, processing, analysis and visualization of structured data. When a natural choice of the graph is not readily available from the datasets, it is thus desirable to infer or learn a graph topology from the data. In this tutorial overview, we survey solutions to the problem of graph learning, including classical viewpoints from statistics and physics, and more recent approaches that adopt a graph signal processing (GSP) perspective. We further emphasize the conceptual similarities and differences between classical and GSP graph inference methods and highlight the potential advantage of the latter in a number of theoretical and practical scenarios. We conclude with several open issues and challenges that are keys to the design of future signal processing and machine learning algorithms for learning graphs from data.

Graph signals offer a very generic and natural representation for data that lives on networks or irregular structures. The actual data structure is however often unknown a priori but can sometimes be estimated from the knowledge of the application domain. If this is not possible, the data structure has to be inferred from the mere signal observations. This is exactly the problem that we address in this paper, under the assumption that the graph signals can be represented as a sparse linear combination of a few atoms of a structured graph dictionary. The dictionary is constructed on polynomials of the graph Laplacian, which can sparsely represent a general class of graph signals composed of localized patterns on the graph. We formulate a graph learning problem, whose solution provides an ideal fit between the signal observations and the sparse graph signal model. As the problem is non-convex, we propose to solve it by alternating between a signal sparse coding and a graph update step. We provide experimental results that outline the good graph recovery performance of our method, which generally compares favourably to other recent network inference algorithms.

Effective information analysis generally boils down to properly identifying the structure or geometry of the data, which is often represented by a graph. In some applications, this structure may be partly determined by design constraints or pre-determined sensing arrangements, like in road transportation networks for example. In general though, the data structure is not readily available and becomes pretty difficult to define. In particular, the global smoothness assumptions, that most of the existing works adopt, are often too general and unable to properly capture localized properties of data. In this paper, we go beyond this classical data model and rather propose to represent information as a sparse combination of localized functions that live on a data structure represented by a graph. Based on this model, we focus on the problem of inferring the connectivity that best explains the data samples at different vertices of a graph that is a priori unknown. We concentrate on the case where the observed data is actually the sum of heat diffusion processes, which is a quite common model for data on networks or other irregular structures. We cast a new graph learning problem and solve it with an efficient nonconvex optimization algorithm. Experiments on both synthetic and real world data finally illustrate the benefits of the proposed graph learning framework and confirm that the data structure can be efficiently learned from data observations only. We believe that our algorithm will help solving key questions in diverse application domains such as social and biological network analysis where it is crucial to unveil proper geometry for data understanding and inference.