Denoising diffusion generative models are state-of-the-art methods for generating synthetic images that have also proved successful in tabular and graph synthetic data generation. However, their computational complexity has limited the application of these techniques to graph data, focusing usually on smaller graphs, such as those used in molecular modeling. In this paper, we propose SaGess, a discrete denoising diffusion approach, which is able to generate large real-world networks. Through a generalized divide-and-conquer framework, SaGess overcomes the scaling limitations of the diffusion model DiGress, by sampling a covering of subgraphs of the initial graph, training a DiGress module, and finally reconstructing a synthetic graph using the subgraphs that have been generated using the DiGress module. We evaluate the quality of the synthetic data sets against several competitor methods by comparing graph statistics between the original and synthetic samples, as well as evaluating the utility of the synthetic data set produced by using it to train a task-driven model, namely link prediction. In our experiments, SaGess outperforms most of the one-shot state-of-the-art graph generating methods by a significant factor, both on the graph metrics and on the link prediction task.

In several domains, data objects can be decomposed into sets of simpler objects. It is then natural to represent each object as the set of its components or parts. Many conventional machine learning algorithms are unable to process this kind of representations, since sets may vary in cardinality and elements lack a meaningful ordering. In this paper, we present a new neural network architecture, called RepSet, that can handle examples that are represented as sets of vectors. The proposed model computes the correspondences between an input set and some hidden sets by solving a series of network flow problems. This representation is then fed to a standard neural network architecture to produce the output. The architecture allows end-to-end gradient-based learning. We demonstrate RepSet on classification tasks, including text categorization, and graph classification, and we show that the proposed neural network achieves performance better or comparable to state-of-the-art algorithms.

Neural networks have become a very popular tool for many machine learning tasks, as in recent years we witnessed many novel architectures, learning and optimization techniques for deep learning. Capitalizing on the fact that neural networks inherently constitute multipartite graphs among neuron layers, we aim to analyze directly their structure to extract meaningful information that can improve the learning process. To our knowledge graph mining techniques for enhancing learning in neural networks have not been thoroughly investigated. In this paper we propose an adapted version of the k-core structure for the complete weighted multipartite graph extracted from a deep learning architecture. As a multipartite graph is a combination of bipartite graphs, that are in turn the incidence graphs of hypergraphs, we design k-hypercore decomposition, the hypergraph analogue of k-core degeneracy. We applied k-hypercore to several neural network architectures, more specifically to convolutional neural networks and multilayer perceptrons for image recognition tasks after a very short pretraining. Then we used the information provided by the hypercore numbers of the neurons to re-initialize the weights of the neural network, thus biasing the gradient optimization scheme. Extensive experiments proved that k-hypercore outperforms the state-of-the-art initialization methods.

The problem of accurately measuring the similarity between graphs is at the core of many applications in a variety of disciplines. Graph kernels have recently emerged as a promising approach to this problem. There are now many kernels, each focusing on different structural aspects of graphs. Here, we present GraKeL, a library that unifies several graph kernels into a common framework. The library is written in Python and adheres to the scikit-learn interface. It is simple to use and can be naturally combined with scikit-learn's modules to build a complete machine learning pipeline for tasks such as graph classification and clustering. The code is BSD licensed and is available at: https://github.com/ysig/GraKeL.

Graph autoencoders (AE) and variational autoencoders (VAE) recently emerged as powerful node embedding methods. In particular, graph AE and VAE were successfully leveraged to tackle the challenging link prediction problem, aiming at figuring out whether some pairs of nodes from a graph are connected by unobserved edges. However, these models focus on undirected graphs and therefore ignore the potential direction of the link, which is limiting for numerous real-life applications. In this paper, we extend the graph AE and VAE frameworks to address link prediction in directed graphs. We present a new gravity-inspired decoder scheme that can effectively reconstruct directed graphs from a node embedding. We empirically evaluate our method on three different directed link prediction tasks, for which standard graph AE and VAE perform poorly. We achieve competitive results on three real-world graphs, outperforming several popular baselines.

The problem of accurately measuring the similarity between graphs is at the core of many applications in a variety of disciplines. Most existing methods for graph similarity focus either on local or on global properties of graphs. However, even if graphs seem very similar from a local or a global perspective, they may exhibit different structure at different scales. In this paper, we present a general framework for graph similarity which takes into account structure at multiple different scales. The proposed framework capitalizes on the well-known k-core decomposition of graphs in order to build a hierarchy of nested subgraphs. We apply the framework to derive variants of four graph kernels, namely graphlet kernel, shortest-path kernel, Weisfeiler-Lehman subtree kernel, and pyramid match graph kernel. The framework is not limited to graph kernels, but can be applied to any graph comparison algorithm. The proposed framework is evaluated on several benchmark datasets for graph classification. In most cases, the core-based kernels achieve significant improvements in terms of classification accuracy over the base kernels, while their time complexity remains very attractive.