Fabrizio Frasca

Fabrizio Frasca, Beatrice Bevilacqua, Michael M. Bronstein et al. · nvidia

Subgraph GNNs are a recent class of expressive Graph Neural Networks (GNNs) which model graphs as collections of subgraphs. So far, the design space of possible Subgraph GNN architectures as well as their basic theoretical properties are still largely unexplored. In this paper, we study the most prominent form of subgraph methods, which employs node-based subgraph selection policies such as ego-networks or node marking and deletion. We address two central questions: (1) What is the upper-bound of the expressive power of these methods? and (2) What is the family of equivariant message passing layers on these sets of subgraphs?. Our first step in answering these questions is a novel symmetry analysis which shows that modelling the symmetries of node-based subgraph collections requires a significantly smaller symmetry group than the one adopted in previous works. This analysis is then used to establish a link between Subgraph GNNs and Invariant Graph Networks (IGNs). We answer the questions above by first bounding the expressive power of subgraph methods by 3-WL, and then proposing a general family of message-passing layers for subgraph methods that generalises all previous node-based Subgraph GNNs. Finally, we design a novel Subgraph GNN dubbed SUN, which theoretically unifies previous architectures while providing better empirical performance on multiple benchmarks.

Moshe Eliasof, Fabrizio Frasca, Beatrice Bevilacqua et al. · nvidia

Two main families of node feature augmentation schemes have been explored for enhancing GNNs: random features and spectral positional encoding. Surprisingly, however, there is still no clear understanding of the relation between these two augmentation schemes. Here we propose a novel family of positional encoding schemes which draws a link between the above two approaches and improves over both. The new approach, named Random Feature Propagation (RFP), is inspired by the power iteration method and its generalizations. It concatenates several intermediate steps of an iterative algorithm for computing the dominant eigenvectors of a propagation matrix, starting from random node features. Notably, these propagation steps are based on graph-dependent propagation operators that can be either predefined or learned. We explore the theoretical and empirical benefits of RFP. First, we provide theoretical justifications for using random features, for incorporating early propagation steps, and for using multiple random initializations. Then, we empirically demonstrate that RFP significantly outperforms both spectral PE and random features in multiple node classification and graph classification benchmarks.

Yam Eitan, Yoav Gelberg, Guy Bar-Shalom et al.

Topological deep learning (TDL) is a rapidly growing field that seeks to leverage topological structure in data and facilitate learning from data supported on topological objects, ranging from molecules to 3D shapes. Most TDL architectures can be unified under the framework of higher-order message-passing (HOMP), which generalizes graph message-passing to higher-order domains. In the first part of the paper, we explore HOMP's expressive power from a topological perspective, demonstrating the framework's inability to capture fundamental topological and metric invariants such as diameter, orientability, planarity, and homology. In addition, we demonstrate HOMP's limitations in fully leveraging lifting and pooling methods on graphs. To the best of our knowledge, this is the first work to study the expressivity of TDL from a \emph{topological} perspective. In the second part of the paper, we develop two new classes of architectures -- multi-cellular networks (MCN) and scalable MCN (SMCN) -- which draw inspiration from expressive GNNs. MCN can reach full expressivity, but scaling it to large data objects can be computationally expansive. Designed as a more scalable alternative, SMCN still mitigates many of HOMP's expressivity limitations. Finally, we create new benchmarks for evaluating models based on their ability to learn topological properties of complexes. We then evaluate SMCN on these benchmarks and on real-world graph datasets, demonstrating improvements over both HOMP baselines and expressive graph methods, highlighting the value of expressively leveraging topological information. Code and data are available at https://github.com/yoavgelberg/SMCN.

Benjamin Paul Chamberlain, Sergey Shirobokov, Emanuele Rossi et al.

Many Graph Neural Networks (GNNs) perform poorly compared to simple heuristics on Link Prediction (LP) tasks. This is due to limitations in expressive power such as the inability to count triangles (the backbone of most LP heuristics) and because they can not distinguish automorphic nodes (those having identical structural roles). Both expressiveness issues can be alleviated by learning link (rather than node) representations and incorporating structural features such as triangle counts. Since explicit link representations are often prohibitively expensive, recent works resorted to subgraph-based methods, which have achieved state-of-the-art performance for LP, but suffer from poor efficiency due to high levels of redundancy between subgraphs. We analyze the components of subgraph GNN (SGNN) methods for link prediction. Based on our analysis, we propose a novel full-graph GNN called ELPH (Efficient Link Prediction with Hashing) that passes subgraph sketches as messages to approximate the key components of SGNNs without explicit subgraph construction. ELPH is provably more expressive than Message Passing GNNs (MPNNs). It outperforms existing SGNN models on many standard LP benchmarks while being orders of magnitude faster. However, it shares the common GNN limitation that it is only efficient when the dataset fits in GPU memory. Accordingly, we develop a highly scalable model, called BUDDY, which uses feature precomputation to circumvent this limitation without sacrificing predictive performance. Our experiments show that BUDDY also outperforms SGNNs on standard LP benchmarks while being highly scalable and faster than ELPH.

Timo Stoll, Chendi Qian, Ben Finkelshtein et al.

Machine learning on graphs has recently achieved impressive progress in various domains, including molecular property prediction and chip design. However, benchmarking practices remain fragmented, often relying on narrow, task-specific datasets and inconsistent evaluation protocols, which hampers reproducibility and broader progress. To address this, we introduce GraphBench, a comprehensive benchmarking suite that spans diverse domains and prediction tasks, including node-level, edge-level, graph-level, and generative settings. GraphBench provides standardized evaluation protocols -- with consistent dataset splits and performance metrics that account for out-of-distribution generalization -- as well as a unified hyperparameter tuning framework. Additionally, we benchmark GraphBench using message-passing neural networks and graph transformer models, providing principled baselines and establishing a reference performance. See www.graphbench.io for further details.

Guy Bar-Shalom, Fabrizio Frasca, Derek Lim et al.

The automated detection of hallucinations and training data contamination is pivotal to the safe deployment of Large Language Models (LLMs). These tasks are particularly challenging in settings where no access to model internals is available. Current approaches in this setup typically leverage only the probabilities of actual tokens in the text, relying on simple task-specific heuristics. Crucially, they overlook the information contained in the full sequence of next-token probability distributions. We propose to go beyond hand-crafted decision rules by learning directly from the complete observable output of LLMs -- consisting not only of next-token probabilities, but also the full sequence of next-token distributions. We refer to this as the LLM Output Signature (LOS), and treat it as a reference data type for detecting hallucinations and data contamination. To that end, we introduce LOS-Net, a lightweight attention-based architecture trained on an efficient encoding of the LOS, which can provably approximate a broad class of existing techniques for both tasks. Empirically, LOS-Net achieves superior performance across diverse benchmarks and LLMs, while maintaining extremely low detection latency. Furthermore, it demonstrates promising transfer capabilities across datasets and LLMs. Full code is available at https://github.com/BarSGuy/Beyond-next-token-probabilities.

Guy Bar-Shalom, Fabrizio Frasca, Yaniv Galron et al.

Detecting hallucinations in Large Language Model-generated text is crucial for their safe deployment. While probing classifiers show promise, they operate on isolated layer-token pairs and are LLM-specific, limiting their effectiveness and hindering cross-LLM applications. In this paper, we introduce a novel approach to address these shortcomings. We build on the natural sequential structure of activation data in both axes (layers $\times$ tokens) and advocate treating full activation tensors akin to images. We design ACT-ViT, a Vision Transformer-inspired model that can be effectively and efficiently applied to activation tensors and supports training on data from multiple LLMs simultaneously. Through comprehensive experiments encompassing diverse LLMs and datasets, we demonstrate that ACT-ViT consistently outperforms traditional probing techniques while remaining extremely efficient for deployment. In particular, we show that our architecture benefits substantially from multi-LLM training, achieves strong zero-shot performance on unseen datasets, and can be transferred effectively to new LLMs through fine-tuning. Full code is available at https://github.com/BarSGuy/ACT-ViT.

Guy Bar-Shalom, Yam Eitan, Fabrizio Frasca et al.

Subgraph GNNs enhance message-passing GNNs expressivity by representing graphs as sets of subgraphs, demonstrating impressive performance across various tasks. However, their scalability is hindered by the need to process large numbers of subgraphs. While previous approaches attempted to generate smaller subsets of subgraphs through random or learnable sampling, these methods often yielded suboptimal selections or were limited to small subset sizes, ultimately compromising their effectiveness. This paper introduces a new Subgraph GNN framework to address these issues. Our approach diverges from most previous methods by associating subgraphs with node clusters rather than with individual nodes. We show that the resulting collection of subgraphs can be viewed as the product of coarsened and original graphs, unveiling a new connectivity structure on which we perform generalized message passing. Crucially, controlling the coarsening function enables meaningful selection of any number of subgraphs. In addition, we reveal novel permutation symmetries in the resulting node feature tensor, characterize associated linear equivariant layers, and integrate them into our Subgraph GNN. We also introduce novel node marking strategies and provide a theoretical analysis of their expressive power and other key aspects of our approach. Extensive experiments on multiple graph learning benchmarks demonstrate that our method is significantly more flexible than previous approaches, as it can seamlessly handle any number of subgraphs, while consistently outperforming baseline approaches. Our code is available at https://github.com/BarSGuy/Efficient-Subgraph-GNNs.

Giorgos Bouritsas, Fabrizio Frasca, Stefanos Zafeiriou et al.

While Graph Neural Networks (GNNs) have achieved remarkable results in a variety of applications, recent studies exposed important shortcomings in their ability to capture the structure of the underlying graph. It has been shown that the expressive power of standard GNNs is bounded by the Weisfeiler-Leman (WL) graph isomorphism test, from which they inherit proven limitations such as the inability to detect and count graph substructures. On the other hand, there is significant empirical evidence, e.g. in network science and bioinformatics, that substructures are often intimately related to downstream tasks. To this end, we propose "Graph Substructure Networks" (GSN), a topologically-aware message passing scheme based on substructure encoding. We theoretically analyse the expressive power of our architecture, showing that it is strictly more expressive than the WL test, and provide sufficient conditions for universality. Importantly, we do not attempt to adhere to the WL hierarchy; this allows us to retain multiple attractive properties of standard GNNs such as locality and linear network complexity, while being able to disambiguate even hard instances of graph isomorphism. We perform an extensive experimental evaluation on graph classification and regression tasks and obtain state-of-the-art results in diverse real-world settings including molecular graphs and social networks. The code is publicly available at https://github.com/gbouritsas/graph-substructure-networks.

Daniel Herbst, Lea Karbeska, Divyanshu Kumar et al.

While promising, graph reasoners based on Large Language Models (LLMs) lack built-in invariance to symmetries in graph representations. Operating on sequential graph serializations, LLMs can produce different outputs under node reindexing, edge reordering, or formatting changes, raising robustness concerns. We systematically analyze these effects, studying how fine-tuning impacts encoding sensitivity as well generalization on unseen tasks. We propose a principled decomposition of graph serializations into node labeling, edge encoding, and syntax, and evaluate LLM robustness to variations of each of these factors on a comprehensive benchmarking suite. We also contribute a novel set of spectral tasks to further assess generalization abilities of fine-tuned reasoners. Results show that larger (non-fine-tuned) models are more robust. Fine-tuning reduces sensitivity to node relabeling but may increase it to variations in structure and format, while it does not consistently improve performance on unseen tasks.

Maya Bechler-Speicher, Ben Finkelshtein, Fabrizio Frasca et al. · deepmind

While machine learning on graphs has demonstrated promise in drug design and molecular property prediction, significant benchmarking challenges hinder its further progress and relevance. Current benchmarking practices often lack focus on transformative, real-world applications, favoring narrow domains like two-dimensional molecular graphs over broader, impactful areas such as combinatorial optimization, relational databases, or chip design. Additionally, many benchmark datasets poorly represent the underlying data, leading to inadequate abstractions and misaligned use cases. Fragmented evaluations and an excessive focus on accuracy further exacerbate these issues, incentivizing overfitting rather than fostering generalizable insights. These limitations have prevented the development of truly useful graph foundation models. This position paper calls for a paradigm shift toward more meaningful benchmarks, rigorous evaluation protocols, and stronger collaboration with domain experts to drive impactful and reliable advances in graph learning research, unlocking the potential of graph learning.

Christopher Morris, Fabrizio Frasca, Nadav Dym et al. · nvidia

Machine learning on graphs, especially using graph neural networks (GNNs), has seen a surge in interest due to the wide availability of graph data across a broad spectrum of disciplines, from life to social and engineering sciences. Despite their practical success, our theoretical understanding of the properties of GNNs remains highly incomplete. Recent theoretical advancements primarily focus on elucidating the coarse-grained expressive power of GNNs, predominantly employing combinatorial techniques. However, these studies do not perfectly align with practice, particularly in understanding the generalization behavior of GNNs when trained with stochastic first-order optimization techniques. In this position paper, we argue that the graph machine learning community needs to shift its attention to developing a balanced theory of graph machine learning, focusing on a more thorough understanding of the interplay of expressive power, generalization, and optimization.

Joshua Southern, Yam Eitan, Guy Bar-Shalom et al.

Subgraph GNNs have emerged as promising architectures that overcome the expressiveness limitations of Graph Neural Networks (GNNs) by processing bags of subgraphs. Despite their compelling empirical performance, these methods are afflicted by a high computational complexity: they process bags whose size grows linearly in the number of nodes, hindering their applicability to larger graphs. In this work, we propose an effective and easy-to-implement approach to dramatically alleviate the computational cost of Subgraph GNNs and unleash broader applications thereof. Our method, dubbed HyMN, leverages walk-based centrality measures to sample a small number of relevant subgraphs and drastically reduce the bag size. By drawing a connection to perturbation analysis, we highlight the strength of the proposed centrality-based subgraph sampling, and further prove that these walk-based centralities can be additionally used as Structural Encodings for improved discriminative power. A comprehensive set of experimental results demonstrates that HyMN provides an effective synthesis of expressiveness, efficiency, and downstream performance, unlocking the application of Subgraph GNNs to dramatically larger graphs. Not only does our method outperform more sophisticated subgraph sampling approaches, it is also competitive, and sometimes better, than other state-of-the-art approaches for a fraction of their runtime.

Fabrizio Frasca, Fabian Jogl, Moshe Eliasof et al.

To develop a preliminary understanding towards Graph Foundation Models, we study the extent to which pretrained Graph Neural Networks can be applied across datasets, an effort requiring to be agnostic to dataset-specific features and their encodings. We build upon a purely structural pretraining approach and propose an extension to capture feature information while still being feature-agnostic. We evaluate pretrained models on downstream tasks for varying amounts of training samples and choices of pretraining datasets. Our preliminary results indicate that embeddings from pretrained models improve generalization only with enough downstream data points and in a degree which depends on the quantity and properties of pretraining data. Feature information can lead to improvements, but currently requires some similarities between pretraining and downstream feature spaces.

Yaniv Galron, Fabrizio Frasca, Haggai Maron et al.

Temporal graph learning has applications in recommendation systems, traffic forecasting, and social network analysis. Although multiple architectures have been introduced, progress in positional encoding for temporal graphs remains limited. Extending static Laplacian eigenvector approaches to temporal graphs through the supra-Laplacian has shown promise, but also poses key challenges: high eigendecomposition costs, limited theoretical understanding, and ambiguity about when and how to apply these encodings. In this paper, we address these issues by (1) offering a theoretical framework that connects supra-Laplacian encodings to per-time-slice encodings, highlighting the benefits of leveraging additional temporal connectivity, (2) introducing novel methods to reduce the computational overhead, achieving up to 56x faster runtimes while scaling to graphs with 50,000 active nodes, and (3) conducting an extensive experimental study to identify which models, tasks, and datasets benefit most from these encodings. Our findings reveal that while positional encodings can significantly boost performance in certain scenarios, their effectiveness varies across different models.

Yam Eitan, Moshe Eliasof, Yoav Gelberg et al.

Despite significant advances in Graph Neural Networks (GNNs), their limited expressivity remains a fundamental challenge. Research on GNN expressivity has produced many expressive architectures, leading to architecture hierarchies with models of increasing expressive power. Separately, derivatives of GNNs with respect to node features have been widely studied in the context of the oversquashing and over-smoothing phenomena, GNN explainability, and more. To date, these derivatives remain unexplored as a means to enhance GNN expressivity. In this paper, we show that these derivatives provide a natural way to enhance the expressivity of GNNs. We introduce High-Order Derivative GNN (HOD-GNN), a novel method that enhances the expressivity of Message Passing Neural Networks (MPNNs) by leveraging high-order node derivatives of the base model. These derivatives generate expressive structure-aware node embeddings processed by a second GNN in an end-to-end trainable architecture. Theoretically, we show that the resulting architecture family's expressive power aligns with the WL hierarchy. We also draw deep connections between HOD-GNN, Subgraph GNNs, and popular structural encoding schemes. For computational efficiency, we develop a message-passing algorithm for computing high-order derivatives of MPNNs that exploits graph sparsity and parallelism. Evaluations on popular graph learning benchmarks demonstrate HOD-GNN's strong performance on popular graph learning tasks.

Fabrizio Frasca, Guy Bar-Shalom, Yftah Ziser et al.

Large Language Models (LLMs) often generate incorrect or unsupported content, known as hallucinations. Existing detection methods rely on heuristics or simple models over isolated computational traces such as activations, or attention maps. We unify these signals by representing them as attributed graphs, where tokens are nodes, edges follow attentional flows, and both carry features from attention scores and activations. Our approach, CHARM, casts hallucination detection as a graph learning task and tackles it by applying GNNs over the above attributed graphs. We show that CHARM provably subsumes prior attention-based heuristics and, experimentally, it consistently outperforms other leading approaches across diverse benchmarks. Our results shed light on the relevant role played by the graph structure and on the benefits of combining computational traces, whilst showing CHARM exhibits promising zero-shot performance on cross-dataset transfer.

Ran Elbaz, Guy Bar-Shalom, Yam Eitan et al.

Permutation equivariant neural networks employing parameter-sharing schemes have emerged as powerful models for leveraging a wide range of data symmetries, significantly enhancing the generalization and computational efficiency of the resulting models. Recently, Kolmogorov-Arnold Networks (KANs) have demonstrated promise through their improved interpretability and expressivity compared to traditional architectures based on MLPs. While equivariant KANs have been explored in recent literature for a few specific data types, a principled framework for applying them to data with permutation symmetries in a general context remains absent. This paper introduces Function Sharing KAN (FS-KAN), a principled approach to constructing equivariant and invariant KA layers for arbitrary permutation symmetry groups, unifying and significantly extending previous work in this domain. We derive the basic construction of these FS-KAN layers by generalizing parameter-sharing schemes to the Kolmogorov-Arnold setup and provide a theoretical analysis demonstrating that FS-KANs have the same expressive power as networks that use standard parameter-sharing layers, allowing us to transfer well-known and important expressivity results from parameter-sharing networks to FS-KANs. Empirical evaluations on multiple data types and symmetry groups show that FS-KANs exhibit superior data efficiency compared to standard parameter-sharing layers, by a wide margin in certain cases, while preserving the interpretability and adaptability of KANs, making them an excellent architecture choice in low-data regimes.

Emanuele Rossi, Bertrand Charpentier, Francesco Di Giovanni et al.

Graph Neural Networks (GNNs) have become the de-facto standard tool for modeling relational data. However, while many real-world graphs are directed, the majority of today's GNN models discard this information altogether by simply making the graph undirected. The reasons for this are historical: 1) many early variants of spectral GNNs explicitly required undirected graphs, and 2) the first benchmarks on homophilic graphs did not find significant gain from using direction. In this paper, we show that in heterophilic settings, treating the graph as directed increases the effective homophily of the graph, suggesting a potential gain from the correct use of directionality information. To this end, we introduce Directed Graph Neural Network (Dir-GNN), a novel general framework for deep learning on directed graphs. Dir-GNN can be used to extend any Message Passing Neural Network (MPNN) to account for edge directionality information by performing separate aggregations of the incoming and outgoing edges. We prove that Dir-GNN matches the expressivity of the Directed Weisfeiler-Lehman test, exceeding that of conventional MPNNs. In extensive experiments, we validate that while our framework leaves performance unchanged on homophilic datasets, it leads to large gains over base models such as GCN, GAT and GraphSage on heterophilic benchmarks, outperforming much more complex methods and achieving new state-of-the-art results.

Beatrice Bevilacqua, Fabrizio Frasca, Derek Lim et al.

Message-passing neural networks (MPNNs) are the leading architecture for deep learning on graph-structured data, in large part due to their simplicity and scalability. Unfortunately, it was shown that these architectures are limited in their expressive power. This paper proposes a novel framework called Equivariant Subgraph Aggregation Networks (ESAN) to address this issue. Our main observation is that while two graphs may not be distinguishable by an MPNN, they often contain distinguishable subgraphs. Thus, we propose to represent each graph as a set of subgraphs derived by some predefined policy, and to process it using a suitable equivariant architecture. We develop novel variants of the 1-dimensional Weisfeiler-Leman (1-WL) test for graph isomorphism, and prove lower bounds on the expressiveness of ESAN in terms of these new WL variants. We further prove that our approach increases the expressive power of both MPNNs and more expressive architectures. Moreover, we provide theoretical results that describe how design choices such as the subgraph selection policy and equivariant neural architecture affect our architecture's expressive power. To deal with the increased computational cost, we propose a subgraph sampling scheme, which can be viewed as a stochastic version of our framework. A comprehensive set of experiments on real and synthetic datasets demonstrates that our framework improves the expressive power and overall performance of popular GNN architectures.

Cristian Bodnar, Fabrizio Frasca, Nina Otter et al.

Graph Neural Networks (GNNs) are limited in their expressive power, struggle with long-range interactions and lack a principled way to model higher-order structures. These problems can be attributed to the strong coupling between the computational graph and the input graph structure. The recently proposed Message Passing Simplicial Networks naturally decouple these elements by performing message passing on the clique complex of the graph. Nevertheless, these models can be severely constrained by the rigid combinatorial structure of Simplicial Complexes (SCs). In this work, we extend recent theoretical results on SCs to regular Cell Complexes, topological objects that flexibly subsume SCs and graphs. We show that this generalisation provides a powerful set of graph "lifting" transformations, each leading to a unique hierarchical message passing procedure. The resulting methods, which we collectively call CW Networks (CWNs), are strictly more powerful than the WL test and not less powerful than the 3-WL test. In particular, we demonstrate the effectiveness of one such scheme, based on rings, when applied to molecular graph problems. The proposed architecture benefits from provably larger expressivity than commonly used GNNs, principled modelling of higher-order signals and from compressing the distances between nodes. We demonstrate that our model achieves state-of-the-art results on a variety of molecular datasets.

Cristian Bodnar, Fabrizio Frasca, Yu Guang Wang et al.

The pairwise interaction paradigm of graph machine learning has predominantly governed the modelling of relational systems. However, graphs alone cannot capture the multi-level interactions present in many complex systems and the expressive power of such schemes was proven to be limited. To overcome these limitations, we propose Message Passing Simplicial Networks (MPSNs), a class of models that perform message passing on simplicial complexes (SCs). To theoretically analyse the expressivity of our model we introduce a Simplicial Weisfeiler-Lehman (SWL) colouring procedure for distinguishing non-isomorphic SCs. We relate the power of SWL to the problem of distinguishing non-isomorphic graphs and show that SWL and MPSNs are strictly more powerful than the WL test and not less powerful than the 3-WL test. We deepen the analysis by comparing our model with traditional graph neural networks (GNNs) with ReLU activations in terms of the number of linear regions of the functions they can represent. We empirically support our theoretical claims by showing that MPSNs can distinguish challenging strongly regular graphs for which GNNs fail and, when equipped with orientation equivariant layers, they can improve classification accuracy in oriented SCs compared to a GNN baseline.

Emanuele Rossi, Ben Chamberlain, Fabrizio Frasca et al.

Graph Neural Networks (GNNs) have recently become increasingly popular due to their ability to learn complex systems of relations or interactions arising in a broad spectrum of problems ranging from biology and particle physics to social networks and recommendation systems. Despite the plethora of different models for deep learning on graphs, few approaches have been proposed thus far for dealing with graphs that present some sort of dynamic nature (e.g. evolving features or connectivity over time). In this paper, we present Temporal Graph Networks (TGNs), a generic, efficient framework for deep learning on dynamic graphs represented as sequences of timed events. Thanks to a novel combination of memory modules and graph-based operators, TGNs are able to significantly outperform previous approaches being at the same time more computationally efficient. We furthermore show that several previous models for learning on dynamic graphs can be cast as specific instances of our framework. We perform a detailed ablation study of different components of our framework and devise the best configuration that achieves state-of-the-art performance on several transductive and inductive prediction tasks for dynamic graphs.

Fabrizio Frasca, Emanuele Rossi, Davide Eynard et al.

Graph representation learning has recently been applied to a broad spectrum of problems ranging from computer graphics and chemistry to high energy physics and social media. The popularity of graph neural networks has sparked interest, both in academia and in industry, in developing methods that scale to very large graphs such as Facebook or Twitter social networks. In most of these approaches, the computational cost is alleviated by a sampling strategy retaining a subset of node neighbors or subgraphs at training time. In this paper we propose a new, efficient and scalable graph deep learning architecture which sidesteps the need for graph sampling by using graph convolutional filters of different size that are amenable to efficient precomputation, allowing extremely fast training and inference. Our architecture allows using different local graph operators (e.g. motif-induced adjacency matrices or Personalized Page Rank diffusion matrix) to best suit the task at hand. We conduct extensive experimental evaluation on various open benchmarks and show that our approach is competitive with other state-of-the-art architectures, while requiring a fraction of the training and inference time. Moreover, we obtain state-of-the-art results on ogbn-papers100M, the largest public graph dataset, with over 110 million nodes and 1.5 billion edges.

Fabrizio Frasca, Diego Galeano, Guadalupe Gonzalez et al.

Drug repositioning is an attractive cost-efficient strategy for the development of treatments for human diseases. Here, we propose an interpretable model that learns disease self-representations for drug repositioning. Our self-representation model represents each disease as a linear combination of a few other diseases. We enforce proximity in the learnt representations in a way to preserve the geometric structure of the human phenome network - a domain-specific knowledge that naturally adds relational inductive bias to the disease self-representations. We prove that our method is globally optimal and show results outperforming state-of-the-art drug repositioning approaches. We further show that the disease self-representations are biologically interpretable.

Federico Monti, Fabrizio Frasca, Davide Eynard et al.

Social media are nowadays one of the main news sources for millions of people around the globe due to their low cost, easy access and rapid dissemination. This however comes at the cost of dubious trustworthiness and significant risk of exposure to 'fake news', intentionally written to mislead the readers. Automatically detecting fake news poses challenges that defy existing content-based analysis approaches. One of the main reasons is that often the interpretation of the news requires the knowledge of political or social context or 'common sense', which current NLP algorithms are still missing. Recent studies have shown that fake and real news spread differently on social media, forming propagation patterns that could be harnessed for the automatic fake news detection. Propagation-based approaches have multiple advantages compared to their content-based counterparts, among which is language independence and better resilience to adversarial attacks. In this paper we show a novel automatic fake news detection model based on geometric deep learning. The underlying core algorithms are a generalization of classical CNNs to graphs, allowing the fusion of heterogeneous data such as content, user profile and activity, social graph, and news propagation. Our model was trained and tested on news stories, verified by professional fact-checking organizations, that were spread on Twitter. Our experiments indicate that social network structure and propagation are important features allowing highly accurate (92.7% ROC AUC) fake news detection. Second, we observe that fake news can be reliably detected at an early stage, after just a few hours of propagation. Third, we test the aging of our model on training and testing data separated in time. Our results point to the promise of propagation-based approaches for fake news detection as an alternative or complementary strategy to content-based approaches.