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Antonio Longa

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7 papers

2 author rows

TMLR Journal 2025 Journal Article

A Self-Explainable Heterogeneous GNN for Relational Deep Learning

Francesco Ferrini
Antonio Longa
Andrea Passerini
Manfred Jaeger

Recently, significant attention has been given to the idea of viewing relational databases as heterogeneous graphs, enabling the application of graph neural network (GNN) technology for predictive tasks. However, existing GNN methods struggle with the complexity of the heterogeneous graphs induced by databases with numerous tables and relations. Traditional approaches either consider all possible relational meta-paths, thus failing to scale with the number of relations, or rely on domain experts to identify relevant meta-paths. A recent solution does manage to learn informative meta-paths without expert supervision, but assumes that a node’s class depends solely on the existence of a meta-path occurrence. In this work, we present a self-explainable heterogeneous GNN for relational data, that supports models in which class membership depends on aggregate information obtained from multiple occurrences of a meta-path. Experimental results show that in the context of relational databases, our approach effectively identifies informative meta-paths that faithfully capture the model’s reasoning mechanisms. It significantly outperforms existing methods in both synthetic and real-world scenarios.

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NeurIPS Conference 2025 Conference Paper

Bridging Theory and Practice in Link Representation with Graph Neural Networks

Veronica Lachi
Francesco Ferrini
Antonio Longa
Bruno Lepri
Andrea Passerini
Manfred Jaeger

Graph Neural Networks (GNNs) are widely used to compute representations of node pairs for downstream tasks such as link prediction. Yet, theoretical understanding of their expressive power has focused almost entirely on graph-level representations. In this work, we shift the focus to links and provide the first comprehensive study of GNN expressiveness in link representation. We introduce a unifying framework, the $k_\phi$-$k_\rho$-$m$ framework, that subsumes existing message-passing link models and enables formal expressiveness comparisons. Using this framework, we derive a hierarchy of state-of-the-art methods and offer theoretical tools to analyze future architectures. To complement our analysis, we propose a synthetic evaluation protocol comprising the first benchmark specifically designed to assess link-level expressiveness. Finally, we ask: does expressiveness matter in practice? We use a graph symmetry metric that quantifies the difficulty of distinguishing links and show that while expressive models may underperform on standard benchmarks, they significantly outperform simpler ones as symmetry increases, highlighting the need for dataset-aware model selection.

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ICLR Conference 2025 Conference Paper

Reconsidering Faithfulness in Regular, Self-Explainable and Domain Invariant GNNs

Steve Azzolin
Antonio Longa
Stefano Teso
Andrea Passerini

As Graph Neural Networks (GNNs) become more pervasive, it becomes paramount to build reliable tools for explaining their predictions. A core desideratum is that explanations are *faithful*, i.e., that they portray an accurate picture of the GNN's reasoning process. However, a number of different faithfulness metrics exist, begging the question of what is faithfulness exactly and how to achieve it. We make three key contributions. We begin by showing that *existing metrics are not interchangeable* -- i.e., explanations attaining high faithfulness according to one metric may be unfaithful according to others -- and can *systematically ignore important properties of explanations*. We proceed to show that, surprisingly, *optimizing for faithfulness is not always a sensible design goal*. Specifically, we prove that for injective regular GNN architectures, perfectly faithful explanations are completely uninformative. This does not apply to modular GNNs, such as self-explainable and domain-invariant architectures, prompting us to study the relationship between architectural choices and faithfulness. Finally, we show that *faithfulness is tightly linked to out-of-distribution generalization*, in that simply ensuring that a GNN can correctly recognize the domain-invariant subgraph, as prescribed by the literature, does not guarantee that it is invariant unless this subgraph is also faithful. All our code can be found in the supplementary material.

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ICML Conference 2025 Conference Paper

Simple Path Structural Encoding for Graph Transformers

Louis Airale
Antonio Longa
Mattia Rigon
Andrea Passerini
Roberto Passerone

Graph transformers extend global self-attention to graph-structured data, achieving notable success in graph learning. Recently, Relative Random Walk Probabilities (RRWP) has been found to further enhance their predictive power by encoding both structural and positional information into the edge representation. However, RRWP cannot always distinguish between edges that belong to different local graph patterns, which reduces its ability to capture the full structural complexity of graphs. This work introduces Simple Path Structural Encoding (SPSE), a novel method that utilizes simple path counts for edge encoding. We show theoretically and experimentally that SPSE overcomes the limitations of RRWP, providing a richer representation of graph structures, particularly in capturing local cyclic patterns. To make SPSE computationally tractable, we propose an efficient approximate algorithm for simple path counting. SPSE demonstrates significant performance improvements over RRWP on various benchmarks, including molecular and long-range graph datasets, achieving statistically significant gains in discriminative tasks. These results pose SPSE as a powerful edge encoding alternative for enhancing the expressivity of graph transformers.

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EAAI Journal 2024 Journal Article

A unified active learning framework for annotating graph data for regression tasks

Peter Samoaa
Linus Aronsson
Antonio Longa
Philipp Leitner
Morteza Haghir Chehreghani

In many domains, effectively applying machine learning models requires a large number of annotations and labelled data, which might not be available in advance. Acquiring annotations often requires significant time, effort, and computational resources, making it challenging. Active learning strategies are pivotal in addressing these challenges, particularly for diverse data types such as graphs. Although active learning has been extensively explored for node-level classification, its application to graph-level learning, especially for regression tasks, is not well-explored. We develop a unified active learning framework specializing in graph annotating and graph-level learning for regression tasks on both standard and expanded graphs, which are more detailed representations. We begin with graph collection and construction. Then, we construct various graph embeddings (unsupervised and supervised) into a latent space. Given such an embedding, the framework becomes task agnostic and active learning can be performed using any regression method and query strategy suited for regression. Within this framework, we investigate the impact of using different levels of information for active and passive learning, e. g. , partially available labels and unlabelled test data. Despite our framework being domain agnostic, we validate it on a real-world application of software performance prediction, where the execution time of the source code is predicted. Thus, the graph is constructed as an intermediate source code representation. We support our methodology with a real-world dataset to underscore the applicability of our approach. Our real-world experiments reveal that satisfactory performance can be achieved by querying labels for only a small subset of all the data. A key finding is that Graph2Vec (an unsupervised embedding approach for graph data) performs the best, but only when all train and test features are used. However, Graph Neural Networks (GNNs) are the most flexible embedding techniques when used for different levels of information with and without label access. In addition, we find that the benefit of active learning increases for larger datasets (more graphs) and when the graphs are more complex, which is arguably when active learning is the most important.

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ICLR Conference 2023 Conference Paper

Global Explainability of GNNs via Logic Combination of Learned Concepts

Steve Azzolin
Antonio Longa
Pietro Barbiero
Pietro Liò
Andrea Passerini

While instance-level explanation of GNN is a well-studied problem with plenty of approaches being developed, providing a global explanation for the behaviour of a GNN is much less explored, despite its potential in interpretability and debugging. Existing solutions either simply list local explanations for a given class, or generate a synthetic prototypical graph with maximal score for a given class, completely missing any combinatorial aspect that the GNN could have learned. In this work, we propose GLGExplainer (Global Logic-based GNN Explainer), the first Global Explainer capable of generating explanations as arbitrary Boolean combinations of learned graphical concepts. GLGExplainer is a fully differentiable architecture that takes local explanations as inputs and combines them into a logic formula over graphical concepts, represented as clusters of local explanations. Contrary to existing solutions, GLGExplainer provides accurate and human-interpretable global explanations that are perfectly aligned with ground-truth explanations (on synthetic data) or match existing domain knowledge (on real-world data). Extracted formulas are faithful to the model predictions, to the point of providing insights into some occasionally incorrect rules learned by the model, making GLGExplainer a promising diagnostic tool for learned GNNs.

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TMLR Journal 2023 Journal Article

Graph Neural Networks for Temporal Graphs: State of the Art, Open Challenges, and Opportunities

Antonio Longa
Veronica Lachi
Gabriele Santin
Monica Bianchini
Bruno Lepri
Pietro Lio
franco scarselli
Andrea Passerini

Graph Neural Networks (GNNs) have become the leading paradigm for learning on (static) graph-structured data. However, many real-world systems are dynamic in nature, since the graph and node/edge attributes change over time. In recent years, GNN-based models for temporal graphs have emerged as a promising area of research to extend the capabilities of GNNs. In this work, we provide the first comprehensive overview of the current state-of-the-art of temporal GNN, introducing a rigorous formalization of learning settings and tasks and a novel taxonomy categorizing existing approaches in terms of how the temporal aspect is represented and processed. We conclude the survey with a discussion of the most relevant open challenges for the field, from both research and application perspectives.

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