Antonio Longa

Hazem Peter Samoaa, Antonio Longa, Mazen Mohamad et al.

Predicting the performance of production code prior to actually executing or benchmarking it is known to be highly challenging. In this paper, we propose a predictive model, dubbed TEP-GNN, which demonstrates that high-accuracy performance prediction is possible for the special case of predicting unit test execution times. TEP-GNN uses FA-ASTs, or flow-augmented ASTs, as a graph-based code representation approach, and predicts test execution times using a powerful graph neural network (GNN) deep learning model. We evaluate TEP-GNN using four real-life Java open source programs, based on 922 test files mined from the projects' public repositories. We find that our approach achieves a high Pearson correlation of 0.789, considerable outperforming a baseline deep learning model. However, we also find that more work is needed for trained models to generalize to unseen projects. Our work demonstrates that FA-ASTs and GNNs are a feasible approach for predicting absolute performance values, and serves as an important intermediary step towards being able to predict the performance of arbitrary code prior to execution.

Antonio Longa, Veronica Lachi, Gabriele Santin et al.

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.

Steve Azzolin, Antonio Longa, Pietro Barbiero et al.

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.

Antonio Longa, Steve Azzolin, Gabriele Santin et al.

Following a fast initial breakthrough in graph based learning, Graph Neural Networks (GNNs) have reached a widespread application in many science and engineering fields, prompting the need for methods to understand their decision process. GNN explainers have started to emerge in recent years, with a multitude of methods both novel or adapted from other domains. To sort out this plethora of alternative approaches, several studies have benchmarked the performance of different explainers in terms of various explainability metrics. However, these earlier works make no attempts at providing insights into why different GNN architectures are more or less explainable, or which explainer should be preferred in a given setting. In this survey, we fill these gaps by devising a systematic experimental study, which tests ten explainers on eight representative architectures trained on six carefully designed graph and node classification datasets. With our results we provide key insights on the choice and applicability of GNN explainers, we isolate key components that make them usable and successful and provide recommendations on how to avoid common interpretation pitfalls. We conclude by highlighting open questions and directions of possible future research.

Peter Samoaa, Linus Aronsson, Antonio Longa et al.

Most machine learning and data analytics applications, including performance engineering in software systems, require 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. We develop a unified active learning framework specializing in software performance prediction to address this task. We begin by parsing the source code to an Abstract Syntax Tree (AST) and augmenting it with data and control flow edges. Then, we convert the tree representation of the source code to a Flow Augmented-AST graph (FA-AST) representation. Based on the graph representation, we construct various graph embeddings (unsupervised and supervised) into a latent space. Given such an embedding, the framework becomes task agnostic since 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 unlabeled test data. Our approach aims to improve the investment in AI models for different software performance predictions (execution time) based on the structure of the source code. Our real-world experiments reveal that respectable performance can be achieved by querying labels for only a small subset of all the data.

Vincenzo Marco De Luca, Antonio Longa, Giovanna Varni et al.

Surgical team performance arises from complex interactions between technical execution and non-technical skills, including communication and coordination dynamics. However, current surgical AI systems predominantly model visual workflow signals, lacking structured representations of intraoperative team interactions over time. We propose a real-time actionable approach for modeling surgical team dynamics using time-expanded interaction graphs, where team members are modeled as time-indexed nodes and communication exchanges define directed edges. This spatio-temporal expansion enables dynamic interaction modeling, while allowing efficient inference with a static graph neural network. The model predicts procedural efficiency as the deviation from the expected duration and supports real-time deployment. Beyond prediction, we perform a counterfactual analysis to identify minimal changes in communication structure and interpretable behavioral variables associated with improved predicted outcomes. Experiments on recorded surgical procedures show that structured modeling of team interactions improves early identification of prolonged interventions and provides coherent, actionable explanations. This work advances surgical AI toward real-time, team-aware, and actionable decision support in the operating room.

Anna Nguyen, Antonio Longa, Massimiliano Luca et al.

Anticipating audience reaction towards a certain piece of text is integral to several facets of society ranging from politics, research, and commercial industries. Sentiment analysis (SA) is a useful natural language processing (NLP) technique that utilizes both lexical/statistical and deep learning methods to determine whether different sized texts exhibit a positive, negative, or neutral emotion. However, there is currently a lack of tools that can be used to analyse groups of independent texts and extract the primary emotion from the whole set. Therefore, the current paper proposes a novel algorithm referred to as the Multi-Layered Tweet Analyzer (MLTA) that graphically models social media text using multi-layered networks (MLNs) in order to better encode relationships across independent sets of tweets. Graph structures are capable of capturing meaningful relationships in complex ecosystems compared to other representation methods. State of the art Graph Neural Networks (GNNs) are used to extract information from the Tweet-MLN and make predictions based on the extracted graph features. Results show that not only does the MLTA predict from a larger set of possible emotions, delivering a more accurate sentiment compared to the standard positive, negative or neutral, it also allows for accurate group-level predictions of Twitter data.

Francesco Ferrini, Antonio Longa, Andrea Passerini et al.

Existing multi-relational graph neural networks use one of two strategies for identifying informative relations: either they reduce this problem to low-level weight learning, or they rely on handcrafted chains of relational dependencies, called meta-paths. However, the former approach faces challenges in the presence of many relations (e.g., knowledge graphs), while the latter requires substantial domain expertise to identify relevant meta-paths. In this work we propose a novel approach to learn meta-paths and meta-path GNNs that are highly accurate based on a small number of informative meta-paths. Key element of our approach is a scoring function for measuring the potential informativeness of a relation in the incremental construction of the meta-path. Our experimental evaluation shows that the approach manages to correctly identify relevant meta-paths even with a large number of relations, and substantially outperforms existing multi-relational GNNs on synthetic and real-world experiments.

Vincenzo Marco De Luca, Antonio Longa, Andrea Passerini et al.

Graph Neural Networks (GNNs) have emerged as the predominant paradigm for learning from graph-structured data, offering a wide range of applications from social network analysis to bioinformatics. Despite their versatility, GNNs face challenges such as lack of generalization and poor interpretability, which hinder their wider adoption and reliability in critical applications. Dropping has emerged as an effective paradigm for improving the generalization capabilities of GNNs. However, existing approaches often rely on random or heuristic-based selection criteria, lacking a principled method to identify and exclude nodes that contribute to noise and over-complexity in the model. In this work, we argue that explainability should be a key indicator of a model's quality throughout its training phase. To this end, we introduce xAI-Drop, a novel topological-level dropping regularizer that leverages explainability to pinpoint noisy network elements to be excluded from the GNN propagation mechanism. An empirical evaluation on diverse real-world datasets demonstrates that our method outperforms current state-of-the-art dropping approaches in accuracy, and improves explanation quality.

Francesco Ferrini, Veronica Lachi, Antonio Longa et al.

Handling missing node features is a key challenge for deploying Graph Neural Networks (GNNs) in real-world domains such as healthcare and sensor networks. Existing studies mostly address relatively benign scenarios, namely benchmark datasets with (a) high-dimensional but sparse node features and (b) incomplete data generated under Missing Completely At Random (MCAR) mechanisms. For (a), we theoretically prove that high sparsity substantially limits the information loss caused by missingness, making all models appear robust and preventing a meaningful comparison of their performance. To overcome this limitation, we introduce one synthetic and three real-world datasets with dense, semantically meaningful features. For (b), we move beyond MCAR and design evaluation protocols with more realistic missingness mechanisms. Moreover, we provide a theoretical background to state explicit assumptions on the missingness process and analyze their implications for different methods. Building on this analysis, we propose GNNmim, a simple yet effective baseline for node classification with incomplete feature data. Experiments show that GNNmim is competitive with respect to specialized architectures across diverse datasets and missingness regimes.

Francesco Ferrini, Antonio Longa, Andrea Passerini et al.

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 scenario.

Louis Airale, Antonio Longa, Mattia Rigon et al.

Graph transformers extend global self-attention to graph-structured data, achieving notable success in graph learning. Recently, random walk structural encoding (RWSE) has been found to further enhance their predictive power by encoding both structural and positional information into the edge representation. However, RWSE 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 RWSE, providing a richer representation of graph structures, particularly for 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 RWSE 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.

Veronica Lachi, Antonio Longa, Beatrice Bevilacqua et al.

Relational databases, organized into tables connected by primary-foreign key relationships, are a common format for organizing data. Making predictions on relational data often involves transforming them into a flat tabular format through table joins and feature engineering, which serve as input to tabular methods. However, designing features that fully capture complex relational patterns remains challenging. Graph Neural Networks (GNNs) offer a compelling alternative by inherently modeling these relationships, but their time overhead during inference limits their applicability for real-time scenarios. In this work, we aim to bridge this gap by leveraging existing feature engineering efforts to enhance the efficiency of GNNs in relational databases. Specifically, we use GNNs to capture complex relationships within relational databases, patterns that are difficult to featurize, while employing engineered features to encode temporal information, thereby avoiding the need to retain the entire historical graph and enabling the use of smaller, more efficient graphs. Our \textsc{LightRDL} approach not only improves efficiency, but also outperforms existing models. Experimental results on the RelBench benchmark demonstrate that our framework achieves up to $33\%$ performance improvement and a $526\times$ inference speedup compared to GNNs, making it highly suitable for real-time inference.

Nicolò Penzo, Antonio Longa, Bruno Lepri et al.

Current text classification approaches usually focus on the content to be classified. Contextual aspects (both linguistic and extra-linguistic) are usually neglected, even in tasks based on online discussions. Still in many cases the multi-party and multi-turn nature of the context from which these elements are selected can be fruitfully exploited. In this work, we propose a series of experiments on a large dataset for stance detection in English, in which we evaluate the contribution of different types of contextual information, i.e. linguistic, structural and temporal, by feeding them as natural language input into a transformer-based model. We also experiment with different amounts of training data and analyse the topology of local discussion networks in a privacy-compliant way. Results show that structural information can be highly beneficial to text classification but only under certain circumstances (e.g. depending on the amount of training data and on discussion chain complexity). Indeed, we show that contextual information on smaller datasets from other classification tasks does not yield significant improvements. Our framework, based on local discussion networks, allows the integration of structural information, while minimising user profiling, thus preserving their privacy.

Francesco Ferrini, Veronica Lachi, Antonio Longa et al.

Graph Neural Networks (GNNs) often struggle to capture the link-specific structural patterns crucial for accurate link prediction, as their node-centric message-passing schemes overlook the subgraph structures connecting a pair of nodes. Existing methods to inject such structural context either incur high computational cost or rely on simplistic heuristics (e.g., common neighbor counts) that fail to model multi-hop dependencies. We introduce SP4LP (Shortest Path for Link Prediction), a novel framework that combines GNN-based node encodings with sequence modeling over shortest paths. Specifically, SP4LP first applies a GNN to compute representations for all nodes, then extracts the shortest path between each candidate node pair and processes the resulting sequence of node embeddings using a sequence model. This design enables SP4LP to capture expressive multi-hop relational patterns with computational efficiency. Empirically, SP4LP achieves state-of-the-art performance across link prediction benchmarks. Theoretically, we prove that SP4LP is strictly more expressive than standard message-passing GNNs and several state-of-the-art structural features methods, establishing it as a general and principled approach for link prediction in graphs.

Veronica Lachi, Francesco Ferrini, Antonio Longa et al.

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 $k_φ$-$k_ρ$-$m$ 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.

Peter Samoaa, Marcus Vukojevic, Morteza Haghir Chehreghani et al.

Graph-level regression underpins many real-world applications, yet public benchmarks remain heavily skewed toward molecular graphs and citation networks. This limited diversity hinders progress on models that must generalize across both homogeneous and heterogeneous graph structures. We introduce RelSC, a new graph-regression dataset built from program graphs that combine syntactic and semantic information extracted from source code. Each graph is labelled with the execution-time cost of the corresponding program, providing a continuous target variable that differs markedly from those found in existing benchmarks. RelSC is released in two complementary variants. RelSC-H supplies rich node features under a single (homogeneous) edge type, while RelSC-M preserves the original multi-relational structure, connecting nodes through multiple edge types that encode distinct semantic relationships. Together, these variants let researchers probe how representation choice influences model behaviour. We evaluate a diverse set of graph neural network architectures on both variants of RelSC. The results reveal consistent performance differences between the homogeneous and multi-relational settings, emphasising the importance of structural representation. These findings demonstrate RelSC's value as a challenging and versatile benchmark for advancing graph regression methods.

Steve Azzolin, Antonio Longa, Stefano Teso et al.

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 \textit{faithful}, \ie 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 \textit{existing metrics are not interchangeable} -- \ie 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, \textit{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 \textit{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.The code is publicly available on GitHub

Peter Samoaa, Mehrdad Farahani, Antonio Longa et al.

The landscape of deep learning has vastly expanded the frontiers of source code analysis, particularly through the utilization of structural representations such as Abstract Syntax Trees (ASTs). While these methodologies have demonstrated effectiveness in classification tasks, their efficacy in regression applications, such as execution time prediction from source code, remains underexplored. This paper endeavours to decode the behaviour of tree-based neural network models in the context of such regression challenges. We extend the application of established models--tree-based Convolutional Neural Networks (CNNs), Code2Vec, and Transformer-based methods--to predict the execution time of source code by parsing it to an AST. Our comparative analysis reveals that while these models are benchmarks in code representation, they exhibit limitations when tasked with regression. To address these deficiencies, we propose a novel dual-transformer approach that operates on both source code tokens and AST representations, employing cross-attention mechanisms to enhance interpretability between the two domains. Furthermore, we explore the adaptation of Graph Neural Networks (GNNs) to this tree-based problem, theorizing the inherent compatibility due to the graphical nature of ASTs. Empirical evaluations on real-world datasets showcase that our dual-transformer model outperforms all other tree-based neural networks and the GNN-based models. Moreover, our proposed dual transformer demonstrates remarkable adaptability and robust performance across diverse datasets.

Giovanni Mauro, Massimiliano Luca, Antonio Longa et al.

The increasingly crucial role of human displacements in complex societal phenomena, such as traffic congestion, segregation, and the diffusion of epidemics, is attracting the interest of scientists from several disciplines. In this article, we address mobility network generation, i.e., generating a city's entire mobility network, a weighted directed graph in which nodes are geographic locations and weighted edges represent people's movements between those locations, thus describing the entire mobility set flows within a city. Our solution is MoGAN, a model based on Generative Adversarial Networks (GANs) to generate realistic mobility networks. We conduct extensive experiments on public datasets of bike and taxi rides to show that MoGAN outperforms the classical Gravity and Radiation models regarding the realism of the generated networks. Our model can be used for data augmentation and performing simulations and what-if analysis.