arXiv subjects

Alessio Micheli

Publications and source records attributed to Alessio Micheli.

At least 19 recordsLinked to original sources

arXiv2025

Water Quality Estimation Through Machine Learning Multivariate Analysis

The quality of water is key for the quality of agrifood sector. Water is used in agriculture for fertigation, for animal husbandry, and in the agrifood processing industry. In the context of the progressive digitalization of this sector, the automatic assessment of the quality of water is thus becoming an important asset. In this work, we present the integration of Ultraviolet-Visible (UV-Vis) spectroscopy with Machine Learning in the context of water quality assessment aiming at ensuring water safety and the compliance of water regulation. Furthermore, we emphasize the importance of model interpretability by employing SHapley Additive exPlanations (SHAP) to understand the contribution of absorbance at different wavelengths to the predictions. Our approach demonstrates the potential for rapid, accurate, and interpretable assessment of key water quality parameters.

cs.LG↗

arXiv2025

Efficient quantification on large-scale networks

Network quantification (NQ) is the problem of estimating the proportions of nodes belonging to each class in subsets of unlabelled graph nodes. When prior probability shift is at play, this task cannot be effectively addressed by first classifying the nodes and then counting the class predictions. In addition, unlike non-relational quantification, NQ demands enhanced flexibility in order to capture a broad range of connectivity patterns, resilience to the challenge of heterophily, and scalability to large networks. In order to meet these stringent requirements, we introduce XNQ, a novel method that synergizes the flexibility and efficiency of the unsupervised node embeddings computed by randomized recursive Graph Neural Networks, with an Expectation-Maximization algorithm that provides a robust quantification-aware adjustment to the output probabilities of a calibrated node classifier. In an extensive evaluation, in which we also validate the design choices underpinning XNQ through comprehensive ablation experiments, we find that XNQ consistently and significantly improves on the best network quantification methods to date, thereby setting the new state of the art for this challenging task. XNQ also provides a training speed-up of up to 10x-100x over other methods based on graph learning.

cs.LG↗

arXiv2025

A method for the systematic generation of graph XAI benchmarks via Weisfeiler-Leman coloring

Graph neural networks have become the de facto model for learning from structured data. However, the decision-making process of GNNs remains opaque to the end user, which undermines their use in safety-critical applications. Several explainable AI techniques for graphs have been developed to address this major issue. Focusing on graph classification, these explainers identify subgraph motifs that explain predictions. Therefore, a robust benchmarking of graph explainers is required to ensure that the produced explanations are of high quality, i.e., aligned with the GNN's decision process. However, current graph-XAI benchmarks are limited to simplistic synthetic datasets or a few real-world tasks curated by domain experts, hindering rigorous and reproducible evaluation, and consequently stalling progress in the field. To overcome these limitations, we propose a method to automate the construction of graph XAI benchmarks from generic graph classification datasets. Our approach leverages the Weisfeiler-Leman color refinement algorithm to efficiently perform approximate subgraph matching and mine class-discriminating motifs, which serve as proxy ground-truth class explanations. At the same time, we ensure that these motifs can be learned by GNNs because their discriminating power aligns with WL expressiveness. This work also introduces the OpenGraphXAI benchmark suite, which consists of 15 ready-made graph-XAI datasets derived by applying our method to real-world molecular classification datasets. The suite is available to the public along with a codebase to generate over 2,000 additional graph-XAI benchmarks. Finally, we present a use case that illustrates how the suite can be used to assess the effectiveness of a selection of popular graph explainers, demonstrating the critical role of a sufficiently large benchmark collection for improving the significance of experimental results.

cs.LG↗

arXiv2025

An Empirical Evaluation of Rewiring Approaches in Graph Neural Networks

Graph neural networks compute node representations by performing multiple message-passing steps that consist in local aggregations of node features. Having deep models that can leverage longer-range interactions between nodes is hindered by the issues of over-smoothing and over-squashing. In particular, the latter is attributed to the graph topology which guides the message-passing, causing a node representation to become insensitive to information contained at distant nodes. Many graph rewiring methods have been proposed to remedy or mitigate this problem. However, properly evaluating the benefits of these methods is made difficult by the coupling of over-squashing with other issues strictly related to model training, such as vanishing gradients. Therefore, we propose an evaluation setting based on message-passing models that do not require training to compute node and graph representations. We perform a systematic experimental comparison on real-world node and graph classification tasks, showing that rewiring the underlying graph rarely does confer a practical benefit for message-passing.

cs.LG↗

arXiv2023

Modeling Edge Features with Deep Bayesian Graph Networks

We propose an extension of the Contextual Graph Markov Model, a deep and probabilistic machine learning model for graphs, to model the distribution of edge features. Our approach is architectural, as we introduce an additional Bayesian network mapping edge features into discrete states to be used by the original model. In doing so, we are also able to build richer graph representations even in the absence of edge features, which is confirmed by the performance improvements on standard graph classification benchmarks. Moreover, we successfully test our proposal in a graph regression scenario where edge features are of fundamental importance, and we show that the learned edge representation provides substantial performance improvements against the original model on three link prediction tasks. By keeping the computational complexity linear in the number of edges, the proposed model is amenable to large-scale graph processing.

cs.LG↗

arXiv2023

Addressing Heterophily in Node Classification with Graph Echo State Networks

Node classification tasks on graphs are addressed via fully-trained deep message-passing models that learn a hierarchy of node representations via multiple aggregations of a node's neighbourhood. While effective on graphs that exhibit a high ratio of intra-class edges, this approach poses challenges in the opposite case, i.e. heterophily, where nodes belonging to the same class are usually further apart. In graphs with a high degree of heterophily, the smoothed representations based on close neighbours computed by convolutional models are no longer effective. So far, architectural variations in message-passing models to reduce excessive smoothing or rewiring the input graph to improve longer-range message passing have been proposed. In this paper, we address the challenges of heterophilic graphs with Graph Echo State Network (GESN) for node classification. GESN is a reservoir computing model for graphs, where node embeddings are recursively computed by an untrained message-passing function. Our experiments show that reservoir models are able to achieve better or comparable accuracy with respect to most fully trained deep models that implement ad hoc variations in the architectural bias or perform rewiring as a preprocessing step on the input graph, with an improvement in terms of efficiency/accuracy trade-off. Furthermore, our analysis shows that GESN is able to effectively encode the structural relationships of a graph node, by showing a correlation between iterations of the recursive embedding function and the distribution of shortest paths in a graph.

cs.LG↗

arXiv2022

Leave Graphs Alone: Addressing Over-Squashing without Rewiring

Recent works have investigated the role of graph bottlenecks in preventing long-range information propagation in message-passing graph neural networks, causing the so-called `over-squashing' phenomenon. As a remedy, graph rewiring mechanisms have been proposed as preprocessing steps. Graph Echo State Networks (GESNs) are a reservoir computing model for graphs, where node embeddings are recursively computed by an untrained message-passing function. In this paper, we show that GESNs can achieve a significantly better accuracy on six heterophilic node classification tasks without altering the graph connectivity, thus suggesting a different route for addressing the over-squashing problem.

cs.LG↗

arXiv2022

Dynamic Graph Echo State Networks

Dynamic temporal graphs represent evolving relations between entities, e.g. interactions between social network users or infection spreading. We propose an extension of graph echo state networks for the efficient processing of dynamic temporal graphs, with a sufficient condition for their echo state property, and an experimental analysis of reservoir layout impact. Compared to temporal graph kernels that need to hold the entire history of vertex interactions, our model provides a vector encoding for the dynamic graph that is updated at each time-step without requiring training. Experiments show accuracy comparable to approximate temporal graph kernels on twelve dissemination process classification tasks.

cs.LG↗

arXiv2022

Beyond Homophily with Graph Echo State Networks

Graph Echo State Networks (GESN) have already demonstrated their efficacy and efficiency in graph classification tasks. However, semi-supervised node classification brought out the problem of over-smoothing in end-to-end trained deep models, which causes a bias towards high homophily graphs. We evaluate for the first time GESN on node classification tasks with different degrees of homophily, analyzing also the impact of the reservoir radius. Our experiments show that reservoir models are able to achieve better or comparable accuracy with respect to fully trained deep models that implement ad hoc variations in the architectural bias, with a gain in terms of efficiency.

cs.LG↗

arXiv2022

A Fair Comparison of Graph Neural Networks for Graph Classification

Experimental reproducibility and replicability are critical topics in machine learning. Authors have often raised concerns about their lack in scientific publications to improve the quality of the field. Recently, the graph representation learning field has attracted the attention of a wide research community, which resulted in a large stream of works. As such, several Graph Neural Network models have been developed to effectively tackle graph classification. However, experimental procedures often lack rigorousness and are hardly reproducible. Motivated by this, we provide an overview of common practices that should be avoided to fairly compare with the state of the art. To counter this troubling trend, we ran more than 47000 experiments in a controlled and uniform framework to re-evaluate five popular models across nine common benchmarks. Moreover, by comparing GNNs with structure-agnostic baselines we provide convincing evidence that, on some datasets, structural information has not been exploited yet. We believe that this work can contribute to the development of the graph learning field, by providing a much needed grounding for rigorous evaluations of graph classification models.

cs.LG↗

arXiv2021

TEACHING -- Trustworthy autonomous cyber-physical applications through human-centred intelligence

This paper discusses the perspective of the H2020 TEACHING project on the next generation of autonomous applications running in a distributed and highly heterogeneous environment comprising both virtual and physical resources spanning the edge-cloud continuum. TEACHING puts forward a human-centred vision leveraging the physiological, emotional, and cognitive state of the users as a driver for the adaptation and optimization of the autonomous applications. It does so by building a distributed, embedded and federated learning system complemented by methods and tools to enforce its dependability, security and privacy preservation. The paper discusses the main concepts of the TEACHING approach and singles out the main AI-related research challenges associated with it. Further, we provide a discussion of the design choices for the TEACHING system to tackle the aforementioned challenges

cs.AI↗

arXiv2021

Graph Mixture Density Networks

We introduce the Graph Mixture Density Networks, a new family of machine learning models that can fit multimodal output distributions conditioned on graphs of arbitrary topology. By combining ideas from mixture models and graph representation learning, we address a broader class of challenging conditional density estimation problems that rely on structured data. In this respect, we evaluate our method on a new benchmark application that leverages random graphs for stochastic epidemic simulations. We show a significant improvement in the likelihood of epidemic outcomes when taking into account both multimodality and structure. The empirical analysis is complemented by two real-world regression tasks showing the effectiveness of our approach in modeling the output prediction uncertainty. Graph Mixture Density Networks open appealing research opportunities in the study of structure-dependent phenomena that exhibit non-trivial conditional output distributions.

cs.LG↗

arXiv2021

Phase Transition Adaptation

Artificial Recurrent Neural Networks are a powerful information processing abstraction, and Reservoir Computing provides an efficient strategy to build robust implementations by projecting external inputs into high dimensional dynamical system trajectories. In this paper, we propose an extension of the original approach, a local unsupervised learning mechanism we call Phase Transition Adaptation, designed to drive the system dynamics towards the `edge of stability'. Here, the complex behavior exhibited by the system elicits an enhancement in its overall computational capacity. We show experimentally that our approach consistently achieves its purpose over several datasets.

cs.LG↗

arXiv2021

Pyramidal Reservoir Graph Neural Network

We propose a deep Graph Neural Network (GNN) model that alternates two types of layers. The first type is inspired by Reservoir Computing (RC) and generates new vertex features by iterating a non-linear map until it converges to a fixed point. The second type of layer implements graph pooling operations, that gradually reduce the support graph and the vertex features, and further improve the computational efficiency of the RC-based GNN. The architecture is, therefore, pyramidal. In the last layer, the features of the remaining vertices are combined into a single vector, which represents the graph embedding. Through a mathematical derivation introduced in this paper, we show formally how graph pooling can reduce the computational complexity of the model and speed-up the convergence of the dynamical updates of the vertex features. Our proposed approach to the design of RC-based GNNs offers an advantageous and principled trade-off between accuracy and complexity, which we extensively demonstrate in experiments on a large set of graph datasets.

cs.LG↗

arXiv2020

Deep Echo State Network (DeepESN): A Brief Survey

The study of deep recurrent neural networks (RNNs) and, in particular, of deep Reservoir Computing (RC) is gaining an increasing research attention in the neural networks community. The recently introduced Deep Echo State Network (DeepESN) model opened the way to an extremely efficient approach for designing deep neural networks for temporal data. At the same time, the study of DeepESNs allowed to shed light on the intrinsic properties of state dynamics developed by hierarchical compositions of recurrent layers, i.e. on the bias of depth in RNNs architectural design. In this paper, we summarize the advancements in the development, analysis and applications of DeepESNs.

cs.LG↗

arXiv2020

Accelerating the identification of informative reduced representations of proteins with deep learning for graphs

The limits of molecular dynamics (MD) simulations of macromolecules are steadily pushed forward by the relentless developments of computer architectures and algorithms. This explosion in the number and extent (in size and time) of MD trajectories induces the need of automated and transferable methods to rationalise the raw data and make quantitative sense out of them. Recently, an algorithmic approach was developed by some of us to identify the subset of a protein's atoms, or mapping, that enables the most informative description of it. This method relies on the computation, for a given reduced representation, of the associated mapping entropy, that is, a measure of the information loss due to the simplification. Albeit relatively straightforward, this calculation can be time consuming. Here, we describe the implementation of a deep learning approach aimed at accelerating the calculation of the mapping entropy. The method relies on deep graph networks, which provide extreme flexibility in the input format. We show that deep graph networks are accurate and remarkably efficient, with a speedup factor as large as $10^5$ with respect to the algorithmic computation of the mapping entropy. Applications of this method, which entails a great potential in the study of biomolecules when used to reconstruct its mapping entropy landscape, reach much farther than this, being the scheme easily transferable to the computation of arbitrary functions of a molecule's structure.

physics.comp-ph↗

arXiv2020

A Gentle Introduction to Deep Learning for Graphs

The adaptive processing of graph data is a long-standing research topic which has been lately consolidated as a theme of major interest in the deep learning community. The snap increase in the amount and breadth of related research has come at the price of little systematization of knowledge and attention to earlier literature. This work is designed as a tutorial introduction to the field of deep learning for graphs. It favours a consistent and progressive introduction of the main concepts and architectural aspects over an exposition of the most recent literature, for which the reader is referred to available surveys. The paper takes a top-down view to the problem, introducing a generalized formulation of graph representation learning based on a local and iterative approach to structured information processing. It introduces the basic building blocks that can be combined to design novel and effective neural models for graphs. The methodological exposition is complemented by a discussion of interesting research challenges and applications in the field.

cs.LG↗

arXiv2020

Ring Reservoir Neural Networks for Graphs

Machine Learning for graphs is nowadays a research topic of consolidated relevance. Common approaches in the field typically resort to complex deep neural network architectures and demanding training algorithms, highlighting the need for more efficient solutions. The class of Reservoir Computing (RC) models can play an important role in this context, enabling to develop fruitful graph embeddings through untrained recursive architectures. In this paper, we study progressive simplifications to the design strategy of RC neural networks for graphs. Our core proposal is based on shaping the organization of the hidden neurons to follow a ring topology. Experimental results on graph classification tasks indicate that ring-reservoirs architectures enable particularly effective network configurations, showing consistent advantages in terms of predictive performance.

cs.LG↗