arXiv subjects

Francesca Chiaromonte

Publications and source records attributed to Francesca Chiaromonte.

At least 19 recordsLinked to original sources

arXiv2026

GravityGraphSAGE: Link Prediction in Directed Attributed Graphs

Link prediction (inferring missing or future connections between nodes in a graph) is a fundamental problem in network science with widespread applications in, e.g., biological systems, recommender systems, finance and cybersecurity. The ability to accurately predict links has significant real-world applications, such as detecting fraudulent financial transactions or identifying drug-target interactions in biomedicine. Despite a rich literature, link prediction is still challenging, especially for graphs enriched with information on edges (direction) and nodes (attributes). In fact, research on link prediction, especially the one based on Graph Deep Learning (GDL), has mostly focused on undirected graphs, without fully leveraging node attributes. Here, we fill this gap by proposing Gravity-GraphSAGE (GG-SAGE), a modified version of GraphSAGE, a GDL model for node embeddings, composed of a gravity-inspired decoder. This implementation is the first example in the literature of a GraphSAGE backbone adopted for directed link prediction. Using the benchmark datasets Cora, Citeseer, PubMed and 16 real-world graphs from the online Netzschleuder repository, we show that our proposed model outperforms state-of-the-art GDL link prediction techniques. Using further experimental evidence, we relate the quality of the output of our model with various characteristics of the graph, suggesting that our framework scales well when applied to data of increasing complexity.

cs.LG↗

arXiv2026

RAwR: Role-Aware Rewiring via Approximate Equitable Partition

While Graph Neural Networks (GNNs) have demonstrated significant efficacy in node classification tasks, where predictions rely on local neighborhood information, the performance of GNNs often drops when prediction tasks depend on long-range interactions. These limitations are attributed to phenomena such as oversquashing, where structural bottlenecks restrict signal propagation across the network topology. To address this challenge, we introduce RAwR, a computationally efficient rewiring framework that augments the input graph with a quotient graph derived from equitable partitions. This approach facilitates accelerated communication between nodes that share identical structural roles, as identified by the Weisfeiler-Leman graph coloring, and thereby reduces the total effective resistance of the system. Furthermore, by employing an approximate definition of the equitable partition, RAwR enables a controllable reduction of the quotient graph, which, in its most condensed state, recovers the conventional Master Node rewiring technique. Empirical evaluations across a diverse suite of benchmarks -- including homophilic, heterophilic, and synthetic long-range datasets -- demonstrate that RAwR achieves state-of-the-art results. Our contribution is further supported by an analytical investigation using a teacher-student model of linear GNNs, which elucidates the theoretical foundations of role-based rewiring. This analysis leads to the formulation of Spectral Role Lift (SRL), a metric designed to identify the optimal approximate equitable partition for maximizing predictive performance.

cs.LG↗

arXiv2026

A Doubly Robust Machine Learning Approach for Disentangling Treatment Effect Heterogeneity with Functional Outcomes

Causal inference is paramount for understanding the effects of interventions, yet extracting personalized insights from increasingly complex data remains a significant challenge for modern machine learning. This is the case, in particular, when considering functional outcomes observed over a continuous domain (e.g., time, or space). Estimation of heterogeneous treatment effects, known as CATE, has emerged as a crucial tool for personalized decision-making, but existing meta-learning frameworks are largely limited to scalar outcomes, failing to provide satisfying results in scientific applications that leverage the rich, continuous information encoded in functional data. Here, we introduce FOCaL (Functional Outcome Causal Learning), a novel, doubly robust meta-learner specifically engineered to estimate a functional heterogeneous treatment effect (F-CATE). FOCaL integrates advanced functional regression techniques for both outcome modeling and functional pseudo-outcome reconstruction, thereby enabling the direct and robust estimation of F-CATE. We provide a rigorous theoretical derivation of FOCaL, demonstrate its performance and robustness compared to existing non-robust functional methods through comprehensive simulation studies, and illustrate its practical utility on diverse real-world functional datasets. FOCaL advances the capabilities of machine intelligence to infer nuanced, individualized causal effects from complex data, paving the way for more precise and trustworthy AI systems in personalized medicine, adaptive policy design, and fundamental scientific discovery.

stat.ME↗

arXiv2026

Aligned explanations in neural networks

As artificial intelligence increasingly drives critical decisions, the ability to genuinely explain how neural networks make predictions is essential for trust. Yet, most current explanation methods offer post-hoc rationalizations rather than guaranteeing a true reflection of the model's reasoning. We introduce the notion of explanatory alignment, a requirement that explanations directly construct predictions rather than rationalize them. To achieve this in complex data domains, we present Pointwise-interpretable Networks (PiNets), a pseudo-linear architecture that forms linear models instance-wise. Evaluated on image classification and segmentation tasks, PiNets demonstrate that their explanations are deeply faithful across four criteria: meaningfulness, alignment, robustness, and sufficiency (MARS). Our contributions pave the way for promising avenues: by reconciling the predictive power of deep learning with the interpretability of linear models, PiNets provide a principled foundation for trustworthy AI and data-driven scientific discovery.

cs.LG↗

arXiv2025

Sparse Bayesian Partially Identified Models for Sequence Count Data

In genomics, differential abundance and expression analyses are complicated by the compositional nature of sequence count data, which reflect only relative-not absolute-abundances or expression levels. Many existing methods attempt to address this limitation through data normalizations, but we have shown that such approaches imply strong, often biologically implausible assumptions about total microbial load or total gene expression. Even modest violations of these assumptions can inflate Type I and Type II error rates to over 70%. Sparse estimators have been proposed as an alternative, leveraging the assumption that only a small subset of taxa (or genes) change between conditions. However, we show that current sparse methods suffer from similar pathologies because they treat sparsity assumptions as fixed and ignore the uncertainty inherent in these assumptions. We introduce a sparse Bayesian Partially Identified Model (PIM) that addresses this limitation by explicitly modeling uncertainty in sparsity assumptions. Our method extends the Scale-Reliant Inference (SRI) framework to the sparse setting, providing a principled approach to differential analysis under scale uncertainty. We establish theoretical consistency of the proposed estimator and, through extensive simulations and real data analyses, demonstrate substantial reductions in both Type I and Type II errors compared to existing methods.

stat.ME↗

arXiv2025

Rescuing double robustness: safe estimation under complete misspecification

Double robustness is a major selling point of semiparametric and missing data methodology. Its virtues lie in protection against partial nuisance misspecification and asymptotic semiparametric efficiency under correct nuisance specification. However, in many applications, complete nuisance misspecification should be regarded as the norm (or at the very least the expected default), and thus doubly robust estimators may behave fragilely. In fact, it has been amply verified empirically that these estimators can perform poorly when all nuisance functions are misspecified. Here, we first characterize this phenomenon of double fragility, and then propose a solution based on adaptive correction clipping (DR+ACC). We argue that our DR+ACC proposal is safe, in that it inherits the favorable properties of doubly robust estimators under correct nuisance specification, but its error is guaranteed to be bounded by a convex combination of the individual nuisance model errors, which prevents the instability caused by the compounding product of errors of doubly robust estimators. We also show that our proposal comes with no reduction in semiparametric efficiency compared to doubly robust estimators, and thus valid inference based on asymptotic normality can be conducted when nuisances are well-specified. We showcase the efficacy of our DR+ACC estimator both through extensive simulations and by applying it to the analysis of Alzheimer's disease proteomics data.

stat.ME↗

arXiv2025

Global p-Values in Multi-Design Studies

Replicability issues -- referring to the difficulty or failure of independent researchers to corroborate the results of published studies -- have hindered the meaningful progression of science and eroded public trust in scientific findings. In response to the replicability crisis, one approach is the use of multi-design studies, which incorporate multiple analysis strategies to address a single research question. However, there remains a lack of methods for effectively combining outcomes in multi-design studies. In this paper, we propose a unified framework based on the g-value, for global p-value, which enables meaningful aggregation of outcomes from all the considered analysis strategies in multi-design studies. Our framework mitigates the risk of selective reporting while rigorously controlling type I error rates. At the same time, it maintains statistical power and reduces the likelihood of overlooking true positive effects. Importantly, our method is flexible and broadly applicable across various scientific domains and outcome results.

stat.ME↗

arXiv2025

Doubly-Robust Functional Average Treatment Effect Estimation

Understanding causal relationships in the presence of complex, structured data remains a central challenge in modern statistics and science in general. While traditional causal inference methods are well-suited for scalar outcomes, many scientific applications demand tools capable of handling functional data -- outcomes observed as functions over continuous domains such as time or space. Motivated by this need, we propose DR-FoS, a novel method for estimating the Functional Average Treatment Effect (FATE) in observational studies with functional outcomes. DR-FoS exhibits double robustness properties, ensuring consistent estimation of FATE even if either the outcome or the treatment assignment model is misspecified. By leveraging recent advances in functional data analysis and causal inference, we establish the asymptotic properties of the estimator, proving its convergence to a Gaussian process. This guarantees valid inference with simultaneous confidence bands across the entire functional domain. Through extensive simulations, we show that DR-FoS achieves robust performance under a wide range of model specifications. Finally, we illustrate the utility of DR-FoS in a real-world application, analyzing functional outcomes to uncover meaningful causal insights in the SHARE ({\em Survey of Health, Aging and Retirement in Europe}) dataset.

stat.ME↗

arXiv2024

ARMAr-LASSO: Mitigating the Impact of Predictor Serial Correlation on the LASSO

We explore estimation and forecast accuracy for sparse linear models, focusing on scenarios where both predictors and errors carry serial correlations. We establish a clear link between predictor serial correlation and the performance of the LASSO, showing that even orthogonal or weakly correlated stationary AR processes can lead to significant spurious correlations due to their serial correlations. To address this challenge, we propose a novel approach named ARMAr-LASSO ({\em ARMA residuals LASSO}), which applies the LASSO to predictors that have been pre-whitened with ARMA filters and lags of dependent variable. We derive both asymptotic results and oracle inequalities for the ARMAr-LASSO, demonstrating that it effectively reduces estimation errors while also providing an effective forecasting and feature selection strategy. Our findings are supported by extensive simulations and an application to real-world macroeconomic data, which highlight the superior performance of the ARMAr-LASSO for handling sparse linear models in the context of time series.

math.ST↗

arXiv2024

Accurate and fast anomaly detection in industrial processes and IoT environments

We present a novel, simple and widely applicable semi-supervised procedure for anomaly detection in industrial and IoT environments, SAnD (Simple Anomaly Detection). SAnD comprises 5 steps, each leveraging well-known statistical tools, namely; smoothing filters, variance inflation factors, the Mahalanobis distance, threshold selection algorithms and feature importance techniques. To our knowledge, SAnD is the first procedure that integrates these tools to identify anomalies and help decipher their putative causes. We show how each step contributes to tackling technical challenges that practitioners face when detecting anomalies in industrial contexts, where signals can be highly multicollinear, have unknown distributions, and intertwine short-lived noise with the long(er)-lived actual anomalies. The development of SAnD was motivated by a concrete case study from our industrial partner, which we use here to show its effectiveness. We also evaluate the performance of SAnD by comparing it with a selection of semi-supervised methods on public datasets from the literature on anomaly detection. We conclude that SAnD is effective, broadly applicable, and outperforms existing approaches in both anomaly detection and runtime.

cs.LG↗

arXiv2024

White-box validation of quantitative product lines by statistical model checking and process mining

We propose a novel methodology for validating software product line (PL) models by integrating Statistical Model Checking (SMC) with Process Mining (PM). Our approach focuses on the feature-oriented language QFLan in the PL engineering domain, allowing modeling of PLs with rich cross-tree and quantitative constraints, as well as aspects of dynamic PLs like staged configurations. This richness leads to models with infinite state-space, requiring simulation-based analysis techniques like SMC. For instance, we illustrate with a running example involving infinite state space. SMC involves generating samples of system dynamics to estimate properties such as event probabilities or expected values. On the other hand, PM uses data-driven techniques on execution logs to identify and reason about the underlying execution process. In this paper, we propose, for the first time, applying PM techniques to SMC simulations' byproducts to enhance the utility of SMC analyses. Typically, when SMC results are unexpected, modelers must determine whether they stem from actual system characteristics or model bugs in a black-box manner. We improve on this by using PM to provide a white-box perspective on the observed system dynamics. Samples from SMC are fed into PM tools, producing a compact graphical representation of observed dynamics. The mined PM model is then transformed into a QFLan model, accessible to PL engineers. Using two well-known PL models, we demonstrate the effectiveness and scalability of our methodology in pinpointing issues and suggesting fixes. Additionally, we show its generality by applying it to the security domain.

cs.SE↗

arXiv2023

An efficient approach to characterize spatio-temporal dependence in cortical surface fMRI data

Functional magnetic resonance imaging (fMRI) is a neuroimaging technique known for its ability to capture brain activity non-invasively and at fine spatial resolution (2-3mm). Cortical surface fMRI (cs-fMRI) is a recent development of fMRI that focuses on signals from tissues that have neuronal activities, as opposed to the whole brain. cs-fMRI data is plagued with non-stationary spatial correlations and long temporal dependence which, if inadequately accounted for, can hinder downstream statistical analyses. We propose a fully integrated approach that captures both spatial non-stationarity and varying ranges of temporal dependence across regions of interest. More specifically, we impose non-stationary spatial priors on the latent activation fields and model temporal dependence via fractional Gaussian errors of varying Hurst parameters, which can be studied through a wavelet transformation and its coefficients' variances at different scales. We demonstrate the performance of our proposed approach through simulations and an application to a visual working memory task cs-fMRI dataset.

stat.AP↗

arXiv2023

Automated and Distributed Statistical Analysis of Economic Agent-Based Models

We propose a novel approach to the statistical analysis of stochastic simulation models and, especially, agent-based models (ABMs). Our main goal is to provide fully automated, model-independent and tool-supported techniques and algorithms to inspect simulations and perform counterfactual analysis. Our approach: (i) is easy-to-use by the modeller, (ii) improves reproducibility of results, (iii) optimizes running time given the modeller's machine, (iv) automatically chooses the number of required simulations and simulation steps to reach user-specified statistical confidence, and (v) automates a variety of statistical tests. In particular, our techniques are designed to distinguish the transient dynamics of the model from its steady-state behaviour (if any), estimate properties in both 'phases', and provide indications on the (non-)ergodic nature of the simulated processes - which, in turn, allows one to gauge the reliability of a steady-state analysis. Estimates are equipped with statistical guarantees, allowing for robust comparisons across computational experiments. To demonstrate the effectiveness of our approach, we apply it to two models from the literature: a large-scale macro-financial ABM and a small scale prediction market model. Compared to prior analyses of these models, we obtain new insights and we are able to identify and fix some erroneous conclusions.

econ.GN↗

arXiv2023

Contrasting pre-vaccine COVID-19 waves in Italy through Functional Data Analysis

We use data from 107 Italian provinces to characterize and compare mortality patterns in the first two COVID-19 epidemic waves, which occurred prior to the introduction of vaccines. We also associate these patterns with mobility, timing of government restrictions, and socio-demographic, infrastructural, and environmental covariates. Notwithstanding limitations in the accuracy and reliability of publicly available data, we are able to exploit information in curves and shapes through Functional Data Analysis techniques. Specifically, we document differences in magnitude and variability between the two waves; while both were characterized by a co-occurrence of 'exponential' and 'mild' mortality patterns, the second spread much more broadly and asynchronously through the country. Moreover, we find evidence of a significant positive association between local mobility and mortality in both epidemic waves and corroborate the effectiveness of timely restrictions in curbing mortality. The techniques we describe could capture additional signals of interest if applied, for instance, to data on cases and positivity rates. However, we show that the quality of such data, at least in the case of Italian provinces, was too poor to support meaningful analyses.

stat.AP↗

arXiv2023

smoothEM: a new approach for the simultaneous assessment of smooth patterns and spikes

We consider functional data where an underlying smooth curve is composed not just with errors, but also with irregular spikes. We propose an approach that, combining regularized spline smoothing and an Expectation-Maximization algorithm, allows one to both identify spikes and estimate the smooth component. Imposing some assumptions on the error distribution, we prove consistency of EM estimates. Next, we demonstrate the performance of our proposal on finite samples and its robustness to assumptions violations through simulations. Finally, we apply our proposal to data on the annual heatwaves index in the US and on weekly electricity consumption in Ireland. In both datasets, we are able to characterize underlying smooth trends and to pinpoint irregular/extreme behaviors.

stat.ME↗

arXiv2023

funBIalign: a hierachical algorithm for functional motif discovery based on mean squared residue scores

Motif discovery is gaining increasing attention in the domain of functional data analysis. Functional motifs are typical "shapes" or "patterns" that recur multiple times in different portions of a single curve and/or in misaligned portions of multiple curves. In this paper, we define functional motifs using an additive model and we propose funBIalign for their discovery and evaluation. Inspired by clustering and biclustering techniques, funBIalign is a multi-step procedure which uses agglomerative hierarchical clustering with complete linkage and a functional distance based on mean squared residue scores to discover functional motifs, both in a single curve (e.g., time series) and in a set of curves. We assess its performance and compare it to other recent methods through extensive simulations. Moreover, we use funBIalign for discovering motifs in two real-data case studies; one on food price inflation and one on temperature changes.

stat.ME↗

arXiv2023

FAStEN: An Efficient Adaptive Method for Feature Selection and Estimation in High-Dimensional Functional Regressions

Functional regression analysis is an established tool for many contemporary scientific applications. Regression problems involving large and complex data sets are ubiquitous, and feature selection is crucial for avoiding overfitting and achieving accurate predictions. We propose a new, flexible and ultra-efficient approach to perform feature selection in a sparse high dimensional function-on-function regression problem, and we show how to extend it to the scalar-on-function framework. Our method, called FAStEN, combines functional data, optimization, and machine learning techniques to perform feature selection and parameter estimation simultaneously. We exploit the properties of Functional Principal Components and the sparsity inherent to the Dual Augmented Lagrangian problem to significantly reduce computational cost, and we introduce an adaptive scheme to improve selection accuracy. In addition, we derive asymptotic oracle properties, which guarantee estimation and selection consistency for the proposed FAStEN estimator. Through an extensive simulation study, we benchmark our approach to the best existing competitors and demonstrate a massive gain in terms of CPU time and selection performance, without sacrificing the quality of the coefficients' estimation. The theoretical derivations and the simulation study provide a strong motivation for our approach. Finally, we present an application to brain fMRI data from the AOMIC PIOP1 study. Complete FAStEN code is provided at https://github.com/IBM/funGCN.

stat.ME↗

arXiv2023

On the Impact of Serial Dependence on Penalized Regression Methods

This paper characterizes the impact of covariate serial dependence on the non-asymptotic estimation error bound of penalized regressions (PRs). Focusing on the direct relationship between the degree of cross-correlation between covariates and the estimation error bound of PRs, we show that orthogonal or weakly cross-correlated stationary AR processes can exhibit high spurious correlations caused by serial dependence. We provide analytical results on the distribution of the sample cross-correlation in the case of two orthogonal Gaussian AR(1) processes, and extend and validate them through an extensive simulation study. Furthermore, we introduce a new procedure to mitigate spurious correlations in a time series setting, applying PRs to pre-whitened (ARMA filtered) time series. We show that under mild assumptions our procedure allows both to reduce the estimation error and to develop an effective forecasting strategy. The estimation accuracy of our proposal is validated through additional simulations, as well as an empirical application to a large set of monthly macroeconomic time series relative to the Euro Area.

math.ST↗