Antonietta Mira

Antonio Di Noia, Iuri Macocco, Aldo Glielmo et al. · eth-zurich

The Intrinsic Dimension (ID) is a key concept in unsupervised learning and feature selection, as it is a lower bound to the number of variables which are necessary to describe a system. However, in almost any real-world dataset the ID depends on the scale at which the data are analysed. Quite typically at a small scale, the ID is very large, as the data are affected by measurement errors. At large scale, the ID can also appear erroneously large, due to the curvature and the topology of the manifold containing the data. In this work, we introduce an automatic protocol to select the sweet spot, namely the correct range of scales in which the ID is meaningful and useful. This protocol is based on imposing that for distances smaller than the correct scale the density of the data is constant. In the presented framework, to estimate the density it is necessary to know the ID, therefore, this condition is imposed self-consistently. We illustrate the usefulness and robustness of this procedure to noise by benchmarks on artificial and real-world datasets.

Simon Dirmeier, Simone Ulzega, Antonietta Mira et al.

Neural simulation-based inference (SBI) describes an emerging family of methods for Bayesian inference with intractable likelihood functions that use neural networks as surrogate models. Here we introduce sbijax, a Python package that implements a wide variety of state-of-the-art methods in neural simulation-based inference using a user-friendly programming interface. sbijax offers high-level functionality to quickly construct SBI estimators, and compute and visualize posterior distributions with only a few lines of code. In addition, the package provides functionality for conventional approximate Bayesian computation, to compute model diagnostics, and to automatically estimate summary statistics. By virtue of being entirely written in JAX, sbijax is extremely computationally efficient, allowing rapid training of neural networks and executing code automatically in parallel on both CPU and GPU.

Antonio Di Noia, Federico Ravenda, Antonietta Mira

Dimensionality reduction is a fundamental task in modern data science. Several projection methods specifically tailored to take into account the non-linearity of the data via local embeddings have been proposed. Such methods are often based on local neighbourhood structures and require tuning the number of neighbours that define this local structure, and the dimensionality of the lower-dimensional space onto which the data are projected. Such choices critically influence the quality of the resulting embedding. In this paper, we exploit a recently proposed intrinsic dimension estimator which also returns the optimal locally adaptive neighbourhood sizes according to some desirable criteria. In principle, this adaptive framework can be employed to perform an optimal hyper-parameter tuning of any dimensionality reduction algorithm that relies on local neighbourhood structures. Numerical experiments on both real-world and simulated datasets show that the proposed method can be used to significantly improve well-known projection methods when employed for various learning tasks, with improvements measurable through both quantitative metrics and the quality of low-dimensional visualizations.

Federico Ravenda, Seyed Ali Bahrainian, Andrea Raballo et al.

In psychological practices, standardized questionnaires serve as essential tools for assessing mental health through structured, clinically-validated questions (i.e., items). While social media platforms offer rich data for mental health screening, computational approaches often bypass these established clinical assessment tools in favor of black-box classification. We propose a novel questionnaire-guided screening framework that bridges psychological practice and computational methods through adaptive Retrieval-Augmented Generation (\textit{aRAG}). Our approach links unstructured social media content and standardized clinical assessments by retrieving relevant posts for each questionnaire item and using Large Language Models (LLMs) to complete validated psychological instruments. Our findings demonstrate two key advantages of questionnaire-guided screening: First, when completing the Beck Depression Inventory-II (BDI-II), our approach matches or outperforms state-of-the-art performance on Reddit-based benchmarks without requiring training data. Second, we show that guiding LLMs through standardized questionnaires can yield superior results compared to directly prompting them for depression screening, while also providing a more interpretable assessment by linking model outputs to clinically validated diagnostic criteria. Additionally, we show, as a proof-of-concept, how our questionnaire-based methodology can be extended to other mental conditions' screening, highlighting the promising role of LLMs as psychological assessors.

Conor Hassan, Matthew Sutton, Antonietta Mira et al.

Vertical federated learning (VFL) has emerged as a paradigm for collaborative model estimation across multiple clients, each holding a distinct set of covariates. This paper introduces the first comprehensive framework for fitting Bayesian models in the VFL setting. We propose a novel approach that leverages data augmentation techniques to transform VFL problems into a form compatible with existing Bayesian federated learning algorithms. We present an innovative model formulation for specific VFL scenarios where the joint likelihood factorizes into a product of client-specific likelihoods. To mitigate the dimensionality challenge posed by data augmentation, which scales with the number of observations and clients, we develop a factorized amortized variational approximation that achieves scalability independent of the number of observations. We showcase the efficacy of our framework through extensive numerical experiments on logistic regression, multilevel regression, and a novel hierarchical Bayesian split neural net model. Our work paves the way for privacy-preserving, decentralized Bayesian inference in vertically partitioned data scenarios, opening up new avenues for research and applications in various domains.

Federico Ravenda, Seyed Ali Bahrainian, Andrea Raballo et al.

The rapid evolution of Large Language Models (LLMs) is transforming AI, opening new opportunities in sensitive and high-impact areas such as Mental Health (MH). Yet, despite these advancements, recent evidence reveals that smaller-scale models still struggle to deliver optimal performance in domain-specific applications. In this study, we present a cost-efficient yet powerful approach to improve MH assessment capabilities of an LLM, without relying on any computationally intensive techniques. Our lightweight method consists of a linear transformation applied to a specific layer's activations, leveraging steering vectors to guide the model's output. Remarkably, this intervention enables the model to achieve improved results across two distinct tasks: (1) identifying whether a Reddit post is useful for detecting the presence or absence of depressive symptoms (relevance prediction task), and (2) completing a standardized psychological screening questionnaire for depression based on users' Reddit post history (questionnaire completion task). Results highlight the untapped potential of steering mechanisms as computationally efficient tools for LLMs' MH domain adaptation.

Simon Dirmeier, Antonietta Mira

We present Causal Posterior Estimation (CPE), a novel method for Bayesian inference in simulator models, i.e., models where the evaluation of the likelihood function is intractable or too computationally expensive, but where one can simulate model outputs given parameter values. CPE utilizes a normalizing flow-based (NF) approximation to the posterior distribution which carefully incorporates the conditional dependence structure induced by the graphical representation of the model into the neural network. Thereby it is possible to improve the accuracy of the approximation. We introduce both discrete and continuous NF architectures for CPE and propose a constant-time sampling procedure for the continuous case which reduces the computational complexity of drawing samples to O(1) as for discrete NFs. We show, through an extensive experimental evaluation, that by incorporating the conditional dependencies induced by the graphical model directly into the neural network, rather than learning them from data, CPE is able to conduct highly accurate posterior inference either outperforming or matching the state of the art in the field.

Carlo Albert, Simone Ulzega, Firat Ozdemir et al.

For stochastic models with intractable likelihood functions, approximate Bayesian computation offers a way of approximating the true posterior through repeated comparisons of observations with simulated model outputs in terms of a small set of summary statistics. These statistics need to retain the information that is relevant for constraining the parameters but cancel out the noise. They can thus be seen as thermodynamic state variables, for general stochastic models. For many scientific applications, we need strictly more summary statistics than model parameters to reach a satisfactory approximation of the posterior. Therefore, we propose to use the inner dimension of deep neural network based Autoencoders as summary statistics. To create an incentive for the encoder to encode all the parameter-related information but not the noise, we give the decoder access to explicit or implicit information on the noise that has been used to generate the training data. We validate the approach empirically on two types of stochastic models.

Ritabrata Dutta, Karim Zouaoui-Boudjeltia, Christos Kotsalos et al.

Cardio/cerebrovascular diseases (CVD) have become one of the major health issue in our societies. But recent studies show that the present pathology tests to detect CVD are ineffectual as they do not consider different stages of platelet activation or the molecular dynamics involved in platelet interactions and are incapable to consider inter-individual variability. Here we propose a stochastic platelet deposition model and an inferential scheme to estimate the biologically meaningful model parameters using approximate Bayesian computation with a summary statistic that maximally discriminates between different types of patients. Inferred parameters from data collected on healthy volunteers and different patient types help us to identify specific biological parameters and hence biological reasoning behind the dysfunction for each type of patients. This work opens up an unprecedented opportunity of personalized pathology test for CVD detection and medical treatment.

Michele Allegra, Elena Facco, Francesco Denti et al.

One of the founding paradigms of machine learning is that a small number of variables is often sufficient to describe high-dimensional data. The minimum number of variables required is called the intrinsic dimension (ID) of the data. Contrary to common intuition, there are cases where the ID varies within the same data set. This fact has been highlighted in technical discussions, but seldom exploited to analyze large data sets and obtain insight into their structure. Here we develop a robust approach to discriminate regions with different local IDs and segment the points accordingly. Our approach is computationally efficient and can be proficiently used even on large data sets. We find that many real-world data sets contain regions with widely heterogeneous dimensions. These regions host points differing in core properties: folded vs unfolded configurations in a protein molecular dynamics trajectory, active vs non-active regions in brain imaging data, and firms with different financial risk in company balance sheets. A simple topological feature, the local ID, is thus sufficient to achieve an unsupervised segmentation of high-dimensional data, complementary to the one given by clustering algorithms.

Maksym Byshkin, Alex Stivala, Antonietta Mira et al.

A major line of contemporary research on complex networks is based on the development of statistical models that specify the local motifs associated with macro-structural properties observed in actual networks. This statistical approach becomes increasingly problematic as network size increases. In the context of current research on efficient estimation of models for large network data sets, we propose a fast algorithm for maximum likelihood estimation (MLE) that afords a signifcant increase in the size of networks amenable to direct empirical analysis. The algorithm we propose in this paper relies on properties of Markov chains at equilibrium, and for this reason it is called equilibrium expectation (EE). We demonstrate the performance of the EE algorithm in the context of exponential random graphmodels (ERGMs) a family of statistical models commonly used in empirical research based on network data observed at a single period in time. Thus far, the lack of efcient computational strategies has limited the empirical scope of ERGMs to relatively small networks with a few thousand nodes. The approach we propose allows a dramatic increase in the size of networks that may be analyzed using ERGMs. This is illustrated in an analysis of several biological networks and one social network with 104,103 nodes

Ritabrata Dutta, Antonietta Mira, Jukka-Pekka Onnela

Infectious diseases are studied to understand their spreading mechanisms, to evaluate control strategies and to predict the risk and course of future outbreaks. Because people only interact with a small number of individuals, and because the structure of these interactions matters for spreading processes, the pairwise relationships between individuals in a population can be usefully represented by a network. Although the underlying processes of transmission are different, the network approach can be used to study the spread of pathogens in a contact network or the spread of rumors in an online social network. We study simulated simple and complex epidemics on synthetic networks and on two empirical networks, a social / contact network in an Indian village and an online social network in the U.S. Our goal is to learn simultaneously about the spreading process parameters and the source node (first infected node) of the epidemic, given a fixed and known network structure, and observations about state of nodes at several points in time. Our inference scheme is based on approximate Bayesian computation (ABC), an inference technique for complex models with likelihood functions that are either expensive to evaluate or analytically intractable. ABC enables us to adopt a Bayesian approach to the problem despite the posterior distribution being very complex. Our method is agnostic about the topology of the network and the nature of the spreading process. It generally performs well and, somewhat counter-intuitively, the inference problem appears to be easier on more heterogeneous network topologies, which enhances its future applicability to real-world settings where few networks have homogeneous topologies.