Álex Rodríguez

Aldo Glielmo, Iuri Macocco, Diego Doimo et al.

DADApy is a python software package for analysing and characterising high-dimensional data manifolds. It provides methods for estimating the intrinsic dimension and the probability density, for performing density-based clustering and for comparing different distance metrics. We review the main functionalities of the package and exemplify its usage in toy cases and in a real-world application. DADApy is freely available under the open-source Apache 2.0 license.

Matteo Carli, Alex Rodriguez, Alessandro Laio et al.

We introduce the Binless Multidimensional Thermodynamic Integration (BMTI) method for nonparametric, robust, and data-efficient density estimation. BMTI estimates the logarithm of the density by initially computing log-density differences between neighbouring data points. Subsequently, such differences are integrated, weighted by their associated uncertainties, using a maximum-likelihood formulation. This procedure can be seen as an extension to a multidimensional setting of the thermodynamic integration, a technique developed in statistical physics. The method leverages the manifold hypothesis, estimating quantities within the intrinsic data manifold without defining an explicit coordinate map. It does not rely on any binning or space partitioning, but rather on the construction of a neighbourhood graph based on an adaptive bandwidth selection procedure. BMTI mitigates the limitations commonly associated with traditional nonparametric density estimators, effectively reconstructing smooth profiles even in high-dimensional embedding spaces. The method is tested on a variety of complex synthetic high-dimensional datasets, where it is shown to outperform traditional estimators, and is benchmarked on realistic datasets from the chemical physics literature.

Michele Alessi, Alessio Ansuini, Alex Rodriguez

We introduce Density-Informed VAE (DiVAE), a lightweight, data-driven regularizer that aligns the VAE log-prior probability $\log p_Z(z)$ with a log-density estimated from data. Standard VAEs match latents to a simple prior, overlooking density structure in the data-space. DiVAE encourages the encoder to allocate posterior mass in proportion to data-space density and, when the prior is learnable, nudges the prior toward high-density regions. This is realized by adding a robust, precision-weighted penalty to the ELBO, incurring negligible computational overhead. On synthetic datasets, DiVAE (i) improves distributional alignment of latent log-densities to its ground truth counterpart, (ii) improves prior coverage, and (iii) yields better OOD uncertainty calibration. On MNIST, DiVAE improves alignment of the prior with external estimates of the density, providing better interpretability, and improves OOD detection for learnable priors.

Santiago Acevedo, Alex Rodriguez, Alessandro Laio

In real-world data, information is stored in extremely large feature vectors. These variables are typically correlated due to complex interactions involving many features simultaneously. Such correlations qualitatively correspond to semantic roles and are naturally recognized by both the human brain and artificial neural networks. This recognition enables, for instance, the prediction of missing parts of an image or text based on their context. We present a method to detect these correlations in high-dimensional data represented as binary numbers. We estimate the binary intrinsic dimension of a dataset, which quantifies the minimum number of independent coordinates needed to describe the data, and is therefore a proxy of semantic complexity. The proposed algorithm is largely insensitive to the so-called curse of dimensionality, and can therefore be used in big data analysis. We test this approach identifying phase transitions in model magnetic systems and we then apply it to the detection of semantic correlations of images and text inside deep neural networks.

Lorenzo Basile, Santiago Acevedo, Luca Bortolussi et al.

To gain insight into the mechanisms behind machine learning methods, it is crucial to establish connections among the features describing data points. However, these correlations often exhibit a high-dimensional and strongly nonlinear nature, which makes them challenging to detect using standard methods. This paper exploits the entanglement between intrinsic dimensionality and correlation to propose a metric that quantifies the (potentially nonlinear) correlation between high-dimensional manifolds. We first validate our method on synthetic data in controlled environments, showcasing its advantages and drawbacks compared to existing techniques. Subsequently, we extend our analysis to large-scale applications in neural network representations. Specifically, we focus on latent representations of multimodal data, uncovering clear correlations between paired visual and textual embeddings, whereas existing methods struggle significantly in detecting similarity. Our results indicate the presence of highly nonlinear correlation patterns between latent manifolds.

Lorenzo Basile, Nikos Karantzas, Alberto d'Onofrio et al.

Despite their impressive performance in classification tasks, neural networks are known to be vulnerable to adversarial attacks, subtle perturbations of the input data designed to deceive the model. In this work, we investigate the correlation between these perturbations and the implicit bias of neural networks trained with gradient-based algorithms. To this end, we analyse a representation of the network's implicit bias through the lens of the Fourier transform. Specifically, we identify unique fingerprints of implicit bias and adversarial attacks by calculating the minimal, essential frequencies needed for accurate classification of each image, as well as the frequencies that drive misclassification in its adversarially perturbed counterpart. This approach enables us to uncover and analyse the correlation between these essential frequencies, providing a precise map of how the network's biases align or contrast with the frequency components exploited by adversarial attacks. To this end, among other methods, we use a newly introduced technique capable of detecting nonlinear correlations between high-dimensional datasets. Our results provide empirical evidence that the network bias in Fourier space and the target frequencies of adversarial attacks are highly correlated and suggest new potential strategies for adversarial defence.

Elena Facco, Maria d'Errico, Alex Rodriguez et al.

Analyzing large volumes of high-dimensional data is an issue of fundamental importance in data science, molecular simulations and beyond. Several approaches work on the assumption that the important content of a dataset belongs to a manifold whose Intrinsic Dimension (ID) is much lower than the crude large number of coordinates. Such manifold is generally twisted and curved, in addition points on it will be non-uniformly distributed: two factors that make the identification of the ID and its exploitation really hard. Here we propose a new ID estimator using only the distance of the first and the second nearest neighbor of each point in the sample. This extreme minimality enables us to reduce the effects of curvature, of density variation, and the resulting computational cost. The ID estimator is theoretically exact in uniformly distributed datasets, and provides consistent measures in general. When used in combination with block analysis, it allows discriminating the relevant dimensions as a function of the block size. This allows estimating the ID even when the data lie on a manifold perturbed by a high-dimensional noise, a situation often encountered in real world data sets. We demonstrate the usefulness of the approach on molecular simulations and image analysis.

Maria d'Errico, Elena Facco, Alessandro Laio et al.

Data analysis in high-dimensional spaces aims at obtaining a synthetic description of a data set, revealing its main structure and its salient features. We here introduce an approach providing this description in the form of a topography of the data, namely a human-readable chart of the probability density from which the data are harvested. The approach is based on an unsupervised extension of Density Peak clustering and a non-parametric density estimator that measures the probability density in the manifold containing the data. This allows finding automatically the number and the height of the peaks of the probability density, and the depth of the "valleys" separating them. Importantly, the density estimator provides a measure of the error, which allows distinguishing genuine density peaks from density fluctuations due to finite sampling. The approach thus provides robust and visual information about the density peaks' height, their statistical reliability, and their hierarchical organization, offering a conceptually powerful extension of the standard clustering partitions. We show that this framework is particularly useful in the analysis of complex data sets.