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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.

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.

The increase of legislative concerns towards the usage of Artificial Intelligence (AI) has recently led to a series of regulations striving for a more transparent, trustworthy and accountable AI. Along with these proposals, the field of Explainable AI (XAI) has seen a rapid growth but the usage of its techniques has at times led to unexpected results. The robustness of the approaches is, in fact, a key property often overlooked: it is necessary to evaluate the stability of an explanation (to random and adversarial perturbations) to ensure that the results are trustable. To this end, we propose a test to evaluate the robustness to non-adversarial perturbations and an ensemble approach to analyse more in depth the robustness of XAI methods applied to neural networks and tabular datasets. We will show how leveraging manifold hypothesis and ensemble approaches can be beneficial to an in-depth analysis of the robustness., Comment: 8 pages, 3 figures

We show that every Jordan quadrilateral $Q\subset\mathbb{C}$ contains a disk $D$ so that $\partial D\cap\partial Q$ contains points of three different sides of $Q$. As a consequence, together with some modulus estimates from Lehto and Virtanen, we offer a short proof of the main result obtained by Chrontsios-Garitsis and Hinkkanen in 2024 and it also improves the bounds on their result., Comment: 9 pages, 5 figures

The use of computer simulations to study the properties of aqueous systems is, today more than ever, an active area of research. In this context, during the last decade there has been a tremendous growth in the use of data-driven approaches to develop more accurate potentials for water as well as to characterize its complexity in chemical and biological contexts. We highlight the progress, giving a historical context, on the path to the development of many-body and reactive potentials to model aqueous chemistry, including the role of machine learning strategies. We focus specifically on conceptual and methodological challenges along the way in performing simulations that seek to tackle problems in modeling the chemistry of aqueous solutions. In conclusion, we summarize our perspectives on the use and integration of advanced data-science techniques to provide chemical insights in physical chemistry and how this will influence computer simulations of aqueous systems in the future., Comment: 37 Pages. 7 Figures. Submitted to Chemical Physics Reviews

The presence of a second critical point in water has been a topic of intense investigation for the last few decades. The molecular origins underlying this phenomenon are typically rationalized in terms of the competition between local high-density (HD) and low-density (LD) structures. Their identification often require designing parameters that are subject to human intervention. Herein, we use unsupervised learning to discover structures in atomistic simulations of water close to the Liquid-Liquid Critical point (LLCP). Encoding the information of the environment using local descriptors, we do not find evidence for two distinct thermodynamic structures. In contrast, when we deploy non-local descriptors that probe instead heterogeneities on the nanometer length scale, this leads to the emergence of LD and HD domains rationalizing the microscopic origins of the density fluctuations close to criticality.

Optimizing the probability of quantum tunneling between two states, while keeping the resources of the underlying physical system constant, is a task of key importance due to its critical role in various applications. We show that, by applying Machine Learning techniques when the system is coupled to an ancilla, one optimizes the parameters of both the ancillary component and the coupling, ultimately resulting in the maximization of the tunneling probability. We provide illustrative examples for the paradigmatic scenario involving a two-mode system and a two-mode ancilla in the presence of several interacting particles. Physically, the increase of the tunneling probability is rooted in the decrease of the two-well asymmetry due to the coherent oscillations induced by the coupling to the ancilla. We also argue that the enhancement of the tunneling probability is not hampered by weak coupling to noisy environments., Comment: Added new results, moved calculations in supplemetary and methods. arXiv admin note: substantial text overlap with arXiv:2308.06060

The structure of the excess proton in liquid water has been the subject of lively debate from both experimental and theoretical fronts for the last century. Fluctuations of the proton are typically interpreted in terms of limiting states referred to as the Eigen and Zundel species. Here we put these ideas under the microscope taking advantage of recent advances in unsupervised learning that use local atomic descriptors to characterize environments of acidic water combined with advanced clustering techniques. Our agnostic approach leads to the observation of only a single charged cluster and two neutral ones. We demonstrate that the charged cluster involving the excess proton, is best seen as an ionic topological defect in water's hydrogen bond network forming a single local minimum on the global free-energy landscape. This charged defect is a highly fluxional moiety where the idealized Eigen and Zundel species are neither limiting configurations nor distinct thermodynamic states. Instead, the ionic defect enhances the presence of neutral water defects through strong interactions with the network. We dub the combination of the charged and neutral defect clusters as ZundEig demonstrating that the fluctuations between these local environments provide a general framework for rationalizing more descriptive notions of the proton in the existing literature.

We provide and critically analyze a framework to learn critical behavior in classical partition functions through the application of non-parametric methods to data sets of thermal configurations. We illustrate our approach in phase transitions in 2D and 3D Ising models. First, we extend previous studies on the intrinsic dimension of 2D partition function data sets, by exploring the effect of volume in 3D Ising data. We find that as opposed to 2D systems for which this quantity has been successfully used in unsupervised characterizations of critical phenomena, in the 3D case its estimation is far more challenging. To circumvent this limitation, we then use the principal component analysis (PCA) entropy, a "Shannon entropy" of the normalized spectrum of the covariance matrix. We find a striking qualitative similarity to the thermodynamic entropy, which the PCA entropy approaches asymptotically. The latter allows us to extract -- through a conventional finite-size scaling analysis with modest lattice sizes -- the critical temperature with less than $1\%$ error for both 2D and 3D models while being computationally efficient. The PCA entropy can readily be applied to characterize correlations and critical phenomena in a huge variety of many-body problems and suggests a (direct) link between easy-to-compute quantities and entropies., Comment: 20 pages, 10 figures, Submission to SciPost. Comments are welcome

Network science provides very powerful tools for extracting information from interacting data. Although recently the unsupervised detection of phases of matter using machine learning has raised significant interest, the full prediction power of network science has not yet been systematically explored in this context. Here we fill this gap by providing an in-depth statistical, combinatorial, geometrical and topological characterization of 2D Ising snapshot networks (IsingNets) extracted from Monte Carlo simulations of the $2$D Ising model at different temperatures, going across the phase transition. Our analysis reveals the complex organization properties of IsingNets in both the ferromagnetic and paramagnetic phases and demonstrates the significant deviations of the IsingNets with respect to randomized null models. In particular percolation properties of the IsingNets reflect the existence of the symmetry between configurations with opposite magnetization below the critical temperature and the very compact nature of the two emerging giant clusters revealed by our persistent homology analysis of the IsingNets. Moreover, the IsingNets display a very broad degree distribution and significant degree-degree correlations and weight-degree correlations demonstrating that they encode relevant information present in the configuration space of the $2$D Ising model. The geometrical organization of the critical IsingNets is reflected in their spectral properties deviating from the one of the null model. This work reveals the important insights that network science can bring to the characterization of phases of matter. The set of tools described hereby can be applied as well to numerical and experimental data., Comment: 17 pages, 18 figures

Given the key role that quantum tunneling plays in a wide range of applications, a crucial objective is to maximize the probability of tunneling from one quantum state/level to another, while keeping the resources of the underlying physical system fixed. In this work, we demonstrate that an effective solution to this challenge can be achieved by coupling the tunneling system with an ancillary system of the same kind. By utilizing machine learning techniques, the parameters of both the ancillary system and the coupling can be optimized, leading to the maximization of the tunneling probability. We provide illustrative examples for the paradigmatic scenario involving a two-mode system and a two-mode ancilla with arbitrary couplings and in the presence of several interacting particles. Importantly, the enhancement of the tunneling probability appears to be minimally affected by noise and decoherence in both the system and the ancilla., Comment: Submitted

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 relation between these perturbations and the implicit bias of neural networks trained with gradient-based algorithms. To this end, we analyse the network's implicit bias through the lens of the Fourier transform. Specifically, we identify the minimal and most critical frequencies necessary for accurate classification or misclassification respectively for each input image and its adversarially perturbed version, and uncover the correlation among those. To this end, among other methods, we use a newly introduced technique capable of detecting non-linear 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.

Topology plays a fundamental role in our understanding of many-body physics, from vortices and solitons in classical field theory, to phases and excitations in quantum matter. Topological phenomena are intimately connected to the distribution of information content - that, differently from ordinary matter, is now governed by non-local degrees of freedom. However, a precise characterization of how topological effects govern the complexity of a many-body state - i.e., its partition function - is presently unclear. In this work, we show how topology and complexity are directly intertwined concepts in the context of classical statistical mechanics. In concrete, we present a theory that shows how the Kolmogorov complexity of a classical partition function sampling carries unique, distinctive features depending on the presence of topological excitations in the system. We confront two-dimensional Ising, Heisenberg, and XY models on several topologies and study the corresponding samplings as high-dimensional manifolds in configuration space, quantifying their complexity via the intrinsic dimension. While for the Ising and Heisenberg models the intrinsic dimension is independent of the real-space topology, for the XY model it depends crucially on temperature: across the Berezkinskii-Kosterlitz-Thouless (BKT) transition, complexity becomes topology dependent. In the BKT phase, it displays a characteristic dependence on the homology of the real-space manifold, and, for $g$-torii, it follows a scaling that is solely genus dependent. We argue that this behavior is intimately connected to the emergence of an order parameter in data space, the conditional connectivity, that displays scaling behavior., Comment: 12 pages, 8 figures

We study the Hamiltonian dynamics of a many-body quantum system subjected to periodic projective measurements which leads to probabilistic cellular automata dynamics. Given a sequence of measured values, we characterize their dynamics by performing a principal component analysis. The number of principal components required for an almost complete description of the system, which is a measure of complexity we refer to as PCA complexity, is studied as a function of the Hamiltonian parameters and measurement intervals. We consider different Hamiltonians that describe interacting, non-interacting, integrable, and non-integrable systems, including random local Hamiltonians and translational invariant random local Hamiltonians. In all these scenarios, we find that the PCA complexity grows rapidly in time before approaching a plateau. The dynamics of the PCA complexity can vary quantitatively and qualitatively as a function of the Hamiltonian parameters and measurement protocol. Importantly, the dynamics of PCA complexity present behavior that is considerably less sensitive to the specific system parameters for models which lack simple local dynamics, as is often the case in non-integrable models. In particular, we point out a figure of merit that considers the local dynamics and the measurement direction to predict the sensitivity of the PCA complexity dynamics to the system parameters., Comment: 9 pages, 8 figures

Billions of people remain without Internet access due to availability or affordability of service. In this paper, we present Magma, an open and flexible system for building low-cost wireless access networks. Magma aims to connect users where operator economics are difficult due to issues such as low population density or income levels, while preserving features expected in cellular networks such as authentication and billing policies. To achieve this, and in contrast to traditional cellular networks, Magma adopts an approach that extensively leverages Internet design patterns, terminating access network-specific protocols at the edge and abstracting the access network from the core architecture. This decision allows Magma to refactor the wireless core using SDN (software-defined networking) principles and leverage other techniques from modern distributed systems. In doing so, Magma lowers cost and operational complexity for network operators while achieving resilience, scalability, and rich policy support., Comment: 15 pages, 10 figures, to be published in the 20th USENIX Symposium on Networked Systems Design and Implementation (2023), source code available at https://github.com/magma/magma

Understanding the microscopic origins of collective reorientational motions in aqueous systems requires techniques that allow us to reach beyond our chemical imagination. Herein, we elucidate a mechanism using unsupervised learning, showing that large angular jumps in liquid water involve highly cooperative orchestrated motions. Our automatized detection of angular fluctuations, unravels a heterogeneity in the type of angular jumps occurring concertedly in the system. We show that large orientational motions require a highly collective dynamic process involving correlated motion of up to 10% of water molecules in the hydrogen-bond network that form spatially connected clusters. This phenomenon is rooted in the collective fluctuations of the network topology which results in the creation of defects in waves on the ThZ timescale. The mechanism we propose involves a cascade of hydrogen-bond fluctuations underlying angular jumps and provides new insights into the current localized picture of angular jumps, and in its wide use in the interpretations of numerous spectroscopies as well in reorientational dynamics of water near biological and inorganic systems., Comment: 12 pages, 7 figures, Supplementary Information as ancillary file

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., Comment: 9 pages, 6 figures. Patterns (2022)

The microscopic description of the local structure of water remains an open challenge. Here, we adopt an agnostic approach to understanding water's hydrogen bond network using data harvested from molecular dynamics simulations of an empirical water model. A battery of state-of-the-art unsupervised data-science techniques are used to characterize the free energy landscape of water starting from encoding the water environment using local-atomic descriptors, through dimensionality reduction and finally the use of advanced clustering techniques. Analysis of the free energy at ambient conditions was found to be consistent with a rough single basin and independent of the choice of the water model. We find that the fluctuations of the water network occur in a high-dimensional space which we characterize using a combination of both atomic descriptors and chemical-intuition based coordinates. We demonstrate that a combination of both types of variables are needed in order to adequately capture the complexity of the fluctuations in the hydrogen bond network at different length-scales both at room temperature and also close to the critical point of water. Our results provide a general framework for examining fluctuations in water under different conditions., Comment: 41+8 pages, 10+11 figures

Quantum many-body systems are characterized by patterns of correlations that define highly-non trivial manifolds when interpreted as data structures. Physical properties of phases and phase transitions are typically retrieved via simple correlation functions, that are related to observable response functions. Recent experiments have demonstrated capabilities to fully characterize quantum many-body systems via wave-function snapshots, opening new possibilities to analyze quantum phenomena. Here, we introduce a method to data mine the correlation structure of quantum partition functions via their path integral (or equivalently, stochastic series expansion) manifold. We characterize path-integral manifolds generated via state-of-the-art Quantum Monte Carlo methods utilizing the intrinsic dimension (ID) and the variance of distances from nearest neighbors (NN): the former is related to dataset complexity, while the latter is able to diagnose connectivity features of points in configuration space. We show how these properties feature universal patterns in the vicinity of quantum criticality, that reveal how data structures {\it simplify} systematically at quantum phase transitions. This is further reflected by the fact that both ID and variance of NN-distances exhibit universal scaling behavior in the vicinity of second-order and Berezinskii-Kosterlitz-Thouless critical points. Finally, we show how non-Abelian symmetries dramatically influence quantum data sets, due to the nature of (non-commuting) conserved charges in the quantum case. Complementary to neural network representations, our approach represents a first, elementary step towards a systematic characterization of path integral manifolds before any dimensional reduction is taken, that is informative about universal behavior and complexity, and can find immediate application to both experiments and Monte Carlo simulations., Comment: 19 pages, 13 figures, version accepted for publication in Phys. Rev. X Quantum

The identification of universal properties from minimally processed data sets is one goal of machine learning techniques applied to statistical physics. Here, we study how the minimum number of variables needed to accurately describe the important features of a data set - the intrinsic dimension ($I_d$) - behaves in the vicinity of phase transitions. We employ state-of-the-art nearest neighbors-based $I_d$-estimators to compute the $I_d$ of raw Monte Carlo thermal configurations across different phase transitions: first-, second-order and Berezinskii-Kosterlitz-Thouless. For all the considered cases, we find that the $I_d$ uniquely characterizes the transition regime. The finite-size analysis of the $I_d$ allows not just to identify critical points with an accuracy comparable with methods that rely on {\it a priori} identification of order parameters, but also to determine the corresponding (critical) exponent $\nu$ in case of continuous transitions. For the case of topological transitions, this analysis overcomes the reported limitations affecting other unsupervised learning methods. Our work reveals how raw data sets display unique signatures of universal behavior in the absence of any dimensional reduction scheme, and suggest direct parallelism between conventional order parameters in real space, and the intrinsic dimension in the data space.

We study the focusing stochastic nonlinear Schr\"odinger equation in one spatial dimension with multiplicative noise, driven by a Wiener process white in time and colored in space, in the $L^2$-critical and supercritical cases. The mass ($L^2$-norm) is conserved due to the multiplicative noise defined via the Stratonovich integral, the energy (Hamiltonian) is not preserved. We first investigate how the energy is affected by various spatially correlated random perturbations. We then study the influence of the noise on the global dynamics measuring the probability of blow-up versus scattering behavior depending on various parameters of correlation kernels. Finally, we study the effect of the spatially correlated noise on the blow-up behavior, and conclude that such random perturbations do not influence the blow-up dynamics, except for shifting of the blow-up center location. This is similar to what we observed in [32] for a space-time white driving noise.

The process of RNA base fraying (i.e. the transient opening of the termini of a helix) is involved in many aspects of RNA dynamics. We here use molecular dynamics simulations and Markov state models to characterize the kinetics of RNA fraying and its sequence and direction dependence. In particular, we first introduce a method for determining biomolecular dynamics employing core-set Markov state models constructed using an advanced clustering technique. The method is validated on previously reported simulations. We then use the method to analyze extensive trajectories for four different RNA model duplexes. Results obtained using D. E. Shaw research and AMBER force fields are compared and discussed in detail, and show a non-trivial interplay between the stability of intermediate states and the overall fraying kinetics., Comment: Supporting information included in ancillary files

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., Comment: Scientific Reports 2017

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., Comment: There is a Supplementary Information document in the ancillary files folder