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Beatriz Seoane

Publications and source records attributed to Beatriz Seoane.

29 records · Page 2Linked to original sources

Equilibrium and non-Equilibrium regimes in the learning of Restricted Boltzmann Machines

Training Restricted Boltzmann Machines (RBMs) has been challenging for a long time due to the difficulty of computing precisely the log-likelihood gradient. Over the past decades, many works have proposed more or less successful training recipes but without studying the crucial quantity of the problem: the mixing time, i.e. the number of Monte Carlo iterations needed to sample new configurations from a model. In this work, we show that this mixing time plays a crucial role in the dynamics and stability of the trained model, and that RBMs operate in two well-defined regimes, namely equilibrium and out-of-equilibrium, depending on the interplay between this mixing time of the model and the number of steps, $k$, used to approximate the gradient. We further show empirically that this mixing time increases with the learning, which often implies a transition from one regime to another as soon as $k$ becomes smaller than this time. In particular, we show that using the popular $k$ (persistent) contrastive divergence approaches, with $k$ small, the dynamics of the learned model are extremely slow and often dominated by strong out-of-equilibrium effects. On the contrary, RBMs trained in equilibrium display faster dynamics, and a smooth convergence to dataset-like configurations during the sampling. Finally we discuss how to exploit in practice both regimes depending on the task one aims to fulfill: (i) short $k$ can be used to generate convincing samples in short learning times, (ii) large $k$ (or increasingly large) is needed to learn the correct equilibrium distribution of the RBM. Finally, the existence of these two operational regimes seems to be a general property of energy based models trained via likelihood maximization.

cs.LG↗

A scaling approach to estimate the COVID-19 infection fatality ratio from incomplete data

SARS-CoV-2 has disrupted the life of billions of people around the world since the first outbreak was officially declared in China at the beginning of 2020. Yet, important questions such as how deadly it is or its degree of spread within different countries remain unanswered. In this work, we exploit the `universal' growth of the mortality rate with age observed in different countries since the beginning of their respective outbreaks, combined with the results of the antibody prevalence tests in the population of Spain, to unveil both unknowns. We validate these results with an analogous antibody rate survey in the canton of Geneva, Switzerland. We also argue that the official number of deaths over 70 years old is importantly underestimated in most of the countries, and we use the comparison between the official records with the number of deaths mentioning COVID-19 in the death certificates to quantify by how much. Using this information, we estimate the fatality infection ratio (IFR) for the different age segments and the fraction of the population infected in different countries assuming a uniform exposure to the virus in all age segments. We also give estimations for the non-uniform IFR using the sero-epidemiological results of Spain, showing a very similar growth of the fatality ratio with age. Only for Spain, we estimate the probability (if infected) of being identified as a case, being hospitalized or admitted in the intensive care units as function of age. In general, we observe a nearly exponential growth of the fatality ratio with age, which anticipates large differences in total IFR in countries with different demographic distributions, with numbers that range from 1.82\% in Italy, to 0.62\% in China or even 0.14\% in middle Africa.

q-bio.PE↗

The complexity of protein interactions unravelled from structural disorder

The idea that structural disorder might be a novel mechanism of protein interaction is widespread in the Literature, although the number of statistically significant structural studies supporting this is surprisingly low. At variance with previous works, our conclusions rely exclusively on a large-scale analysis of all the 134337 X-ray crystallographic structures of the Protein Data Bank averaged over clusters of almost identical protein sequences. In this work, we explore the complexity of the organization of all the interaction interfaces observed when a protein lies in alternative complexes, showing that interfaces progressively add up in a hierarchical way. We further investigate the connection of this complexity with different measures of structural disorder: the standard missing residues and a new definition, called "soft disorder", that covers all the flexible and structurally amorphous residues of a protein. We show evidences that both the interaction interfaces and the soft disordered regions tend to involve roughly the same amino-acids of the protein, and preliminary results suggesting that soft disorder spots those surface regions where new interfaces are progressively accommodated by complex formation. Our results suggest that disordered regions not only carry crucial information about the location of alternative interfaces within complexes, but also of the order of the assembly. We verify these hypotheses in several examples. We finally compare our measures of disorder with several disorder predictors, showing that these latter are optimized to predict the residues that are missing in all the alternative structures of a protein, and they are not able to catch the progressive evolution of the disordered regions upon complex formation. Yet, the predicted residues, if not missing, tend to be characterized as soft disordered.

cond-mat.dis-nn↗

Learning a Local Symmetry with Neural-Networks

We explore the capacity of neural networks to detect a symmetry with complex local and non-local patterns : the gauge symmetry Z 2 . This symmetry is present in physical problems from topological transitions to QCD, and controls the computational hardness of instances of spin-glasses. Here, we show how to design a neural network, and a dataset, able to learn this symmetry and to find compressed latent representations of the gauge orbits. Our method pays special attention to system-wrapping loops, the so-called Polyakov loops, known to be particularly relevant for computational complexity.

cond-mat.dis-nn↗

Spin-glass--like aging in colloidal and granular glasses

Motivated by the mean field prediction of a Gardner phase transition between a "normal glass" and a "marginally stable glass", we investigate the off-equilibrium dynamics of three-dimensional polydisperse hard spheres, used as a model for colloidal or granular glasses. Deep inside the glass phase, we find that a sharp crossover pressure $P_{\rm G}$ separates two distinct dynamical regimes. For pressure $P < P_{\rm G}$, the glass behaves as a normal solid, displaying fast dynamics that quickly equilibrates within the glass free energy basin. For $P>P_{\rm G}$, instead, the dynamics becomes strongly anomalous, displaying very large equilibration time scales, aging, and a constantly increasing dynamical susceptibility. The crossover at $P_{\rm G}$ is strongly reminiscent of the one observed in three-dimensional spin-glasses in an external field, suggesting that the two systems could be in the same universality class, consistently with theoretical expectations.

cond-mat.soft↗

Low-temperature anomalies of a vapor deposited glass

We investigate the low temperature properties of two-dimensional Lennard-Jones glass films, prepared in silico both by liquid cooling and by physical vapor deposition. We identify deep in the solid phase a crossover temperature $T^*$, at which slow dynamics and enhanced heterogeneity emerge. Around $T^*$, localized defects become visible, leading to vibrational anomalies as compared to standard solids. We find that on average, $T^*$ decreases in samples with lower inherent structure energy, suggesting that such anomalies will be suppressed in ultra-stable glass films, prepared both by very slow liquid cooling and vapor deposition.

cond-mat.soft↗

An Ising Model for Metal-Organic Frameworks

We present a three-dimensional Ising model where lines of equal spins are frozen in such that they form an ordered framework structure. The frame spins impose an external field on the rest of the spins (active spins). We demonstrate that this "porous Ising model" can be seen as a minimal model for condensation transitions of gas molecules in metal-organic frameworks. Using Monte Carlo simulation techniques, we compare the phase behavior of a porous Ising model with that of a particle-based model for the condensation of methane (CH$_4$) in the isoreticular metal-organic framework IRMOF-16. For both models, we find a line of first-order phase transitions that end in a critical point. We show that the critical behavior in both cases belongs to the 3D Ising universality class, in contrast to other phase transitions in confinement such as capillary condensation.

cond-mat.mtrl-sci↗

Growing timescales and lengthscales characterizing vibrations of amorphous solids

Low-temperature properties of crystalline solids can be understood using harmonic perturbations around a perfect lattice, as in Debye's theory. Low-temperature properties of amorphous solids, however, strongly depart from such descriptions, displaying enhanced transport, activated slow dynamics across energy barriers, excess vibrational modes with respect to Debye's theory (i.e., a Boson Peak), and complex irreversible responses to small mechanical deformations. These experimental observations indirectly suggest that the dynamics of amorphous solids becomes anomalous at low temperatures. Here, we present direct numerical evidence that vibrations change nature at a well-defined location deep inside the glass phase of a simple glass former. We provide a real-space description of this transition and of the rapidly growing time and length scales that accompany it. Our results provide the seed for a universal understanding of low-temperature glass anomalies within the theoretical framework of the recently discovered Gardner phase transition.

cond-mat.soft↗

First Principle Computation of Random Pinning Glass Transition, Glass Cooperative Length-Scales and Numerical Comparisons

As a guideline for experimental tests of the ideal glass transition (Random Pinning Glass Transition, RPGT) that shall be induced in a system by randomly pinning particles, we performed first-principle computations within the Hypernetted chain approximation and numerical simulations of a Hard Sphere model of glass-former. We obtain confirmation of the expected enhancement of glassy behaviour under the procedure of random pinning, which consists in freezing a fraction $c$ of randomly chosen particles in the positions they have in an equilibrium configuration. We present the analytical phase diagram as a function of $c$ and of the packing fraction $ϕ$, showing a line of RPGT ending in a critical point. We also obtain first microscopic results on cooperative length-scales characterizing medium-range amorphous order in Hard Spere glasses and indirect quantitative information on a key thermodynamic quantity defined in proximity of ideal glass transitions, the amorphous surface tension. Finally, we present numerical results of pair correlation functions able to differentiate the liquid and the glass phases, as predicted by the analytic computations.

cond-mat.dis-nn↗

Numerical detection of the Gardner transition in a mean-field glass former

Recent theoretical advances predict the existence, deep into the glass phase, of a novel phase transition, the so-called Gardner transition. This transition is associated with the emergence of a complex free energy landscape composed of many marginally stable sub-basins within a glass metabasin. In this study, we explore several methods to detect numerically the Gardner transition in a simple structural glass former, the infinite-range Mari-Kurchan model. The transition point is robustly located from three independent approaches: (i) the divergence of the characteristic relaxation time, (ii) the divergence of the caging susceptibility, and (iii) the abnormal tail in the probability distribution function of cage order parameters. We show that the numerical results are fully consistent with the theoretical expectation. The methods we propose may also be generalized to more realistic numerical models as well as to experimental systems.

cond-mat.dis-nn↗

Many-body transverse interactions in the quantum annealing of the p-spin ferromagnet

We study the performance of quantum annealing for the simple $p$-body infinite-range ferromagnetic Ising model. In particular, we generalize the transverse antiferromagnetic interactions proposed by Seki and Nishimori as a quantum driver to many-body transverse interactions to understand if the two-body interactions are essential to allow the system to avoid troublesome first-order quantum phase transitions. We conclude that the general many-body interactions are effective to let the system evolve only through second-order transitions as long as a few minor conditions are satisfied. It is also discussed whether the overlap of the ground-state wave function of the new driver term with the target ground state is an essential factor for the success.

quant-ph↗