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Francesc Font-Clos

Publications and source records attributed to Francesc Font-Clos.

At least 19 recordsLinked to original sources

Predicting the failure of two-dimensional silica glasses

Being able to predict the failure of materials based on structural information is a fundamental issue with enormous practical and industrial relevance for the monitoring of devices and components. Thanks to recent advances in deep learning, accurate failure predictions are becoming possible even for strongly disordered solids, but the sheer number of parameters used in the process renders a physical interpretation of the results impossible. Here we address this issue and use machine learning methods to predict the failure of simulated two dimensional silica glasses from their initial undeformed structure. We then exploit Gradient-weighted Class Activation Mapping (Grad-CAM) to build attention maps associated with the predictions, and we demonstrate that these maps are amenable to physical interpretation in terms of topological defects and local potential energies. We show that our predictions can be transferred to samples with different shape or size than those used in training, as well as to experimental images. Our strategy illustrates how artificial neural networks trained with numerical simulation results can provide interpretable predictions of the behavior of experimentally measured structures.

cond-mat.mtrl-sci

A standardized Project Gutenberg corpus for statistical analysis of natural language and quantitative linguistics

The use of Project Gutenberg (PG) as a text corpus has been extremely popular in statistical analysis of language for more than 25 years. However, in contrast to other major linguistic datasets of similar importance, no consensual full version of PG exists to date. In fact, most PG studies so far either consider only a small number of manually selected books, leading to potential biased subsets, or employ vastly different pre-processing strategies (often specified in insufficient details), raising concerns regarding the reproducibility of published results. In order to address these shortcomings, here we present the Standardized Project Gutenberg Corpus (SPGC), an open science approach to a curated version of the complete PG data containing more than 50,000 books and more than $3 \times 10^9$ word-tokens. Using different sources of annotated metadata, we not only provide a broad characterization of the content of PG, but also show different examples highlighting the potential of SPGC for investigating language variability across time, subjects, and authors. We publish our methodology in detail, the code to download and process the data, as well as the obtained corpus itself on 3 different levels of granularity (raw text, timeseries of word tokens, and counts of words). In this way, we provide a reproducible, pre-processed, full-size version of Project Gutenberg as a new scientific resource for corpus linguistics, natural language processing, and information retrieval.

cs.CL

Dependence of exponents on text length versus finite-size scaling for word-frequency distributions

Some authors have recently argued that a finite-size scaling law for the text-length dependence of word-frequency distributions cannot be conceptually valid. Here we give solid quantitative evidence for the validity of such scaling law, both using careful statistical tests and analytical arguments based on the generalized central-limit theorem applied to the moments of the distribution (and obtaining a novel derivation of Heaps' law as a by-product). We also find that the picture of word-frequency distributions with power-law exponents that decrease with text length [Yan and Minnhagen, Physica A 444, 828 (2016)] does not stand with rigorous statistical analysis. Instead, we show that the distributions are perfectly described by power-law tails with stable exponents, whose values are close to 2, in agreement with the classical Zipf's law. Some misconceptions about scaling are also clarified.

physics.data-an

Phase transition, scaling of moments, and order-parameter distributions in Brownian particles and branching processes with finite-size effects

We revisit the problem of Brownian diffusion with drift in order to study finite-size effects in the geometric Galton-Watson branching process. This is possible because of an exact mapping between one-dimensional random walks and geometric branching processes, known as the Harris walk. In this way, first-passage times of Brownian particles are equivalent to sizes of trees in the branching process (up to a factor of proportionality). Brownian particles that reach a distant boundary correspond to percolating trees, and those that do not correspond to non-percolating trees. In fact, both systems display a second-order phase transition between "insulating" and "conducting" phases, controlled by the drift velocity in the Brownian system. In the limit of large system size, we obtain exact expressions for the Laplace transforms of the probability distributions and their first and second moments. These quantities are also shown to obey finite-size scaling laws.

cond-mat.stat-mech

Percolation on trees as a Brownian excursion: from Gaussian to Kolmogorov-Smirnov to Exponential statistics

We calculate the distribution of the size of the percolating cluster on a tree in the subcritical, critical and supercritical phase. We do this by exploiting a mapping between continuum trees and Brownian excursions, and arrive at a diffusion equation with suitable boundary conditions. The exact solution to this equation can be conveniently represented as a characteristic function, from which the following distributions are clearly visible: Gaussian (subcritical), Kolmogorov-Smirnov (critical) and exponential (supercritical). In this way we provide an intuitive explanation for the result reported in R. Botet and M. Ploszajczak, Phys. Rev. Lett 95, 185702 (2005) for critical percolation.

cond-mat.stat-mech

Exact derivation of a finite-size-scaling law and corrections to scaling in the geometric Galton-Watson process

The theory of finite-size scaling explains how the singular behavior of thermodynamic quantities in the critical point of a phase transition emerges when the size of the system becomes infinite. Usually, this theory is presented in a phenomenological way. Here, we exactly demonstrate the existence of a finite-size scaling law for the Galton-Watson branching processes when the number of offsprings of each individual follows either a geometric distribution or a generalized geometric distribution. We also derive the corrections to scaling and the limits of validity of the finite-size scaling law away the critical point. A mapping between branching processes and random walks allows us to establish that these results also hold for the latter case, for which the order parameter turns out to be the probability of hitting a distant boundary.

cond-mat.stat-mech

Similarity of symbol frequency distributions with heavy tails

Quantifying the similarity between symbolic sequences is a traditional problem in Information Theory which requires comparing the frequencies of symbols in different sequences. In numerous modern applications, ranging from DNA over music to texts, the distribution of symbol frequencies is characterized by heavy-tailed distributions (e.g., Zipf's law). The large number of low-frequency symbols in these distributions poses major difficulties to the estimation of the similarity between sequences, e.g., they hinder an accurate finite-size estimation of entropies. Here we show analytically how the systematic (bias) and statistical (fluctuations) errors in these estimations depend on the sample size~$N$ and on the exponent~$γ$ of the heavy-tailed distribution. Our results are valid for the Shannon entropy $(α=1)$, its corresponding similarity measures (e.g., the Jensen-Shanon divergence), and also for measures based on the generalized entropy of order $α$. For small $α$'s, including $α=1$, the errors decay slower than the $1/N$-decay observed in short-tailed distributions. For $α$ larger than a critical value $α^* = 1+1/γ\leq 2$, the $1/N$-decay is recovered. We show the practical significance of our results by quantifying the evolution of the English language over the last two centuries using a complete $α$-spectrum of measures. We find that frequent words change more slowly than less frequent words and that $α=2$ provides the most robust measure to quantify language change.

physics.soc-ph

Large-scale analysis of Zipf's law in English texts

Despite being a paradigm of quantitative linguistics, Zipf's law for words suffers from three main problems: its formulation is ambiguous, its validity has not been tested rigorously from a statistical point of view, and it has not been confronted to a representatively large number of texts. So, we can summarize the current support of Zipf's law in texts as anecdotic. We try to solve these issues by studying three different versions of Zipf's law and fitting them to all available English texts in the Project Gutenberg database (consisting of more than 30000 texts). To do so we use state-of-the art tools in fitting and goodness-of-fit tests, carefully tailored to the peculiarities of text statistics. Remarkably, one of the three versions of Zipf's law, consisting of a pure power-law form in the complementary cumulative distribution function of word frequencies, is able to fit more than 40% of the texts in the database (at the 0.05 significance level), for the whole domain of frequencies (from 1 to the maximum value) and with only one free parameter (the exponent).

stat.AP

Mapping high-growth phenotypes in the flux space of microbial metabolism

Experimental and empirical observations on cell metabolism cannot be understood as a whole without their integration into a consistent systematic framework. However, the characterization of metabolic flux phenotypes is typically reduced to the study of a single optimal state, like maximum biomass yield that is by far the most common assumption. Here we confront optimal growth solutions to the whole set of feasible flux phenotypes (FFP), which provides a benchmark to assess the likelihood of optimal and high-growth states and their agreement with experimental results. In addition, FFP maps are able to uncover metabolic behaviors, such as aerobic fermentation accompanying exponential growth on sugars at nutrient excess conditions, that are unreachable using standard models based on optimality principles. The information content of the full FFP space provides us with a map to explore and evaluate metabolic behavior and capabilities, and so it opens new avenues for biotechnological and biomedical applications.

q-bio.MN

Log-log Convexity of Type-Token Growth in Zipf's Systems

It is traditionally assumed that Zipf's law implies the power-law growth of the number of different elements with the total number of elements in a system - the so-called Heaps' law. We show that a careful definition of Zipf's law leads to the violation of Heaps' law in random systems, and obtain alternative growth curves. These curves fulfill universal data collapses that only depend on the value of the Zipf's exponent. We observe that real books behave very much in the same way as random systems, despite the presence of burstiness in word occurrence. We advance an explanation for this unexpected correspondence.

physics.soc-ph

Finite-size scaling of survival probability in branching processes

Branching processes pervade many models in statistical physics. We investigate the survival probability of a Galton-Watson branching process after a finite number of generations. We reveal the finite-size scaling law of the survival probability for a given branching process ruled by a probability distribution of the number of offspring per element whose standard deviation is finite, obtaining the exact scaling function as well as the critical exponents. Our findings prove the universal behavior of branching processes concerning the survival probability.

cond-mat.stat-mech

The perils of thresholding

The thresholding of time series of activity or intensity is frequently used to define and differentiate events. This is either implicit, for example due to resolution limits, or explicit, in order to filter certain small scale physics from the supposed true asymptotic events. Thresholding the birth-death process, however, introduces a scaling region into the event size distribution, which is characterised by an exponent that is unrelated to the actual asymptote and is rather an artefact of thresholding. As a result, numerical fits of simulation data produce a range of exponents, with the true asymptote visible only in the tail of the distribution. This tail is increasingly difficult to sample as the threshold is increased. In the present case, the exponents and the spurious nature of the scaling region can be determined analytically, thus demonstrating the way in which thresholding conceals the true asymptote. The analysis also suggests a procedure for detecting the influence of the threshold by means of a data collapse involving the threshold-imposed scale.

physics.data-an

The configuration multi-edge model: Assessing the effect of fixing node strengths on weighted network magnitudes

Complex networks grow subject to structural constraints which affect their measurable properties. Assessing the effect that such constraints impose on their observables is thus a crucial aspect to be taken into account in their analysis. To this end,we examine the effect of fixing the strength sequence in multi-edge networks on several network observables such as degrees, disparity, average neighbor properties and weight distribution using an ensemble approach. We provide a general method to calculate any desired weighted network metric and we show that several features detected in real data could be explained solely by structural constraints. We thus justify the need of analytical null models to be used as basis to assess the relevance of features found in real data represented in weighted network form.

physics.soc-ph

Reply to "Comment on 'A Scaling law beyond Zipf's law and its relation to Heaps' law'"

In [arXiv:1404.1461], Yan and Minnhagen argue that the scaling law for the text-length dependence of word-frequency distributions proposed in [New J. Phys. 15 093033, arXiv:1303.0705] is "fundamentally incorrect" and "fundamentally impossible". In this note, we reason that such claims are clearly unjustified, with the scaling law being clearly valid for absolute frequencies greater than about 10. Further, we show that the very counter-example provided by Yan and Minnhagen [arXiv:1404.1461] fulfils our scaling hypothesis with excellent accuracy, at odds with Yan and Minnhagen's criticisms, and supporting our approach.

physics.soc-ph

A Novel Methodology to Estimate Metabolic Flux Distributions in Constraint-Based Models

Quite generally, constraint-based metabolic flux analysis describes the space of viable flux configurations for a metabolic network as a high-dimensional polytope defined by the linear constraints that enforce the balancing of production and consumption fluxes for each chemical species in the system. In some cases, the complexity of the solution space can be reduced by performing an additional optimization, while in other cases, knowing the range of variability of fluxes over the polytope provides a sufficient characterization of the allowed configurations. There are cases, however, in which the thorough information encoded in the individual distributions of viable fluxes over the polytope is required. Obtaining such distributions is known to be a highly challenging computational task when the dimensionality of the polytope is sufficiently large, and the problem of developing cost-effective {\it ad hoc} algorithms has recently seen a major surge of interest. Here, we propose a method that allows us to perform the required computation heuristically in a time scaling {\it linearly} with the number of reactions in the network, overcoming some limitations of similar techniques employed in recent years. As a case study, we apply it to the analysis of the human red blood cell metabolic network, whose solution space can be sampled by different exact techniques, like Hit-and-Run Monte Carlo (scaling roughly like the third power of the system size). Remarkably accurate estimates for the true distributions of viable reaction fluxes are obtained, suggesting that, although further improvements are desirable, our method enhances our ability to analyze the space of allowed configurations for large biochemical reaction networks.

q-bio.MN

A scaling law beyond Zipf's law and its relation to Heaps' law

The dependence with text length of the statistical properties of word occurrences has long been considered a severe limitation quantitative linguistics. We propose a simple scaling form for the distribution of absolute word frequencies which uncovers the robustness of this distribution as text grows. In this way, the shape of the distribution is always the same and it is only a scale parameter which increases linearly with text length. By analyzing very long novels we show that this behavior holds both for raw, unlemmatized texts and for lemmatized texts. For the latter case, the word-frequency distribution is well fit by a double power law, maintaining the Zipf's exponent value $γ\simeq 2$ for large frequencies but yielding a smaller exponent in the low frequency regime. The growth of the distribution with text length allows us to estimate the size of the vocabulary at each step and to propose an alternative to Heaps' law, which turns out to be intimately connected to Zipf's law, thanks to the scaling behavior.

physics.soc-ph

A weighted belief-propagation algorithm to estimate volume-related properties of random polytopes

In this work we introduce a novel weighted message-passing algorithm based on the cavity method to estimate volume-related properties of random polytopes, properties which are relevant in various research fields ranging from metabolic networks, to neural networks, to compressed sensing. Unlike the usual approach consisting in approximating the real-valued cavity marginal distributions by a few parameters, we propose an algorithm to faithfully represent the entire marginal distribution. We explain various alternatives to implement the algorithm and benchmark the theoretical findings by showing concrete applications to random polytopes. The results obtained with our approach are found to be in very good agreement with the estimates produced by the Hit-and-Run algorithm, known to produce uniform sampling.

cond-mat.dis-nn

Criticality and self-organization in branching processes: application to natural hazards

The statistics of natural catastrophes contains very counter-intuitive results. Using earthquakes as a working example, we show that the energy radiated by such events follows a power-law or Pareto distribution. This means, in theory, that the expected value of the energy does not exist (is infinite), and in practice, that the mean of a finite set of data in not representative of the full population. Also, the distribution presents scale invariance, which implies that it is not possible to define a characteristic scale for the energy. A simple model to account for this peculiar statistics is a branching process: the activation or slip of a fault segment can trigger other segments to slip, with a certain probability, and so on. Although not recognized initially by seismologists, this is a particular case of the stochastic process studied by Galton and Watson one hundred years in advance, in order to model the extinction of (prominent) families. Using the formalism of probability generating functions we will be able to derive, in an accessible way, the main properties of these models. Remarkably, a power-law distribution of energies is only recovered in a very special case, when the branching process is at the onset of attenuation and intensification, i.e., at criticality. In order to account for this fact, we introduce the self-organized critical models, in which, by means of some feedback mechanism, the critical state becomes an attractor in the evolution of such systems. Analogies with statistical physics are drawn. The bulk of the material presented here is self-contained, as only elementary probability and mathematics are needed to start to read.

cond-mat.stat-mech