Inference of the sparse kinetic Ising model using the decimation method

In this paper we study the inference of the kinetic Ising model on sparse graphs by the decimation method. The decimation method, which was first proposed in [Phys. Rev. Lett. 112, 070603] for the static inverse Ising problem, tries to recover the topology of the inferred system by setting the weakest couplings to zero iteratively. During the decimation process the likelihood function is maximized over the remaining couplings. Unlike the $\ell_1$-optimization based methods, the decimation method does not use the Laplace distribution as a heuristic choice of prior to select a sparse solution. In our case, the whole process can be done automatically without fixing any parameters by hand. We show that in the dynamical inference problem, where the task is to reconstruct the couplings of an Ising model given the data, the decimation process can be applied naturally into a maximum-likelihood optimization algorithm, as opposed to the static case where pseudo-likelihood method needs to be adopted. We also use extensive numerical studies to validate the accuracy of our methods in dynamical inference problems. Our results illustrate that on various topologies and with different distribution of couplings, the decimation method outperforms the widely-used $\ell _1$-optimization based methods.Comment: 11 pages, 5 figure

Solving the inverse Ising problem by mean-field methods in a clustered phase space with many states

In this work we explain how to properly use mean-field methods to solve the inverse Ising problem when the phase space is clustered, that is many states are present. The clustering of the phase space can occur for many reasons, e.g. when a system undergoes a phase transition. Mean-field methods for the inverse Ising problem are typically used without taking into account the eventual clustered structure of the input configurations and may led to very bad inference (for instance in the low temperature phase of the Curie-Weiss model). In the present work we explain how to modify mean-field approaches when the phase space is clustered and we illustrate the effectiveness of the new method on different clustered structures (low temperature phases of Curie-Weiss and Hopfield models).Comment: 6 pages, 5 figure

Ensemble renormalization group for the random field hierarchical model

The Renormalization Group (RG) methods are still far from being completely understood in quenched disordered systems. In order to gain insight into the nature of the phase transition of these systems, it is common to investigate simple models. In this work we study a real-space RG transformation on the Dyson hierarchical lattice with a random field, which led to a reconstruction of the RG flow and to an evaluation of the critical exponents of the model at T = 0. We show that this method gives very accurate estimations of the critical exponents, by comparing our results with the ones obtained by some of us using an independent method

Pseudolikelihood Decimation Algorithm Improving the Inference of the Interaction Network in a General Class of Ising Models

In this Letter we propose a new method to infer the topology of the interaction network in pairwise models with Ising variables. By using the pseudolikelihood method (PLM) at high temperature, it is generally possible to distinguish between zero and nonzero couplings because a clear gap separate the two groups. However at lower temperatures the PLM is much less effective and the result depends on subjective choices, such as the value of the $\ell_1$ regularizer and that of the threshold to separate nonzero couplings from null ones. We introduce a decimation procedure based on the PLM that recursively sets to zero the less significant couplings, until the variation of the pseudolikelihood signals that relevant couplings are being removed. The new method is fully automated and does not require any subjective choice by the user. Numerical tests have been performed on a wide class of Ising models, having different topologies (from random graphs to finite dimensional lattices) and different couplings (both diluted ferromagnets in a field and spin glasses). These numerical results show that the new algorithm performs better than standard PLMComment: 5 pages, 4 figure

La macchina di Boltzmann: quando il modello di Ising incontra il Machine Learning

International audienceMachine Learning is becoming more and more important in research and in daily life, yet the learning process remains largely misunderstood and many important questions are still unresolved. Statistical physicists, in a long tradition of looking for universal behavior and simple mechanisms to understand complex collective phenomena, have taken their turn in trying to understand these models with their own language. It is therefore natural that the Boltzmann Machine - or the inverse Ising problem- enters at the crossroad of statistical physics and machine learningIl machine learning sta diventando sempre più importante nella ricerca e nella vita quotidiana, tuttavia il processo dell’apprendimento rimane in gran parte oscuro e molte questioni importanti sono ancora irrisolte. I meccanici statistici, in una lunga tradizione di ricerca di comportamenti universali e meccanismi semplici per comprendere fenomeni collettivi complessi, hanno provato a comprendere questi modelli con il loro linguaggio. È quindi naturale che la macchina di Boltzmann - o il problema inverso di Ising- si inserisca nell’intersezione tra meccanica statistica e machine learning

Unsupervised hierarchical clustering using the learning dynamics of RBMs

Datasets in the real world are often complex and to some degree hierarchical, with groups and sub-groups of data sharing common characteristics at different levels of abstraction. Understanding and uncovering the hidden structure of these datasets is an important task that has many practical applications. To address this challenge, we present a new and general method for building relational data trees by exploiting the learning dynamics of the Restricted Boltzmann Machine (RBM). Our method is based on the mean-field approach, derived from the Plefka expansion, and developed in the context of disordered systems. It is designed to be easily interpretable. We tested our method in an artificially created hierarchical dataset and on three different real-world datasets (images of digits, mutations in the human genome, and a homologous family of proteins). The method is able to automatically identify the hierarchical structure of the data. This could be useful in the study of homologous protein sequences, where the relationships between proteins are critical for understanding their function and evolution.Comment: Version accepted in Physical Review

Fast and Functional Structured Data Generators Rooted in Out-of-Equilibrium Physics

In this study, we address the challenge of using energy-based models to produce high-quality, label-specific data in complex structured datasets, such as population genetics, RNA or protein sequences data. Traditional training methods encounter difficulties due to inefficient Markov chain Monte Carlo mixing, which affects the diversity of synthetic data and increases generation times. To address these issues, we use a novel training algorithm that exploits non-equilibrium effects. This approach, applied on the Restricted Boltzmann Machine, improves the model's ability to correctly classify samples and generate high-quality synthetic data in only a few sampling steps. The effectiveness of this method is demonstrated by its successful application to four different types of data: handwritten digits, mutations of human genomes classified by continental origin, functionally characterized sequences of an enzyme protein family, and homologous RNA sequences from specific taxonomies.Comment: 15 page

Cosmology with cosmic web environments I. Real-space power spectra

We undertake the first comprehensive and quantitative real-space analysis of the cosmological information content in the environments of the cosmic web (voids, filaments, walls, and nodes) up to non-linear scales, $k = 0.5$ $h$/Mpc. Relying on the large set of $N$-body simulations from the Quijote suite, the environments are defined through the eigenvalues of the tidal tensor and the Fisher formalism is used to assess the constraining power of the power spectra derived in each of the four environments and their combination. Our results show that there is more information available in the environment-dependent power spectra, both individually and when combined all together, than in the matter power spectrum. By breaking some key degeneracies between parameters of the cosmological model such as $M_\nu$--$\sigma_\mathrm{8}$ or $\Omega_\mathrm{m}$--$\sigma_8$, the power spectra computed in identified environments improve the constraints on cosmological parameters by factors $\sim 15$ for the summed neutrino mass $M_\nu$ and $\sim 8$ for the matter density $\Omega_\mathrm{m}$ over those derived from the matter power spectrum. We show that these tighter constraints are obtained for a wide range of the maximum scale, from $k_\mathrm{max} = 0.1$ $h$/Mpc to highly non-linear regimes with $k_\mathrm{max} = 0.5$ $h$/Mpc. We also report an eight times higher value of the signal-to-noise ratio for the combination of spectra compared to the matter one. Importantly, we show that all the presented results are robust to variations of the parameters defining the environments hence suggesting a robustness to the definition we chose to define them.Comment: 15 pages, 11 figure