Predicting large scale cosmological structure evolution with GAN-based autoencoders

Cosmological simulations play a key role in the prediction and understanding of large scale structure formation from initial conditions. We make use of GAN-based Autoencoders (AEs) in an attempt to predict structure evolution within simulations. The AEs are trained on images and cubes issued from respectively 2D and 3D N-body simulations describing the evolution of the dark matter (DM) field. We find that while the AEs can predict structure evolution for 2D simulations of DM fields well, using only the density fields as input, they perform significantly more poorly in similar conditions for 3D simulations. However, additionally providing velocity fields as inputs greatly improves results, with similar predictions regardless of time-difference between input and target.

Inferring effective couplings with Restricted Boltzmann Machines

Generative models offer a direct way to model complex data. Among them, energy-based models provide us with a neural network model that aims to accurately reproduce all statistical correlations observed in the data at the level of the Boltzmann weight of the model. However, one challenge is to understand the physical interpretation of such models. In this study, we propose a simple solution by implementing a direct mapping between the energy function of the Restricted Boltzmann Machine and an effective Ising spin Hamiltonian that includes high-order interactions between spins. This mapping includes interactions of all possible orders, going beyond the conventional pairwise interactions typically considered in the inverse Ising approach, and allowing the description of complex datasets. Earlier works attempted to achieve this goal, but the proposed mappings did not do properly treat the complexity of the problem or did not contain direct prescriptions for practical application. To validate our method, we performed several controlled numerical experiments where we trained the RBMs using equilibrium samples of predefined models containing local external fields, two-body and three-body interactions in various low-dimensional topologies. The results demonstrate the effectiveness of our proposed approach in learning the correct interaction network and pave the way for its application in modeling interesting datasets. We also evaluate the quality of the inferred model based on different training methods.

The Copycat Perceptron: Smashing Barriers Through Collective Learning

We characterize the equilibrium properties of a model of $y$ coupled binary perceptrons in the teacher-student scenario, subject to a suitable learning rule, with an explicit ferromagnetic coupling proportional to the Hamming distance between the students' weights. In contrast to recent works, we analyze a more general setting in which a thermal noise is present that affects the generalization performance of each student. Specifically, in the presence of a nonzero temperature, which assigns nonzero probability to configurations that misclassify samples with respect to the teacher's prescription, we find that the coupling of replicas leads to a shift of the phase diagram to smaller values of $\alpha$: This suggests that the free energy landscape gets smoother around the solution with good generalization (i.e., the teacher) at a fixed fraction of reviewed examples, which allows local update algorithms such as Simulated Annealing to reach the solution before the dynamics gets frozen. Finally, from a learning perspective, these results suggest that more students (in this case, with the same amount of data) are able to learn the same rule when coupled together with a smaller amount of data.

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.

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.

Explaining the effects of non-convergent sampling in the training of Energy-Based Models

In this paper, we quantify the impact of using non-convergent Markov chains to train Energy-Based models (EBMs). In particular, we show analytically that EBMs trained with non-persistent short runs to estimate the gradient can perfectly reproduce a set of empirical statistics of the data, not at the level of the equilibrium measure, but through a precise dynamical process. Our results provide a first-principles explanation for the observations of recent works proposing the strategy of using short runs starting from random initial conditions as an efficient way to generate high-quality samples in EBMs, and lay the groundwork for using EBMs as diffusion models. After explaining this effect in generic EBMs, we analyze two solvable models in which the effect of the non-convergent sampling in the trained parameters can be described in detail. Finally, we test these predictions numerically on the Boltzmann machine.

Thermodynamics of bidirectional associative memories

In this paper we investigate the equilibrium properties of bidirectional associative memories (BAMs). Introduced by Kosko in 1988 as a generalization of the Hopfield model to a bipartite structure, the simplest architecture is defined by two layers of neurons, with synaptic connections only between units of different layers: even without internal connections within each layer, information storage and retrieval are still possible through the reverberation of neural activities passing from one layer to another. We characterize the computational capabilities of a stochastic extension of this model in the thermodynamic limit, by applying rigorous techniques from statistical physics. A detailed picture of the phase diagram at the replica symmetric level is provided, both at finite temperature and in the noiseless regime. An analytical and numerical inspection of the transition curves (namely critical lines splitting the various modes of operation of the machine) is carried out as the control parameters - noise, load and asymmetry between the two layer sizes - are tuned. In particular, with a finite asymmetry between the two layers, it is shown how the BAM can store information more efficiently than the Hopfield model by requiring less parameters to encode a fixed number of patterns. Comparisons are made with numerical simulations of neural dynamics. Finally, a low-load analysis is carried out to explain the retrieval mechanism in the BAM by analogy with two interacting Hopfield models. A potential equivalence with two coupled Restricted Boltmzann Machines is also discussed.

Learning a Restricted Boltzmann Machine using biased Monte Carlo sampling

Restricted Boltzmann Machines are simple and powerful generative models capable of encoding any complex dataset. Despite all their advantages, in practice, trainings are often unstable, and it is hard to assess their quality because dynamics are hampered by extremely slow time-dependencies. This situation becomes critical when dealing with low-dimensional clustered datasets, where the time needed to sample ergodically the trained models becomes computationally prohibitive. In this work, we show that this divergence of Monte Carlo mixing times is related to a phase coexistence phenomenon, similar to that encountered in Physics in the vicinity of a first order phase transition. We show that sampling the equilibrium distribution via Markov Chain Monte Carlo can be dramatically accelerated using biased sampling techniques, in particular, the Tethered Monte Carlo method (TMC). This sampling technique solves efficiently the problem of evaluating the quality of a given trained model and the generation of new samples in reasonable times. In addition, we show that this sampling technique can be exploited to improve the computation of the log-likelihood gradient during the training too, which produces dramatic improvements when training RBMs with artificial clustered datasets. When dealing with real low-dimensional datasets, this new training procedure fits RBM models with significantly faster relaxational dynamics than those obtained with standard PCD recipes. We also show that TMC sampling can be used to recover free-energy profile of the RBM, which turns out to be extremely useful to compute the probability distribution of a given model and to improve the generation of new decorrelated samples on slow PCD trained models.

Regularization of Mixture Models for Robust Principal Graph Learning

A regularized version of Mixture Models is proposed to learn a principal graph from a distribution of $D$-dimensional data points. In the particular case of manifold learning for ridge detection, we assume that the underlying manifold can be modeled as a graph structure acting like a topological prior for the Gaussian clusters turning the problem into a maximum a posteriori estimation. Parameters of the model are iteratively estimated through an Expectation-Maximization procedure making the learning of the structure computationally efficient with guaranteed convergence for any graph prior in a polynomial time. We also embed in the formalism a natural way to make the algorithm robust to outliers of the pattern and heteroscedasticity of the manifold sampling coherently with the graph structure. The method uses a graph prior given by the minimum spanning tree that we extend using random sub-samplings of the dataset to take into account cycles that can be observed in the spatial distribution.