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Recent research has developed several Monte Carlo methods for estimating the normalization constant (partition function) based on the idea of annealing. This means sampling successively from a path of distributions that interpolate between a tractable "proposal" distribution and the unnormalized "target" distribution. Prominent estimators in this family include annealed importance sampling and annealed noise-contrastive estimation (NCE). Such methods hinge on a number of design choices: which estimator to use, which path of distributions to use and whether to use a path at all; so far, there is no definitive theory on which choices are efficient. Here, we evaluate each design choice by the asymptotic estimation error it produces. First, we show that using NCE is more efficient than the importance sampling estimator, but in the limit of infinitesimal path steps, the difference vanishes. Second, we find that using the geometric path brings down the estimation error from an exponential to a polynomial function of the parameter distance between the target and proposal distributions. Third, we find that the arithmetic path, while rarely used, can offer optimality properties over the universally-used geometric path. In fact, in a particular limit, the optimal path is arithmetic. Based on this theory, we finally propose a two-step estimator to approximate the optimal path in an efficient way.

A central problem in unsupervised deep learning is how to find useful representations of high-dimensional data, sometimes called "disentanglement". Most approaches are heuristic and lack a proper theoretical foundation. In linear representation learning, independent component analysis (ICA) has been successful in many applications areas, and it is principled, i.e., based on a well-defined probabilistic model. However, extension of ICA to the nonlinear case has been problematic due to the lack of identifiability, i.e., uniqueness of the representation. Recently, nonlinear extensions that utilize temporal structure or some auxiliary information have been proposed. Such models are in fact identifiable, and consequently, an increasing number of algorithms have been developed. In particular, some self-supervised algorithms can be shown to estimate nonlinear ICA, even though they have initially been proposed from heuristic perspectives. This paper reviews the state-of-the-art of nonlinear ICA theory and algorithms., Comment: Revised version, to appear in Patterns

Self-supervised learning is an increasingly popular approach to unsupervised learning, achieving state-of-the-art results. A prevalent approach consists in contrasting data points and noise points within a classification task: this requires a good noise distribution which is notoriously hard to specify. While a comprehensive theory is missing, it is widely assumed that the optimal noise distribution should in practice be made equal to the data distribution, as in Generative Adversarial Networks (GANs). We here empirically and theoretically challenge this assumption. We turn to Noise-Contrastive Estimation (NCE) which grounds this self-supervised task as an estimation problem of an energy-based model of the data. This ties the optimality of the noise distribution to the sample efficiency of the estimator, which is rigorously defined as its asymptotic variance, or mean-squared error. In the special case where the normalization constant only is unknown, we show that NCE recovers a family of Importance Sampling estimators for which the optimal noise is indeed equal to the data distribution. However, in the general case where the energy is also unknown, we prove that the optimal noise density is the data density multiplied by a correction term based on the Fisher score. In particular, the optimal noise distribution is different from the data distribution, and is even from a different family. Nevertheless, we soberly conclude that the optimal noise may be hard to sample from, and the gain in efficiency can be modest compared to choosing the noise distribution equal to the data's., Comment: arXiv admin note: text overlap with arXiv:2203.01110

Learning a parametric model of a data distribution is a well-known statistical problem that has seen renewed interest as it is brought to scale in deep learning. Framing the problem as a self-supervised task, where data samples are discriminated from noise samples, is at the core of state-of-the-art methods, beginning with Noise-Contrastive Estimation (NCE). Yet, such contrastive learning requires a good noise distribution, which is hard to specify; domain-specific heuristics are therefore widely used. While a comprehensive theory is missing, it is widely assumed that the optimal noise should in practice be made equal to the data, both in distribution and proportion. This setting underlies Generative Adversarial Networks (GANs) in particular. Here, we empirically and theoretically challenge this assumption on the optimal noise. We show that deviating from this assumption can actually lead to better statistical estimators, in terms of asymptotic variance. In particular, the optimal noise distribution is different from the data's and even from a different family.

We introduce a new general identifiable framework for principled disentanglement referred to as Structured Nonlinear Independent Component Analysis (SNICA). Our contribution is to extend the identifiability theory of deep generative models for a very broad class of structured models. While previous works have shown identifiability for specific classes of time-series models, our theorems extend this to more general temporal structures as well as to models with more complex structures such as spatial dependencies. In particular, we establish the major result that identifiability for this framework holds even in the presence of noise of unknown distribution. Finally, as an example of our framework's flexibility, we introduce the first nonlinear ICA model for time-series that combines the following very useful properties: it accounts for both nonstationarity and autocorrelation in a fully unsupervised setting; performs dimensionality reduction; models hidden states; and enables principled estimation and inference by variational maximum-likelihood., Comment: Accepted for publication at NeurIPS 2021

We posit that autoregressive flow models are well-suited to performing a range of causal inference tasks - ranging from causal discovery to making interventional and counterfactual predictions. In particular, we exploit the fact that autoregressive architectures define an ordering over variables, analogous to a causal ordering, in order to propose a single flow architecture to perform all three aforementioned tasks. We first leverage the fact that flow models estimate normalized log-densities of data to derive a bivariate measure of causal direction based on likelihood ratios. Whilst traditional measures of causal direction often require restrictive assumptions on the nature of causal relationships (e.g., linearity),the flexibility of flow models allows for arbitrary causal dependencies. Our approach compares favourably against alternative methods on synthetic data as well as on the Cause-Effect Pairs bench-mark dataset. Subsequently, we demonstrate that the invertible nature of flows naturally allows for direct evaluation of both interventional and counterfactual predictions, which require marginalization and conditioning over latent variables respectively. We present examples over synthetic data where autoregressive flows, when trained under the correct causal ordering, are able to make accurate interventional and counterfactual predictions, Comment: 6 pages, 3 figures. Accepted at the 2nd ICML Workshop on Invertible Neural Networks, Normalizing Flows, and Explicit Likelihood Models

Neuroimaging-driven prediction of brain age, defined as the predicted biological age of a subject using only brain imaging data, is an exciting avenue of research. In this work we seek to build models of brain age based on functional connectivity while prioritizing model interpretability and understanding. This way, the models serve to both provide accurate estimates of brain age as well as allow us to investigate changes in functional connectivity which occur during the ageing process. The methods proposed in this work consist of a two-step procedure: first, linear latent variable models, such as PCA and its extensions, are employed to learn reproducible functional connectivity networks present across a cohort of subjects. The activity within each network is subsequently employed as a feature in a linear regression model to predict brain age. The proposed framework is employed on the data from the CamCAN repository and the inferred brain age models are further demonstrated to generalize using data from two open-access repositories: the Human Connectome Project and the ATR Wide-Age-Range., Comment: 21 pages, 11 figures

Many statistical models are given in the form of non-normalized densities with an intractable normalization constant. Since maximum likelihood estimation is computationally intensive for these models, several estimation methods have been developed which do not require explicit computation of the normalization constant, such as noise contrastive estimation (NCE) and score matching. However, model selection methods for general non-normalized models have not been proposed so far. In this study, we develop information criteria for non-normalized models estimated by NCE or score matching. They are approximately unbiased estimators of discrepancy measures for non-normalized models. Simulation results and applications to real data demonstrate that the proposed criteria enable selection of the appropriate non-normalized model in a data-driven manner.

We consider the problem of inferring causal relationships between two or more passively observed variables. While the problem of such causal discovery has been extensively studied especially in the bivariate setting, the majority of current methods assume a linear causal relationship, and the few methods which consider non-linear dependencies usually make the assumption of additive noise. Here, we propose a framework through which we can perform causal discovery in the presence of general non-linear relationships. The proposed method is based on recent progress in non-linear independent component analysis and exploits the non-stationarity of observations in order to recover the underlying sources or latent disturbances. We show rigorously that in the case of bivariate causal discovery, such non-linear ICA can be used to infer the causal direction via a series of independence tests. We further propose an alternative measure of causal direction based on asymptotic approximations to the likelihood ratio, as well as an extension to multivariate causal discovery. We demonstrate the capabilities of the proposed method via a series of simulation studies and conclude with an application to neuroimaging data.

We unify $\textit{kernel density estimation}$ and $\textit{empirical Bayes}$ and address a set of problems in unsupervised learning with a geometric interpretation of those methods, rooted in the $\textit{concentration of measure}$ phenomenon. Kernel density is viewed symbolically as $X\rightharpoonup Y$ where the random variable $X$ is smoothed to $Y= X+N(0,\sigma^2 I_d)$, and empirical Bayes is the machinery to denoise in a least-squares sense, which we express as $X \leftharpoondown Y$. A learning objective is derived by combining these two, symbolically captured by $X \rightleftharpoons Y$. Crucially, instead of using the original nonparametric estimators, we parametrize $\textit{the energy function}$ with a neural network denoted by $\phi$; at optimality, $\nabla \phi \approx -\nabla \log f$ where $f$ is the density of $Y$. The optimization problem is abstracted as interactions of high-dimensional spheres which emerge due to the concentration of isotropic gaussians. We introduce two algorithmic frameworks based on this machinery: (i) a "walk-jump" sampling scheme that combines Langevin MCMC (walks) and empirical Bayes (jumps), and (ii) a probabilistic framework for $\textit{associative memory}$, called NEBULA, defined \`{a} la Hopfield by the $\textit{gradient flow}$ of the learned energy to a set of attractors. We finish the paper by reporting the emergence of very rich "creative memories" as attractors of NEBULA for highly-overlapping spheres., Comment: 23 pages, 10 figures

Nonlinear ICA is a fundamental problem for unsupervised representation learning, emphasizing the capacity to recover the underlying latent variables generating the data (i.e., identifiability). Recently, the very first identifiability proofs for nonlinear ICA have been proposed, leveraging the temporal structure of the independent components. Here, we propose a general framework for nonlinear ICA, which, as a special case, can make use of temporal structure. It is based on augmenting the data by an auxiliary variable, such as the time index, the history of the time series, or any other available information. We propose to learn nonlinear ICA by discriminating between true augmented data, or data in which the auxiliary variable has been randomized. This enables the framework to be implemented algorithmically through logistic regression, possibly in a neural network. We provide a comprehensive proof of the identifiability of the model as well as the consistency of our estimation method. The approach not only provides a general theoretical framework combining and generalizing previously proposed nonlinear ICA models and algorithms, but also brings practical advantages., Comment: Camera-ready version of article accepted for AISTATS2019

We develop a general method for estimating a finite mixture of non-normalized models. Here, a non-normalized model is defined to be a parametric distribution with an intractable normalization constant. Existing methods for estimating non-normalized models without computing the normalization constant are not applicable to mixture models because they contain more than one intractable normalization constant. The proposed method is derived by extending noise contrastive estimation (NCE), which estimates non-normalized models by discriminating between the observed data and some artificially generated noise. We also propose an extension of NCE with multiple noise distributions. Then, based on the observation that conventional classification learning with neural networks is implicitly assuming an exponential family as a generative model, we introduce a method for clustering unlabeled data by estimating a finite mixture of distributions in an exponential family. Estimation of this mixture model is attained by the proposed extensions of NCE where the training data of neural networks are used as noise. Thus, the proposed method provides a probabilistically principled clustering method that is able to utilize a deep representation. Application to image clustering using a deep neural network gives promising results.

Nonlinear independent component analysis (ICA) provides an appealing framework for unsupervised feature learning, but the models proposed so far are not identifiable. Here, we first propose a new intuitive principle of unsupervised deep learning from time series which uses the nonstationary structure of the data. Our learning principle, time-contrastive learning (TCL), finds a representation which allows optimal discrimination of time segments (windows). Surprisingly, we show how TCL can be related to a nonlinear ICA model, when ICA is redefined to include temporal nonstationarities. In particular, we show that TCL combined with linear ICA estimates the nonlinear ICA model up to point-wise transformations of the sources, and this solution is unique --- thus providing the first identifiability result for nonlinear ICA which is rigorous, constructive, as well as very general.

Structural equation models and Bayesian networks have been widely used to analyze causal relations between continuous variables. In such frameworks, linear acyclic models are typically used to model the datagenerating process of variables. Recently, it was shown that use of non-Gaussianity identifies a causal ordering of variables in a linear acyclic model without using any prior knowledge on the network structure, which is not the case with conventional methods. However, existing estimation methods are based on iterative search algorithms and may not converge to a correct solution in a finite number of steps. In this paper, we propose a new direct method to estimate a causal ordering based on non-Gaussianity. In contrast to the previous methods, our algorithm requires no algorithmic parameters and is guaranteed to converge to the right solution within a small fixed number of steps if the data strictly follows the model., Comment: Appears in Proceedings of the Twenty-Fifth Conference on Uncertainty in Artificial Intelligence (UAI2009)

Model selection based on classical information criteria, such as BIC, is generally computationally demanding, but its properties are well studied. On the other hand, model selection based on parameter shrinkage by $\ell_1$-type penalties is computationally efficient. In this paper we make an attempt to combine their strengths, and propose a simple approach that penalizes the likelihood with data-dependent $\ell_1$ penalties as in adaptive Lasso and exploits a fixed penalization parameter. Even for finite samples, its model selection results approximately coincide with those based on information criteria; in particular, we show that in some special cases, this approach and the corresponding information criterion produce exactly the same model. One can also consider this approach as a way to directly determine the penalization parameter in adaptive Lasso to achieve information criteria-like model selection. As extensions, we apply this idea to complex models including Gaussian mixture model and mixture of factor analyzers, whose model selection is traditionally difficult to do; by adopting suitable penalties, we provide continuous approximators to the corresponding information criteria, which are easy to optimize and enable efficient model selection., Comment: 16 pages, 3 figures

We consider learning a causal ordering of variables in a linear non-Gaussian acyclic model called LiNGAM. Several existing methods have been shown to consistently estimate a causal ordering assuming that all the model assumptions are correct. But, the estimation results could be distorted if some assumptions actually are violated. In this paper, we propose a new algorithm for learning causal orders that is robust against one typical violation of the model assumptions: latent confounders. The key idea is to detect latent confounders by testing independence between estimated external influences and find subsets (parcels) that include variables that are not affected by latent confounders. We demonstrate the effectiveness of our method using artificial data and simulated brain imaging data., Comment: A revised version of this was accepted in Neural Computation. 18 pages and 5 figures. arXiv admin note: substantial text overlap with arXiv:1204.1795

In recent years, several methods have been proposed for the discovery of causal structure from non-experimental data (Spirtes et al. 2000; Pearl 2000). Such methods make various assumptions on the data generating process to facilitate its identification from purely observational data. Continuing this line of research, we show how to discover the complete causal structure of continuous-valued data, under the assumptions that (a) the data generating process is linear, (b) there are no unobserved confounders, and (c) disturbance variables have non-gaussian distributions of non-zero variances. The solution relies on the use of the statistical method known as independent component analysis (ICA), and does not require any pre-specified time-ordering of the variables. We provide a complete Matlab package for performing this LiNGAM analysis (short for Linear Non-Gaussian Acyclic Model), and demonstrate the effectiveness of the method using artificially generated data., Comment: Appears in Proceedings of the Twenty-First Conference on Uncertainty in Artificial Intelligence (UAI2005)

An important task in data analysis is the discovery of causal relationships between observed variables. For continuous-valued data, linear acyclic causal models are commonly used to model the data-generating process, and the inference of such models is a well-studied problem. However, existing methods have significant limitations. Methods based on conditional independencies (Spirtes et al. 1993; Pearl 2000) cannot distinguish between independence-equivalent models, whereas approaches purely based on Independent Component Analysis (Shimizu et al. 2006) are inapplicable to data which is partially Gaussian. In this paper, we generalize and combine the two approaches, to yield a method able to learn the model structure in many cases for which the previous methods provide answers that are either incorrect or are not as informative as possible. We give exact graphical conditions for when two distinct models represent the same family of distributions, and empirically demonstrate the power of our method through thorough simulations., Comment: Appears in Proceedings of the Twenty-Fourth Conference on Uncertainty in Artificial Intelligence (UAI2008)

By taking into account the nonlinear effect of the cause, the inner noise effect, and the measurement distortion effect in the observed variables, the post-nonlinear (PNL) causal model has demonstrated its excellent performance in distinguishing the cause from effect. However, its identifiability has not been properly addressed, and how to apply it in the case of more than two variables is also a problem. In this paper, we conduct a systematic investigation on its identifiability in the two-variable case. We show that this model is identifiable in most cases; by enumerating all possible situations in which the model is not identifiable, we provide sufficient conditions for its identifiability. Simulations are given to support the theoretical results. Moreover, in the case of more than two variables, we show that the whole causal structure can be found by applying the PNL causal model to each structure in the Markov equivalent class and testing if the disturbance is independent of the direct causes for each variable. In this way the exhaustive search over all possible causal structures is avoided., Comment: Appears in Proceedings of the Twenty-Fifth Conference on Uncertainty in Artificial Intelligence (UAI2009)

We consider to learn a causal ordering of variables in a linear non-Gaussian acyclic model called LiNGAM. Several existing methods have been shown to consistently estimate a causal ordering assuming that all the model assumptions are correct. But, the estimation results could be distorted if some assumptions actually are violated. In this paper, we propose a new algorithm for learning causal orders that is robust against one typical violation of the model assumptions: latent confounders. We demonstrate the effectiveness of our method using artificial data., Comment: 8 pages, 2 figures

Separation of the sources and analysis of their connectivity have been an important topic in EEG/MEG analysis. To solve this problem in an automatic manner, we propose a two-layer model, in which the sources are conditionally uncorrelated from each other, but not independent; the dependence is caused by the causality in their time-varying variances (envelopes). The model is identified in two steps. We first propose a new source separation technique which takes into account the autocorrelations (which may be time-varying) and time-varying variances of the sources. The causality in the envelopes is then discovered by exploiting a special kind of multivariate GARCH (generalized autoregressive conditional heteroscedasticity) model. The resulting causal diagram gives the effective connectivity between the separated sources; in our experimental results on MEG data, sources with similar functions are grouped together, with negative influences between groups, and the groups are connected via some interesting sources., Comment: Appears in Proceedings of the Twenty-Sixth Conference on Uncertainty in Artificial Intelligence (UAI2010)

We introduce a new family of estimators for unnormalized statistical models. Our family of estimators is parameterized by two nonlinear functions and uses a single sample from an auxiliary distribution, generalizing Maximum Likelihood Monte Carlo estimation of Geyer and Thompson (1992). The family is such that we can estimate the partition function like any other parameter in the model. The estimation is done by optimizing an algebraically simple, well defined objective function, which allows for the use of dedicated optimization methods. We establish consistency of the estimator family and give an expression for the asymptotic covariance matrix, which enables us to further analyze the influence of the nonlinearities and the auxiliary density on estimation performance. Some estimators in our family are particularly stable for a wide range of auxiliary densities. Interestingly, a specific choice of the nonlinearity establishes a connection between density estimation and classification by nonlinear logistic regression. Finally, the optimal amount of auxiliary samples relative to the given amount of the data is considered from the perspective of computational efficiency., Comment: Appears in Proceedings of the Twenty-Sixth Conference on Uncertainty in Artificial Intelligence (UAI2010)

Structural equation models and Bayesian networks have been widely used to analyze causal relations between continuous variables. In such frameworks, linear acyclic models are typically used to model the data-generating process of variables. Recently, it was shown that use of non-Gaussianity identifies the full structure of a linear acyclic model, i.e., a causal ordering of variables and their connection strengths, without using any prior knowledge on the network structure, which is not the case with conventional methods. However, existing estimation methods are based on iterative search algorithms and may not converge to a correct solution in a finite number of steps. In this paper, we propose a new direct method to estimate a causal ordering and connection strengths based on non-Gaussianity. In contrast to the previous methods, our algorithm requires no algorithmic parameters and is guaranteed to converge to the right solution within a small fixed number of steps if the data strictly follows the model., Comment: A revised version of this was accepted in Journal of Machine Learning Research

Many statistical methods have been proposed to estimate causal models in classical situations with fewer variables than observations (p>n). In this paper, we propose a method to find exogenous variables in a linear non-Gaussian causal model, which requires much smaller sample sizes than conventional methods and works even when p>>n. The key idea is to identify which variables are exogenous based on non-Gaussianity instead of estimating the entire structure of the model. Exogenous variables work as triggers that activate a causal chain in the model, and their identification leads to more efficient experimental designs and better understanding of the causal mechanism. We present experiments with artificial data and real-world gene expression data to evaluate the method., Comment: A revised version of this was published in Proc. ICANN2010