We propose a method for recovering the structure of a sparse undirected graphical model when very few samples are available. The method decides about the presence or absence of bonds between pairs of variable by considering one pair at a time and using a closed form formula, analytically derived by calculating the posterior probability for every possible model explaining a two body system using Jeffreys prior. The approach does not rely on the optimization of any cost functions and consequently is much faster than existing algorithms. Despite this time and computational advantage, numerical results show that for several sparse topologies the algorithm is comparable to the best existing algorithms, and is more accurate in the presence of hidden variables. We apply this approach to the analysis of US stock market data and to neural data, in order to show its efficiency in recovering robust statistical dependencies in real data with non-stationary correlations in time and/or space.

In neuroscience, the similarity matrix of neural activity patterns in response to different sensory stimuli or under different cognitive states reflects the structure of neural representational space. Existing methods derive point estimations of neural activity patterns from noisy neural imaging data, and the similarity is calculated from these point estimations. We show that this approach translates structured noise from estimated patterns into spurious bias structure in the resulting similarity matrix, which is especially severe when signal-to-noise ratio is low and experimental conditions cannot be fully randomized in a cognitive task. We propose an alternative Bayesian framework for computing representational similarity in which we treat the covariance structure of neural activity patterns as a hyper-parameter in a generative model of the neural data, and directly estimate this covariance structure from imaging data while marginalizing over the unknown activity patterns. Converting the estimated covariance structure into a correlation matrix offers a much less biased estimate of neural representational similarity. Our method can also simultaneously estimate a signal-to-noise map that informs where the learned representational structure is supported more strongly, and the learned covariance matrix can be used as a structured prior to constrain Bayesian estimation of neural activity patterns. Our code is freely available in Brain Imaging Analysis Kit (Brainiak) (https://github.com/IntelPNI/brainiak), a python toolkit for brain imaging analysis.

In recent years, a rapidly increasing number of applications in practice requires solving non-convex objectives, like training neural networks, learning graphical models, maximum likelihood estimation etc. Though simple heuristics such as gradient descent with very few modifications tend to work well, theoretical understanding is very weak. We consider possibly the most natural class of non-convex functions where one could hope to obtain provable guarantees: functions that are ``approximately convex'', i.e. functions $\tf: \Real^d \to \Real$ for which there exists a \emph{convex function} $f$ such that for all $x$, $|\tf(x) - f(x)| \le \errnoise$ for a fixed value $\errnoise$. We then want to minimize $\tf$, i.e. output a point $\tx$ such that $\tf(\tx) \le \min_{x} \tf(x) + \err$. It is quite natural to conjecture that for fixed $\err$, the problem gets harder for larger $\errnoise$, however, the exact dependency of $\err$ and $\errnoise$ is not known. In this paper, we strengthen the known \emph{information theoretic} lower bounds on the trade-off between $\err$ and $\errnoise$ substantially, and exhibit an algorithm that matches these lower bounds for a large class of convex bodies.

We introduce the Forget-me-not Process, an efficient, non-parametric meta-algorithm for online probabilistic sequence prediction for piecewise stationary, repeating sources. Our method works by taking a Bayesian approach to partition a stream of data into postulated task-specific segments, while simultaneously building a model for each task. We provide regret guarantees with respect to piecewise stationary data sources under the logarithmic loss, and validate the method empirically across a range of sequence prediction and task identification problems.

In this work, we propose an infinite restricted Boltzmann machine (RBM), whose maximum likelihood estimation (MLE) corresponds to a constrained convex optimization. We consider the Frank-Wolfe algorithm to solve the program, which provides a sparse solution that can be interpreted as inserting a hidden unit at each iteration, so that the optimization process takes the form of a sequence of finite models of increasing complexity. As a side benefit, this can be used to easily and efficiently identify an appropriate number of hidden units during the optimization. The resulting model can also be used as an initialization for typical state-of-the-art RBM training algorithms such as contrastive divergence, leading to models with consistently higher test likelihood than random initialization.

A fundamental problem in cognitive neuroscience is how humans make decisions, act, and behave in relation to other humans. Here we adopt the hypothesis that when we are in an interactive social setting, our brains perform Bayesian inference of the intentions and cooperativeness of others using probabilistic representations. We employ the framework of partially observable Markov decision processes (POMDPs) to model human decision making in a social context, focusing specifically on the volunteer's dilemma in a version of the classic Public Goods Game. We show that the POMDP model explains both the behavior of subjects as well as neural activity recorded using fMRI during the game. The decisions of subjects can be modeled across all trials using two interpretable parameters. Furthermore, the expected reward predicted by the model for each subject was correlated with the activation of brain areas related to reward expectation in social interactions. Our results suggest a probabilistic basis for human social decision making within the framework of expected reward maximization.

Probabilistic graphical models have been widely used to model complex systems and aid scientific discoveries. As a result, there is a large body of literature focused on consistent model selection. However, scientists are often interested in understanding uncertainty associated with the estimated parameters, which current literature has not addressed thoroughly. In this paper, we propose a novel estimator for edge parameters for pairwise graphical models based on Hyv\"arinen scoring rule. Hyv\"arinen scoring rule is especially useful in cases where the normalizing constant cannot be obtained efficiently in a closed form. We prove that the estimator is $\sqrt{n}$-consistent and asymptotically Normal. This result allows us to construct confidence intervals for edge parameters, as well as, hypothesis tests. We establish our results under conditions that are typically assumed in the literature for consistent estimation. However, we do not require that the estimator consistently recovers the graph structure. In particular, we prove that the asymptotic distribution of the estimator is robust to model selection mistakes and uniformly valid for a large number of data-generating processes. We illustrate validity of our estimator through extensive simulation studies.

Markov chain Monte Carlo (MCMC) is one of the main workhorses of probabilistic inference, but it is notoriously hard to measure the quality of approximate posterior samples. This challenge is particularly salient in black box inference methods, which can hide details and obscure inference failures. In this work, we extend the recently introduced bidirectional Monte Carlo technique to evaluate MCMC-based posterior inference algorithms. By running annealed importance sampling (AIS) chains both from prior to posterior and vice versa on simulated data, we upper bound in expectation the symmetrized KL divergence between the true posterior distribution and the distribution of approximate samples. We integrate our method into two probabilistic programming languages, WebPPL and Stan, and validate it on several models and datasets. As an example of how our method be used to guide the design of inference algorithms, we apply it to study the effectiveness of different model representations in WebPPL and Stan.

Probabilistic inference algorithms such as Sequential Monte Carlo (SMC) provide powerful tools for constraining procedural models in computer graphics, but they require many samples to produce desirable results. In this paper, we show how to create procedural models which learn how to satisfy constraints. We augment procedural models with neural networks which control how the model makes random choices based on the output it has generated thus far. We call such models neurally-guided procedural models. As a pre-computation, we train these models to maximize the likelihood of example outputs generated via SMC. They are then used as efficient SMC importance samplers, generating high-quality results with very few samples. We evaluate our method on L-system-like models with image-based constraints. Given a desired quality threshold, neurally-guided models can generate satisfactory results up to 10x faster than unguided models.

The reparameterization gradient has become a widely used method to obtain Monte Carlo gradients to optimize the variational objective. However, this technique does not easily apply to commonly used distributions such as beta or gamma without further approximations, and most practical applications of the reparameterization gradient fit Gaussian distributions. In this paper, we introduce the generalized reparameterization gradient, a method that extends the reparameterization gradient to a wider class of variational distributions. Generalized reparameterizations use invertible transformations of the latent variables which lead to transformed distributions that weakly depend on the variational parameters. This results in new Monte Carlo gradients that combine reparameterization gradients and score function gradients. We demonstrate our approach on variational inference for two complex probabilistic models. The generalized reparameterization is effective: even a single sample from the variational distribution is enough to obtain a low-variance gradient.