Mechanistic models of single-neuron dynamics have been extensively studied in computational neuroscience. However, identifying which models can quantitatively reproduce empirically measured data has been challenging. We propose to overcome this limitation by using likelihood-free inference approaches (also known as Approximate Bayesian Computation, ABC) to perform full Bayesian inference on single-neuron models. Our approach builds on recent advances in ABC by learning a neural network which maps features of the observed data to the posterior distribution over parameters. We learn a Bayesian mixture-density network approximating the posterior over multiple rounds of adaptively chosen simulations. Furthermore, we propose an efficient approach for handling missing features and parameter settings for which the simulator fails, as well as a strategy for automatically learning relevant features using recurrent neural networks. On synthetic data, our approach efficiently estimates posterior distributions and recovers ground-truth parameters. On in-vitro recordings of membrane voltages, we recover multivariate posteriors over biophysical parameters, which yield model-predicted voltage traces that accurately match empirical data. Our approach will enable neuroscientists to perform Bayesian inference on complex neuron models without having to design model-specific algorithms, closing the gap between mechanistic and statistical approaches to single-neuron modelling.

Calcium imaging permits optical measurement of neural activity. Since intracellular calcium concentration is an indirect measurement of neural activity, computational tools are necessary to infer the true underlying spiking activity from fluorescence measurements. Bayesian model inversion can be used to solve this problem, but typically requires either computationally expensive MCMC sampling, or faster but approximate maximum-a-posteriori optimization. Here, we introduce a flexible algorithmic framework for fast, efficient and accurate extraction of neural spikes from imaging data. Using the framework of variational autoencoders, we propose to amortize inference by training a deep neural network to perform model inversion efficiently. The recognition network is trained to produce samples from the posterior distribution over spike trains. Once trained, performing inference amounts to a fast single forward pass through the network, without the need for iterative optimization or sampling. We show that amortization can be applied flexibly to a wide range of nonlinear generative models and significantly improves upon the state of the art in computation time, while achieving competitive accuracy. Our framework is also able to represent posterior distributions over spike-trains. We demonstrate the generality of our method by proposing the first probabilistic approach for separating backpropagating action potentials from putative synaptic inputs in calcium imaging of dendritic spines.

In this paper, we consider the block-sparse signals recovery problem in the context of multiple measurement vectors (MMV) with common row sparsity patterns. We develop a new method for recovery of common row sparsity MMV signals, where a pattern-coupled hierarchical Gaussian prior model is introduced to characterize both the block-sparsity of the coefficients and the statistical dependency between neighboring coefficients of the common row sparsity MMV signals. Unlike many other methods, the proposed method is able to automatically capture the block sparse structure of the unknown signal. Our method is developed using an expectation-maximization (EM) framework. Simulation results show that our proposed method offers competitive performance in recovering block-sparse common row sparsity pattern MMV signals.

While all kinds of mixed data -from personal data, over panel and scientific data, to public and commercial data- are collected and stored, building probabilistic graphical models for these hybrid domains becomes more difficult. Users spend significant amounts of time in identifying the parametric form of the random variables (Gaussian, Poisson, Logit, etc.) involved and learning the mixed models. To make this difficult task easier, we propose the first trainable probabilistic deep architecture for hybrid domains that features tractable queries. It is based on Sum-Product Networks (SPNs) with piecewise polynomial leave distributions together with novel nonparametric decomposition and conditioning steps using the Hirschfeld-Gebelein-R\'enyi Maximum Correlation Coefficient. This relieves the user from deciding a-priori the parametric form of the random variables but is still expressive enough to effectively approximate any continuous distribution and permits efficient learning and inference. Our empirical evidence shows that the architecture, called Mixed SPNs, can indeed capture complex distributions across a wide range of hybrid domains.

Compression and computational efficiency in deep learning have become a problem of great significance. In this work, we argue that the most principled and effective way to attack this problem is by adopting a Bayesian point of view, where through sparsity inducing priors we prune large parts of the network. We introduce two novelties in this paper: 1) we use hierarchical priors to prune nodes instead of individual weights, and 2) we use the posterior uncertainties to determine the optimal fixed point precision to encode the weights. Both factors significantly contribute to achieving the state of the art in terms of compression rates, while still staying competitive with methods designed to optimize for speed or energy efficiency.

This paper is about index policies for minimizing (frequentist) regret in a stochastic multi-armed bandit model, inspired by a Bayesian view on the problem. Our main contribution is to prove that the Bayes-UCB algorithm, which relies on quantiles of posterior distributions, is asymptotically optimal when the reward distributions belong to a one-dimensional exponential family, for a large class of prior distributions. We also show that the Bayesian literature gives new insight on what kind of exploration rates could be used in frequentist, UCB-type algorithms. Indeed, approximations of the Bayesian optimal solution or the Finite Horizon Gittins indices provide a justification for the kl-UCB+ and kl-UCB-H+ algorithms, whose asymptotic optimality is also established.

Implicit probabilistic models are a flexible class of models defined by a simulation process for data. They form the basis for theories which encompass our understanding of the physical world. Despite this fundamental nature, the use of implicit models remains limited due to challenges in specifying complex latent structure in them, and in performing inferences in such models with large data sets. In this paper, we first introduce hierarchical implicit models (HIMs). HIMs combine the idea of implicit densities with hierarchical Bayesian modeling, thereby defining models via simulators of data with rich hidden structure. Next, we develop likelihood-free variational inference (LFVI), a scalable variational inference algorithm for HIMs. Key to LFVI is specifying a variational family that is also implicit. This matches the model's flexibility and allows for accurate approximation of the posterior. We demonstrate diverse applications: a large-scale physical simulator for predator-prey populations in ecology; a Bayesian generative adversarial network for discrete data; and a deep implicit model for text generation.

This paper develops variational continual learning (VCL), a simple but general framework for continual learning that fuses online variational inference (VI) and recent advances in Monte Carlo VI for neural networks. The framework can successfully train both deep discriminative models and deep generative models in complex continual learning settings where existing tasks evolve over time and entirely new tasks emerge. Experimental results show that variational continual learning outperforms state-of-the-art continual learning methods on a variety of tasks, avoiding catastrophic forgetting in a fully automatic way.

Deep neural networks (NNs) are powerful black box predictors that have recently achieved impressive performance on a wide spectrum of tasks. Quantifying predictive uncertainty in NNs is a challenging and yet unsolved problem. Bayesian NNs, which learn a distribution over weights, are currently the state-of-the-art for estimating predictive uncertainty; however these require significant modifications to the training procedure and are computationally expensive compared to standard (non-Bayesian) NNs. We propose an alternative to Bayesian NNs that is simple to implement, readily parallelizable, requires very little hyperparameter tuning, and yields high quality predictive uncertainty estimates. Through a series of experiments on classification and regression benchmarks, we demonstrate that our method produces well-calibrated uncertainty estimates which are as good or better than approximate Bayesian NNs. To assess robustness to dataset shift, we evaluate the predictive uncertainty on test examples from known and unknown distributions, and show that our method is able to express higher uncertainty on out-of-distribution examples. We demonstrate the scalability of our method by evaluating predictive uncertainty estimates on ImageNet.

Mention strong words such as "death" or "praise" to someone who has suicidal thoughts and chances are the neurons in their brains activate in a totally different pattern than those of a non-suicidal person. That's what researchers at University of Pittsburgh and Carnegie Mellon University discovered, and trained algorithms to distinguish, using data from fMRI brain scans. The scientists published the findings of their small-scale study Monday in the journal Nature Human Behaviour. They hope to study a larger group of people and use the data to develop simple tests that doctors can use to more readily identify people at risk of suicide. Suicide is the second-leading cause of death among young adults, according to the U.S. Centers for Disease Control and Prevention.