How do humans perceive the speed of a coherent motion stimulus that contains motion energy in multiple spatiotemporal frequency bands? Here we tested the idea that perceived speed is the result of an integration process that optimally combines speed information across independent spatiotemporal frequency channels. We formalized this hypothesis with a Bayesian observer model that combines the likelihood functions provided by the individual channel responses (cues). We experimentally validated the model with a 2AFC speed discrimination experiment that measured subjects' perceived speed of drifting sinusoidal gratings with different contrasts and spatial frequencies, and of various combinations of these single gratings. We found that the perceived speeds of the combined stimuli are independent of the relative phase of the underlying grating components. The results also show that the discrimination thresholds are smaller for the combined stimuli than for the individual grating components, supporting the cue combination hypothesis. The proposed Bayesian model fits the data well, accounting for the full psychometric functions of both simple and combined stimuli. Fits are improved if we assume that the channel responses are subject to divisive normalization. Our results provide an important step toward a more complete model of visual motion perception that can predict perceived speeds for coherent motion stimuli of arbitrary spatial structure.

We present a non-factorized variational method for full posterior inference in Bayesian hierarchical models, with the goal of capturing the posterior variable dependencies via efficient and possibly parallel computation. Our approach unifies the integrated nested Laplace approximation (INLA) under the variational framework.

With the advent of modern stimulation techniques in neuroscience, the opportunity arises to map neuron to neuron connectivity. In this work, we develop a method for efficiently inferring posterior distributions over synaptic strengths in neural microcircuits. The input to our algorithm is data from experiments in which action potentials from putative presynaptic neurons can be evoked while a subthreshold recording is made from a single postsynaptic neuron. We present a realistic statistical model which accounts for the main sources of variability in this experiment and allows for significant prior information about the connectivity and neuronal cell types to be incorporated if available. Due to the technical challenges and sparsity of these systems, it is important to focus experimental time stimulating the neurons whose synaptic strength is most ambiguous, therefore we also develop an online optimal design algorithm for choosing which neurons to stimulate at each trial.

We introduce a novel variational method that allows to approximately integrate out kernel hyperparameters, such as length-scales, in Gaussian process regression. This approach consists of a novel variant of the variational framework that has been recently developed for the Gaussian process latent variable model which additionally makes use of a standardised representation of the Gaussian process. We consider this technique for learning Mahalanobis distance metrics in a Gaussian process regression setting and provide experimental evaluations and comparisons with existing methods by considering datasets with high-dimensional inputs.

Stochastic variational inference (SVI) uses stochastic optimization to scale up Bayesian computation to massive data. We present an alternative perspective on SVI as approximate parallel coordinate ascent. SVI trades-off bias and variance to step close to the unknown true coordinate optimum given by batch variational Bayes (VB). We define a model to automate this process.

In many problem settings, parameter vectors are not merely sparse, but dependent in such a way that non-zero coefficients tend to cluster together. We refer to this form of dependency as "region sparsity". Classical sparse regression methods, such as the lasso and automatic relevance determination (ARD), model parameters as independent a priori, and therefore do not exploit such dependencies. Here we introduce a hierarchical model for smooth, region-sparse weight vectors and tensors in a linear regression setting. Our approach represents a hierarchical extension of the relevance determination framework, where we add a transformed Gaussian process to model the dependencies between the prior variances of regression weights. We combine this with a structured model of the prior variances of Fourier coefficients, which eliminates unnecessary high frequencies. The resulting prior encourages weights to be region-sparse in two different bases simultaneously. We develop efficient approximate inference methods and show substantial improvements over comparable methods (e.g., group lasso and smooth RVM) for both simulated and real datasets from brain imaging.

The central challenge in probabilistic inference is numerical integration, to average over ensembles of models or unknown (hyper-)parameters (for example to compute the marginal likelihood or a partition function).

We propose a spiking network model capable of performing both approximate inference and learning for any hidden Markov model. The lower layer sensory neurons detect noisy measurements of hidden world states. The higher layer neurons with recurrent connections infer a posterior distribution over world states from spike trains generated by sensory neurons. We show how such a neuronal network with synaptic plasticity can implement a form of Bayesian inference similar to Monte Carlo methods such as particle filtering. Each spike in the population of inference neurons represents a sample of a particular hidden world state.

This paper studies the problem of rank aggregation under the Plackett-Luce model. The goal is to infer a global ranking and related scores of the items, based on partial rankings provided by multiple users over multiple subsets of items. A question of particular interest is how to optimally assign items to users for ranking and how many item assignments are needed to achieve a target estimation error. Without any assumptions on how the items are assigned to users, we derive an oracle lower bound and the Cramér-Rao lower bound of the estimation error. We prove an upper bound on the estimation error achieved by the maximum likelihood estimator, and show that both the upper bound and the Cramér-Rao lower bound inversely depend on the spectral gap of the Laplacian of an appropriately defined comparison graph. Since random comparison graphs are known to have large spectral gaps, this suggests the use of random assignments when we have the control. Precisely, the matching oracle lower bound and the upper bound on the estimation error imply that the maximum likelihood estimator together with a random assignment is minimax-optimal up to a logarithmic factor. We further analyze a popular rankbreaking scheme that decompose partial rankings into pairwise comparisons. We show that even if one applies the mismatched maximum likelihood estimator that assumes independence (on pairwise comparisons that are now dependent due to rank-breaking), minimax optimal performance is still achieved up to a logarithmic factor.

Fluorescent calcium imaging provides a potentially powerful tool for inferring connectivity in neural circuits with up to thousands of neurons. However, a key challenge in using calcium imaging for connectivity detection is that current systems often have a temporal response and frame rate that can be orders of magnitude slower than the underlying neural spiking process. Bayesian inference methods based on expectation-maximization (EM) have been proposed to overcome these limitations, but are often computationally demanding since the E-step in the EM procedure typically involves state estimation for a high-dimensional nonlinear dynamical system. In this work, we propose a computationally fast method for the state estimation based on a hybrid of loopy belief propagation and approximate message passing (AMP). The key insight is that a neural system as viewed through calcium imaging can be factorized into simple scalar dynamical systems for each neuron with linear interconnections between the neurons. Using the structure, the updates in the proposed hybrid AMP methodology can be computed by a set of one-dimensional state estimation procedures and linear transforms with the connectivity matrix. This yields a computationally scalable method for inferring connectivity of large neural circuits. Simulations of the method on realistic neural networks demonstrate good accuracy with computation times that are potentially significantly faster than current approaches based on Markov Chain Monte Carlo methods.