The human brain can be described as containing a number of functional regions. For a given task, these regions, as well as the connections between them, play a key role in information processing in the brain. However, most existing multi-voxel pattern analysis approaches either treat multiple functional regions as one large uniform region or several independent regions, ignoring the connections between regions. In this paper, we propose to model such connections in an Hidden Conditional Random Field (HCRF) framework, where the classifier of one region of interest (ROI) makes predictions based on not only its voxels but also the classifier predictions from ROIs that it connects to. Furthermore, we propose a structural learning method in the HCRF framework to automatically uncover the connections between ROIs. Experiments on fMRI data acquired while human subjects viewing images of natural scenes show that our model can improve the top-level (the classifier combining information from all ROIs) and ROI-level prediction accuracy, as well as uncover some meaningful connections between ROIs.

There is a growing body of experimental evidence to suggest that the brain is capable of approximating optimal Bayesian inference in the face of noisy input stimuli. Despite this progress, the neural underpinnings of this computation are still poorly understood. In this paper we focus on the problem of Bayesian filtering of stochastic time series. In particular we introduce a novel neural network, derived from a line attractor architecture, whose dynamics map directly onto those of the Kalman Filter in the limit where the prediction error is small. When the prediction error is large we show that the network responds robustly to change-points in a way that is qualitatively compatible with the optimal Bayesian model. The model suggests ways in which probability distributions are encoded in the brain and makes a number of testable experimental predictions.

Across a wide range of cognitive tasks, recent experience influences behavior. For example, when individuals repeatedly perform a simple two-alternative forcedchoice task(2AFC), response latencies vary dramatically based on the immediately preceding trial sequence. These sequential effects have been interpreted as adaptation to the statistical structure of an uncertain, changing environment (e.g., Jones and Sieck, 2003; Mozer, Kinoshita, and Shettel, 2007; Yu and Cohen, 2008).The Dynamic Belief Model (DBM) (Yu and Cohen, 2008) explains sequential effects in 2AFC tasks as a rational consequence of a dynamic internal representation that tracks second-order statistics of the trial sequence (repetition rates) and predicts whether the upcoming trial will be a repetition or an alternation ofthe previous trial. Experimental results suggest that first-order statistics (base rates) also influence sequential effects. We propose a model that learns both first-and second-order sequence properties, each according to the basic principles ofthe DBM but under a unified inferential framework. This model, the Dynamic BeliefMixture Model (DBM2), obtains precise, parsimonious fits to data. Furthermore, the model predicts dissociations in behavioral (Maloney, Martello, Sahm, and Spillmann, 2005) and electrophysiological studies (Jentzsch and Sommer, 2002),supporting the psychological and neurobiological reality of its two components.

The nested Chinese restaurant process (nCRP) is a powerful nonparametric Bayesian model for learning tree-based hierarchies from data. Since its posterior distribution is intractable, current inference methods have all relied on MCMC sampling. In this paper, we develop an alternative inference technique based on variational methods. To employ variational methods, we derive a tree-based stick-breaking construction of the nCRP mixture model, and a novel variational algorithm that efficiently explores a posterior over a large set of combinatorial structures. We demonstrate the use of this approach for text and hand written digits modeling, where we show we can adapt the nCRP to continuous data as well.

Implementations of topic models typically use symmetric Dirichlet priors with fixed concentration parameters, with the implicit assumption that such smoothing parameters" have little practical effect. In this paper, we explore several classes of structured priors for topic models. We find that an asymmetric Dirichlet prior over the document-topic distributions has substantial advantages over a symmetric prior, while an asymmetric prior over the topic-word distributions provides no real benefit. Approximation of this prior structure through simple, efficient hyperparameter optimization steps is sufficient to achieve these performance gains. The prior structure we advocate substantially increases the robustness of topic models to variations in the number of topics and to the highly skewed word frequency distributions common in natural language. Since this prior structure can be implemented using efficient algorithms that add negligible cost beyond standard inference techniques, we recommend it as a new standard for topic modeling."

In the last few decades, model complexity has received a lot of press. While many methods have been proposed that jointly measure a model’s descriptive adequacy and its complexity, few measures exist that measure complexity in itself. Moreover, existing measures ignore the parameter prior, which is an inherent part of the model and affects the complexity. This paper presents a stand alone measure for model complexity, that takes the number of parameters, the functional form, the range of the parameters and the parameter prior into account. This Prior Predictive Complexity (PPC) is an intuitive and easy to compute measure. It starts from the observation that model complexity is the property of the model that enables it to fit a wide range of outcomes. The PPC then measures how wide this range exactly is.

When individuals independently recollect events or retrieve facts from memory, how can we aggregate these retrieved memories to reconstruct the actual set of events or facts? In this research, we report the performance of individuals in a series of general knowledge tasks, where the goal is to reconstruct from memory the order of historic events, or the order of items along some physical dimension. We introduce two Bayesian models for aggregating order information based on a Thurstonian approach and Mallows model. Both models assume that each individuals reconstruction is based on either a random permutation of the unobserved ground truth, or by a pure guessing strategy. We apply MCMC to make inferences about the underlying truth and the strategies employed by individuals. The models demonstrate a wisdom of crowds" effect, where the aggregated orderings are closer to the true ordering than the orderings of the best individual."

Directed graphical models such as Bayesian networks are a favored formalism to model the dependency structures in complex multivariate systems such as those encountered in biology and neural sciences. When the system is undergoing dynamic transformation, often a temporally rewiring network is needed for capturing the dynamic causal influences between covariates. In this paper, we propose a time-varying dynamic Bayesian network (TV-DBN) for modeling the structurally varying directed dependency structures underlying non-stationary biological/neural time series. This is a challenging problem due the non-stationarity and sample scarcity of the time series. We present a kernel reweighted $\ell_1$ regularized auto-regressive procedure for learning the TV-DBN model. Our method enjoys nice properties such as computational efficiency and provable asymptotic consistency. Applying TV-DBN to time series measurements during yeast cell cycle and brain response to visual stimuli reveals interesting dynamics underlying the respective biological systems.

The goal of perception is to infer the hidden states in the hierarchical process by which sensory data are generated. Human behavior is consistent with the optimal statistical solution to this problem in many tasks, including cue combination and orientation detection. Understanding the neural mechanisms underlying this behavior is of particular importance, since probabilistic computations are notoriously challenging. Here we propose a simple mechanism for Bayesian inference which involves averaging over a few feature detection neurons which fire at a rate determined by their similarity to a sensory stimulus. This mechanism is based on a Monte Carlo method known as importance sampling, commonly used in computer science and statistics. Moreover, a simple extension to recursive importance sampling can be used to perform hierarchical Bayesian inference. We identify a scheme for implementing importance sampling with spiking neurons, and show that this scheme can account for human behavior in cue combination and oblique effect.

We present a general Bayesian approach to probabilistic matrix factorization subject to linear constraints. The approach is based on a Gaussian observation model and Gaussian priors with bilinear equality and inequality constraints. We present an efficient Markov chain Monte Carlo inference procedure based on Gibbs sampling. Special cases of the proposed model are Bayesian formulations of non-negative matrix factorization and factor analysis. The method is evaluated on a blind source separation problem. We demonstrate that our algorithm can be used to extract meaningful and interpretable features that are remarkably different from features extracted using existing related matrix factorization techniques.