In a variety of behavioral tasks, subjects exhibit an automatic and apparently sub-optimal sequential effect: they respond more rapidly and accurately to a stimulus if it reinforces a local pattern in stimulus history, such as a string of repetitions or alternations, compared to when it violates such a pattern. This is often the case even if the local trends arise by chance in the context of a randomized design, such that stimulus history has no predictive power. In this work, we use a normative Bayesian framework to examine the hypothesis that such idiosyncrasies may reflect the inadvertent engagement of fundamental mechanisms critical for adapting to changing statistics in the natural environment. We show that prior belief in non-stationarity can induce experimentally observed sequential effects in an otherwise Bayes-optimal algorithm. The Bayesian algorithm is shown to be well approximated by linear-exponential filtering of past observations, a feature also apparent in the behavioral data. We derive an explicit relationship between the parameters and computations of the exact Bayesian algorithm and those of the approximate linear-exponential filter. Since the latter is equivalent to a leaky-integration process, a commonly used model of neuronal dynamics underlying perceptual decision-making and trial-to-trial dependencies, our model provides a principled account of why such dynamics are useful. We also show that near-optimal tuning of the leaky-integration process is possible, using stochastic gradient descent based only on the noisy binary inputs. This is a proof of concept that not only can neurons implement near-optimal prediction based on standard neuronal dynamics, but that they can also learn to tune the processing parameters without explicitly representing probabilities.

In cognitive science, empirical data collected from participants are the arbiters in model selection. Model discrimination thus depends on designing maximally informative experiments. It has been shown that adaptive design optimization (ADO) allows one to discriminate models as efficiently as possible in simulation experiments. In this paper we use ADO in a series of experiments with people to discriminate the Power, Exponential, and Hyperbolic models of memory retention, which has been a long-standing problem in cognitive science, providing an ideal setting in which to test the application of ADO for addressing questions about human cognition. Using an optimality criterion based on mutual information, ADO is able to find designs that are maximally likely to increase our certainty about the true model upon observation of the experiment outcomes. Results demonstrate the usefulness of ADO and also reveal some challenges in its implementation.

Most of existing methods for DNA motif discovery consider only a single set of sequences to find an over-represented motif. In contrast, we consider multiple sets of sequences where we group sets associated with the same motif into a cluster, assuming that each set involves a single motif. Clustering sets of sequences yields clusters of coherent motifs, improving signal-to-noise ratio or enabling us to identify multiple motifs. We present a probabilistic model for DNA motif discovery where we identify multiple motifs through searching for patterns which are shared across multiple sets of sequences. Our model infers cluster-indicating latent variables and learns motifs simultaneously, where these two tasks interact with each other. We show that our model can handle various motif discovery problems, depending on how to construct multiple sets of sequences. Experiments on three different problems for discovering DNA motifs emphasize the useful behavior and confirm the substantial gains over existing methods where only single set of sequences is considered.

Many nonlinear dynamical phenomena can be effectively modeled by a system that switches among a set of conditionally linear dynamical modes. We consider two such models: the switching linear dynamical system (SLDS) and the switching vector autoregressive (VAR) process. In this paper, we present a nonparametric approach to the learning of an unknown number of persistent, smooth dynamical modes by utilizing a hierarchical Dirichlet process prior. We develop a sampling algorithm that combines a truncated approximation to the Dirichlet process with an efficient joint sampling of the mode and state sequences. The utility and flexibility of our model are demonstrated on synthetic data, sequences of dancing honey bees, and the IBOVESPA stock index.

In this paper we make several contributions towards accelerating approximate Bayesian structural inference for non-decomposable GGMs. Our first contribution is to show how to efficiently compute a BIC or Laplace approximation to the marginal likelihood of non-decomposable graphs using convex methods for precision matrix estimation. This optimization technique can be used as a fast scoring function inside standard Stochastic Local Search (SLS) for generating posterior samples. Our second contribution is a novel framework for efficiently generating large sets of high-quality graph topologies without performing local search. This graph proposal method, which we call Neighborhood Fusion" (NF), samples candidate Markov blankets at each node using sparse regression techniques. Our final contribution is a hybrid method combining the complementary strengths of NF and SLS. Experimental results in structural recovery and prediction tasks demonstrate that NF and hybrid NF/SLS out-perform state-of-the-art local search methods, on both synthetic and real-world datasets, when realistic computational limits are imposed."

Non-parametric Bayesian techniques are considered for learning dictionaries for sparse image representations, with applications in denoising, inpainting and compressive sensing (CS). The beta process is employed as a prior for learning the dictionary, and this non-parametric method naturally infers an appropriate dictionary size. The Dirichlet process and a probit stick-breaking process are also considered to exploit structure within an image. The proposed method can learn a sparse dictionary in situ; training images may be exploited if available, but they are not required. Further, the noise variance need not be known, and can be non-stationary. Another virtue of the proposed method is that sequential inference can be readily employed, thereby allowing scaling to large images. Several example results are presented, using both Gibbs and variational Bayesian inference, with comparisons to other state-of-the-art approaches.

While many perceptual and cognitive phenomena are well described in terms of Bayesian inference, the necessary computations are intractable at the scale of real-world tasks, and it remains unclear how the human mind approximates Bayesian inference algorithmically. We explore the proposal that for some tasks, humans use a form of Markov Chain Monte Carlo to approximate the posterior distribution over hidden variables. As a case study, we show how several phenomena of perceptual multistability can be explained as MCMC inference in simple graphical models for low-level vision.

Principal Components Analysis (PCA) has become established as one of the key tools for dimensionality reduction when dealing with real valued data. Approaches such as exponential family PCA and non-negative matrix factorisation have successfully extended PCA to non-Gaussian data types, but these techniques fail to take advantage of Bayesian inference and can suffer from problems of overfitting and poor generalisation. This paper presents a fully probabilistic approach to PCA, which is generalised to the exponential family, based on Hybrid Monte Carlo sampling. We describe the model which is based on a factorisation of the observed data matrix, and show performance of the model on both synthetic and real data.

Everyday social interactions are heavily influenced by our snap judgments about others' goals. Even young infants can infer the goals of intentional agents from observing how they interact with objects and other agents in their environment: e.g., that one agent is'helping' or'hindering' another's attempt to get up a hill or open a box. We propose a model for how people can infer these social goals from actions, based on inverse planning in multiagent Markov decision problems (MDPs). The model infers the goal most likely to be driving an agent's behavior byassuming the agent acts approximately rationally given environmental constraints andits model of other agents present.

Recent work on the statistical modeling of neural responses has focused on modulated renewal processes in which the spike rate is a function of the stimulus and recent spiking history. Typically, these models incorporate spike-history dependencies via either: (A) a conditionally-Poisson process with rate dependent on a linear projection of the spike train history (e.g., generalized linear model); or (B) a modulated non-Poisson renewal process (e.g., inhomogeneous gamma process). Here we show that the two approaches can be combined, resulting in a {\it conditional renewal} (CR) model for neural spike trains. This model captures both real and rescaled-time effects, and can be fit by maximum likelihood using a simple application of the time-rescaling theorem [1]. We show that for any modulated renewal process model, the log-likelihood is concave in the linear filter parameters only under certain restrictive conditions on the renewal density (ruling out many popular choices, e.g. gamma with $\kappa \neq1$), suggesting that real-time history effects are easier to estimate than non-Poisson renewal properties. Moreover, we show that goodness-of-fit tests based on the time-rescaling theorem [1] quantify relative-time effects, but do not reliably assess accuracy in spike prediction or stimulus-response modeling. We illustrate the CR model with applications to both real and simulated neural data.