We propose a high dimensional classification method that involves nonparametric feature augmentation. Knowing that marginal density ratios are the most powerful univariate classifiers, we use the ratio estimates to transform the original feature measurements. Subsequently, penalized logistic regression is invoked, taking as input the newly transformed or augmented features. This procedure trains models equipped with local complexity and global simplicity, thereby avoiding the curse of dimensionality while creating a flexible nonlinear decision boundary. The resulting method is called Feature Augmentation via Nonparametrics and Selection (FANS). We motivate FANS by generalizing the Naive Bayes model, writing the log ratio of joint densities as a linear combination of those of marginal densities. It is related to generalized additive models, but has better interpretability and computability. Risk bounds are developed for FANS. In numerical analysis, FANS is compared with competing methods, so as to provide a guideline on its best application domain. Real data analysis demonstrates that FANS performs very competitively on benchmark email spam and gene expression data sets. Moreover, FANS is implemented by an extremely fast algorithm through parallel computing.

Neural population activity in cortical circuits is not solely driven by external inputs, but is also modulated by endogenous states which vary on multiple time-scales. To understand information processing in cortical circuits, we need to understand the statistical structure of internal states and their interaction with sensory inputs. Here, we present a statistical model for extracting hierarchically organised neural population states from multi-channel recordings of neural spiking activity. Population states are modelled using a hidden Markov decision tree with state-dependent tuning parameters and a generalised linear observation model. We present a variational Bayesian inference algorithm for estimating the posterior distribution over parameters from neural population recordings. On simulated data, we show that we can identify the underlying sequence of population states and reconstruct the ground truth parameters. Using population recordings from visual cortex, we find that a model with two levels of population states outperforms both a one-state and a two-state generalised linear model. Finally, we find that modelling of state-dependence also improves the accuracy with which sensory stimuli can be decoded from the population response.

Performance metrics for binary classification are designed to capture tradeoffs between four fundamental population quantities: true positives, false positives, true negatives and false negatives. Despite significant interest from theoretical and applied communities, little is known about either optimal classifiers or consistent algorithms for optimizing binary classification performance metrics beyond a few special cases. We consider a fairly large family of performance metrics given by ratios of linear combinations of the four fundamental population quantities. This family includes many well known binary classification metrics such as classification accuracy, AM measure, F-measure and the Jaccard similarity coefficient as special cases. Our analysis identifies the optimal classifiers as the sign of the thresholded conditional probability of the positive class, with a performance metric-dependent threshold. The optimal threshold can be constructed using simple plug-in estimators when the performance metric is a linear combination of the population quantities, but alternative techniques are required for the general case. We propose two algorithms for estimating the optimal classifiers, and prove their statistical consistency. Both algorithms are straightforward modifications of standard approaches to address the key challenge of optimal threshold selection, thus are simple to implement in practice. The first algorithm combines a plug-in estimate of the conditional probability of the positive class with optimal threshold selection. The second algorithm leverages recent work on calibrated asymmetric surrogate losses to construct candidate classifiers. We present empirical comparisons between these algorithms on benchmark datasets.

This work presents novel algorithms for learning Bayesian networks of bounded treewidth. Both exact and approximate methods are developed. The exact method combines mixed integer linear programming formulations for structure learning and treewidth computation. The approximate method consists in sampling k-trees (maximal graphs of treewidth k), and subsequently selecting, exactly or approximately, the best structure whose moral graph is a subgraph of that k-tree. The approaches are empirically compared to each other and to state-of-the-art methods on a collection of public data sets with up to 100 variables.

We propose a technique for decomposing the parameter learning problem in Bayesian networks into independent learning problems. Our technique applies to incomplete datasets and exploits variables that are either hidden or observed in the given dataset. We show empirically that the proposed technique can lead to orders-of-magnitude savings in learning time. We explain, analytically and empirically, the reasons behind our reported savings, and compare the proposed technique to related ones that are sometimes used by inference algorithms.

We consider the problem of inferring direct neural network connections from Calcium imaging time series. Inverse covariance estimation has proven to be a fast and accurate method for learning macro- and micro-scale network connectivity in the brain and in a recent Kaggle Connectomics competition inverse covariance was the main component of several top ten solutions, including our own and the winning team's algorithm. However, the accuracy of inverse covariance estimation is highly sensitive to signal preprocessing of the Calcium fluorescence time series. Furthermore, brute force optimization methods such as grid search and coordinate ascent over signal processing parameters is a time intensive process, where learning may take several days and parameters that optimize one network may not generalize to networks with different size and parameters. In this paper we show how inverse covariance estimation can be dramatically improved using a simple convolution filter prior to applying sample covariance. Furthermore, these signal processing parameters can be learned quickly using a supervised optimization algorithm. In particular, we maximize a binomial log-likelihood loss function with respect to a convolution filter of the time series and the inverse covariance regularization parameter. Our proposed algorithm is relatively fast on networks the size of those in the competition (1000 neurons), producing AUC scores with similar accuracy to the winning solution in training time under 2 hours on a cpu. Prediction on new networks of the same size is carried out in less than 15 minutes, the time it takes to read in the data and write out the solution.

The prediction of time-changing variances is an important task in the modeling of financial data. Standard econometric models are often limited as they assume rigid functional relationships for the evolution of the variance. Moreover, functional parameters are usually learned by maximum likelihood, which can lead to overfitting. To address these problems we introduce GP-Vol, a novel non-parametric model for time-changing variances based on Gaussian Processes. This new model can capture highly flexible functional relationships for the variances. Furthermore, we introduce a new online algorithm for fast inference in GP-Vol. This method is much faster than current offline inference procedures and it avoids overfitting problems by following a fully Bayesian approach. Experiments with financial data show that GP-Vol performs significantly better than current standard alternatives.

State-space models have been successfully used for more than fifty years in different areas of science and engineering. We present a procedure for efficient variational Bayesian learning of nonlinear state-space models based on sparse Gaussian processes. The result of learning is a tractable posterior over nonlinear dynamical systems. In comparison to conventional parametric models, we offer the possibility to straightforwardly trade off model capacity and computational cost whilst avoiding overfitting. Our main algorithm uses a hybrid inference approach combining variational Bayes and sequential Monte Carlo. We also present stochastic variational inference and online learning approaches for fast learning with long time series.

Even though heterogeneous databases can be found in a broad variety of applications, there exists a lack of tools for estimating missing data in such databases. In this paper, we provide an efficient and robust table completion tool, based on a Bayesian nonparametric latent feature model. In particular, we propose a general observation model for the Indian buffet process (IBP) adapted to mixed continuous (real-valued and positive real-valued) and discrete (categorical, ordinal and count) observations. Then, we propose an inference algorithm that scales linearly with the number of observations. Finally, our experiments over five real databases show that the proposed approach provides more robust and accurate estimates than the standard IBP and the Bayesian probabilistic matrix factorization with Gaussian observations.

Any reinforcement learning algorithm that applies to all Markov decision processes (MDPs) will suffer $\Omega(\sqrt{SAT})$ regret on some MDP, where $T$ is the elapsed time and $S$ and $A$ are the cardinalities of the state and action spaces. This implies $T = \Omega(SA)$ time to guarantee a near-optimal policy. In many settings of practical interest, due to the curse of dimensionality, $S$ and $A$ can be so enormous that this learning time is unacceptable. We establish that, if the system is known to be a \emph{factored} MDP, it is possible to achieve regret that scales polynomially in the number of \emph{parameters} encoding the factored MDP, which may be exponentially smaller than $S$ or $A$. We provide two algorithms that satisfy near-optimal regret bounds in this context: posterior sampling reinforcement learning (PSRL) and an upper confidence bound algorithm (UCRL-Factored).