Inspired by the success of deep learning techniques in the physical and chemical sciences, we apply a modification of an autoencoder type deep neural network to the task of dimension reduction of molecular dynamics data. We can show that our time-lagged autoencoder reliably finds low-dimensional embeddings for highdimensional feature spaces which capture the slow dynamics of the underlying stochastic processes-beyond the capabilities of linear dimension reduction techniques. Molecular dynamics (MD) simulation allows us to probe the full spatiotemporal detail of molecular processes, but its usefulness has long been limited by the sampling problem. If we do not want to choose the library of feature functions by hand, but instead want to optimize the nonlinear mapping E by employing a neural network, we have again two options: (1) employ the variational approach. In this paper we investigate option (2), which naturally leads to using a time-lagged autoencoder (TAE).

We introduce a new formulation of the Hidden Parameter Markov Decision Process (HiP-MDP), a framework for modeling families of related tasks using low-dimensional latent embeddings. Our new framework correctly models the joint uncertainty in the latent parameters and the state space. We also replace the original Gaussian Process-based model with a Bayesian Neural Network, enabling more scalable inference. Thus, we expand the scope of the HiP-MDP to applications with higher dimensions and more complex dynamics.

This work constructs a hypothesis test for detecting whether an data-generating function $h: R^p \rightarrow R$ belongs to a specific reproducing kernel Hilbert space $\mathcal{H}_0$ , where the structure of $\mathcal{H}_0$ is only partially known. Utilizing the theory of reproducing kernels, we reduce this hypothesis to a simple one-sided score test for a scalar parameter, develop a testing procedure that is robust against the mis-specification of kernel functions, and also propose an ensemble-based estimator for the null model to guarantee test performance in small samples. To demonstrate the utility of the proposed method, we apply our test to the problem of detecting nonlinear interaction between groups of continuous features. We evaluate the finite-sample performance of our test under different data-generating functions and estimation strategies for the null model. Our results reveal interesting connections between notions in machine learning (model underfit/overfit) and those in statistical inference (i.e. Type I error/power of hypothesis test), and also highlight unexpected consequences of common model estimating strategies (e.g. estimating kernel hyperparameters using maximum likelihood estimation) on model inference.

Reward augmented maximum likelihood (RAML), a simple and effective learning framework to directly optimize towards the reward function in structured prediction tasks, has led to a number of impressive empirical successes. RAML incorporates task-specific reward by performing maximum-likelihood updates on candidate outputs sampled according to an exponentiated payoff distribution, which gives higher probabilities to candidates that are close to the reference output. While RAML is notable for its simplicity, efficiency, and its impressive empirical successes, the theoretical properties of RAML, especially the behavior of the exponentiated payoff distribution, has not been examined thoroughly. In this work, we introduce softmax Q-distribution estimation, a novel theoretical interpretation of RAML, which reveals the relation between RAML and Bayesian decision theory. The softmax Q-distribution can be regarded as a smooth approximation of the Bayes decision boundary, and the Bayes decision rule is achieved by decoding with this Q-distribution. We further show that RAML is equivalent to approximately estimating the softmax Q-distribution, with the temperature $\tau$ controlling approximation error. We perform two experiments, one on synthetic data of multi-class classification and one on real data of image captioning, to demonstrate the relationship between RAML and the proposed softmax Q-distribution estimation method, verifying our theoretical analysis. Additional experiments on three structured prediction tasks with rewards defined on sequential (named entity recognition), tree-based (dependency parsing) and irregular (machine translation) structures show notable improvements over maximum likelihood baselines.

We propose a probabilistic framework for domain adaptation that blends both generative and discriminative modeling in a principled way. Under this framework, generative and discriminative models correspond to specific choices of the prior over parameters. This provides us a very general way to interpolate between generative and discriminative extremes through different choices of priors. By maximizing both the marginal and the conditional log-likelihoods, models derived from this framework can use both labeled instances from the source domain as well as unlabeled instances from both source and target domains. Under this framework, we show that the popular reconstruction loss of autoencoder corresponds to an upper bound of the negative marginal log-likelihoods of unlabeled instances, where marginal distributions are given by proper kernel density estimations. This provides a way to interpret the empirical success of autoencoders in domain adaptation and semi-supervised learning. We instantiate our framework using neural networks, and build a concrete model, DAuto. Empirically, we demonstrate the effectiveness of DAuto on text, image and speech datasets, showing that it outperforms related competitors when domain adaptation is possible.

This work addresses the problem of segmentation in time series data with respect to a statistical parameter of interest in Bayesian models. It is common to assume that the parameters are distinct within each segment. As such, many Bayesian change point detection models do not exploit the segment parameter patterns, which can improve performance. This work proposes a Bayesian mean-shift change point detection algorithm that makes use of repetition in segment parameters, by introducing segment class labels that utilise a Dirichlet process prior. The performance of the proposed approach was assessed on both synthetic and real world data, highlighting the enhanced performance when using parameter labelling.

This paper examines fundamental error characteristics for a general class of matrix completion problems, where the matrix of interest is a product of two a priori unknown matrices, one of which is sparse, and the observations are noisy. Our main contributions come in the form of minimax lower bounds for the expected per-element squared error for this problem under under several common noise models. Specifically, we analyze scenarios where the corruptions are characterized by additive Gaussian noise or additive heavier-tailed (Laplace) noise, Poisson-distributed observations, and highly-quantized (e.g., one-bit) observations, as instances of our general result. Our results establish that the error bounds derived in (Soni et al., 2016) for complexity-regularized maximum likelihood estimators achieve, up to multiplicative constants and logarithmic factors, the minimax error rates in each of these noise scenarios, provided that the nominal number of observations is large enough, and the sparse factor has (on an average) at least one non-zero per column.

This work provides a simplified proof of the statistical minimax optimality of (iterate averaged) stochastic gradient descent (SGD), for the special case of least squares. This result is obtained by analyzing SGD as a stochastic process and by sharply characterizing the stationary covariance matrix of this process. The finite rate optimality characterization captures the constant factors and addresses model mis-specification.

The original problem of supervised classification considers the task of automatically assigning objects to their respective classes on the basis of numerical measurements derived from these objects. Classifiers are the tools that implement the actual functional mapping from these measurements---also called features or inputs---to the so-called class label---or output. The fields of pattern recognition and machine learning study ways of constructing such classifiers. The main idea behind supervised methods is that of learning from examples: given a number of example input-output relations, to what extent can the general mapping be learned that takes any new and unseen feature vector to its correct class? This chapter provides a basic introduction to the underlying ideas of how to come to a supervised classification problem. In addition, it provides an overview of some specific classification techniques, delves into the issues of object representation and classifier evaluation, and (very) briefly covers some variations on the basic supervised classification task that may also be of interest to the practitioner.

Building classification models is an intrinsically practical exercise that requires many design decisions prior to deployment. We aim to provide some guidance in this decision making process. Specifically, given a classification problem with real valued attributes, we consider which classifier or family of classifiers should one use. Strong contenders are tree based homogeneous ensembles, support vector machines or deep neural networks. All three families of model could claim to be state-of-the-art, and yet it is not clear when one is preferable to the others. Our extensive experiments with over 200 data sets from two distinct archives demonstrate that, rather than choose a single family and expend computing resources on optimising that model, it is significantly better to build simpler versions of classifiers from each family and ensemble. We show that the Heterogeneous Ensembles of Standard Classification Algorithms (HESCA), which ensembles based on error estimates formed on the train data, is significantly better (in terms of error, balanced error, negative log likelihood and area under the ROC curve) than its individual components, picking the component that is best on train data, and a support vector machine tuned over 1089 different parameter configurations. We demonstrate HESCA+, which contains a deep neural network, a support vector machine and two decision tree forests, is significantly better than its components, picking the best component, and HESCA. We analyse the results further and find that HESCA and HESCA+ are of particular value when the train set size is relatively small and the problem has multiple classes. HESCA is a fast approach that is, on average, as good as state-of-the-art classifiers, whereas HESCA+ is significantly better than average and represents a strong benchmark for future research.