An important problem in machine learning and statistics is to identify features that causally affect the outcome. This is often impossible to do from purely observational data, and a natural relaxation is to identify features that are correlated with the outcome even conditioned on all other observed features. For example, we want to identify that smoking really is correlated with cancer conditioned on demographics. The knockoff procedure is a recent breakthrough in statistics that, in theory, can identify truly correlated features while guaranteeing that the false discovery is limited. The idea is to create synthetic data -- knockoffs -- that captures correlations amongst the features. However there are substantial computational and practical challenges to generating and using knockoffs. This paper makes several key advances that enable knockoff application to be more efficient and powerful. We develop an efficient algorithm to generate valid knockoffs from Bayesian Networks. Then we systematically evaluate knockoff test statistics and develop new statistics with improved power. The paper combines new mathematical guarantees with systematic experiments on real and synthetic data.

Estimating the uncertainty of a Bayesian model has been investigated for decades. The model posterior is almost always intractable, such that approximation is necessary. In many real-world cases, even though a decent estimation of the model posterior is obtained, another approximation is required to compute the predictive distribution over the desired output. A common accurate solution is to use Monte Carlo (MC) integration. However, it needs to maintain a large number of samples, evaluate the model repeatedly and average multiple model outputs. In this paper, we propose a method to approximate the probability distribution over the simplex induced by model posterior, enabling tractable computation of the predictive distribution for classification. The aim is to approximate the induced uncertainty of a specific Bayesian model, meanwhile alleviating the heavy workload of MC integration in testing time. Methodologically, we adapt Wasserstein distance to learn the induced conditional distributions, which is novel for Bayesian learning. The proposed method is universally applicable to Bayesian classification models that allow for posterior sampling. Empirical results validate the strong practical performance of our approach.

Behavioral cloning reduces policy learning to supervised learning by training a discriminative model to predict expert actions given observations. Such discriminative models are non-causal: the training procedure is unaware of the causal structure of the interaction between the expert and the environment. We point out that ignoring causality is particularly damaging because of the distributional shift in imitation learning. In particular, it leads to a counter-intuitive "causal confusion" phenomenon: access to more information can yield worse performance. We investigate how this problem arises, and propose a solution to combat it through targeted interventions---either environment interaction or expert queries---to determine the correct causal model. We show that causal confusion occurs in several benchmark control domains as well as realistic driving settings, and validate our solution against DAgger and other baselines and ablations.

Massively multi-label prediction/classification problems arise in environments like health-care or biology where very precise predictions are useful. One challenge with massively multi-label problems is that there is often a long-tailed frequency distribution for the labels, which results in few positive examples for the rare labels. We propose a solution to this problem by modifying the output layer of a neural network to create a Bayesian network of sigmoids which takes advantage of ontology relationships between the labels to help share information between the rare and the more common labels. We apply this method to the two massively multi-label tasks of disease prediction (ICD-9 codes) and protein function prediction (Gene Ontology terms) and obtain significant improvements in per-label AUROC and average precision for less common labels.

Data-driven anomaly detection methods typically build a model for the normal behavior of the target system, and score each data instance with respect to this model. A threshold is invariably needed to identify data instances with high (or low) scores as anomalies. This presents a practical limitation on the applicability of such methods, since most methods are sensitive to the choice of the threshold, and it is challenging to set optimal thresholds. We present a probabilistic framework to explicitly model the normal and anomalous behaviors and probabilistically reason about the data. An extreme value theory based formulation is proposed to model the anomalous behavior as the extremes of the normal behavior. As a specific instantiation, a joint non-parametric clustering and anomaly detection algorithm (INCAD) is proposed that models the normal behavior as a Dirichlet Process Mixture Model. A pseudo-Gibbs sampling based strategy is used for inference. Results on a variety of data sets show that the proposed method provides effective clustering and anomaly detection without requiring strong initialization and thresholding parameters.

The normalizing constants of these distributions depend on gamma functions whose arguments include shape (gamma, inverse gamma) and concentration (beta, Dirichlet) parameters. Bayesian learning of parameters nested inside the gamma function presents significant technical difficulties, since there is no known conjugate prior distribution. In fact, inferring the shape parameter in the gamma distribution is a long-studied problem in Bayesian inference (Damsleth, 1975; Rossell et al., 2009; Miller, 2018). In this paper, we develop the theoretical and algorithmic foundation of a P olya-inverse Gamma (PIG) data augmentation scheme for fully Bayesian inference of shape and concentration parameters in gamma, inverse gamma, and Dirichlet models, respectively . PIG data augmentation may be utilized to design efficient Markov chain Monte Carlo (MCMC) algorithms in latent Dirichlet allocation (Blei et al., 2003), Beta-negative binomial models (Zhou et al., 2012), and Gamma-Gamma (GaGa) hierarchical models (Rossell et al., 2009).

We introduce a flexible, scalable Bayesian inference framework for nonlinear dynamical systems characterised by distinct and hierarchical variability at the individual, group, and population levels. Our model class is a generalisation of nonlinear mixed-effects (NLME) dynamical systems, the statistical workhorse for many experimental sciences. We cast parameter inference as stochastic optimisation of an end-to-end differentiable, block-conditional variational autoencoder. We specify the dynamics of the data-generating process as an ordinary differential equation (ODE) such that both the ODE and its solver are fully differentiable. This model class is highly flexible: the ODE right-hand sides can be a mixture of user-prescribed or "white-box" sub-components and neural network or "black-box" sub-components. Using stochastic optimisation, our amortised inference algorithm could seamlessly scale up to massive data collection pipelines (common in labs with robotic automation). Finally, our framework supports interpretability with respect to the underlying dynamics, as well as predictive generalization to unseen combinations of group components (also called "zero-shot" learning). We empirically validate our method by predicting the dynamic behaviour of bacteria that were genetically engineered to function as biosensors.

We construct a new distribution for the simplex using the Kumaraswamy distribution and an ordered stick-breaking process. We explore and develop the theoretical properties of this new distribution and prove that it exhibits symmetry under the same conditions as the well-known Dirichlet. Like the Dirichlet, the new distribution is adept at capturing sparsity but, unlike the Dirichlet, has an exact and closed form reparameterization--making it well suited for deep variational Bayesian modeling. We demonstrate the distribution's utility in a variety of semi-supervised auto-encoding tasks. In all cases, the resulting models achieve competitive performance commensurate with their simplicity, use of explicit probability models, and abstinence from adversarial training.

We introduce a unified probabilistic approach for deep continual learning based on variational Bayesian inference with open set recognition. Our model combines a probabilistic encoder with a generative model and a generative linear classifier that get shared across tasks. The open set recognition bounds the approximate posterior by fitting regions of high density on the basis of correctly classified data points and balances open-space risk with recognition errors. Catastrophic inference for both generative models is significantly alleviated through generative replay, where the open set recognition is used to sample from high density areas of the class specific posterior and reject statistical outliers. Our approach naturally allows for forward and backward transfer while maintaining past knowledge without the necessity of storing old data, regularization or inferring task labels. We demonstrate compelling results in the challenging scenario of incrementally expanding the single-head classifier for both class incremental visual and audio classification tasks, as well as incremental learning of datasets across modalities.

We consider Bayesian classification with Gaussian processes (GPs) and define robustness of a classifier in terms of the worst-case difference in the classification probabilities with respect to input perturbations. For a subset of the input space $T\subseteq \mathbb{R}^m$ such properties reduce to computing the infimum and supremum of the classification probabilities for all points in $T$. Unfortunately, computing the above values is very challenging, as the classification probabilities cannot be expressed analytically. Nevertheless, using the theory of Gaussian processes, we develop a framework that, for a given dataset $\mathcal{D}$, a compact set of input points $T\subseteq \mathbb{R}^m$ and an error threshold $\epsilon>0$, computes lower and upper bounds of the classification probabilities by over-approximating the exact range with an error bounded by $\epsilon$. We provide experimental comparison of several approximate inference methods for classification on tasks associated to MNIST and SPAM datasets showing that our results enable quantification of uncertainty in adversarial classification settings.