Learning meaningful representations of data that can address challenges such as batch effect correction, data integration and counterfactual inference is a central problem in many domains including computational biology. Adopting a Conditional VAE framework, we identify the mathematical principle that unites these challenges: learning a representation that is marginally independent of a condition variable. We therefore propose the Contrastive Mixture of Posteriors (CoMP) method that uses a novel misalignment penalty to enforce this independence. This penalty is defined in terms of mixtures of the variational posteriors themselves, unlike prior work which uses external discrepancy measures such as MMD to ensure independence in latent space. We show that CoMP has attractive theoretical properties compared to previous approaches, especially when there is complex global structure in latent space. We further demonstrate state of the art performance on a number of real-world problems, including the challenging tasks of aligning human tumour samples with cancer cell-lines and performing counterfactual inference on single-cell RNA sequencing data. Incidentally, we find parallels with the fair representation learning literature, and demonstrate CoMP has competitive performance in learning fair yet expressive latent representations.

Designing provably efficient algorithms with general function approximation is an important open problem in reinforcement learning. Recently, Wang et al.~[2020c] establish a value-based algorithm with general function approximation that enjoys $\widetilde{O}(\mathrm{poly}(dH)\sqrt{K})$\footnote{Throughout the paper, we use $\widetilde{O}(\cdot)$ to suppress logarithm factors. } regret bound, where $d$ depends on the complexity of the function class, $H$ is the planning horizon, and $K$ is the total number of episodes. However, their algorithm requires $\Omega(K)$ computation time per round, rendering the algorithm inefficient for practical use. In this paper, by applying online sub-sampling techniques, we develop an algorithm that takes $\widetilde{O}(\mathrm{poly}(dH))$ computation time per round on average, and enjoys nearly the same regret bound. Furthermore, the algorithm achieves low switching cost, i.e., it changes the policy only $\widetilde{O}(\mathrm{poly}(dH))$ times during its execution, making it appealing to be implemented in real-life scenarios. Moreover, by using an upper-confidence based exploration-driven reward function, the algorithm provably explores the environment in the reward-free setting. In particular, after $\widetilde{O}(\mathrm{poly}(dH))/\epsilon^2$ rounds of exploration, the algorithm outputs an $\epsilon$-optimal policy for any given reward function.

A graph generative model defines a distribution over graphs. One type of generative model is constructed by autoregressive neural networks, which sequentially add nodes and edges to generate a graph. However, the likelihood of a graph under the autoregressive model is intractable, as there are numerous sequences leading to the given graph; this makes maximum likelihood estimation challenging. Instead, in this work we derive the exact joint probability over the graph and the node ordering of the sequential process. From the joint, we approximately marginalize out the node orderings and compute a lower bound on the log-likelihood using variational inference. We train graph generative models by maximizing this bound, without using the ad-hoc node orderings of previous methods. Our experiments show that the log-likelihood bound is significantly tighter than the bound of previous schemes. Moreover, the models fitted with the proposed algorithm can generate high-quality graphs that match the structures of target graphs not seen during training. We have made our code publicly available at \hyperref[https://github.com/tufts-ml/graph-generation-vi]{https://github.com/tufts-ml/graph-generation-vi}.

We propose a model-free reinforcement learning algorithm inspired by the popular randomized least squares value iteration (RLSVI) algorithm as well as the optimism principle. Unlike existing upper-confidence-bound (UCB) based approaches, which are often computationally intractable, our algorithm drives exploration by simply perturbing the training data with judiciously chosen i.i.d. scalar noises. To attain optimistic value function estimation without resorting to a UCB-style bonus, we introduce an optimistic reward sampling procedure. When the value functions can be represented by a function class $\mathcal{F}$, our algorithm achieves a worst-case regret bound of $\widetilde{O}(\mathrm{poly}(d_EH)\sqrt{T})$ where $T$ is the time elapsed, $H$ is the planning horizon and $d_E$ is the $\textit{eluder dimension}$ of $\mathcal{F}$. In the linear setting, our algorithm reduces to LSVI-PHE, a variant of RLSVI, that enjoys an $\widetilde{\mathcal{O}}(\sqrt{d^3H^3T})$ regret. We complement the theory with an empirical evaluation across known difficult exploration tasks.

We focus on the problem of efficient sampling and learning of probability densities by incorporating symmetries in probabilistic models. We first introduce Equivariant Stein Variational Gradient Descent algorithm -- an equivariant sampling method based on Stein's identity for sampling from densities with symmetries. Equivariant SVGD explicitly incorporates symmetry information in a density through equivariant kernels which makes the resultant sampler efficient both in terms of sample complexity and the quality of generated samples. Subsequently, we define equivariant energy based models to model invariant densities that are learned using contrastive divergence. By utilizing our equivariant SVGD for training equivariant EBMs, we propose new ways of improving and scaling up training of energy based models. We apply these equivariant energy models for modelling joint densities in regression and classification tasks for image datasets, many-body particle systems and molecular structure generation.

We propose a fast algorithm for the probabilistic solution of boundary value problems (BVPs), which are ordinary differential equations subject to boundary conditions. In contrast to previous work, we introduce a Gauss--Markov prior and tailor it specifically to BVPs, which allows computing a posterior distribution over the solution in linear time, at a quality and cost comparable to that of well-established, non-probabilistic methods. Our model further delivers uncertainty quantification, mesh refinement, and hyperparameter adaptation. We demonstrate how these practical considerations positively impact the efficiency of the scheme. Altogether, this results in a practically usable probabilistic BVP solver that is (in contrast to non-probabilistic algorithms) natively compatible with other parts of the statistical modelling tool-chain.

Learning the causal structure that underlies data is a crucial step towards robust real-world decision making. The majority of existing work in causal inference focuses on determining a single directed acyclic graph (DAG) or a Markov equivalence class thereof. However, a crucial aspect to acting intelligently upon the knowledge about causal structure which has been inferred from finite data demands reasoning about its uncertainty. For instance, planning interventions to find out more about the causal mechanisms that govern our data requires quantifying epistemic uncertainty over DAGs. While Bayesian causal inference allows to do so, the posterior over DAGs becomes intractable even for a small number of variables. Aiming to overcome this issue, we propose a form of variational inference over the graphs of Structural Causal Models (SCMs). To this end, we introduce a parametric variational family modelled by an autoregressive distribution over the space of discrete DAGs. Its number of parameters does not grow exponentially with the number of variables and can be tractably learned by maximising an Evidence Lower Bound (ELBO). In our experiments, we demonstrate that the proposed variational posterior is able to provide a good approximation of the true posterior.

Actor-critic methods integrating target networks have exhibited a stupendous empirical success in deep reinforcement learning. However, a theoretical understanding of the use of target networks in actor-critic methods is largely missing in the literature. In this paper, we bridge this gap between theory and practice by proposing the first theoretical analysis of an online target-based actor-critic algorithm with linear function approximation in the discounted reward setting. Our algorithm uses three different timescales: one for the actor and two for the critic. Instead of using the standard single timescale temporal difference (TD) learning algorithm as a critic, we use a two timescales target-based version of TD learning closely inspired from practical actor-critic algorithms implementing target networks. First, we establish asymptotic convergence results for both the critic and the actor under Markovian sampling. Then, we provide a finite-time analysis showing the impact of incorporating a target network into actor-critic methods.

Bridge sampling is a powerful Monte Carlo method for estimating ratios of normalizing constants. Various methods have been introduced to improve its efficiency. These methods aim to increase the overlap between the densities by applying appropriate transformations to them without changing their normalizing constants. In this paper, we first give a new estimator of the asymptotic relative mean square error (RMSE) of the optimal Bridge estimator by equivalently estimating an $f$-divergence between the two densities. We then utilize this framework and propose $f$-GAN-Bridge estimator ($f$-GB) based on a bijective transformation that maps one density to the other. Such transformation is chosen to minimize a specific $f$-divergence between them using an $f$-GAN \citep{nowozin2016f}. We show it is equivalent to minimizing the asymptotic RMSE of the optimal Bridge estimator with respect to the densities. In other words, $f$-GB is optimal in the sense that asymptotically, it can achieve an RMSE lower than that achieved by Bridge estimators based on any transformed density within the class of densities generated by the candidate transformations. Numerical experiments show that $f$-GB outperforms existing methods in simulated and real-world examples. In addition, we discuss how Bridge estimators naturally arise from the problem of $f$-divergence estimation.

Marginalising over families of Gaussian Process kernels produces flexible model classes with well-calibrated uncertainty estimates. Existing approaches require likelihood evaluations of many kernels, rendering them prohibitively expensive for larger datasets. We propose a Bayesian Quadrature scheme to make this marginalisation more efficient and thereby more practical. Through use of the maximum mean discrepancies between distributions, we define a kernel over kernels that captures invariances between Spectral Mixture (SM) Kernels. Kernel samples are selected by generalising an information-theoretic acquisition function for warped Bayesian Quadrature. We show that our framework achieves more accurate predictions with better calibrated uncertainty than state-of-the-art baselines, especially when given limited (wall-clock) time budgets.