Uncertainty estimation in large deep-learning models is a computationally challenging task, where it is difficult to form even a Gaussian approximation to the posterior distribution. In such situations, existing methods usually resort to a diagonal approximation of the covariance matrix despite, the fact that these matrices are known to result in poor uncertainty estimates. To address this issue, we propose a new stochastic, low-rank, approximate natural-gradient (SLANG) method for variational inference in large, deep models. Our method estimates a "diagonal plus low-rank" structure based solely on back-propagated gradients of the network log-likelihood. This requires strictly less gradient computations than methods that compute the gradient of the whole variational objective. Empirical evaluations on standard benchmarks confirm that SLANG enables faster and more accurate estimation of uncertainty than mean-field methods, and performs comparably to state-of-the-art methods.
The benefits of automating design cycles for Bayesian inference-based algorithms are becoming increasingly recognized by the machine learning community. As a result, interest in probabilistic programming frameworks has much increased over the past few years. This paper explores a specific probabilistic programming paradigm, namely message passing in Forney-style factor graphs (FFGs), in the context of automated design of efficient Bayesian signal processing algorithms. To this end, we developed "ForneyLab" (https://github.com/biaslab/ForneyLab.jl) as a Julia toolbox for message passing-based inference in FFGs. We show by example how ForneyLab enables automatic derivation of Bayesian signal processing algorithms, including algorithms for parameter estimation and model comparison. Crucially, due to the modular makeup of the FFG framework, both the model specification and inference methods are readily extensible in ForneyLab. In order to test this framework, we compared variational message passing as implemented by ForneyLab with automatic differentiation variational inference (ADVI) and Monte Carlo methods as implemented by state-of-the-art tools "Edward" and "Stan". In terms of performance, extensibility and stability issues, ForneyLab appears to enjoy an edge relative to its competitors for automated inference in state-space models.
Extracting common narratives from multi-author dynamic text corpora requires complex models, such as the Dynamic Author Persona (DAP) topic model. However, such models are complex and can struggle to scale to large corpora, often because of challenging non-conjugate terms. To overcome such challenges, in this paper we adapt new ideas in approximate inference to the DAP model, resulting in the DAP Performed Exceedingly Rapidly (DAPPER) topic model. Specifically, we develop Conjugate-Computation Variational Inference (CVI) based variational Expectation-Maximization (EM) for learning the model, yielding fast, closed form updates for each document, replacing iterative optimization in earlier work. Our results show significant improvements in model fit and training time without needing to compromise the model's temporal structure or the application of Regularized Variation Inference (RVI). We demonstrate the scalability and effectiveness of the DAPPER model by extracting health journeys from the CaringBridge corpus --- a collection of 9 million journals written by 200,000 authors during health crises.
Applying probabilistic models to reinforcement learning (RL) enables the application of powerful optimisation tools such as variational inference to RL. However, existing inference frameworks and their algorithms pose significant challenges for learning optimal policies, e.g., the absence of mode capturing behaviour in pseudo-likelihood methods and difficulties learning deterministic policies in maximum entropy RL based approaches. We propose VIREL, a novel, theoretically grounded probabilistic inference framework for RL that utilises a parametrised action-value function to summarise future dynamics of the underlying MDP. This gives VIREL a mode-seeking form of KL divergence, the ability to learn deterministic optimal polices naturally from inference and the ability to optimise value functions and policies in separate, iterative steps. In applying variational expectation-maximisation to VIREL we thus show that the actor-critic algorithm can be reduced to expectation-maximisation, with policy improvement equivalent to an E-step and policy evaluation to an M-step. We then derive a family of actor-critic methods from VIREL, including a scheme for adaptive exploration. Finally, we demonstrate that actor-critic algorithms from this family outperform state-of-the-art methods based on soft value functions in several domains.
This work explores non-negative low-rank matrix factorization based on regularized Poisson models (PF or "Poisson factorization" for short) for recommender systems with implicit-feedback data. The properties of Poisson likelihood allow a shortcut for very fast computations over zero-valued inputs, and oftentimes results in very sparse factors for both users and items. Compared to HPF (a popular Bayesian formulation of the problem with hierarchical priors), the frequentist optimization-based approach presented here tends to produce better top-N recommendations with significantly shorter fitting times, on top of having sparse solutions.
We introduce Kalman Gradient Descent, a stochastic optimization algorithm that uses Kalman filtering to adaptively reduce gradient variance in stochastic gradient descent by filtering the gradient estimates. We present both a theoretical analysis of convergence in a non-convex setting and experimental results which demonstrate improved performance on a variety of machine learning areas including neural networks and black box variational inference. We also present a distributed version of our algorithm that enables large-dimensional optimization, and we extend our algorithm to SGD with momentum and RMSProp.
We consider the semi-supervised clustering problem where crowdsourcing provides noisy information about the pairwise comparisons on a small subset of data, i.e., whether a sample pair is in the same cluster. We propose a new approach that includes a deep generative model (DGM) to characterize low-level features of the data, and a statistical relational model for noisy pairwise annotations on its subset. The two parts share the latent variables. To make the model automatically trade-off between its complexity and fitting data, we also develop its fully Bayesian variant. The challenge of inference is addressed by fast (natural-gradient) stochastic variational inference algorithms, where we effectively combine variational message passing for the relational part and amortized learning of the DGM under a unified framework. Empirical results on synthetic and real-world datasets show that our model outperforms previous crowdsourced clustering methods.
Variational inference with {\alpha}-divergences has been widely used in modern probabilistic machine learning. Compared to Kullback-Leibler (KL) divergence, a major advantage of using {\alpha}-divergences (with positive {\alpha} values) is their mass-covering property. However, estimating and optimizing {\alpha}-divergences require to use importance sampling, which could have extremely large or infinite variances due to heavy tails of importance weights. In this paper, we propose a new class of tail-adaptive f-divergences that adaptively change the convex function f with the tail of the importance weights, in a way that theoretically guarantees finite moments, while simultaneously achieving mass-covering properties. We test our methods on Bayesian neural networks, as well as deep reinforcement learning in which our method is applied to improve a recent soft actor-critic (SAC) algorithm. Our results show that our approach yields significant advantages compared with existing methods based on classical KL and {\alpha}-divergences.
Many probabilistic models of interest in scientific computing and machine learning have expensive, black-box likelihoods that prevent the application of standard techniques for Bayesian inference, such as MCMC, which would require access to the gradient or a large number of likelihood evaluations. We introduce here a novel sample-efficient inference framework, Variational Bayesian Monte Carlo (VBMC). VBMC combines variational inference with Gaussian-process based, active-sampling Bayesian quadrature, using the latter to efficiently approximate the intractable integral in the variational objective. Our method produces both a nonparametric approximation of the posterior distribution and an approximate lower bound of the model evidence, useful for model selection. We demonstrate VBMC both on several synthetic likelihoods and on a neuronal model with data from real neurons. Across all tested problems and dimensions (up to $D = 10$), VBMC performs consistently well in reconstructing the posterior and the model evidence with a limited budget of likelihood evaluations, unlike other methods that work only in very low dimensions. Our framework shows great promise as a novel tool for posterior and model inference with expensive, black-box likelihoods.
Bayesian neural networks (BNNs) hold great promise as a flexible and principled solution to deal with uncertainty when learning from finite data. Among approaches to realize probabilistic inference in deep neural networks, variational Bayes (VB) is theoretically grounded, generally applicable, and computationally efficient. With wide recognition of potential advantages, why is it that variational Bayes has seen very limited practical use for BNNs in real applications? We argue that variational inference in neural networks is fragile: successful implementations require careful initialization and tuning of prior variances, as well as controlling the variance of Monte Carlo gradient estimates. We provide two innovations that aim to turn VB into a robust inference tool for Bayesian neural networks: first, we introduce a novel deterministic method to approximate moments in neural networks, eliminating gradient variance; second, we introduce a hierarchical prior for parameters and a novel Empirical Bayes procedure for automatically selecting prior variances. Combining these two innovations, the resulting method is highly efficient and robust. On the application of heteroscedastic regression we demonstrate good predictive performance over alternative approaches.
Stochastic optimization techniques are standard in variational inference algorithms. These methods estimate gradients by approximating expectations with independent Monte Carlo samples. In this paper, we explore a technique that uses correlated, but more representative , samples to reduce estimator variance. Specifically, we show how to generate antithetic samples that match sample moments with the true moments of an underlying importance distribution. Combining a differentiable antithetic sampler with modern stochastic variational inference, we showcase the effectiveness of this approach for learning a deep generative model.
Stan is a probabilistic programming language that is popular in the statistics community, with a high-level syntax for expressing probabilistic models. Stan differs by nature from generative probabilistic programming languages like Church, Anglican, or Pyro. This paper presents a comprehensive compilation scheme to compile any Stan model to a generative language and proves its correctness. We use our compilation scheme to build two new backends for the Stanc3 compiler targeting Pyro and NumPyro. Experimental results show that the NumPyro backend yields a 2.3x speedup compared to Stan in geometric mean over 26 benchmarks. Building on Pyro we extend Stan with support for explicit variational inference guides and deep probabilistic models. That way, users familiar with Stan get access to new features without having to learn a fundamentally new language.
Gaussian processes (GPs) provide a powerful non-parametric framework for reasoning over functions. Despite appealing theory, its superlinear computational and memory complexities have presented a long-standing challenge. State-of-the-art sparse variational inference methods trade modeling accuracy against complexity. However, the complexities of these methods still scale superlinearly in the number of basis functions, implying that that sparse GP methods are able to learn from large datasets only when a small model is used. Recently, a decoupled approach was proposed that removes the unnecessary coupling between the complexities of modeling the mean and the covariance functions of a GP. It achieves a linear complexity in the number of mean parameters, so an expressive posterior mean function can be modeled. While promising, this approach suffers from optimization difficulties due to ill-conditioning and non-convexity. In this work, we propose an alternative decoupled parametrization. It adopts an orthogonal basis in the mean function to model the residues that cannot be learned by the standard coupled approach. Therefore, our method extends, rather than replaces, the coupled approach to achieve strictly better performance. This construction admits a straightforward natural gradient update rule, so the structure of the information manifold that is lost during decoupling can be leveraged to speed up learning. Empirically, our algorithm demonstrates significantly faster convergence in multiple experiments.
Extending spatio-temporal scale limitations of models for complex atomistic systems considered in biochemistry and materials science necessitates the development of enhanced sampling methods. The potential acceleration in exploring the configurational space by enhanced sampling methods depends on the choice of collective variables (CVs). In this work, we formulate the discovery of CVs as a Bayesian inference problem and consider the CVs as hidden generators of the full-atomistic trajectory. The ability to generate samples of the fine-scale atomistic configurations using limited training data allows us to compute estimates of observables as well as our probabilistic confidence on them. The methodology is based on emerging methodological advances in machine learning and variational inference. The discovered CVs are related to physicochemical properties which are essential for understanding mechanisms especially in unexplored complex systems. We provide a quantitative assessment of the CVs in terms of their predictive ability for alanine dipeptide (ALA-2) and ALA-15 peptide.
We explore a new research direction in Bayesian variational inference with discrete latent variable priors where we exploit Kronecker matrix algebra for efficient and exact computations of the evidence lower bound (ELBO). The proposed "DIRECT" approach has several advantages over its predecessors; (i) it can exactly compute ELBO gradients (i.e. unbiased, zero-variance gradient estimates), eliminating the need for high-variance stochastic gradient estimators and enabling the use of quasi-Newton optimization methods; (ii) its training complexity is independent of the number of training points, permitting inference on large datasets; and (iii) its posterior samples consist of sparse and low-precision quantized integers which permit fast inference on hardware limited devices. In addition, our DIRECT models can exactly compute statistical moments of the parameterized predictive posterior without relying on Monte Carlo sampling. The DIRECT approach is not practical for all likelihoods, however, we identify a popular model structure which is practical, and demonstrate accurate inference using latent variables discretized as extremely low-precision 4-bit quantized integers. While the ELBO computations considered in the numerical studies require over $10^{2352}$ log-likelihood evaluations, we train on datasets with over two-million points in just seconds.
Group factor analysis (GFA) methods have been widely used to infer the common structure and the group-specific signals from multiple related datasets in various fields including systems biology and neuroimaging. To date, most available GFA models require Gibbs sampling or slice sampling to perform inference, which prevents the practical application of GFA to large-scale data. In this paper we present an efficient collapsed variational inference (CVI) algorithm for the nonparametric Bayesian group factor analysis (NGFA) model built upon an hierarchical beta Bernoulli process. Our CVI algorithm proceeds by marginalizing out the group-specific beta process parameters, and then approximating the true posterior in the collapsed space using mean field methods. Experimental results on both synthetic and real-world data demonstrate the effectiveness of our CVI algorithm for the NGFA compared with state-of-the-art GFA methods.
Non-negative matrix factorization (NMF) is a knowledge discovery method that is used in many fields. Variational inference and Gibbs sampling methods for it are also wellknown. However, the variational approximation error has not been clarified yet, because NMF is not statistically regular and the prior distribution used in variational Bayesian NMF (VBNMF) has zero or divergence points. In this paper, using algebraic geometrical methods, we theoretically analyze the difference in negative log evidence (a.k.a. free energy) between VBNMF and Bayesian NMF, i.e., the Kullback-Leibler divergence between the variational posterior and the true posterior. We derive an upper bound for the learning coefficient (a.k.a. the real log canonical threshold) in Bayesian NMF. By using the upper bound, we find a lower bound for the approximation error, asymptotically. The result quantitatively shows how well the VBNMF algorithm can approximate Bayesian NMF; the lower bound depends on the hyperparameters and the true nonnegative rank. A numerical experiment demonstrates the theoretical result.
We develop unbiased implicit variational inference (UIVI), a method that expands the applicability of variational inference by defining an expressive variational family. UIVI considers an implicit variational distribution obtained in a hierarchical manner using a simple reparameterizable distribution whose variational parameters are defined by arbitrarily flexible deep neural networks. Unlike previous works, UIVI directly optimizes the evidence lower bound (ELBO) rather than an approximation to the ELBO. We demonstrate UIVI on several models, including Bayesian multinomial logistic regression and variational autoencoders, and show that UIVI achieves both tighter ELBO and better predictive performance than existing approaches at a similar computational cost.
To backpropagate the gradients through stochastic binary layers, we propose the augment-REINFORCE-merge (ARM) estimator that is unbiased, exhibits low variance, and has low computational complexity. Exploiting variable augmentation, REINFORCE, and reparameterization, the ARM estimator achieves adaptive variance reduction for Monte Carlo integration by merging two expectations via common random numbers. The variance-reduction mechanism of the ARM estimator can also be attributed to either antithetic sampling in an augmented space, or the use of an optimal anti-symmetric "self-control" baseline function together with the REINFORCE estimator in that augmented space. Experimental results show the ARM estimator provides state-of-the-art performance in auto-encoding variational inference and maximum likelihood estimation, for discrete latent variable models with one or multiple stochastic binary layers. Python code for reproducible research is publicly available.
We present a deep generative model of bilingual sentence pairs for machine translation. The model generates source and target sentences jointly from a shared latent representation and is parameterised by neural networks. We perform efficient training using amortised variational inference and reparameterised gradients. Additionally, we discuss the statistical implications of joint modelling and propose an efficient approximation to maximum a posteriori decoding for fast test-time predictions. We demonstrate the effectiveness of our model in three machine translation scenarios: in-domain training, mixed-domain training, and learning from a mix of gold-standard and synthetic data. Our experiments show consistently that our joint formulation outperforms conditional modelling (i.e. standard neural machine translation) in all such scenarios.