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Given overlapping subsets of a set of taxa (e.g. species), and posterior distributions on phylogenetic tree topologies for each of these taxon sets, how can we infer a posterior distribution on phylogenetic tree topologies for the entire taxon set? Although the equivalent problem for in the non-Bayesian case has attracted substantial research, the Bayesian case has not attracted the attention it deserves. In this paper we develop a variational Bayes approach to this problem and demonstrate its effectiveness.
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Variational Bayesian neural networks (BNNs) perform variational inference over weights, but it is difficult to specify meaningful priors and approximate posteriors in a high-dimensional weight space. We introduce functional variational Bayesian neural networks (fBNNs), which maximize an Evidence Lower BOund (ELBO) defined directly on stochastic processes, i.e. distributions over functions. We prove that the KL divergence between stochastic processes equals the supremum of marginal KL divergences over all finite sets of inputs. Based on this, we introduce a practical training objective which approximates the functional ELBO using finite measurement sets and the spectral Stein gradient estimator. With fBNNs, we can specify priors entailing rich structures, including Gaussian processes and implicit stochastic processes. Empirically, we find fBNNs extrapolate well using various structured priors, provide reliable uncertainty estimates, and scale to large datasets.
Variational dropout (VD) is a generalization of Gaussian dropout, which aims at inferring the posterior of network weights based on a log-uniform prior on them to learn these weights as well as dropout rate simultaneously. The log-uniform prior not only interprets the regularization capacity of Gaussian dropout in network training, but also underpins the inference of such posterior. However, the log-uniform prior is an improper prior (i.e., its integral is infinite) which causes the inference of posterior to be ill-posed, thus restricting the regularization performance of VD. To address this problem, we present a new generalization of Gaussian dropout, termed variational Bayesian dropout (VBD), which turns to exploit a hierarchical prior on the network weights and infer a new joint posterior. Specifically, we implement the hierarchical prior as a zero-mean Gaussian distribution with variance sampled from a uniform hyper-prior. Then, we incorporate such a prior into inferring the joint posterior over network weights and the variance in the hierarchical prior, with which both the network training and the dropout rate estimation can be cast into a joint optimization problem. More importantly, the hierarchical prior is a proper prior which enables the inference of posterior to be well-posed. In addition, we further show that the proposed VBD can be seamlessly applied to network compression. Experiments on both classification and network compression tasks demonstrate the superior performance of the proposed VBD in terms of regularizing network training.
We develop a variational Bayesian (VB) approach for estimating large-scale dynamic network models in the network autoregression framework. The VB approach allows for the automatic identification of the dynamic structure of such a model and obtains a direct approximation of the posterior density. Compared to Markov Chain Monte Carlo (MCMC) based sampling approaches, the VB approach achieves enhanced computational efficiency without sacrificing estimation accuracy. In the simulation study conducted here, the proposed VB approach detects various types of proper active structures for dynamic network models. Compared to the alternative approach, the proposed method achieves similar or better accuracy, and its computational time is halved. In a real data analysis scenario of day-ahead natural gas flow prediction in the German gas transmission network with 51 nodes between October 2013 and September 2015, the VB approach delivers promising forecasting accuracy along with clearly detected structures in terms of dynamic dependence.
Approximate inference in deep Bayesian networks exhibits a dilemma of how to yield high fidelity posterior approximations while maintaining computational efficiency and scalability. We tackle this challenge by introducing a novel variational structured approximation inspired by the Bayesian interpretation of Dropout regularization. Concretely, we focus on the inflexibility of the factorized structure in Dropout posterior and then propose an improved method called Variational Structured Dropout (VSD). VSD employs an orthogonal transformation to learn a structured representation on the variational noise and consequently induces statistical dependencies in the approximate posterior. Theoretically, VSD successfully addresses the pathologies of previous Variational Dropout methods and thus offers a standard Bayesian justification. We further show that VSD induces an adaptive regularization term with several desirable properties which contribute to better generalization. Finally, we conduct extensive experiments on standard benchmarks to demonstrate the effectiveness of VSD over state-of-the-art variational methods on predictive accuracy, uncertainty estimation, and out-of-distribution detection.
Variational inference enables approximate posterior inference of the highly over-parameterized neural networks that are popular in modern machine learning. Unfortunately, such posteriors are known to exhibit various pathological behaviors. We prove that as the number of hidden units in a single-layer Bayesian neural network tends to infinity, the function-space posterior mean under mean-field variational inference actually converges to zero, completely ignoring the data. This is in contrast to the true posterior, which converges to a Gaussian process. Our work provides insight into the over-regularization of the KL divergence in variational inference.
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