Gaussian Process Factor Analysis (GPFA) has been broadly applied to the problem of identifying smooth, low-dimensional temporal structure underlying large-scale neural recordings. However, spike trains are non-Gaussian, which motivates combining GPFA with discrete observation models for binned spike count data. The drawback to this approach is that GPFA priors are not conjugate to count model likelihoods, which makes inference challenging. Here we address this obstacle by introducing a fast, approximate inference method for non-conjugate GPFA models. Our approach uses orthogonal second-order polynomials to approximate the nonlinear terms in the non-conjugate log-likelihood, resulting in a method we refer to as \textit{polynomial approximate log-likelihood} (PAL) estimators. This approximation allows for accurate closed-form evaluation of marginal likelihoods and fast numerical optimization for parameters and hyperparameters. We derive PAL estimators for GPFA models with binomial, Poisson, and negative binomial observations and find the PAL estimation is highly accurate, and achieves faster convergence times compared to existing state-of-the-art inference methods. We also find that PAL hyperparameters can provide sensible initialization for black box variational inference (BBVI), which improves BBVI accuracy. We demonstrate that PAL estimators achieve fast and accurate extraction of latent structure from multi-neuron spike train data.
We develop a data driven approach to perform clustering and end-to-end feature learning simultaneously for streaming data that can adaptively detect novel clusters in emerging data. Our approach, Adaptive Nonparametric Variational Autoencoder (AdapVAE), learns the cluster membership through a Bayesian Nonparametric (BNP) modeling framework with Deep Neural Networks (DNNs) for feature learning. We develop a joint online variational inference algorithm to learn feature representations and clustering assignments simultaneously via iteratively optimizing the Evidence Lower Bound (ELBO). We resolve the catastrophic forgetting \citep{kirkpatrick2017overcoming} challenges with streaming data by adopting generative samples from the trained AdapVAE using previous data, which avoids the need of storing and reusing past data. We demonstrate the advantages of our model including adaptive novel cluster detection without discarding useful information learned from past data, high quality sample generation and comparable clustering performance as end-to-end batch mode clustering methods on both image and text corpora benchmark datasets.
Specifying utility functions is a key step towards applying the discrete choice framework for understanding the behaviour processes that govern user choices. However, identifying the utility function specifications that best model and explain the observed choices can be a very challenging and time-consuming task. This paper seeks to help modellers by leveraging the Bayesian framework and the concept of automatic relevance determination (ARD), in order to automatically determine an optimal utility function specification from an exponentially large set of possible specifications in a purely data-driven manner. Based on recent advances in approximate Bayesian inference, a doubly stochastic variational inference is developed, which allows the proposed DCM-ARD model to scale to very large and high-dimensional datasets. Using semi-artificial choice data, the proposed approach is shown to very accurately recover the true utility function specifications that govern the observed choices. Moreover, when applied to real choice data, DCM-ARD is shown to be able discover high quality specifications that can outperform previous ones from the literature according to multiple criteria, thereby demonstrating its practical applicability.
In this note, we study the relationship between the variational gap and the variance of the (log) likelihood ratio. We show that the gap can be upper bounded by some form of dispersion measure of the likelihood ratio, which suggests the bias of variational inference can be reduced by making the distribution of the likelihood ratio more concentrated, such as via averaging and variance reduction.
A normalizing flow models a complex probability density as an invertible transformation of a simple base density. Flows based on either coupling or autoregressive transforms both offer exact density evaluation and sampling, but rely on the parameterization of an easily invertible elementwise transformation, whose choice determines the flexibility of these models. Building upon recent work, we propose a fully-differentiable module based on monotonic rational-quadratic splines, which enhances the flexibility of both coupling and autoregressive transforms while retaining analytic invertibility. We demonstrate that neural spline flows improve density estimation, variational inference, and generative modeling of images.
We propose a scalable framework for inference in an inhomogeneous Poisson process modeled by a continuous sigmoidal Cox process that assumes the corresponding intensity function is given by a Gaussian process (GP) prior transformed with a scaled logistic sigmoid function. We present a tractable representation of the likelihood through augmentation with a superposition of Poisson processes. This view enables a structured variational approximation capturing dependencies across variables in the model. Our framework avoids discretization of the domain, does not require accurate numerical integration over the input space and is not limited to GPs with squared exponential kernels. We evaluate our approach on synthetic and real-world data showing that its benefits are particularly pronounced on multivariate input settings where it overcomes the limitations of mean-field methods and sampling schemes. We provide the state of-the-art in terms of speed, accuracy and uncertainty quantification trade-offs.
A novel variational inference based resampling framework is proposed to evaluate the robustness and generalization capability of deep learning models with respect to distribution shift. We use Auto Encoding Variational Bayes to find a latent representation of the data, on which a Variational Gaussian Mixture Model is applied to deliberately create distribution shift by dividing the dataset into different clusters. Wasserstein distance is used to characterize the extent of distribution shift between the generated data splits. We compare several popular Convolutional Neural Network (CNN) architectures and Bayesian CNN models for image classification on the Fashion-MNIST dataset, to assess their robustness and generalization behavior under the deliberately created distribution shift, as well as under random Cross Validation. Our method of creating artificial domain splits of a single dataset can also be used to establish novel model selection criteria and assessment tools in machine learning, as well as benchmark methods for domain adaptation and domain generalization approaches.
Natural-gradient methods enable fast and simple algorithms for variational inference, but due to computational difficulties, their use is mostly limited to \emph{minimal} exponential-family (EF) approximations. In this paper, we extend their application to estimate \emph{structured} approximations such as mixtures of EF distributions. Such approximations can fit complex, multimodal posterior distributions and are generally more accurate than unimodal EF approximations. By using a \emph{minimal conditional-EF} representation of such approximations, we derive simple natural-gradient updates. Our empirical results demonstrate a faster convergence of our natural-gradient method compared to black-box gradient-based methods with reparameterization gradients. Our work expands the scope of natural gradients for Bayesian inference and makes them more widely applicable than before.
Supervised models of NLP rely on large collections of text which closely resemble the intended testing setting. Unfortunately matching text is often not available in sufficient quantity, and moreover, within any domain of text, data is often highly heterogenous. In this paper we propose a method to distill the important domain signal as part of a multi-domain learning system, using a latent variable model in which parts of a neural model are stochastically gated based on the inferred domain. We compare the use of discrete versus continuous latent variables, operating in a domain-supervised or a domain semi-supervised setting, where the domain is known only for a subset of training inputs. We show that our model leads to substantial performance improvements over competitive benchmark domain adaptation methods, including methods using adversarial learning.
Bayesian methods promise to fix many shortcomings of deep learning, but they are impractical and rarely match the performance of standard methods, let alone improve them. In this paper, we demonstrate practical training of deep networks with natural-gradient variational inference. By applying techniques such as batch normalisation, data augmentation, and distributed training, we achieve similar performance in about the same number of epochs as the Adam optimiser, even on large datasets such as ImageNet. Importantly, the benefits of Bayesian principles are preserved: predictive probabilities are well-calibrated, uncertainties on out-of-distribution data are improved, and continual-learning performance is boosted. This work enables practical deep learning while preserving benefits of Bayesian principles. A PyTorch implementation is available as a plug-and-play optimiser.
Classical approaches for approximate inference depend on cleverly designed variational distributions and bounds. Modern approaches employ amortized variational inference, which uses a neural network to approximate any posterior without leveraging the structures of the generative models. In this paper, we propose Amortized Conjugate Posterior (ACP), a hybrid approach taking advantages of both types of approaches. Specifically, we use the classical methods to derive specific forms of posterior distributions and then learn the variational parameters using amortized inference. We study the effectiveness of the proposed approach on the noisy-or model and compare to both the classical and the modern approaches for approximate inference and parameter learning. Our results show that the proposed method outperforms or are at par with other approaches.
We propose a framework that lifts the capabilities of graph convolutional networks (GCNs) to scenarios where no input graph is given and increases their robustness to adversarial attacks. We formulate a joint probabilistic model that considers a prior distribution over graphs along with a GCN-based likelihood and develop a stochastic variational inference algorithm to estimate the graph posterior and the GCN parameters jointly. To address the problem of propagating gradients through latent variables drawn from discrete distributions, we use their continuous relaxations known as Concrete distributions. We show that, on real datasets, our approach can outperform state-of-the-art Bayesian and non-Bayesian graph neural network algorithms on the task of semi-supervised classification in the absence of graph data and when the network structure is subjected to adversarial perturbations.
Efficient approximation lies at the heart of large-scale machine learning problems. In this paper, we propose a novel, robust maximum entropy algorithm, which is capable of dealing with hundreds of moments and allows for computationally efficient approximations. We showcase the usefulness of the proposed method, its equivalence to constrained Bayesian variational inference and demonstrate its superiority over existing approaches in two applications, namely, fast log determinant estimation and information-theoretic Bayesian optimisation.
Nonlinear state-space models are powerful tools to describe dynamical structures in complex time series. In a streaming setting where data are processed one sample at a time, simultaneous inference of the state and its nonlinear dynamics has posed significant challenges in practice. We develop a novel online learning framework, leveraging variational inference and sequential Monte Carlo, which enables flexible and accurate Bayesian joint filtering. Our method provides an approximation of the filtering posterior which can be made arbitrarily close to the true filtering distribution for a wide class of dynamics models and observation models. Specifically, the proposed framework can efficiently approximate a posterior over the dynamics using sparse Gaussian processes, allowing for an interpretable model of the latent dynamics. Constant time complexity per sample makes our approach amenable to online learning scenarios and suitable for real-time applications.
Boosting variational inference (BVI) approximates an intractable probability density by iteratively building up a mixture of simple component distributions one at a time, using techniques from sparse convex optimization to provide both computational scalability and approximation error guarantees. But the guarantees have strong conditions that do not often hold in practice, resulting in degenerate component optimization problems; and we show that the ad-hoc regularization used to prevent degeneracy in practice can cause BVI to fail in unintuitive ways. We thus develop universal boosting variational inference (UBVI), a BVI scheme that exploits the simple geometry of probability densities under the Hellinger metric to prevent the degeneracy of other gradient-based BVI methods, avoid difficult joint optimizations of both component and weight, and simplify fully-corrective weight optimizations. We show that for any target density and any mixture component family, the output of UBVI converges to the best possible approximation in the mixture family, even when the mixture family is misspecified. We develop a scalable implementation based on exponential family mixture components and standard stochastic optimization techniques. Finally, we discuss statistical benefits of the Hellinger distance as a variational objective through bounds on posterior probability, moment, and importance sampling errors. Experiments on multiple datasets and models show that UBVI provides reliable, accurate posterior approximations.
Traditional structured prediction models try to learn the conditional likelihood, i.e., p(y|x), to capture the relationship between the structured output y and the input features x. For many models, computing the likelihood is intractable. These models are therefore hard to train, requiring the use of surrogate objectives or variational inference to approximate likelihood. In this paper, we propose conditional Glow (c-Glow), a conditional generative flow for structured output learning. C-Glow benefits from the ability of flow-based models to compute p(y|x) exactly and efficiently. Learning with c-Glow does not require a surrogate objective or performing inference during training. Once trained, we can directly and efficiently generate conditional samples. We develop a sample-based prediction method, which can use this advantage to do efficient and effective inference. In our experiments, we test c-Glow on five different tasks. C-Glow outperforms the state-of-the-art baselines in some tasks and predicts comparable outputs in the other tasks. The results show that c-Glow is versatile and is applicable to many different structured prediction problems.
We construct flexible likelihoods for multi-output Gaussian process models that leverage neural networks as components. We make use of sparse variational inference methods to enable scalable approximate inference for the resulting class of models. An attractive feature of these models is that they can admit analytic predictive means even when the likelihood is non-linear and the predictive distributions are non-Gaussian. We validate the modeling potential of these models in a variety of experiments in both the supervised and unsupervised setting. We demonstrate that the flexibility of these `neural' likelihoods can improve prediction quality as compared to simpler Gaussian process models and that neural likelihoods can be readily combined with a variety of underlying Gaussian process models, including deep Gaussian processes.
Using powerful posterior distributions is a popular approach to achieving better variational inference. However, recent works showed that the aggregated posterior may fail to match unit Gaussian prior, thus learning the prior becomes an alternative way to improve the lower-bound. In this paper, for the first time in the literature, we prove the necessity and effectiveness of learning the prior when aggregated posterior does not match unit Gaussian prior, analyze why this situation may happen, and propose a hypothesis that learning the prior may improve reconstruction loss, all of which are supported by our extensive experiment results. We show that using learned Real NVP prior and just one latent variable in VAE, we can achieve test NLL comparable to very deep state-of-the-art hierarchical VAE, outperforming many previous works with complex hierarchical VAE architectures.
While tasks could come with varying the number of instances and classes in realistic settings, the existing meta-learning approaches for few-shot classification assume that the number of instances per task and class is fixed. Due to such restriction, they learn to equally utilize the meta-knowledge across all the tasks, even when the number of instances per task and class largely varies. Moreover, they do not consider distributional difference in unseen tasks, on which the meta-knowledge may have less usefulness depending on the task relatedness. To overcome these limitations, we propose a novel meta-learning model that adaptively balances the effect of the meta-learning and task-specific learning within each task. Through the learning of the balancing variables, we can decide whether to obtain a solution by relying on the meta-knowledge or task-specific learning. We formulate this objective into a Bayesian inference framework and tackle it using variational inference. We validate our Bayesian Task-Adaptive Meta-Learning (Bayesian TAML) on multiple realistic task- and class-imbalanced datasets, on which it significantly outperforms existing meta-learning approaches. Further ablation study confirms the effectiveness of each balancing component and the Bayesian learning framework.
In classical Hawkes process, the baseline intensity and triggering kernel are assumed to be a constant and parametric function respectively, which limits the model flexibility. To generalize it, we present a fully Bayesian nonparametric model, namely Gaussian process modulated Hawkes process and propose an EM-variational inference scheme. In this model, a transformation of Gaussian process is used as a prior on the baseline intensity and triggering kernel. By introducing a latent branching structure, the inference of baseline intensity and triggering kernel is decoupled and the variational inference scheme is embedded into an EM framework naturally. We also provide a series of schemes to accelerate the inference. Results of synthetic and real data experiments show that the underlying baseline intensity and triggering kernel can be recovered without parametric restriction and our Bayesian nonparametric estimation is superior to other state of the arts.