A simulation is useful when the phenomenon of interest is either expensive to regenerate or irreproducible with the same context. Recently, Bayesian inference on the distribution of the simulation input parameter has been implemented sequentially to minimize the required simulation budget for the task of simulation validation to the real-world. However, the Bayesian inference is still challenging when the ground-truth posterior is multi-modal with a high-dimensional simulation output. This paper introduces a regularization technique, namely Neural Posterior Regularization (NPR), which enforces the model to explore the input parameter space effectively. Afterward, we provide the closed-form solution of the regularized optimization that enables analyzing the effect of the regularization. We empirically validate that NPR attains the statistically significant gain on benchmark performances for diverse simulation tasks.
People have made remarkable progress in game AIs, especially in domain of perfect information game. However, trick-taking poker game, as a popular form of imperfect information game, has been regarded as a challenge for a long time. Since trick-taking game requires high level of not only reasoning, but also inference to excel, it can be a new milestone for imperfect information game AI. We study Gongzhu, a trick-taking game analogous to, but slightly simpler than contract bridge. Nonetheless, the strategies of Gongzhu are complex enough for both human and computer players. We train a strong Gongzhu AI ScrofaZero from \textit{tabula rasa} by deep reinforcement learning, while few previous efforts on solving trick-taking poker game utilize the representation power of neural networks. Also, we introduce new techniques for imperfect information game including stratified sampling, importance weighting, integral over equivalent class, Bayesian inference, etc. Our AI can achieve human expert level performance. The methodologies in building our program can be easily transferred into a wide range of trick-taking games.
Bayesian inference over the reward presents an ideal solution to the ill-posed nature of the inverse reinforcement learning problem. Unfortunately current methods generally do not scale well beyond the small tabular setting due to the need for an inner-loop MDP solver, and even non-Bayesian methods that do themselves scale often require extensive interaction with the environment to perform well, being inappropriate for high stakes or costly applications such as healthcare. In this paper we introduce our method, Approximate Variational Reward Imitation Learning (AVRIL), that addresses both of these issues by jointly learning an approximate posterior distribution over the reward that scales to arbitrarily complicated state spaces alongside an appropriate policy in a completely offline manner through a variational approach to said latent reward. Applying our method to real medical data alongside classic control simulations, we demonstrate Bayesian reward inference in environments beyond the scope of current methods, as well as task performance competitive with focused offline imitation learning algorithms.
We propose a projected Wasserstein gradient descent method (pWGD) for high-dimensional Bayesian inference problems. The underlying density function of a particle system of WGD is approximated by kernel density estimation (KDE), which faces the long-standing curse of dimensionality. We overcome this challenge by exploiting the intrinsic low-rank structure in the difference between the posterior and prior distributions. The parameters are projected into a low-dimensional subspace to alleviate the approximation error of KDE in high dimensions. We formulate a projected Wasserstein gradient flow and analyze its convergence property under mild assumptions. Several numerical experiments illustrate the accuracy, convergence, and complexity scalability of pWGD with respect to parameter dimension, sample size, and processor cores.
We consider adversarial training of deep neural networks through the lens of Bayesian learning, and present a principled framework for adversarial training of Bayesian Neural Networks (BNNs) with certifiable guarantees. We rely on techniques from constraint relaxation of non-convex optimisation problems and modify the standard cross-entropy error model to enforce posterior robustness to worst-case perturbations in $\epsilon$-balls around input points. We illustrate how the resulting framework can be combined with methods commonly employed for approximate inference of BNNs. In an empirical investigation, we demonstrate that the presented approach enables training of certifiably robust models on MNIST, FashionMNIST and CIFAR-10 and can also be beneficial for uncertainty calibration. Our method is the first to directly train certifiable BNNs, thus facilitating their deployment in safety-critical applications.
In images collected by astronomical surveys, stars and galaxies often overlap visually. Deblending is the task of distinguishing and characterizing individual light sources in survey images. We propose StarNet, a Bayesian method to deblend sources in astronomical images of crowded star fields. StarNet leverages recent advances in variational inference, including amortized variational distributions and an optimization objective targeting an expectation of the forward KL divergence. In our experiments with SDSS images of the M2 globular cluster, StarNet is substantially more accurate than two competing methods: Probabilistic Cataloging (PCAT), a method that uses MCMC for inference, and DAOPHOT, a software pipeline employed by SDSS for deblending. In addition, the amortized approach to inference gives StarNet the scaling characteristics necessary to perform Bayesian inference on modern astronomical surveys.
Stacking is a widely used model averaging technique that asymptotically yields optimal predictions among linear averages. We show that stacking is most effective when model predictive performance is heterogeneous in inputs, and we can further improve the stacked mixture with a hierarchical model. We generalize stacking to Bayesian hierarchical stacking. The model weights are varying as a function of data, partially-pooled, and inferred using Bayesian inference. We further incorporate discrete and continuous inputs, other structured priors, and time series and longitudinal data. To verify the performance gain of the proposed method, we derive theory bounds, and demonstrate on several applied problems.
In Bayesian inference, an unknown measurement uncertainty is often quantified in terms of a Gamma distributed precision parameter, which is impractical when prior information on the standard deviation of the measurement uncertainty shall be utilised during inference. This paper thus introduces a method for transforming between a gamma distributed precision parameter and the distribution of the associated standard deviation. The proposed method is based on numerical optimisation and shows adequate results for a wide range of scenarios.
The right to be forgotten has been legislated in many countries but the enforcement in machine learning would cause unbearable costs: companies may need to delete whole models learned from massive resources due to single individual requests. Existing works propose to remove the knowledge learned from the requested data via its influence function which is no longer naturally well-defined in Bayesian inference. This paper proposes a {\it Bayesian inference forgetting} (BIF) framework to realize the right to be forgotten in Bayesian inference. In the BIF framework, we develop forgetting algorithms for variational inference and Markov chain Monte Carlo. We show that our algorithms can provably remove the influence of single datums on the learned models. Theoretical analysis demonstrates that our algorithms have guaranteed generalizability. Experiments of Gaussian mixture models on the synthetic dataset and Bayesian neural networks on the real-world data verify the feasibility of our methods. The source code package is available at \url{https://github.com/fshp971/BIF}.
We develop a generally applicable full-information inference method for heterogeneous agent models, combining aggregate time series data and repeated cross sections of micro data. To handle unobserved aggregate state variables that affect cross-sectional distributions, we compute a numerically unbiased estimate of the model-implied likelihood function. Employing the likelihood estimate in a Markov Chain Monte Carlo algorithm, we obtain fully efficient and valid Bayesian inference. Evaluation of the micro part of the likelihood lends itself naturally to parallel computing. Numerical illustrations in models with heterogeneous households or firms demonstrate that the proposed full-information method substantially sharpens inference relative to using only macro data, and for some parameters micro data is essential for identification.
Bayesian inference applied to microseismic activity monitoring allows the accurate location of microseismic events from recorded seismograms and the estimation of the associated uncertainties. However, the forward modelling of these microseismic events, which is necessary to perform Bayesian source inversion, can be prohibitively expensive in terms of computational resources. A viable solution is to train a surrogate model based on machine learning techniques, to emulate the forward model and thus accelerate Bayesian inference. In this paper, we substantially enhance previous work, which considered only sources with isotropic moment tensors. We train a machine learning algorithm on the power spectrum of the recorded pressure wave and show that the trained emulator allows complete and fast event locations for $\textit{any}$ source mechanism. Moreover, we show that our approach is computationally inexpensive, as it can be run in less than 1 hour on a commercial laptop, while yielding accurate results using less than $10^4$ training seismograms. We additionally demonstrate how the trained emulators can be used to identify the source mechanism through the estimation of the Bayesian evidence. Finally, we demonstrate that our approach is robust to real noise as measured in field data. This work lays the foundations for efficient, accurate future joint determinations of event location and moment tensor, and associated uncertainties, which are ultimately key for accurately characterising human-induced and natural earthquakes, and for enhanced quantitative seismic hazard assessments.
The existence of adversarial examples underscores the importance of understanding the robustness of machine learning models. Bayesian neural networks (BNNs), due to their calibrated uncertainty, have been shown to posses favorable adversarial robustness properties. However, when approximate Bayesian inference methods are employed, the adversarial robustness of BNNs is still not well understood. In this work, we employ gradient-free optimization methods in order to find adversarial examples for BNNs. In particular, we consider genetic algorithms, surrogate models, as well as zeroth order optimization methods and adapt them to the goal of finding adversarial examples for BNNs. In an empirical evaluation on the MNIST and Fashion MNIST datasets, we show that for various approximate Bayesian inference methods the usage of gradient-free algorithms can greatly improve the rate of finding adversarial examples compared to state-of-the-art gradient-based methods.
Bayesian Likelihood-Free Inference (LFI) approaches allow to obtain posterior distributions for stochastic models with intractable likelihood, by relying on model simulations. In Approximate Bayesian Computation (ABC), a popular LFI method, summary statistics are used to reduce data dimensionality. ABC algorithms adaptively tailor simulations to the observation in order to sample from an approximate posterior, whose form depends on the chosen statistics. In this work, we introduce a new way to learn ABC statistics: we first generate parameter-simulation pairs from the model independently on the observation; then, we use Score Matching to train a neural conditional exponential family to approximate the likelihood. The exponential family is the largest class of distributions with fixed-size sufficient statistics; thus, we use them in ABC, which is intuitively appealing and has state-of-the-art performance. In parallel, we insert our likelihood approximation in an MCMC for doubly intractable distributions to draw posterior samples. We can repeat that for any number of observations with no additional model simulations, with performance comparable to related approaches. We validate our methods on toy models with known likelihood and a large-dimensional time-series model.
The characterization of drug-protein interactions is crucial in the high-throughput screening for drug discovery. The deep learning-based approaches have attracted attention because they can predict drug-protein interactions without trial-and-error by humans. However, because data labeling requires significant resources, the available protein data size is relatively small, which consequently decreases model performance. Here we propose two methods to construct a deep learning framework that exhibits superior performance with a small labeled dataset. At first, we use transfer learning in encoding protein sequences with a pretrained model, which trains general sequence representations in an unsupervised manner. Second, we use a Bayesian neural network to make a robust model by estimating the data uncertainty. As a result, our model performs better than the previous baselines for predicting drug-protein interactions. We also show that the quantified uncertainty from the Bayesian inference is related to the confidence and can be used for screening DPI data points.
Latent Factor Model (LFM) is one of the most successful methods for Collaborative filtering (CF) in the recommendation system, in which both users and items are projected into a joint latent factor space. Base on matrix factorization applied usually in pattern recognition, LFM models user-item interactions as inner products of factor vectors of user and item in that space and can be efficiently solved by least square methods with optimal estimation. However, such optimal estimation methods are prone to overfitting due to the extreme sparsity of user-item interactions. In this paper, we propose a Bayesian treatment for LFM, named Bayesian Latent Factor Model (BLFM). Based on observed user-item interactions, we build a probabilistic factor model in which the regularization is introduced via placing prior constraint on latent factors, and the likelihood function is established over observations and parameters. Then we draw samples of latent factors from the posterior distribution with Variational Inference (VI) to predict expected value. We further make an extension to BLFM, called BLFMBias, incorporating user-dependent and item-dependent biases into the model for enhancing performance. Extensive experiments on the movie rating dataset show the effectiveness of our proposed models by compared with several strong baselines.
Many probabilistic inference problems such as stochastic filtering or the computation of rare event probabilities require model analysis under initial and terminal constraints. We propose a solution to this bridging problem for the widely used class of population-structured Markov jump processes. The method is based on a state-space lumping scheme that aggregates states in a grid structure. The resulting approximate bridging distribution is used to iteratively refine relevant and truncate irrelevant parts of the state-space. This way the algorithm learns a well-justified finite-state projection yielding guaranteed lower bounds for the system behavior under endpoint constraints. We demonstrate the method's applicability to a wide range of problems such as Bayesian inference and the analysis of rare events.
In this study, Bayesian inference is developed for structural vector autoregressive models in which the structural parameters are identified via Markov-switching heteroskedasticity. In such a model, restrictions that are just-identifying in the homoskedastic case, become over-identifying and can be tested. A set of parametric restrictions is derived under which the structural matrix is globally or partially identified and a Savage-Dickey density ratio is used to assess the validity of the identification conditions. The latter is facilitated by analytical derivations that make the computations fast and numerical standard errors small. As an empirical example, monetary models are compared using heteroskedasticity as an additional device for identification. The empirical results support models with money in the interest rate reaction function.
Deep Neural Networks (DNNs) have aroused great attention in Compressed Sensing (CS) restoration. However, the working mechanism of DNNs is not explainable, thereby it is unclear that how to design an optimal DNNs for CS restoration. In this paper, we propose a novel statistical framework to explain DNNs, which proves that the hidden layers of DNNs are equivalent to Gibbs distributions and interprets DNNs as a Bayesian hierarchical model. The framework provides a Bayesian perspective to explain the working mechanism of DNNs, namely some hidden layers learn a prior distribution and other layers learn a likelihood distribution. Moreover, the framework provides insights into DNNs and reveals two inherent limitations of DNNs for CS restoration. In contrast to most previous works designing an end-to-end DNNs for CS restoration, we propose a novel DNNs to model a prior distribution only, which can circumvent the limitations of DNNs. Given the prior distribution generated from the DNNs, we design a Bayesian inference algorithm to realize CS restoration in the framework of Bayesian Compressed Sensing. Finally, extensive simulations validate the proposed theory of DNNs and demonstrate that the proposed algorithm outperforms the state-of-the-art CS restoration methods.
Bayesian inference methods rely on numerical algorithms for both model selection and parameter inference. In general, these algorithms require a high computational effort to yield reliable estimates. One of the major challenges in phylogenetics is the estimation of the marginal likelihood. This quantity is commonly used for comparing different evolutionary models, but its calculation, even for simple models, incurs high computational cost. Another interesting challenge relates to the estimation of the posterior distribution. Often, long Markov chains are required to get sufficient samples to carry out parameter inference, especially for tree distributions. In general, these problems are addressed separately by using different procedures. Nested sampling (NS) is a Bayesian computation algorithm which provides the means to estimate marginal likelihoods together with their uncertainties, and to sample from the posterior distribution at no extra cost. The methods currently used in phylogenetics for marginal likelihood estimation lack in practicality due to their dependence on many tuning parameters and the inability of most implementations to provide a direct way to calculate the uncertainties associated with the estimates. To address these issues, we introduce NS to phylogenetics. Its performance is assessed under different scenarios and compared to established methods. We conclude that NS is a competitive and attractive algorithm for phylogenetic inference. An implementation is available as a package for BEAST 2 under the LGPL licence, accessible at https://github.com/BEAST2-Dev/nested-sampling.
Background: Species abundance distributions in chemical reaction network models cannot usually be computed analytically. Instead, stochas- tic simulation algorithms allow sample from the the system configuration. Although many algorithms have been described, no fast implementation has been provided for {\tau}-leaping which i) is Matlab-compatible, ii) adap- tively alternates between SSA, implicit and explicit {\tau}-leaping, and iii) provides summary statistics necessary for Bayesian inference. Results: We provide a Matlab-compatible implementation of the adap- tive explicit-implicit {\tau}-leaping algorithm to address the above-mentioned deficits. matLeap provides equal or substantially faster results compared to two widely used simulation packages while maintaining accuracy. Lastly, matLeap yields summary statistics of the stochastic process unavailable with other methods, which are indispensable for Bayesian inference. Conclusions: matLeap addresses shortcomings in existing Matlab-compatible stochastic simulation software, providing significant speedups and sum- mary statistics that are especially useful for researchers utilizing particle- filter based methods for Bayesian inference. Code is available for download at https://github.com/claassengroup/matLeap. Contact: [email omitted]