We apply the technique of implicit differentiation to boost performance, reduce numerical error, and remove required user-tuning in the Marginal Unbiased Score Expansion (MUSE) algorithm for hierarchical Bayesian inference. We demonstrate these improvements on three representative inference problems: 1) an extended Neal's funnel 2) Bayesian neural networks, and 3) probabilistic principal component analysis. On our particular test cases, MUSE with implicit differentiation is faster than Hamiltonian Monte Carlo by factors of 155, 397, and 5, respectively, or factors of 65, 278, and 1 without implicit differentiation, and yields good approximate marginal posteriors. The Julia and Python MUSE packages have been updated to use implicit differentiation, and can solve problems defined by hand or with any of a number of popular probabilistic programming languages and automatic differentiation backends.
Although the no-u-turn sampler (NUTS) is a widely adopted method for performing Bayesian inference, it requires numerous posterior gradients which can be expensive to compute in practice. Recently, there has been a significant interest in physics-based machine learning of dynamical (or Hamiltonian) systems and Hamiltonian neural networks (HNNs) is a noteworthy architecture. But these types of architectures have not been applied to solve Bayesian inference problems efficiently. We propose the use of HNNs for performing Bayesian inference efficiently without requiring numerous posterior gradients. We introduce latent variable outputs to HNNs (L-HNNs) for improved expressivity and reduced integration errors. We integrate L-HNNs in NUTS and further propose an online error monitoring scheme to prevent sampling degeneracy in regions where L-HNNs may have little training data. We demonstrate L-HNNs in NUTS with online error monitoring considering several complex high-dimensional posterior densities and compare its performance to NUTS.
Epidemic models are powerful tools in understanding infectious disease. However, as they increase in size and complexity, they can quickly become computationally intractable. Recent progress in modelling methodology has shown that surrogate models can be used to emulate complex epidemic models with a high-dimensional parameter space. We show that deep sequence-to-sequence (seq2seq) models can serve as accurate surrogates for complex epidemic models with sequence based model parameters, effectively replicating seasonal and long-term transmission dynamics. Once trained, our surrogate can predict scenarios a several thousand times faster than the original model, making them ideal for policy exploration. We demonstrate that replacing a traditional epidemic model with a learned simulator facilitates robust Bayesian inference.
Transductive Few-Shot learning has gained increased attention nowadays considering the cost of data annotations along with the increased accuracy provided by unlabelled samples in the domain of few shot. Especially in Few-Shot Classification (FSC), recent works explore the feature distributions aiming at maximizing likelihoods or posteriors with respect to the unknown parameters. Following this vein, and considering the parallel between FSC and clustering, we seek for better taking into account the uncertainty in estimation due to lack of data, as well as better statistical properties of the clusters associated with each class. Therefore in this paper we propose a new clustering method based on Variational Bayesian inference, further improved by Adaptive Dimension Reduction based on Probabilistic Linear Discriminant Analysis. Our proposed method significantly improves accuracy in the realistic unbalanced transductive setting on various Few-Shot benchmarks when applied to features used in previous studies, with a gain of up to $6\%$ in accuracy. In addition, when applied to balanced setting, we obtain very competitive results without making use of the class-balance artefact which is disputable for practical use cases. We also provide the performance of our method on a high performing pretrained backbone, with the reported results further surpassing the current state-of-the-art accuracy, suggesting the genericity of the proposed method.
The comparison of local characteristics of two random processes can shed light on periods of time or space at which the processes differ the most. This paper proposes a method that learns about regions with a certain volume, where the marginal attributes of two processes are less similar. The proposed methods are devised in full generality for the setting where the data of interest are themselves stochastic processes, and thus the proposed method can be used for pointing out the regions of maximum dissimilarity with a certain volume, in the contexts of functional data, time series, and point processes. The parameter functions underlying both stochastic processes of interest are modeled via a basis representation, and Bayesian inference is conducted via an integrated nested Laplace approximation. The numerical studies validate the proposed methods, and we showcase their application with case studies on criminology, finance, and medicine.
In this paper we present BayesLDM, a system for Bayesian longitudinal data modeling consisting of a high-level modeling language with specific features for modeling complex multivariate time series data coupled with a compiler that can produce optimized probabilistic program code for performing inference in the specified model. BayesLDM supports modeling of Bayesian network models with a specific focus on the efficient, declarative specification of dynamic Bayesian Networks (DBNs). The BayesLDM compiler combines a model specification with inspection of available data and outputs code for performing Bayesian inference for unknown model parameters while simultaneously handling missing data. These capabilities have the potential to significantly accelerate iterative modeling workflows in domains that involve the analysis of complex longitudinal data by abstracting away the process of producing computationally efficient probabilistic inference code. We describe the BayesLDM system components, evaluate the efficiency of representation and inference optimizations and provide an illustrative example of the application of the system to analyzing heterogeneous and partially observed mobile health data.
Bayesian Optimisation (BO) methods seek to find global optima of objective functions which are only available as a black-box or are expensive to evaluate. Such methods construct a surrogate model for the objective function, quantifying the uncertainty in that surrogate through Bayesian inference. Objective evaluations are sequentially determined by maximising an acquisition function at each step. However, this ancilliary optimisation problem can be highly non-trivial to solve, due to the non-convexity of the acquisition function, particularly in the case of batch Bayesian optimisation, where multiple points are selected in every step. In this work we reformulate batch BO as an optimisation problem over the space of probability measures. We construct a new acquisition function based on multipoint expected improvement which is convex over the space of probability measures. Practical schemes for solving this `inner' optimisation problem arise naturally as gradient flows of this objective function. We demonstrate the efficacy of this new method on different benchmark functions and compare with state-of-the-art batch BO methods.
Full waveform inversion (FWI) commonly stands for the state-of-the-art approach for imaging subsurface structures and physical parameters, however, its implementation usually faces great challenges, such as building a good initial model to escape from local minima, and evaluating the uncertainty of inversion results. In this paper, we propose the implicit full waveform inversion (IFWI) algorithm using continuously and implicitly defined deep neural representations. Compared to FWI, which is sensitive to the initial model, IFWI benefits from the increased degrees of freedom with deep learning optimization, thus allowing to start from a random initialization, which greatly reduces the risk of non-uniqueness and being trapped in local minima. Both theoretical and experimental analyses indicates that, given a random initial model, IFWI is able to converge to the global minimum and produce a high-resolution image of subsurface with fine structures. In addition, uncertainty analysis of IFWI can be easily performed by approximating Bayesian inference with various deep learning approaches, which is analyzed in this paper by adding dropout neurons. Furthermore, IFWI has a certain degree of robustness and strong generalization ability that are exemplified in the experiments of various 2D geological models. With proper setup, IFWI can also be well suited for multi-scale joint geophysical inversion.
Standard GPs offer a flexible modelling tool for well-behaved processes. However, deviations from Gaussianity are expected to appear in real world datasets, with structural outliers and shocks routinely observed. In these cases GPs can fail to model uncertainty adequately and may over-smooth inferences. Here we extend the GP framework into a new class of time-changed GPs that allow for straightforward modelling of heavy-tailed non-Gaussian behaviours, while retaining a tractable conditional GP structure through an infinite mixture of non-homogeneous GPs representation. The conditional GP structure is obtained by conditioning the observations on a latent transformed input space and the random evolution of the latent transformation is modelled using a L\'{e}vy process which allows Bayesian inference in both the posterior predictive density and the latent transformation function. We present Markov chain Monte Carlo inference procedures for this model and demonstrate the potential benefits compared to a standard GP.
We propose a novel approach to perform approximate Bayesian inference in complex models such as Bayesian neural networks. The approach is more scalable to large data than Markov Chain Monte Carlo, it embraces more expressive models than Variational Inference, and it does not rely on adversarial training (or density ratio estimation). We adopt the recent approach of constructing two models: (1) a primary model, tasked with performing regression or classification; and (2) a secondary, expressive (e.g. implicit) model that defines an approximate posterior distribution over the parameters of the primary model. However, we optimise the parameters of the posterior model via gradient descent according to a Monte Carlo estimate of the posterior predictive distribution -- which is our only approximation (other than the posterior model). Only a likelihood needs to be specified, which can take various forms such as loss functions and synthetic likelihoods, thus providing a form of a likelihood-free approach. Furthermore, we formulate the approach such that the posterior samples can either be independent of, or conditionally dependent upon the inputs to the primary model. The latter approach is shown to be capable of increasing the apparent complexity of the primary model. We see this being useful in applications such as surrogate and physics-based models. To promote how the Bayesian paradigm offers more than just uncertainty quantification, we demonstrate: uncertainty quantification, multi-modality, as well as an application with a recent deep forecasting neural network architecture.
We propose a deep importance sampling method that is suitable for estimating rare event probabilities in high-dimensional problems. We approximate the optimal importance distribution in a general importance sampling problem as the pushforward of a reference distribution under a composition of order-preserving transformations, in which each transformation is formed by a squared tensor-train decomposition. The squared tensor-train decomposition provides a scalable ansatz for building order-preserving high-dimensional transformations via density approximations. The use of composition of maps moving along a sequence of bridging densities alleviates the difficulty of directly approximating concentrated density functions. To compute expectations over unnormalized probability distributions, we design a ratio estimator that estimates the normalizing constant using a separate importance distribution, again constructed via a composition of transformations in tensor-train format. This offers better theoretical variance reduction compared with self-normalized importance sampling, and thus opens the door to efficient computation of rare event probabilities in Bayesian inference problems. Numerical experiments on problems constrained by differential equations show little to no increase in the computational complexity with the event probability going to zero, and allow to compute hitherto unattainable estimates of rare event probabilities for complex, high-dimensional posterior densities.
Aided by advances in neural density estimation, considerable progress has been made in recent years towards a suite of simulation-based inference (SBI) methods capable of performing flexible, black-box, approximate Bayesian inference for stochastic simulation models. While it has been demonstrated that neural SBI methods can provide accurate posterior approximations, the simulation studies establishing these results have considered only well-specified problems -- that is, where the model and the data generating process coincide exactly. However, the behaviour of such algorithms in the case of model misspecification has received little attention. In this work, we provide the first comprehensive study of the behaviour of neural SBI algorithms in the presence of various forms of model misspecification. We find that misspecification can have a profoundly deleterious effect on performance. Some mitigation strategies are explored, but no approach tested prevents failure in all cases. We conclude that new approaches are required to address model misspecification if neural SBI algorithms are to be relied upon to derive accurate scientific conclusions.
Variational inference (VI) is a specific type of approximate Bayesian inference that approximates an intractable posterior distribution with a tractable one. VI casts the inference problem as an optimization problem, more specifically, the goal is to maximize a lower bound of the logarithm of the marginal likelihood with respect to the parameters of the approximate posterior. Reinforcement learning (RL) on the other hand deals with autonomous agents and how to make them act optimally such as to maximize some notion of expected future cumulative reward. In the non-sequential setting where agents' actions do not have an impact on future states of the environment, RL is covered by contextual bandits and Bayesian optimization. In a proper sequential scenario, however, where agents' actions affect future states, instantaneous rewards need to be carefully traded off against potential long-term rewards. This manuscript shows how the apparently different subjects of VI and RL are linked in two fundamental ways. First, the optimization objective of RL to maximize future cumulative rewards can be recovered via a VI objective under a soft policy constraint in both the non-sequential and the sequential setting. This policy constraint is not just merely artificial but has proven as a useful regularizer in many RL tasks yielding significant improvements in agent performance. And second, in model-based RL where agents aim to learn about the environment they are operating in, the model-learning part can be naturally phrased as an inference problem over the process that governs environment dynamics. We are going to distinguish between two scenarios for the latter: VI when environment states are fully observable by the agent and VI when they are only partially observable through an observation distribution.
Peer grading systems aggregate noisy reports from multiple students to approximate a true grade as closely as possible. Most current systems either take the mean or median of reported grades; others aim to estimate students' grading accuracy under a probabilistic model. This paper extends the state of the art in the latter approach in three key ways: (1) recognizing that students can behave strategically (e.g., reporting grades close to the class average without doing the work); (2) appropriately handling censored data that arises from discrete-valued grading rubrics; and (3) using mixed integer programming to improve the interpretability of the grades assigned to students. We show how to make Bayesian inference practical in this model and evaluate our approach on both synthetic and real-world data obtained by using our implemented system in four large classes. These extensive experiments show that grade aggregation using our model accurately estimates true grades, students' likelihood of submitting uninformative grades, and the variation in their inherent grading error; we also characterize our models' robustness.
A key challenge of continual reinforcement learning (CRL) in dynamic environments is to promptly adapt the RL agent's behavior as the environment changes over its lifetime, while minimizing the catastrophic forgetting of the learned information. To address this challenge, in this article, we propose DaCoRL, i.e., dynamics-adaptive continual RL. DaCoRL learns a context-conditioned policy using progressive contextualization, which incrementally clusters a stream of stationary tasks in the dynamic environment into a series of contexts and opts for an expandable multihead neural network to approximate the policy. Specifically, we define a set of tasks with similar dynamics as an environmental context and formalize context inference as a procedure of online Bayesian infinite Gaussian mixture clustering on environment features, resorting to online Bayesian inference to infer the posterior distribution over contexts. Under the assumption of a Chinese restaurant process prior, this technique can accurately classify the current task as a previously seen context or instantiate a new context as needed without relying on any external indicator to signal environmental changes in advance. Furthermore, we employ an expandable multihead neural network whose output layer is synchronously expanded with the newly instantiated context, and a knowledge distillation regularization term for retaining the performance on learned tasks. As a general framework that can be coupled with various deep RL algorithms, DaCoRL features consistent superiority over existing methods in terms of the stability, overall performance and generalization ability, as verified by extensive experiments on several robot navigation and MuJoCo locomotion tasks.
Gaussian processes are arguably the most important class of spatiotemporal models within machine learning. They encode prior information about the modeled function and can be used for exact or approximate Bayesian learning. In many applications, particularly in physical sciences and engineering, but also in areas such as geostatistics and neuroscience, invariance to symmetries is one of the most fundamental forms of prior information one can consider. The invariance of a Gaussian process' covariance to such symmetries gives rise to the most natural generalization of the concept of stationarity to such spaces. In this work, we develop constructive and practical techniques for building stationary Gaussian processes on a very large class of non-Euclidean spaces arising in the context of symmetries. Our techniques make it possible to (i) calculate covariance kernels and (ii) sample from prior and posterior Gaussian processes defined on such spaces, both in a practical manner. This work is split into two parts, each involving different technical considerations: part I studies compact spaces, while part II studies non-compact spaces possessing certain structure. Our contributions make the non-Euclidean Gaussian process models we study compatible with well-understood computational techniques available in standard Gaussian process software packages, thereby making them accessible to practitioners.
Most sensor calibrations rely on the linearity and steadiness of their response characteristics, but practical sensors are nonlinear, and their response drifts with time, restricting their choices for adoption. To broaden the realm of sensors to allow nonlinearity and time-drift in the underlying dynamics, a Bayesian inference-based nonlinear, non-causal dynamic calibration method is introduced, where the sensed value is estimated as a posterior conditional mean given a finite-length sequence of the sensor measurements and the elapsed time. Additionally, an algorithm is proposed to adjust an already learned calibration map online whenever new data arrives. The effectiveness of the proposed method is validated on continuous-glucose-monitoring (CGM) data from an alive rat equipped with an in-house optical glucose sensor. To allow flexibility in choice, the validation is also performed on a synthetic blood glucose level (BGL) dataset generated using FDA-approved virtual diabetic patient models together with an illustrative CGM sensor model.
We prove that Fisher-Rao natural gradient descent (FR-NGD) optimally approximates the continuous time replicator equation (an essential model of evolutionary dynamics), and term this correspondence "conjugate natural selection". This correspondence promises alternative approaches for evolutionary computation over continuous or high-dimensional hypothesis spaces. As a special case, FR-NGD also provides the optimal approximation of continuous Bayesian inference when hypotheses compete on the basis of predicting actual observations. In this case, the method avoids the need to compute prior probabilities. We demonstrate our findings on a non-convex optimization problem and a system identification task for a stochastic process with time-varying parameters.
This paper describes a framework for the object-goal navigation task, which requires a robot to find and move to the closest instance of a target object class from a random starting position. The framework uses a history of robot trajectories to learn a Spatial Relational Graph (SRG) and Graph Convolutional Network (GCN)-based embeddings for the likelihood of proximity of different semantically-labeled regions and the occurrence of different object classes in these regions. To locate a target object instance during evaluation, the robot uses Bayesian inference and the SRG to estimate the visible regions, and uses the learned GCN embeddings to rank visible regions and select the region to explore next.
We consider learning and compositionality as the key mechanisms towards simulating human-like intelligence. While each mechanism is successfully achieved by neural networks and symbolic AIs, respectively, it is the combination of the two mechanisms that makes human-like intelligence possible. Despite the numerous attempts on building hybrid neuralsymbolic systems, we argue that our true goal should be unifying learning and compositionality, the core mechanisms, instead of neural and symbolic methods, the surface approaches to achieve them. In this work, we review and analyze the strengths and weaknesses of neural and symbolic methods by separating their forms and meanings (structures and semantics), and propose Connectionist Probabilistic Program (CPPs), a framework that connects connectionist structures (for learning) and probabilistic program semantics (for compositionality). Under the framework, we design a CPP extension for small scale sequence modeling and provide a learning algorithm based on Bayesian inference. Although challenges exist in learning complex patterns without supervision, our early results demonstrate CPP's successful extraction of concepts and relations from raw sequential data, an initial step towards compositional learning.