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Paul-Christian Bürkner

Publications and source records attributed to Paul-Christian Bürkner.

At least 55 records · Page 3Linked to original sources
arXiv2024

Leveraging Self-Consistency for Data-Efficient Amortized Bayesian Inference

We propose a method to improve the efficiency and accuracy of amortized Bayesian inference by leveraging universal symmetries in the joint probabilistic model of parameters and data. In a nutshell, we invert Bayes' theorem and estimate the marginal likelihood based on approximate representations of the joint model. Upon perfect approximation, the marginal likelihood is constant across all parameter values by definition. However, errors in approximate inference lead to undesirable variance in the marginal likelihood estimates across different parameter values. We penalize violations of this symmetry with a \textit{self-consistency loss} which significantly improves the quality of approximate inference in low data regimes and can be used to augment the training of popular neural density estimators. We apply our method to a number of synthetic problems and realistic scientific models, discovering notable advantages in the context of both neural posterior and likelihood approximation.

cs.LG↗
arXiv2024

posteriordb: Testing, Benchmarking and Developing Bayesian Inference Algorithms

The generality and robustness of inference algorithms is critical to the success of widely used probabilistic programming languages such as Stan, PyMC, Pyro, and Turing.jl. When designing a new general-purpose inference algorithm, whether it involves Monte Carlo sampling or variational approximation, the fundamental problem arises in evaluating its accuracy and efficiency across a range of representative target models. To solve this problem, we propose posteriordb, a database of models and data sets defining target densities along with reference Monte Carlo draws. We further provide a guide to the best practices in using posteriordb for model evaluation and comparison. To provide a wide range of realistic target densities, posteriordb currently comprises 120 representative models and has been instrumental in developing several general inference algorithms.

stat.CO↗
arXiv2024

Detecting Model Misspecification in Amortized Bayesian Inference with Neural Networks: An Extended Investigation

Recent advances in probabilistic deep learning enable efficient amortized Bayesian inference in settings where the likelihood function is only implicitly defined by a simulation program (simulation-based inference; SBI). But how faithful is such inference if the simulation represents reality somewhat inaccurately, that is, if the true system behavior at test time deviates from the one seen during training? We conceptualize the types of such model misspecification arising in SBI and systematically investigate how the performance of neural posterior approximators gradually deteriorates as a consequence, making inference results less and less trustworthy. To notify users about this problem, we propose a new misspecification measure that can be trained in an unsupervised fashion (i.e., without training data from the true distribution) and reliably detects model misspecification at test time. Our experiments clearly demonstrate the utility of our new measure both on toy examples with an analytical ground-truth and on representative scientific tasks in cell biology, cognitive decision making, disease outbreak dynamics, and computer vision. We show how the proposed misspecification test warns users about suspicious outputs, raises an alarm when predictions are not trustworthy, and guides model designers in their search for better simulators.

cs.LG↗
arXiv2024

Simulation-Based Prior Knowledge Elicitation for Parametric Bayesian Models

A central characteristic of Bayesian statistics is the ability to consistently incorporate prior knowledge into various modeling processes. In this paper, we focus on translating domain expert knowledge into corresponding prior distributions over model parameters, a process known as prior elicitation. Expert knowledge can manifest itself in diverse formats, including information about raw data, summary statistics, or model parameters. A major challenge for existing elicitation methods is how to effectively utilize all of these different formats in order to formulate prior distributions that align with the expert's expectations, regardless of the model structure. To address these challenges, we develop a simulation-based elicitation method that can learn the hyperparameters of potentially any parametric prior distribution from a wide spectrum of expert knowledge using stochastic gradient descent. We validate the effectiveness and robustness of our elicitation method in four representative case studies covering linear models, generalized linear models, and hierarchical models. Our results support the claim that our method is largely independent of the underlying model structure and adaptable to various elicitation techniques, including quantile-based, moment-based, and histogram-based methods.

stat.ME↗
arXiv2024

Inferring Human Intentions from Predicted Action Probabilities

Predicting the next action that a human is most likely to perform is key to human-AI collaboration and has consequently attracted increasing research interests in recent years. An important factor for next action prediction are human intentions: If the AI agent knows the intention it can predict future actions and plan collaboration more effectively. Existing Bayesian methods for this task struggle with complex visual input while deep neural network (DNN) based methods do not provide uncertainty quantifications. In this work we combine both approaches for the first time and show that the predicted next action probabilities contain information that can be used to infer the underlying intention. We propose a two-step approach to human intention prediction: While a DNN predicts the probabilities of the next action, MCMC-based Bayesian inference is used to infer the underlying intention from these predictions. This approach not only allows for independent design of the DNN architecture but also the subsequently fast, design-independent inference of human intentions. We evaluate our method using a series of experiments on the Watch-And-Help (WAH) and a keyboard and mouse interaction dataset. Our results show that our approach can accurately predict human intentions from observed actions and the implicit information contained in next action probabilities. Furthermore, we show that our approach can predict the correct intention even if only few actions have been observed.

cs.HC↗
arXiv2024

Prediction can be safely used as a proxy for explanation in causally consistent Bayesian generalized linear models

Bayesian modeling provides a principled approach to quantifying uncertainty in model parameters and model structure and has seen a surge of applications in recent years. Within the context of a Bayesian workflow, we are concerned with model selection for the purpose of finding models that best explain the data, that is, help us understand the underlying data generating process. Since we rarely have access to the true process, all we are left with during real-world analyses is incomplete causal knowledge from sources outside of the current data and model predictions of said data. This leads to the important question of when the use of prediction as a proxy for explanation for the purpose of model selection is valid. We approach this question by means of large-scale simulations of Bayesian generalized linear models where we investigate various causal and statistical misspecifications. Our results indicate that the use of prediction as proxy for explanation is valid and safe only when the models under consideration are sufficiently consistent with the underlying causal structure of the true data generating process.

stat.ME↗
arXiv2024

The Simplex Projection: Lossless Visualization of 4D Compositional Data on a 2D Canvas

The simplex projection expands the capabilities of simplex plots (also known as ternary plots) to achieve a lossless visualization of 4D compositional data on a 2D canvas. Previously, this was only possible for 3D compositional data. We demonstrate how our approach can be applied to individual data points, point clouds, and continuous probability density functions on simplices. While we showcase our visualization technique specifically for 4D compositional data, we offer rigorous proofs that support its extension to compositional data of any (finite) dimensionality.

cs.GR↗
arXiv2023

A Deep Learning Method for Comparing Bayesian Hierarchical Models

Bayesian model comparison (BMC) offers a principled approach for assessing the relative merits of competing computational models and propagating uncertainty into model selection decisions. However, BMC is often intractable for the popular class of hierarchical models due to their high-dimensional nested parameter structure. To address this intractability, we propose a deep learning method for performing BMC on any set of hierarchical models which can be instantiated as probabilistic programs. Since our method enables amortized inference, it allows efficient re-estimation of posterior model probabilities and fast performance validation prior to any real-data application. In a series of extensive validation studies, we benchmark the performance of our method against the state-of-the-art bridge sampling method and demonstrate excellent amortized inference across all BMC settings. We then showcase our method by comparing four hierarchical evidence accumulation models that have previously been deemed intractable for BMC due to partly implicit likelihoods. Additionally, we demonstrate how transfer learning can be leveraged to enhance training efficiency. We provide reproducible code for all analyses and an open-source implementation of our method.

stat.ML↗
arXiv2023

Posterior accuracy and calibration under misspecification in Bayesian generalized linear models

Generalized linear models (GLMs) are popular for data-analysis in almost all quantitative sciences, but the choice of likelihood family and link function is often difficult. This motivates the search for likelihoods and links that minimize the impact of potential misspecification. We perform a large-scale simulation study on double-bounded and lower-bounded response data where we systematically vary both true and assumed likelihoods and links. In contrast to previous studies, we also study posterior calibration and uncertainty metrics in addition to point-estimate accuracy. Our results indicate that certain likelihoods and links can be remarkably robust to misspecification, performing almost on par with their respective true counterparts. Additionally, normal likelihood models with identity link (i.e., linear regression) often achieve calibration comparable to the more structurally faithful alternatives, at least in the studied scenarios. On the basis of our findings, we provide practical suggestions for robust likelihood and link choices in GLMs.

stat.ME↗
arXiv2023

Some models are useful, but how do we know which ones? Towards a unified Bayesian model taxonomy

Probabilistic (Bayesian) modeling has experienced a surge of applications in almost all quantitative sciences and industrial areas. This development is driven by a combination of several factors, including better probabilistic estimation algorithms, flexible software, increased computing power, and a growing awareness of the benefits of probabilistic learning. However, a principled Bayesian model building workflow is far from complete and many challenges remain. To aid future research and applications of a principled Bayesian workflow, we ask and provide answers for what we perceive as two fundamental questions of Bayesian modeling, namely (a) "What actually is a Bayesian model?" and (b) "What makes a good Bayesian model?". As an answer to the first question, we propose the PAD model taxonomy that defines four basic kinds of Bayesian models, each representing some combination of the assumed joint distribution of all (known or unknown) variables (P), a posterior approximator (A), and training data (D). As an answer to the second question, we propose ten utility dimensions according to which we can evaluate Bayesian models holistically, namely, (1) causal consistency, (2) parameter recoverability, (3) predictive performance, (4) fairness, (5) structural faithfulness, (6) parsimony, (7) interpretability, (8) convergence, (9) estimation speed, and (10) robustness. Further, we propose two example utility decision trees that describe hierarchies and trade-offs between utilities depending on the inferential goals that drive model building and testing.

stat.ME↗
arXiv2023

Neural Superstatistics for Bayesian Estimation of Dynamic Cognitive Models

Mathematical models of cognition are often memoryless and ignore potential fluctuations of their parameters. However, human cognition is inherently dynamic. Thus, we propose to augment mechanistic cognitive models with a temporal dimension and estimate the resulting dynamics from a superstatistics perspective. Such a model entails a hierarchy between a low-level observation model and a high-level transition model. The observation model describes the local behavior of a system, and the transition model specifies how the parameters of the observation model evolve over time. To overcome the estimation challenges resulting from the complexity of superstatistical models, we develop and validate a simulation-based deep learning method for Bayesian inference, which can recover both time-varying and time-invariant parameters. We first benchmark our method against two existing frameworks capable of estimating time-varying parameters. We then apply our method to fit a dynamic version of the diffusion decision model to long time series of human response times data. Our results show that the deep learning approach is very efficient in capturing the temporal dynamics of the model. Furthermore, we show that the erroneous assumption of static or homogeneous parameters will hide important temporal information.

stat.ME↗
arXiv2023

BayesFlow: Amortized Bayesian Workflows With Neural Networks

Modern Bayesian inference involves a mixture of computational techniques for estimating, validating, and drawing conclusions from probabilistic models as part of principled workflows for data analysis. Typical problems in Bayesian workflows are the approximation of intractable posterior distributions for diverse model types and the comparison of competing models of the same process in terms of their complexity and predictive performance. This manuscript introduces the Python library BayesFlow for simulation-based training of established neural network architectures for amortized data compression and inference. Amortized Bayesian inference, as implemented in BayesFlow, enables users to train custom neural networks on model simulations and re-use these networks for any subsequent application of the models. Since the trained networks can perform inference almost instantaneously, the upfront neural network training is quickly amortized.

cs.LG↗
arXiv2023

JANA: Jointly Amortized Neural Approximation of Complex Bayesian Models

This work proposes ``jointly amortized neural approximation'' (JANA) of intractable likelihood functions and posterior densities arising in Bayesian surrogate modeling and simulation-based inference. We train three complementary networks in an end-to-end fashion: 1) a summary network to compress individual data points, sets, or time series into informative embedding vectors; 2) a posterior network to learn an amortized approximate posterior; and 3) a likelihood network to learn an amortized approximate likelihood. Their interaction opens a new route to amortized marginal likelihood and posterior predictive estimation -- two important ingredients of Bayesian workflows that are often too expensive for standard methods. We benchmark the fidelity of JANA on a variety of simulation models against state-of-the-art Bayesian methods and propose a powerful and interpretable diagnostic for joint calibration. In addition, we investigate the ability of recurrent likelihood networks to emulate complex time series models without resorting to hand-crafted summary statistics.

cs.LG↗
arXiv2023

Intuitive Joint Priors for Bayesian Linear Multilevel Models: The R2D2M2 prior

The training of high-dimensional regression models on comparably sparse data is an important yet complicated topic, especially when there are many more model parameters than observations in the data. From a Bayesian perspective, inference in such cases can be achieved with the help of shrinkage prior distributions, at least for generalized linear models. However, real-world data usually possess multilevel structures, such as repeated measurements or natural groupings of individuals, which existing shrinkage priors are not built to deal with. We generalize and extend one of these priors, the R2D2 prior by Zhang et al. (2020), to linear multilevel models leading to what we call the R2D2M2 prior. The proposed prior enables both local and global shrinkage of the model parameters. It comes with interpretable hyperparameters, which we show to be intrinsically related to vital properties of the prior, such as rates of concentration around the origin, tail behavior, and amount of shrinkage the prior exerts. We offer guidelines on how to select the prior's hyperparameters by deriving shrinkage factors and measuring the effective number of non-zero model coefficients. Hence, the user can readily evaluate and interpret the amount of shrinkage implied by a specific choice of hyperparameters. Finally, we perform extensive experiments on simulated and real data, showing that our inference procedure for the prior is well calibrated, has desirable global and local regularization properties and enables the reliable and interpretable estimation of much more complex Bayesian multilevel models than was previously possible.

stat.ME↗
arXiv2023

Detecting and diagnosing prior and likelihood sensitivity with power-scaling

Determining the sensitivity of the posterior to perturbations of the prior and likelihood is an important part of the Bayesian workflow. We introduce a practical and computationally efficient sensitivity analysis approach using importance sampling to estimate properties of posteriors resulting from power-scaling the prior or likelihood. On this basis, we suggest a diagnostic that can indicate the presence of prior-data conflict or likelihood noninformativity and discuss limitations to this power-scaling approach. The approach can be easily included in Bayesian workflows with minimal effort by the model builder and we present an implementation in our new R package priorsense. We further demonstrate the workflow on case studies of real data using models varying in complexity from simple linear models to Gaussian process models.

stat.ME↗
arXiv2023

Prior knowledge elicitation: The past, present, and future

Specification of the prior distribution for a Bayesian model is a central part of the Bayesian workflow for data analysis, but it is often difficult even for statistical experts. In principle, prior elicitation transforms domain knowledge of various kinds into well-defined prior distributions, and offers a solution to the prior specification problem. In practice, however, we are still fairly far from having usable prior elicitation tools that could significantly influence the way we build probabilistic models in academia and industry. We lack elicitation methods that integrate well into the Bayesian workflow and perform elicitation efficiently in terms of costs of time and effort. We even lack a comprehensive theoretical framework for understanding different facets of the prior elicitation problem. Why are we not widely using prior elicitation? We analyse the state of the art by identifying a range of key aspects of prior knowledge elicitation, from properties of the modelling task and the nature of the priors to the form of interaction with the expert. The existing prior elicitation literature is reviewed and categorized in these terms. This allows recognizing under-studied directions in prior elicitation research, finally leading to a proposal of several new avenues to improve prior elicitation methodology.

stat.ME↗
arXiv2023

Meta-Uncertainty in Bayesian Model Comparison

Bayesian model comparison (BMC) offers a principled probabilistic approach to study and rank competing models. In standard BMC, we construct a discrete probability distribution over the set of possible models, conditional on the observed data of interest. These posterior model probabilities (PMPs) are measures of uncertainty, but -- when derived from a finite number of observations -- are also uncertain themselves. In this paper, we conceptualize distinct levels of uncertainty which arise in BMC. We explore a fully probabilistic framework for quantifying meta-uncertainty, resulting in an applied method to enhance any BMC workflow. Drawing on both Bayesian and frequentist techniques, we represent the uncertainty over the uncertain PMPs via meta-models which combine simulated and observed data into a predictive distribution for PMPs on new data. We demonstrate the utility of the proposed method in the context of conjugate Bayesian regression, likelihood-based inference with Markov chain Monte Carlo, and simulation-based inference with neural networks.

stat.ML↗
arXiv2023

A fully Bayesian sparse polynomial chaos expansion approach with joint priors on the coefficients and global selection of terms

Polynomial chaos expansion (PCE) is a versatile tool widely used in uncertainty quantification and machine learning, but its successful application depends strongly on the accuracy and reliability of the resulting PCE-based response surface. High accuracy typically requires high polynomial degrees, demanding many training points especially in high-dimensional problems through the curse of dimensionality. So-called sparse PCE concepts work with a much smaller selection of basis polynomials compared to conventional PCE approaches and can overcome the curse of dimensionality very efficiently, but have to pay specific attention to their strategies of choosing training points. Furthermore, the approximation error resembles an uncertainty that most existing PCE-based methods do not estimate. In this study, we develop and evaluate a fully Bayesian approach to establish the PCE representation via joint shrinkage priors and Markov chain Monte Carlo. The suggested Bayesian PCE model directly aims to solve the two challenges named above: achieving a sparse PCE representation and estimating uncertainty of the PCE itself. The embedded Bayesian regularizing via the joint shrinkage prior allows using higher polynomial degrees for given training points due to its ability to handle underdetermined situations, where the number of considered PCE coefficients could be much larger than the number of available training points. We also explore multiple variable selection methods to construct sparse PCE expansions based on the established Bayesian representations, while globally selecting the most meaningful orthonormal polynomials given the available training data. We demonstrate the advantages of our Bayesian PCE and the corresponding sparsity-inducing methods on several benchmarks.

stat.CO↗