As models of cognition grow in complexity and number of parameters, Bayesian inference with standard methods can become intractable, especially when the data-generating model is of unknown analytic form. Recent advances in simulation-based inference using specialized neural network architectures circumvent many previous problems of approximate Bayesian computation. Moreover, due to the properties of these special neural network estimators, the effort of training the networks via simulations amortizes over subsequent evaluations which can re-use the same network for multiple datasets and across multiple researchers. However, these methods have been largely underutilized in cognitive science and psychology so far, even though they are well suited for tackling a wide variety of modeling problems. With this work, we provide a general introduction to amortized Bayesian parameter estimation and model comparison and demonstrate the applicability of the proposed methods on a well-known class of intractable response-time models.
University of Helsinki（赫尔辛基大学）；ELLIS Institute Finland, Aalto University（芬兰埃利斯研究所、阿尔托大学）；TU Dortmund University（多特蒙德技术大学）；Rensselaer Polytechnic Institute（伦斯勒理工学院）；Independent Scientist（独立研究者）
We develop methods for efficient amortized approximate Bayesian inference over posterior distributions of probabilistic clustering models, such as Dirichlet process mixture models. The approach is based on mapping distributed, symmetry-invariant representations of cluster arrangements into conditional probabilities. The method parallelizes easily, yields iid samples from the approximate posterior of cluster assignments with the same computational cost of a single Gibbs sampler sweep, and can easily be applied to both conjugate and non-conjugate models, as training only requires samples from th…
Neural Architectures for Amortized Bayesian Inference: Statistical Foundations and Empirical Assessments
Department of Mathematics and Statistics, Indian Institute of Technology Kanpur（数学与统计学系，印度理工学院坎浦尔分校）；Marshall School of Business, University of Southern California（马歇尔商学院，南加州大学）
Stellenbosch University（斯泰伦博斯大学）；National Institute for Theoretical and Computational Sciences（国家理论与计算科学研究所）
Initial work on variational autoencoders assumed independent latent variables with simple distributions. Subsequent work has explored incorporating more complex distributions and dependency structures: including normalizing flows in the encoder network allows latent variables to entangle non-linearly, creating a richer class of distributions for the approximate posterior, and stacking layers of latent variables allows more complex priors to be specified for the generative model. This work explores incorporating arbitrary dependency structures, as specified by Bayesian networks, into VAEs. This…
Generalized Bayesian Inference for Scientific Simulators via Amortized Cost Estimation
Tübingen AI Center（图宾根人工智能中心）；Machine Learning in Science, Excellence Cluster Machine Learning, University of Tübingen（图宾根大学机器学习卓越集群科学机器学习系）；Department Empirical Inference, Max Planck Institute for Intelligent Systems（马克斯·普朗克智能系统研究所经验推断系）
Uncertainty-Aware Surrogate-based Amortized Bayesian Inference for Computationally Expensive Models
Department of Stochastic Simulation and Safety Research for Hydrosystems（随机模拟与安全研究部门）；Cluster of Excellence SimTech（卓越中心SimTech）；University of Stuttgart（斯图加特大学）；Department of Statistics（统计学系）；TU Dortmund University（多特蒙德技术大学）
From Mice to Trains: Amortized Bayesian Inference on Graph Data
Department of Statistics, TU Dortmund University（统计系，多特蒙德技术大学）；School of Public Health, Imperial College London（公共卫生学院，伦敦帝国理工学院）；Department of Biology, University of Oxford（生物学系，牛津大学）；Department of Mechanical Engineering, Karlsruhe Institute of Technology（机械工程系，卡尔斯鲁厄理工学院）
Cluster of Excellence SimTech（SimTech卓越集群）；University of Stuttgart（斯图加特大学）；Heidelberg University（海德堡大学）；Cluster of Excellence STRUCTURES（STRUCTURES卓越集群）
Neural density estimators have proven remarkably powerful in performing efficient simulation-based Bayesian inference in various research domains. In particular, the BayesFlow framework uses a two-step approach to enable amortized parameter estimation in settings where the likelihood function is implicitly defined by a simulation program. But how faithful is such inference when simulations are poor representations of reality? In this paper, we conceptualize the types of model misspecification arising in simulation-based inference and systematically investigate the performance of the BayesFlow …
Radboud University（拉德堡德大学）；University of Utrecht（乌得勒支大学）；University of Amsterdam（阿姆斯特丹大学）
In this paper, we introduce a new form of amortized variational inference by using the forward KL divergence in a joint-contrastive variational loss. The resulting forward amortized variational inference is a likelihood-free method as its gradient can be sampled without bias and without requiring any evaluation of either the model joint distribution or its derivatives. We prove that our new variational loss is optimized by the exact posterior marginals in the fully factorized mean-field approximation, a property that is not shared with the more conventional reverse KL inference. Furthermore, w…
With the surge in the number of hyperparameters and training times of modern machine learning models, hyperparameter tuning is becoming increasingly expensive. However, after assessing 40 tuning methods systematically, we find that each faces certain limitations. In particular, methods that speed up tuning via knowledge transfer typically require the final performance of hyperparameters and do not focus on low-fidelity information. As we demonstrate empirically, this common practice is suboptimal and can incur an unnecessary use of resources. It is more cost-efficient to instead leverage low-f…
Department of Statistics（统计学系）；TU Dortmund University（多特蒙德技术大学）；Cluster of Excellence SimTech（卓越中心SimTech）；University of Stuttgart（斯图加特大学）；Institute for Visualisation and Interactive Systems（可视化与交互系统研究所）；Rensselaer Polytechnic Institute（拉特克利夫理工学院）
This paper presents a fast algorithm for estimating hidden states of Bayesian state space models. The algorithm is a variation of amortized simulation-based inference algorithms, where a large number of artificial datasets are generated at the first stage, and then a flexible model is trained to predict the variables of interest. In contrast to those proposed earlier, the procedure described in this paper makes it possible to train estimators for hidden states by concentrating only on certain characteristics of the marginal posterior distributions and introducing inductive bias. Illustrations …
Comparing competing mathematical models of complex natural processes is a shared goal among many branches of science. The Bayesian probabilistic framework offers a principled way to perform model comparison and extract useful metrics for guiding decisions. However, many interesting models are intractable with standard Bayesian methods, as they lack a closed-form likelihood function or the likelihood is computationally too expensive to evaluate. With this work, we propose a novel method for performing Bayesian model comparison using specialized deep learning architectures. Our method is purely …
ALINE: Joint Amortization for Bayesian Inference and Active Data Acquisition
ELLIS Institute Finland（芬兰ELLIS研究所）；Department of Computer Science, Aalto University, Finland（芬兰阿尔托大学计算机科学系）；Department of Computer Science, University of Helsinki, Finland（芬兰赫尔辛基大学计算机科学系）；Department of Computer Science, University of Manchester, UK（英国曼彻斯特大学计算机科学系）
Frequently, population studies feature pyramidally-organized data represented using Hierarchical Bayesian Models (HBM) enriched with plates. These models can become prohibitively large in settings such as neuroimaging, where a sample is composed of a functional MRI signal measured on 300 brain locations, across 4 measurement sessions, and 30 subjects, resulting in around 1 million latent parameters.Such high dimensionality hampers the usage of modern, expressive flow-based techniques.To infer parameter posterior distributions in this challenging class of problems, we designed a novel methodolo…
Scalable Vertical Federated Learning via Data Augmentation and Amortized Inference
Centre for Data Science, Queensland University of Technology（昆士兰科技大学数据科学中心）；School of Mathematical Sciences, Queensland University of Technology（昆士兰科技大学数学科学学院）；Euler Institute, Università della Svizzera italiana (USI)（瑞士意大利语区大学欧拉研究所）；Insubria University（因苏布里亚大学）
State-of-the-art spectral energy distribution (SED) analyses use a Bayesian framework to infer the physical properties of galaxies from observed photometry or spectra. They require sampling from a high-dimensional space of SED model parameters and take $>10-100$ CPU hours per galaxy, which renders them practically infeasible for analyzing the $billions$ of galaxies that will be observed by upcoming galaxy surveys ($e.g.$ DESI, PFS, Rubin, Webb, and Roman). In this work, we present an alternative scalable approach to rigorous Bayesian inference using Amortized Neural Posterior Estimation (ANPE)…
While deep neural networks provide good performance for a range of challenging tasks, calibration and uncertainty estimation remain major challenges, especially under distribution shift. In this paper, we propose the amortized conditional normalized maximum likelihood (ACNML) method as a scalable general-purpose approach for uncertainty estimation, calibration, and out-of-distribution robustness with deep networks. Our algorithm builds on the conditional normalized maximum likelihood (CNML) coding scheme, which has minimax optimal properties according to the minimum description length principl…
University of Tübingen（蒂宾根大学）；Tübingen AI Center（蒂宾根人工智能中心）；University of British Columbia（不列颠哥伦比亚大学）；Max Planck Institute for Intelligent Systems（马克斯·普朗克智能系统研究所）
Overcoming Selection Bias in Statistical Studies With Amortized Bayesian Inference
University of Bonn（波恩大学）；Institut Pasteur（巴斯德研究所）；University of Freiburg（弗赖堡大学）；LMU University Hospital（慕尼黑大学附属医院）；German Center for Infection Research（德国感染研究中心）；Fraunhofer Institute ITMP（弗劳恩霍夫ITMP研究所）；Max von Pettenkofer Institute（马克斯·冯·佩滕科弗研究所）；LMU Munich（慕尼黑大学）；German Research Center for Environmental Health（德国环境健康研究中心）；Institut Necker-Enfants Malades（内克-儿童疾病研究所）
Amortized Simulation-Based Inference in Generalized Bayes via Neural Posterior Estimation
Department of Statistics, University of Oxford, Oxford, United Kingdom（英国牛津大学统计系）；Department of Statistics, University of Auckland, Auckland, New Zealand（新西兰奥克兰大学统计系）
Causal models can compactly and efficiently encode the data-generating process under all interventions and hence may generalize better under changes in distribution. These models are often represented as Bayesian networks and learning them scales poorly with the number of variables. Moreover, these approaches cannot leverage previously learned knowledge to help with learning new causal models. In order to tackle these challenges, we represent a novel algorithm called \textit{causal relational networks} (CRN) for learning causal models using neural networks. The CRN represent causal models usin…
Probabilistic programming languages (PPLs) are a powerful modeling tool, able to represent any computable probability distribution. Unfortunately, probabilistic program inference is often intractable, and existing PPLs mostly rely on expensive, approximate sampling-based methods. To alleviate this problem, one could try to learn from past inferences, so that future inferences run faster. This strategy is known as amortized inference; it has recently been applied to Bayesian networks and deep generative models. This paper proposes a system for amortized inference in PPLs. In our system, amortiz…
