Uncertainty quantification (UQ) is an important component of molecular property prediction, particularly for drug discovery applications where model predictions direct experimental design and where unanticipated imprecision wastes valuable time and resources. The need for UQ is especially acute for neural models, which are becoming increasingly standard yet are challenging to interpret. While several approaches to UQ have been proposed in the literature, there is no clear consensus on the comparative performance of these models. In this paper, we study this question in the context of regression tasks. We systematically evaluate several methods on five benchmark datasets using multiple complementary performance metrics. Our experiments show that none of the methods we tested is unequivocally superior to all others, and none produces a particularly reliable ranking of errors across multiple datasets. While we believe these results show that existing UQ methods are not sufficient for all common use-cases and demonstrate the benefits of further research, we conclude with a practical recommendation as to which existing techniques seem to perform well relative to others.
AWS（亚马逊云科技）；Amazon（亚马逊公司）；New York University（纽约大学）
We present Fortuna, an open-source library for uncertainty quantification in deep learning. Fortuna supports a range of calibration techniques, such as conformal prediction that can be applied to any trained neural network to generate reliable uncertainty estimates, and scalable Bayesian inference methods that can be applied to Flax-based deep neural networks trained from scratch for improved uncertainty quantification and accuracy. By providing a coherent framework for advanced uncertainty quantification methods, Fortuna simplifies the process of benchmarking and helps practitioners build rob…
Language Technologies Institute, Carnegie Mellon University（卡内基梅隆大学语言技术研究所）；Computer Science Department, Stanford University（斯坦福大学计算机科学系）
With increasing deployment of machine learning systems in various real-world tasks, there is a greater need for accurate quantification of predictive uncertainty. While the common goal in uncertainty quantification (UQ) in machine learning is to approximate the true distribution of the target data, many works in UQ tend to be disjoint in the evaluation metrics utilized, and disparate implementations for each metric lead to numerical results that are not directly comparable across different works. To address this, we introduce Uncertainty Toolbox, an open-source python library that helps to ass…
University of Oxford（牛津大学）；Microsoft Research Cambridge（微软研究院剑桥分院）
While causal models are becoming one of the mainstays of machine learning, the problem of uncertainty quantification in causal inference remains challenging. In this paper, we study the causal data fusion problem, where datasets pertaining to multiple causal graphs are combined to estimate the average treatment effect of a target variable. As data arises from multiple sources and can vary in quality and quantity, principled uncertainty quantification becomes essential. To that end, we introduce Bayesian Interventional Mean Processes, a framework which combines ideas from probabilistic integrat…
Harvard Data Science Initiative（哈佛数据科学倡议）；Harvard University（哈佛大学）
Uncertainty quantification has been a core of the statistical machine learning, but its computational bottleneck has been a serious challenge for both Bayesians and frequentists. We propose a model-based framework in quantifying uncertainty, called predictive-matching Generative Parameter Sampler (GPS). This procedure considers an Uncertainty Quantification (UQ) distribution on the targeted parameter, which matches the corresponding predictive distribution to the observed data. This framework adopts a hierarchical modeling perspective such that each observation is modeled by an individual para…
An Axiomatic Assessment of Entropy- and Variance-based Uncertainty Quantification in Regression
LMU Munich（慕尼黑莱布尼茨大学）；Munich Center for Machine Learning (MCML)（慕尼黑机器学习中心）；DLR-German Aerospace Center University of Tromsø（德国航空航天中心图勒大学）；German Research Center for Artificial Intelligence (DFKI, DSA)（德国人工智能研究中心）
German Research Center for Artificial Intelligence（德国人工智能研究中心）
Uncertainty in machine learning is not generally taught as general knowledge in Machine Learning course curricula. In this paper we propose a short curriculum for a course about uncertainty in machine learning, and complement the course with a selection of use cases, aimed to trigger discussion and let students play with the concepts of uncertainty in a programming setting. Our use cases cover the concept of output uncertainty, Bayesian neural networks and weight distributions, sources of uncertainty, and out of distribution detection. We expect that this curriculum and set of use cases motiva…
This work develops rigorous theoretical basis for the fact that deep Bayesian neural network (BNN) is an effective tool for high-dimensional variable selection with rigorous uncertainty quantification. We develop new Bayesian non-parametric theorems to show that a properly configured deep BNN (1) learns the variable importance effectively in high dimensions, and its learning rate can sometimes "break" the curse of dimensionality. (2) BNN's uncertainty quantification for variable importance is rigorous, in the sense that its 95% credible intervals for variable importance indeed covers the truth…
In this paper, we propose a novel data-driven operator learning framework referred to as the \textit{Randomized Prior Wavelet Neural Operator} (RP-WNO). The proposed RP-WNO is an extension of the recently proposed wavelet neural operator, which boasts excellent generalizing capabilities but cannot estimate the uncertainty associated with its predictions. RP-WNO, unlike the vanilla WNO, comes with inherent uncertainty quantification module and hence, is expected to be extremely useful for scientists and engineers alike. RP-WNO utilizes randomized prior networks, which can account for prior info…
University of Munich (LMU)（慕尼黑大学）；Munich Center for Machine Learning（慕尼黑机器学习中心）；Ghent University（根特大学）
Uncertainty quantification has received increasing attention in machine learning in the recent past. In particular, a distinction between aleatoric and epistemic uncertainty has been found useful in this regard. The latter refers to the learner's (lack of) knowledge and appears to be especially difficult to measure and quantify. In this paper, we analyse a recent proposal based on the idea of a second-order learner, which yields predictions in the form of distributions over probability distributions. While standard (first-order) learners can be trained to predict accurate probabilities, namely…
We present a simple and effective approach for posterior uncertainty quantification in deep operator networks (DeepONets); an emerging paradigm for supervised learning in function spaces. We adopt a frequentist approach based on randomized prior ensembles, and put forth an efficient vectorized implementation for fast parallel inference on accelerated hardware. Through a collection of representative examples in computational mechanics and climate modeling, we show that the merits of the proposed approach are fourfold. (1) It can provide more robust and accurate predictions when compared against…
Pohang University of Science and Technology (POSTECH)（浦项科技大学）
We develop a novel deep learning method for uncertainty quantification in stochastic partial differential equations based on Bayesian neural network (BNN) and Hamiltonian Monte Carlo (HMC). A BNN efficiently learns the posterior distribution of the parameters in deep neural networks by performing Bayesian inference on the network parameters. The posterior distribution is efficiently sampled using HMC to quantify uncertainties in the system. Several numerical examples are shown for both forward and inverse problems in high dimension to demonstrate the effectiveness of the proposed method for un…
Uncertainty quantification by ensemble learning is explored in terms of an application from computational optical form measurements. The application requires to solve a large-scale, nonlinear inverse problem. Ensemble learning is used to extend a recently developed deep learning approach for this application in order to provide an uncertainty quantification of its predicted solution to the inverse problem. By systematically inserting out-of-distribution errors as well as noisy data the reliability of the developed uncertainty quantification is explored. Results are encouraging and the proposed…
Harvard Medical School（哈佛医学院）；Google Research（谷歌研究院）；Harvard School of Public Health（哈佛公共卫生学院）
Uncertainty quantification for complex deep learning models is increasingly important as these techniques see growing use in high-stakes, real-world settings. Currently, the quality of a model's uncertainty is evaluated using point-prediction metrics such as negative log-likelihood or the Brier score on heldout data. In this study, we provide the first large scale evaluation of the empirical frequentist coverage properties of well known uncertainty quantification techniques on a suite of regression and classification tasks. We find that, in general, some methods do achieve desirable coverage p…
Oak Ridge National Laboratory（橡树岭国家实验室）；Florida State University（佛罗里达州立大学）；Auburn University（奥本大学）；Jilin University（吉林大学）
We develop a probabilistic machine learning method, which formulates a class of stochastic neural networks by a stochastic optimal control problem. An efficient stochastic gradient descent algorithm is introduced under the stochastic maximum principle framework. Numerical experiments for applications of stochastic neural networks are carried out to validate the effectiveness of our methodology.
We present a new data-driven model to reconstruct nonlinear flow from spatially sparse observations. The model is a version of a conditional variational auto-encoder (CVAE), which allows for probabilistic reconstruction and thus uncertainty quantification of the prediction. We show that in our model, conditioning on the measurements from the complete flow data leads to a CVAE where only the decoder depends on the measurements. For this reason we call the model as Semi-Conditional Variational Autoencoder (SCVAE). The method, reconstructions and associated uncertainty estimates are illustrated o…
Berkeley Center for Cosmological Physics（伯克利宇宙物理中心）；University of California, Berkeley（加州大学伯克利分校）；Lawrence Berkeley National Laboratory（劳伦斯伯克利国家实验室）
We develop a generative model-based approach to Bayesian inverse problems, such as image reconstruction from noisy and incomplete images. Our framework addresses two common challenges of Bayesian reconstructions: 1) It makes use of complex, data-driven priors that comprise all available information about the uncorrupted data distribution. 2) It enables computationally tractable uncertainty quantification in the form of posterior analysis in latent and data space. The method is very efficient in that the generative model only has to be trained once on an uncorrupted data set, after that, the pr…
Georgia Institute of Technology（佐治亚理工学院）；Duke University（杜克大学）
Multivariate Hawkes processes are commonly used to model streaming networked event data in a wide variety of applications. However, it remains a challenge to extract reliable inference from complex datasets with uncertainty quantification. Aiming towards this, we develop a statistical inference framework to learn causal relationships between nodes from networked data, where the underlying directed graph implies Granger causality. We provide uncertainty quantification for the maximum likelihood estimate of the network multivariate Hawkes process by providing a non-asymptotic confidence set. The…
College of Engineering, Peking University（北京大学工学院）；School of Environmental Science and Engineering, Southern University of Science and Technology（南方科技大学环境科学与工程学院）；Peng Cheng Laboratory（鹏城实验室）
Subsurface flow problems usually involve some degree of uncertainty. Consequently, uncertainty quantification is commonly necessary for subsurface flow prediction. In this work, we propose a methodology for efficient uncertainty quantification for dynamic subsurface flow with a surrogate constructed by the Theory-guided Neural Network (TgNN). The TgNN here is specially designed for problems with stochastic parameters. In the TgNN, stochastic parameters, time and location comprise the input of the neural network, while the quantity of interest is the output. The neural network is trained with a…
Paderborn University（帕德博恩大学）；University of Munich (LMU)（慕尼黑大学）
The idea to distinguish and quantify two important types of uncertainty, often referred to as aleatoric and epistemic, has received increasing attention in machine learning research in the last couple of years. In this paper, we consider ensemble-based approaches to uncertainty quantification. Distinguishing between different types of uncertainty-aware learning algorithms, we specifically focus on Bayesian methods and approaches based on so-called credal sets, which naturally suggest themselves from an ensemble learning point of view. For both approaches, we address the question of how to quan…
Aalborg University（奥尔堡大学）；University of Electronic Science and Technology of China（电子科技大学）；Southern University of Science and Technology（南方科技大学）
Uncertainty is an essential consideration for time series forecasting tasks. In this work, we specifically focus on quantifying the uncertainty of traffic forecasting. To achieve this, we develop Deep Spatio-Temporal Uncertainty Quantification (DeepSTUQ), which can estimate both aleatoric and epistemic uncertainty. We first leverage a spatio-temporal model to model the complex spatio-temporal correlations of traffic data. Subsequently, two independent sub-neural networks maximizing the heterogeneous log-likelihood are developed to estimate aleatoric uncertainty. For estimating epistemic uncert…
We introduce a class of acquisition functions for sample selection that leads to faster convergence in applications related to Bayesian experimental design and uncertainty quantification. The approach follows the paradigm of active learning, whereby existing samples of a black-box function are utilized to optimize the next most informative sample. The proposed method aims to take advantage of the fact that some input directions of the black-box function have a larger impact on the output than others, which is important especially for systems exhibiting rare and extreme events. The acquisition …
German Research Center for Artificial Intelligence（德国人工智能研究中心）
Uncertainty quantification in neural network promises to increase safety of AI systems, but it is not clear how performance might vary with the training set size. In this paper we evaluate seven uncertainty methods on Fashion MNIST and CIFAR10, as we sub-sample and produce varied training set sizes. We find that calibration error and out of distribution detection performance strongly depend on the training set size, with most methods being miscalibrated on the test set with small training sets. Gradient-based methods seem to poorly estimate epistemic uncertainty and are the most affected by tr…
We are interested in the development of surrogate models for uncertainty quantification and propagation in problems governed by stochastic PDEs using a deep convolutional encoder-decoder network in a similar fashion to approaches considered in deep learning for image-to-image regression tasks. Since normal neural networks are data intensive and cannot provide predictive uncertainty, we propose a Bayesian approach to convolutional neural nets. A recently introduced variational gradient descent algorithm based on Stein's method is scaled to deep convolutional networks to perform approximate Baye…
Uncertainty and confidence have been shown to be useful metrics in a wide variety of techniques proposed for deep learning testing, including test data selection and system supervision.We present uncertainty-wizard, a tool that allows to quantify such uncertainty and confidence in artificial neural networks. It is built on top of the industry-leading tf.keras deep learning API and it provides a near-transparent and easy to understand interface. At the same time, it includes major performance optimizations that we benchmarked on two different machines and different configurations.
Rule-based classification models described in the language of logic directly predict boolean values, rather than modeling a probability and translating it into a prediction as done in statistical models. The vast majority of existing uncertainty quantification approaches rely on models providing continuous output not available to rule-based models. In this work, we propose an uncertainty quantification framework in the form of a meta-model that takes any binary classifier with binary output as a black box and estimates the prediction accuracy of that base model at a given input along with a le…
Lawrence Berkeley National Laboratory（劳伦斯伯克利国家实验室）；Los Alamos National Laboratory（洛斯阿拉莫斯国家实验室）
The modeling and uncertainty quantification of closed curves is an important problem in the field of shape analysis, and can have significant ramifications for subsequent statistical tasks. Many of these tasks involve collections of closed curves, which often exhibit structural similarities at multiple levels. Modeling multiple closed curves in a way that efficiently incorporates such between-curve dependence remains a challenging problem. In this work, we propose and investigate a multiple-output (a.k.a. multi-output), multi-dimensional Gaussian process modeling framework. We illustrate the p…
Bringing deep neural networks (DNNs) into safety critical applications such as automated driving, medical imaging and finance, requires a thorough treatment of the model's uncertainties. Training deep neural networks is already resource demanding and so is also their uncertainty quantification. In this overview article, we survey methods that we developed to teach DNNs to be uncertain when they encounter new object classes. Additionally, we present training methods to learn from only a few labels with help of uncertainty quantification. Note that this is typically paid with a massive overhead …
Robust data association is critical for analysis of long-term motion trajectories in complex scenes. In its absence, trajectory precision suffers due to periods of kinematic ambiguity degrading the quality of follow-on analysis. Common optimization-based approaches often neglect uncertainty quantification arising from these events. Consequently, we propose the Joint Posterior Tracker (JPT), a Bayesian multi-object tracking algorithm that robustly reasons over the posterior of associations and trajectories. Novel, permutation-based proposals are crafted for exploration of posterior modes that c…
We propose a framework for the assessment of uncertainty quantification in deep regression. The framework is based on regression problems where the regression function is a linear combination of nonlinear functions. Basically, any level of complexity can be realized through the choice of the nonlinear functions and the dimensionality of their domain. Results of an uncertainty quantification for deep regression are compared against those obtained by a statistical reference method. The reference method utilizes knowledge of the underlying nonlinear functions and is based on a Bayesian linear reg…
Seismic imaging is an ill-posed inverse problem that is challenged by noisy data and modeling inaccuracies -- due to errors in the background squared-slowness model. Uncertainty quantification is essential for determining how variability in the background models affects seismic imaging. Due to the costs associated with the forward Born modeling operator as well as the high dimensionality of seismic images, quantification of uncertainty is computationally expensive. As such, the main contribution of this work is a survey-specific Fourier neural operator surrogate to velocity continuation that m…
