Objective Evaluation of Deep Uncertainty Predictions for COVID-19 Detection

Deep neural networks (DNNs) have been widely applied for detecting COVID-19 in medical images. Existing studies mainly apply transfer learning and other data representation strategies to generate accurate point estimates. The generalization power of these networks is always questionable due to being developed using small datasets and failing to report their predictive confidence. Quantifying uncertainties associated with DNN predictions is a prerequisite for their trusted deployment in medical settings. Here we apply and evaluate three uncertainty quantification techniques for COVID-19 detection using chest X-Ray (CXR) images. The novel concept of uncertainty confusion matrix is proposed and new performance metrics for the objective evaluation of uncertainty estimates are introduced. Through comprehensive experiments, it is shown that networks pertained on CXR images outperform networks pretrained on natural image datasets such as ImageNet. Qualitatively and quantitatively evaluations also reveal that the predictive uncertainty estimates are statistically higher for erroneous predictions than correct predictions. Accordingly, uncertainty quantification methods are capable of flagging risky predictions with high uncertainty estimates. We also observe that ensemble methods more reliably capture uncertainties during the inference.Comment: 7 pages, 6 figures, 1 Table, 36 refrence

An Uncertainty-aware Transfer Learning-based Framework for Covid-19 Diagnosis

The early and reliable detection of COVID-19 infected patients is essential to prevent and limit its outbreak. The PCR tests for COVID-19 detection are not available in many countries and also there are genuine concerns about their reliability and performance. Motivated by these shortcomings, this paper proposes a deep uncertainty-aware transfer learning framework for COVID-19 detection using medical images. Four popular convolutional neural networks (CNNs) including VGG16, ResNet50, DenseNet121, and InceptionResNetV2 are first applied to extract deep features from chest X-ray and computed tomography (CT) images. Extracted features are then processed by different machine learning and statistical modelling techniques to identify COVID-19 cases. We also calculate and report the epistemic uncertainty of classification results to identify regions where the trained models are not confident about their decisions (out of distribution problem). Comprehensive simulation results for X-ray and CT image datasets indicate that linear support vector machine and neural network models achieve the best results as measured by accuracy, sensitivity, specificity, and AUC. Also it is found that predictive uncertainty estimates are much higher for CT images compared to X-ray images.Comment: 9 pages, 9 figures, 3 table

A case for new neural network smoothness constraints

How sensitive should machine learning models be to input changes? We tackle the question of model smoothness and show that it is a useful inductive bias which aids generalization, adversarial robustness, generative modeling and reinforcement learning. We explore current methods of imposing smoothness constraints and observe they lack the flexibility to adapt to new tasks, they don't account for data modalities, they interact with losses, architectures and optimization in ways not yet fully understood. We conclude that new advances in the field are hinging on finding ways to incorporate data, tasks and learning into our definitions of smoothness

Bayesian Deep Ensembles via the Neural Tangent Kernel

We explore the link between deep ensembles and Gaussian processes (GPs) through the lens of the Neural Tangent Kernel (NTK): a recent development in understanding the training dynamics of wide neural networks (NNs). Previous work has shown that even in the infinite width limit, when NNs become GPs, there is no GP posterior interpretation to a deep ensemble trained with squared error loss. We introduce a simple modification to standard deep ensembles training, through addition of a computationally-tractable, randomised and untrainable function to each ensemble member, that enables a posterior interpretation in the infinite width limit. When ensembled together, our trained NNs give an approximation to a posterior predictive distribution, and we prove that our Bayesian deep ensembles make more conservative predictions than standard deep ensembles in the infinite width limit. Finally, using finite width NNs we demonstrate that our Bayesian deep ensembles faithfully emulate the analytic posterior predictive when available, and can outperform standard deep ensembles in various out-of-distribution settings, for both regression and classification tasks

SAMBA: Safe Model-Based & Active Reinforcement Learning

In this paper, we propose SAMBA, a novel framework for safe reinforcement learning that combines aspects from probabilistic modelling, information theory, and statistics. Our method builds upon PILCO to enable active exploration using novel(semi-)metrics for out-of-sample Gaussian process evaluation optimised through a multi-objective problem that supports conditional-value-at-risk constraints. We evaluate our algorithm on a variety of safe dynamical system benchmarks involving both low and high-dimensional state representations. Our results show orders of magnitude reductions in samples and violations compared to state-of-the-art methods. Lastly, we provide intuition as to the effectiveness of the framework by a detailed analysis of our active metrics and safety constraints

Simple and Principled Uncertainty Estimation with Deterministic Deep Learning via Distance Awareness

Bayesian neural networks (BNN) and deep ensembles are principled approaches to estimate the predictive uncertainty of a deep learning model. However their practicality in real-time, industrial-scale applications are limited due to their heavy memory and inference cost. This motivates us to study principled approaches to high-quality uncertainty estimation that require only a single deep neural network (DNN). By formalizing the uncertainty quantification as a minimax learning problem, we first identify input distance awareness, i.e., the model's ability to quantify the distance of a testing example from the training data in the input space, as a necessary condition for a DNN to achieve high-quality (i.e., minimax optimal) uncertainty estimation. We then propose Spectral-normalized Neural Gaussian Process (SNGP), a simple method that improves the distance-awareness ability of modern DNNs, by adding a weight normalization step during training and replacing the output layer with a Gaussian process. On a suite of vision and language understanding tasks and on modern architectures (Wide-ResNet and BERT), SNGP is competitive with deep ensembles in prediction, calibration and out-of-domain detection, and outperforms the other single-model approaches

Understanding Softmax Confidence and Uncertainty

It is often remarked that neural networks fail to increase their uncertainty when predicting on data far from the training distribution. Yet naively using softmax confidence as a proxy for uncertainty achieves modest success in tasks exclusively testing for this, e.g., out-of-distribution (OOD) detection. This paper investigates this contradiction, identifying two implicit biases that do encourage softmax confidence to correlate with epistemic uncertainty: 1) Approximately optimal decision boundary structure, and 2) Filtering effects of deep networks. It describes why low-dimensional intuitions about softmax confidence are misleading. Diagnostic experiments quantify reasons softmax confidence can fail, finding that extrapolations are less to blame than overlap between training and OOD data in final-layer representations. Pre-trained/fine-tuned networks reduce this overlap

Advances in Electron Microscopy with Deep Learning

This doctoral thesis covers some of my advances in electron microscopy with deep learning. Highlights include a comprehensive review of deep learning in electron microscopy; large new electron microscopy datasets for machine learning, dataset search engines based on variational autoencoders, and automatic data clustering by t-distributed stochastic neighbour embedding; adaptive learning rate clipping to stabilize learning; generative adversarial networks for compressed sensing with spiral, uniformly spaced and other fixed sparse scan paths; recurrent neural networks trained to piecewise adapt sparse scan paths to specimens by reinforcement learning; improving signal-to-noise; and conditional generative adversarial networks for exit wavefunction reconstruction from single transmission electron micrographs. This thesis adds to my publications by presenting their relationships, reflections, and holistic conclusions. This copy of my thesis is typeset for online dissemination to improve readability, whereas the thesis submitted to the University of Warwick in support of my application for the degree of Doctor of Philosophy in Physics will be typeset for physical printing and binding.Comment: 295 pages, phd thesis, 100 figures + 12 tables, papers are compresse