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This work suggests several methods of uncertainty treatment in multiscale modelling and describes their application to a system of coupled turbulent transport simulations of a tokamak plasma. We propose a method to quantify the usually aleatoric uncertainty of a system in a quasi-stationary state, estimating the mean values and their errors for quantities of interest, which is average heat fluxes in the case of turbulence simulations. The method defines the stationarity of the system and suggests a way to balance the computational cost of simulation and the accuracy of estimation. This allows, contrary to many approaches, to incorporate aleatoric uncertainties in the analysis of the model and to have a quantifiable decision for simulation runtime. Furthermore, the paper describes methods for quantifying the epistemic uncertainty of a model and the results of such a procedure for turbulence simulations, identifying the model's sensitivity to particular input parameters and sensitivity to uncertainties in total. Finally, we introduce a surrogate model approach based on Gaussian Process Regression and present a preliminary result of training and analysing the performance of such a model based on turbulence simulation data. Such an approach shows a potential to significantly decrease the computational cost of the uncertainty propagation for the given model, making it feasible on current HPC systems.

Diffusion models are a class of probabilistic generative models that have been widely used as a prior for image processing tasks like text conditional generation and inpainting. We demonstrate that these models can be adapted to make predictions and provide uncertainty quantification for chaotic dynamical systems. In these applications, diffusion models can implicitly represent knowledge about outliers and extreme events; however, querying that knowledge through conditional sampling or measuring probabilities is surprisingly difficult. Existing methods for conditional sampling at inference time seek mainly to enforce the constraints, which is insufficient to match the statistics of the distribution or compute the probability of the chosen events. To achieve these ends, optimally one would use the conditional score function, but its computation is typically intractable. In this work, we develop a probabilistic approximation scheme for the conditional score function which provably converges to the true distribution as the noise level decreases. With this scheme we are able to sample conditionally on nonlinear userdefined events at inference time, and matches data statistics even when sampling from the tails of the distribution.

We present a framework and algorithms to learn controlled dynamics models using neural stochastic differential equations (SDEs) -- SDEs whose drift and diffusion terms are both parametrized by neural networks. We construct the drift term to leverage a priori physics knowledge as inductive bias, and we design the diffusion term to represent a distance-aware estimate of the uncertainty in the learned model's predictions -- it matches the system's underlying stochasticity when evaluated on states near those from the training dataset, and it predicts highly stochastic dynamics when evaluated on states beyond the training regime. The proposed neural SDEs can be evaluated quickly enough for use in model predictive control algorithms, or they can be used as simulators for model-based reinforcement learning. Furthermore, they make accurate predictions over long time horizons, even when trained on small datasets that cover limited regions of the state space. We demonstrate these capabilities through experiments on simulated robotic systems, as well as by using them to model and control a hexacopter's flight dynamics: A neural SDE trained using only three minutes of manually collected flight data results in a model-based control policy that accurately tracks aggressive trajectories that push the hexacopter's velocity and Euler angles to nearly double the maximum values observed in the training dataset.

Uncertainty quantification (UQ) is important for reliability assessment and enhancement of machine learning models. In deep learning, uncertainties arise not only from data, but also from the training procedure that often injects substantial noises and biases. These hinder the attainment of statistical guarantees and, moreover, impose computational challenges on UQ due to the need for repeated network retraining. Building upon the recent neural tangent kernel theory, we create statistically guaranteed schemes to principally \emph{quantify}, and \emph{remove}, the procedural uncertainty of over-parameterized neural networks with very low computation effort. In particular, our approach, based on what we call a procedural-noise-correcting (PNC) predictor, removes the procedural uncertainty by using only \emph{one} auxiliary network that is trained on a suitably labeled data set, instead of many retrained networks employed in deep ensembles. Moreover, by combining our PNC predictor with suitable light-computation resampling methods, we build several approaches to construct asymptotically exact-coverage confidence intervals using as low as four trained networks without additional overheads.

Segmentation of curvilinear structures such as vasculature and road networks is challenging due to relatively weak signals and complex geometry/topology. To facilitate and accelerate large scale annotation, one has to adopt semi-automatic approaches such as proofreading by experts. In this work, we focus on uncertainty estimation for such tasks, so that highly uncertain, and thus error-prone structures can be identified for human annotators to verify. Unlike most existing works, which provide pixel-wise uncertainty maps, we stipulate it is crucial to estimate uncertainty in the units of topological structures, e.g., small pieces of connections and branches. To achieve this, we leverage tools from topological data analysis, specifically discrete Morse theory (DMT), to first capture the structures, and then reason about their uncertainties. To model the uncertainty, we (1) propose a joint prediction model that estimates the uncertainty of a structure while taking the neighboring structures into consideration (inter-structural uncertainty); (2) propose a novel Probabilistic DMT to model the inherent uncertainty within each structure (intra-structural uncertainty) by sampling its representations via a perturb-and-walk scheme. On various 2D and 3D datasets, our method produces better structure-wise uncertainty maps compared to existing works.

Jointly extracting entity pairs and their relations is challenging when working on distantly-supervised data with ambiguous or noisy labels. To mitigate such impact, we propose uncertainty-aware bootstrap learning, which is motivated by the intuition that the higher uncertainty of an instance, the more likely the model confidence is inconsistent with the ground truths. Specifically, we first explore instance-level data uncertainty to create an initial high-confident examples. Such subset serves as filtering noisy instances and facilitating the model to converge fast at the early stage. During bootstrap learning, we propose self-ensembling as a regularizer to alleviate inter-model uncertainty produced by noisy labels. We further define probability variance of joint tagging probabilities to estimate inner-model parametric uncertainty, which is used to select and build up new reliable training instances for the next iteration. Experimental results on two large datasets reveal that our approach outperforms existing strong baselines and related methods.

Medical image segmentation is a fundamental and critical step in many image-guided clinical approaches. Recent success of deep learning-based segmentation methods usually relies on a large amount of labeled data, which is particularly difficult and costly to obtain especially in the medical imaging domain where only experts can provide reliable and accurate annotations. Semi-supervised learning has emerged as an appealing strategy and been widely applied to medical image segmentation tasks to train deep models with limited annotations. In this paper, we present a comprehensive review of recently proposed semi-supervised learning methods for medical image segmentation and summarized both the technical novelties and empirical results. Furthermore, we analyze and discuss the limitations and several unsolved problems of existing approaches. We hope this review could inspire the research community to explore solutions for this challenge and further promote the developments in medical image segmentation field.

Due to their increasing spread, confidence in neural network predictions became more and more important. However, basic neural networks do not deliver certainty estimates or suffer from over or under confidence. Many researchers have been working on understanding and quantifying uncertainty in a neural network's prediction. As a result, different types and sources of uncertainty have been identified and a variety of approaches to measure and quantify uncertainty in neural networks have been proposed. This work gives a comprehensive overview of uncertainty estimation in neural networks, reviews recent advances in the field, highlights current challenges, and identifies potential research opportunities. It is intended to give anyone interested in uncertainty estimation in neural networks a broad overview and introduction, without presupposing prior knowledge in this field. A comprehensive introduction to the most crucial sources of uncertainty is given and their separation into reducible model uncertainty and not reducible data uncertainty is presented. The modeling of these uncertainties based on deterministic neural networks, Bayesian neural networks, ensemble of neural networks, and test-time data augmentation approaches is introduced and different branches of these fields as well as the latest developments are discussed. For a practical application, we discuss different measures of uncertainty, approaches for the calibration of neural networks and give an overview of existing baselines and implementations. Different examples from the wide spectrum of challenges in different fields give an idea of the needs and challenges regarding uncertainties in practical applications. Additionally, the practical limitations of current methods for mission- and safety-critical real world applications are discussed and an outlook on the next steps towards a broader usage of such methods is given.

Embedding models for deterministic Knowledge Graphs (KG) have been extensively studied, with the purpose of capturing latent semantic relations between entities and incorporating the structured knowledge into machine learning. However, there are many KGs that model uncertain knowledge, which typically model the inherent uncertainty of relations facts with a confidence score, and embedding such uncertain knowledge represents an unresolved challenge. The capturing of uncertain knowledge will benefit many knowledge-driven applications such as question answering and semantic search by providing more natural characterization of the knowledge. In this paper, we propose a novel uncertain KG embedding model UKGE, which aims to preserve both structural and uncertainty information of relation facts in the embedding space. Unlike previous models that characterize relation facts with binary classification techniques, UKGE learns embeddings according to the confidence scores of uncertain relation facts. To further enhance the precision of UKGE, we also introduce probabilistic soft logic to infer confidence scores for unseen relation facts during training. We propose and evaluate two variants of UKGE based on different learning objectives. Experiments are conducted on three real-world uncertain KGs via three tasks, i.e. confidence prediction, relation fact ranking, and relation fact classification. UKGE shows effectiveness in capturing uncertain knowledge by achieving promising results on these tasks, and consistently outperforms baselines on these tasks.

Recent advances in 3D fully convolutional networks (FCN) have made it feasible to produce dense voxel-wise predictions of volumetric images. In this work, we show that a multi-class 3D FCN trained on manually labeled CT scans of several anatomical structures (ranging from the large organs to thin vessels) can achieve competitive segmentation results, while avoiding the need for handcrafting features or training class-specific models. To this end, we propose a two-stage, coarse-to-fine approach that will first use a 3D FCN to roughly define a candidate region, which will then be used as input to a second 3D FCN. This reduces the number of voxels the second FCN has to classify to ~10% and allows it to focus on more detailed segmentation of the organs and vessels. We utilize training and validation sets consisting of 331 clinical CT images and test our models on a completely unseen data collection acquired at a different hospital that includes 150 CT scans, targeting three anatomical organs (liver, spleen, and pancreas). In challenging organs such as the pancreas, our cascaded approach improves the mean Dice score from 68.5 to 82.2%, achieving the highest reported average score on this dataset. We compare with a 2D FCN method on a separate dataset of 240 CT scans with 18 classes and achieve a significantly higher performance in small organs and vessels. Furthermore, we explore fine-tuning our models to different datasets. Our experiments illustrate the promise and robustness of current 3D FCN based semantic segmentation of medical images, achieving state-of-the-art results. Our code and trained models are available for download: //github.com/holgerroth/3Dunet_abdomen_cascade.