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Threshold selection is a fundamental problem in any threshold-based extreme value analysis. While models are asymptotically motivated, selecting an appropriate threshold for finite samples can be difficult through standard methods. Inference can also be highly sensitive to the choice of threshold. Too low a threshold choice leads to bias in the fit of the extreme value model, while too high a choice leads to unnecessary additional uncertainty in the estimation of model parameters. In this paper, we develop a novel methodology for automated threshold selection that directly tackles this bias-variance trade-off. We also develop a method to account for the uncertainty in this threshold choice and propagate this uncertainty through to high quantile inference. Through a simulation study, we demonstrate the effectiveness of our method for threshold selection and subsequent extreme quantile estimation. We apply our method to the well-known, troublesome example of the River Nidd dataset.

We present and analyze a discontinuous Galerkin method for the numerical modeling of the non-linear fully-coupled thermo-hydro-mechanic problem. We propose a high-order symmetric weighted interior penalty scheme that supports general polytopal grids and is robust with respect to strong heteorgeneities in the model coefficients. We focus on the treatment of the non-linear convective transport term in the energy conservation equation and we propose suitable stabilization techniques that make the scheme robust for advection-dominated regimes. The stability analysis of the problem and the convergence of the fixed-point linearization strategy are addressed theoretically under mild requirements on the problem's data. A complete set of numerical simulations is presented in order to assess the convergence and robustness properties of the proposed method.

Constrained optimization of the parameters of a simulator plays a crucial role in a design process. These problems become challenging when the simulator is stochastic, computationally expensive, and the parameter space is high-dimensional. One can efficiently perform optimization only by utilizing the gradient with respect to the parameters, but these gradients are unavailable in many legacy, black-box codes. We introduce the algorithm Scout-Nd (Stochastic Constrained Optimization for N dimensions) to tackle the issues mentioned earlier by efficiently estimating the gradient, reducing the noise of the gradient estimator, and applying multi-fidelity schemes to further reduce computational effort. We validate our approach on standard benchmarks, demonstrating its effectiveness in optimizing parameters highlighting better performance compared to existing methods.

Stochastic Primal-Dual Hybrid Gradient (SPDHG) is an algorithm proposed by Chambolle et al. (2018) to efficiently solve a wide class of nonsmooth large-scale optimization problems. In this paper we contribute to its theoretical foundations and prove its almost sure convergence for convex but neither necessarily strongly convex nor smooth functionals, as well as for any random sampling. In addition, we study SPDHG for parallel Magnetic Resonance Imaging reconstruction, where data from different coils are randomly selected at each iteration. We apply SPDHG using a wide range of random sampling methods and compare its performance across a range of settings, including mini-batch size and step size parameters. We show that the sampling can significantly affect the convergence speed of SPDHG and for many cases an optimal sampling can be identified.

We resurrect the infamous harmonic mean estimator for computing the marginal likelihood (Bayesian evidence) and solve its problematic large variance. The marginal likelihood is a key component of Bayesian model selection to evaluate model posterior probabilities; however, its computation is challenging. The original harmonic mean estimator, first proposed by Newton and Raftery in 1994, involves computing the harmonic mean of the likelihood given samples from the posterior. It was immediately realised that the original estimator can fail catastrophically since its variance can become very large (possibly not finite). A number of variants of the harmonic mean estimator have been proposed to address this issue although none have proven fully satisfactory. We present the \emph{learnt harmonic mean estimator}, a variant of the original estimator that solves its large variance problem. This is achieved by interpreting the harmonic mean estimator as importance sampling and introducing a new target distribution. The new target distribution is learned to approximate the optimal but inaccessible target, while minimising the variance of the resulting estimator. Since the estimator requires samples of the posterior only, it is agnostic to the sampling strategy used. We validate the estimator on a variety of numerical experiments, including a number of pathological examples where the original harmonic mean estimator fails catastrophically. We also consider a cosmological application, where our approach leads to $\sim$ 3 to 6 times more samples than current state-of-the-art techniques in 1/3 of the time. In all cases our learnt harmonic mean estimator is shown to be highly accurate. The estimator is computationally scalable and can be applied to problems of dimension $O(10^3)$ and beyond. Code implementing the learnt harmonic mean estimator is made publicly available

In this study, we propose a novel multi-objective Bayesian optimization (MOBO) method to efficiently identify the Pareto front (PF) defined by risk measures for black-box functions under the presence of input uncertainty (IU). Existing BO methods for Pareto optimization in the presence of IU are risk-specific or without theoretical guarantees, whereas our proposed method addresses general risk measures and has theoretical guarantees. The basic idea of the proposed method is to assume a Gaussian process (GP) model for the black-box function and to construct high-probability bounding boxes for the risk measures using the GP model. Furthermore, in order to reduce the uncertainty of non-dominated bounding boxes, we propose a method of selecting the next evaluation point using a maximin distance defined by the maximum value of a quasi distance based on bounding boxes. As theoretical analysis, we prove that the algorithm can return an arbitrary-accurate solution in a finite number of iterations with high probability, for various risk measures such as Bayes risk, worst-case risk, and value-at-risk. We also give a theoretical analysis that takes into account approximation errors because there exist non-negligible approximation errors (e.g., finite approximation of PFs and sampling-based approximation of bounding boxes) in practice. We confirm that the proposed method outperforms compared with existing methods not only in the setting with IU but also in the setting of ordinary MOBO through numerical experiments.

The characterization of the solution set for a class of algebraic Riccati inequalities is studied. This class arises in the passivity analysis of linear time invariant control systems. Eigenvalue perturbation theory for the Hamiltonian matrix associated with the Riccati inequality is used to analyze the extremal points of the solution set.

Improving the resolution of fluorescence microscopy beyond the diffraction limit can be achievedby acquiring and processing multiple images of the sample under different illumination conditions.One of the simplest techniques, Random Illumination Microscopy (RIM), forms the super-resolvedimage from the variance of images obtained with random speckled illuminations. However, thevalidity of this process has not been fully theorized. In this work, we characterize mathematicallythe sample information contained in the variance of diffraction-limited speckled images as a functionof the statistical properties of the illuminations. We show that an unambiguous two-fold resolutiongain is obtained when the speckle correlation length coincides with the width of the observationpoint spread function. Last, we analyze the difference between the variance-based techniques usingrandom speckled illuminations (as in RIM) and those obtained using random fluorophore activation(as in Super-resolution Optical Fluctuation Imaging, SOFI).

We propose and compare methods for the analysis of extreme events in complex systems governed by PDEs that involve random parameters, in situations where we are interested in quantifying the probability that a scalar function of the system's solution is above a threshold. If the threshold is large, this probability is small and its accurate estimation is challenging. To tackle this difficulty, we blend theoretical results from large deviation theory (LDT) with numerical tools from PDE-constrained optimization. Our methods first compute parameters that minimize the LDT-rate function over the set of parameters leading to extreme events, using adjoint methods to compute the gradient of this rate function. The minimizers give information about the mechanism of the extreme events as well as estimates of their probability. We then propose a series of methods to refine these estimates, either via importance sampling or geometric approximation of the extreme event sets. Results are formulated for general parameter distributions and detailed expressions are provided when Gaussian distributions. We give theoretical and numerical arguments showing that the performance of our methods is insensitive to the extremeness of the events we are interested in. We illustrate the application of our approach to quantify the probability of extreme tsunami events on shore. Tsunamis are typically caused by a sudden, unpredictable change of the ocean floor elevation during an earthquake. We model this change as a random process, which takes into account the underlying physics. We use the one-dimensional shallow water equation to model tsunamis numerically. In the context of this example, we present a comparison of our methods for extreme event probability estimation, and find which type of ocean floor elevation change leads to the largest tsunamis on shore.

Objective: Clinical deep phenotyping and phenotype annotation play a critical role in both the diagnosis of patients with rare disorders as well as in building computationally-tractable knowledge in the rare disorders field. These processes rely on using ontology concepts, often from the Human Phenotype Ontology, in conjunction with a phenotype concept recognition task (supported usually by machine learning methods) to curate patient profiles or existing scientific literature. With the significant shift in the use of large language models (LLMs) for most NLP tasks, we examine the performance of the latest Generative Pre-trained Transformer (GPT) models underpinning ChatGPT as a foundation for the tasks of clinical phenotyping and phenotype annotation. Materials and Methods: The experimental setup of the study included seven prompts of various levels of specificity, two GPT models (gpt-3.5-turbo and gpt-4.0) and two established gold standard corpora for phenotype recognition, one consisting of publication abstracts and the other clinical observations. Results: Our results show that, with an appropriate setup, these models can achieve state of the art performance. The best run, using few-shot learning, achieved 0.58 macro F1 score on publication abstracts and 0.75 macro F1 score on clinical observations, the former being comparable with the state of the art, while the latter surpassing the current best in class tool. Conclusion: While the results are promising, the non-deterministic nature of the outcomes, the high cost and the lack of concordance between different runs using the same prompt and input make the use of these LLMs challenging for this particular task.