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Gaussian process are a widely-used statistical tool for conducting non-parametric inference in applied sciences, with many computational packages available to fit to data and predict future observations. We study the use of the Greta software for Bayesian inference to apply Gaussian process regression to spatio-temporal data of infectious disease outbreaks and predict future disease spread. Greta builds on Tensorflow, making it comparatively easy to take advantage of the significant gain in speed offered by GPUs. In these complex spatio-temporal models, we show a reduction of up to 70\% in computational time relative to fitting the same models on CPUs. We show how the choice of covariance kernel impacts the ability to infer spread and extrapolate to unobserved spatial and temporal units. The inference pipeline is applied to weekly incidence data on tuberculosis in the East and West Midlands regions of England over a period of two years.

Splitting methods are widely used for solving initial value problems (IVPs) due to their ability to simplify complicated evolutions into more manageable subproblems which can be solved efficiently and accurately. Traditionally, these methods are derived using analytic and algebraic techniques from numerical analysis, including truncated Taylor series and their Lie algebraic analogue, the Baker--Campbell--Hausdorff formula. These tools enable the development of high-order numerical methods that provide exceptional accuracy for small timesteps. Moreover, these methods often (nearly) conserve important physical invariants, such as mass, unitarity, and energy. However, in many practical applications the computational resources are limited. Thus, it is crucial to identify methods that achieve the best accuracy within a fixed computational budget, which might require taking relatively large timesteps. In this regime, high-order methods derived with traditional methods often exhibit large errors since they are only designed to be asymptotically optimal. Machine Learning techniques offer a potential solution since they can be trained to efficiently solve a given IVP with less computational resources. However, they are often purely data-driven, come with limited convergence guarantees in the small-timestep regime and do not necessarily conserve physical invariants. In this work, we propose a framework for finding machine learned splitting methods that are computationally efficient for large timesteps and have provable convergence and conservation guarantees in the small-timestep limit. We demonstrate numerically that the learned methods, which by construction converge quadratically in the timestep size, can be significantly more efficient than established methods for the Schr\"{o}dinger equation if the computational budget is limited.

An aspect of interest in surveillance of diseases is whether the survival time distribution changes over time. By following data in health registries over time, this can be monitored, either in real time or retrospectively. With relevant risk factors registered, these can be taken into account in the monitoring as well. A challenge in monitoring survival times based on registry data is that data on cause of death might either be missing or uncertain. To quantify the burden of disease in such cases, excess hazard methods can be used, where the total hazard is modelled as the population hazard plus the excess hazard due to the disease. We propose a CUSUM procedure for monitoring for changes in the survival time distribution in cases where use of excess hazard models is relevant. The procedure is based on a survival log-likelihood ratio and extends previously suggested methods for monitoring of time to event to the excess hazard setting. The procedure takes into account changes in the population risk over time, as well as changes in the excess hazard which is explained by observed covariates. Properties, challenges and an application to cancer registry data will be presented.

In prototype-based federated learning, the exchange of model parameters between clients and the master server is replaced by transmission of prototypes or quantized versions of the data samples to the aggregation server. A fully decentralized deployment of prototype- based learning, without a central agregartor of prototypes, is more robust upon network failures and reacts faster to changes in the statistical distribution of the data, suggesting potential advantages and quick adaptation in dynamic learning tasks, e.g., when the data sources are IoT devices or when data is non-iid. In this paper, we consider the problem of designing a communication-efficient decentralized learning system based on prototypes. We address the challenge of prototype redundancy by leveraging on a twofold data compression technique, i.e., sending only update messages if the prototypes are informationtheoretically useful (via the Jensen-Shannon distance), and using clustering on the prototypes to compress the update messages used in the gossip protocol. We also use parallel instead of sequential gossiping, and present an analysis of its age-of-information (AoI). Our experimental results show that, with these improvements, the communications load can be substantially reduced without decreasing the convergence rate of the learning algorithm.

Partial differential equations (PDEs) are crucial in modeling diverse phenomena across scientific disciplines, including seismic and medical imaging, computational fluid dynamics, image processing, and neural networks. Solving these PDEs at scale is an intricate and time-intensive process that demands careful tuning. This paper introduces automated code-generation techniques specifically tailored for distributed memory parallelism (DMP) to execute explicit finite-difference (FD) stencils at scale, a fundamental challenge in numerous scientific applications. These techniques are implemented and integrated into the Devito DSL and compiler framework, a well-established solution for automating the generation of FD solvers based on a high-level symbolic math input. Users benefit from modeling simulations for real-world applications at a high-level symbolic abstraction and effortlessly harnessing HPC-ready distributed-memory parallelism without altering their source code. This results in drastic reductions both in execution time and developer effort. A comprehensive performance evaluation of Devito's DMP via MPI demonstrates highly competitive strong and weak scaling on CPU and GPU clusters, proving its effectiveness and capability to meet the demands of large-scale scientific simulations.

These last few years, image decomposition algorithms have been proposed to split an image into two parts: the structures and the textures. These algorithms are not adapted to the case of noisy images because the textures are corrupted by noise. In this paper, we propose a new model which decomposes an image into three parts (structures, textures and noise) based on a local regularization scheme. We compare our results with the recent work of Aujol and Chambolle. We finish by giving another model which combines the advantages of the two previous ones.

We address the problem of identifying functional interactions among stochastic neurons with variable-length memory from their spiking activity. The neuronal network is modeled by a stochastic system of interacting point processes with variable-length memory. Each chain describes the activity of a single neuron, indicating whether it spikes at a given time. One neuron's influence on another can be either excitatory or inhibitory. To identify the existence and nature of an interaction between a neuron and its postsynaptic counterpart, we propose a model selection procedure based on the observation of the spike activity of a finite set of neurons over a finite time. The proposed procedure is also based on the maximum likelihood estimator for the synaptic weight matrix of the network neuronal model. In this sense, we prove the consistency of the maximum likelihood estimator followed by a proof of the consistency of the neighborhood interaction estimation procedure. The effectiveness of the proposed model selection procedure is demonstrated using simulated data, which validates the underlying theory. The method is also applied to analyze spike train data recorded from hippocampal neurons in rats during a visual attention task, where a computational model reconstructs the spiking activity and the results reveal interesting and biologically relevant information.

The available data in semi-supervised learning usually consists of relatively small sized labeled data and much larger sized unlabeled data. How to effectively exploit unlabeled data is the key issue. In this paper, we write the regression function in the form of a copula and marginal distributions, and the unlabeled data can be exploited to improve the estimation of the marginal distributions. The predictions based on different copulas are weighted, where the weights are obtained by minimizing an asymptotic unbiased estimator of the prediction risk. Error-ambiguity decomposition of the prediction risk is performed such that unlabeled data can be exploited to improve the prediction risk estimation. We demonstrate the asymptotic normality of copula parameters and regression function estimators of the candidate models under the semi-supervised framework, as well as the asymptotic optimality and weight consistency of the model averaging estimator. Our model averaging estimator achieves faster convergence rates of asymptotic optimality and weight consistency than the supervised counterpart. Extensive simulation experiments and the California housing dataset demonstrate the effectiveness of the proposed method.

We consider goal-oriented optimal design of experiments for infinite-dimensional Bayesian linear inverse problems governed by partial differential equations (PDEs). Specifically, we seek sensor placements that minimize the posterior variance of a prediction or goal quantity of interest. The goal quantity is assumed to be a nonlinear functional of the inversion parameter. We propose a goal-oriented optimal experimental design (OED) approach that uses a quadratic approximation of the goal-functional to define a goal-oriented design criterion. The proposed criterion, which we call the Gq-optimality criterion, is obtained by integrating the posterior variance of the quadratic approximation over the set of likely data. Under the assumption of Gaussian prior and noise models, we derive a closed-form expression for this criterion. To guide development of discretization invariant computational methods, the derivations are performed in an infinite-dimensional Hilbert space setting. Subsequently, we propose efficient and accurate computational methods for computing the Gq-optimality criterion. A greedy approach is used to obtain Gq-optimal sensor placements. We illustrate the proposed approach for two model inverse problems governed by PDEs. Our numerical results demonstrate the effectiveness of the proposed strategy. In particular, the proposed approach outperforms non-goal-oriented (A-optimal) and linearization-based (c-optimal) approaches.

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.