Numerical methods such as the Finite Element Method (FEM) have been successfully adapted to utilize the computational power of GPU accelerators. However, much of the effort around applying FEM to GPU's has been focused on high-order FEM due to higher arithmetic intensity and order of accuracy. For applications such as the simulation of subsurface processes, high levels of heterogeneity results in high-resolution grids characterized by highly discontinuous (cell-wise) material property fields. Moreover, due to the significant uncertainties in the characterization of the domain of interest, e.g. geologic reservoirs, the benefits of high order accuracy are reduced, and low-order methods are typically employed. In this study, we present a strategy for implementing highly performant low-order matrix-free FEM operator kernels in the context of the conjugate gradient (CG) method. Performance results of matrix-free Laplace and isotropic elasticity operator kernels are presented and are shown to compare favorably to matrix-based SpMV operators on V100, A100, and MI250X GPUs.
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Metal artifact correction is a challenging problem in cone beam computed tomography (CBCT) scanning. Metal implants inserted into the anatomy cause severe artifacts in reconstructed images. Widely used inpainting-based metal artifact reduction (MAR) methods require segmentation of metal traces in the projections as a first step, which is a challenging task. One approach is to use a deep learning method to segment metals in the projections. However, the success of deep learning methods is limited by the availability of realistic training data. It is laborious and time consuming to get reliable ground truth annotations due to unclear implant boundaries and large numbers of projections. We propose to use X-ray simulations to generate synthetic metal segmentation training dataset from clinical CBCT scans. We compare the effect of simulations with different numbers of photons and also compare several training strategies to augment the available data. We compare our model's performance on real clinical scans with conventional region growing threshold-based MAR, moving metal artifact reduction method, and a recent deep learning method. We show that simulations with relatively small number of photons are suitable for the metal segmentation task and that training the deep learning model with full size and cropped projections together improves the robustness of the model. We show substantial improvement in the image quality affected by severe motion, voxel size under-sampling, and out-of-FOV metals. Our method can be easily integrated into the existing projection-based MAR pipeline to get improved image quality. This method can provide a novel paradigm to accurately segment metals in CBCT projections.
While well-established methods for time-to-event data are available when the proportional hazards assumption holds, there is no consensus on the best inferential approach under non-proportional hazards (NPH). However, a wide range of parametric and non-parametric methods for testing and estimation in this scenario have been proposed. To provide recommendations on the statistical analysis of clinical trials where non proportional hazards are expected, we conducted a comprehensive simulation study under different scenarios of non-proportional hazards, including delayed onset of treatment effect, crossing hazard curves, subgroups with different treatment effect and changing hazards after disease progression. We assessed type I error rate control, power and confidence interval coverage, where applicable, for a wide range of methods including weighted log-rank tests, the MaxCombo test, summary measures such as the restricted mean survival time (RMST), average hazard ratios, and milestone survival probabilities as well as accelerated failure time regression models. We found a trade-off between interpretability and power when choosing an analysis strategy under NPH scenarios. While analysis methods based on weighted logrank tests typically were favorable in terms of power, they do not provide an easily interpretable treatment effect estimate. Also, depending on the weight function, they test a narrow null hypothesis of equal hazard functions and rejection of this null hypothesis may not allow for a direct conclusion of treatment benefit in terms of the survival function. In contrast, non-parametric procedures based on well interpretable measures as the RMST difference had lower power in most scenarios. Model based methods based on specific survival distributions had larger power, however often gave biased estimates and lower than nominal confidence interval coverage.
We present a coordination method for multiple mobile manipulators to sort objects in clutter. We consider the object rearrangement problem in which the objects must be sorted into different groups in a particular order. In clutter, the order constraints could not be easily satisfied since some objects occlude other objects so the occluded ones are not directly accessible to the robots. Those objects occluding others need to be moved more than once to make the occluded objects accessible. Such rearrangement problems fall into the class of nonmonotone rearrangement problems which are computationally intractable. While the nonmonotone problems with order constraints are harder, involving with multiple robots requires another computation for task allocation. The proposed method first finds a sequence of objects to be sorted using a search such that the order constraint in each group is satisfied. The search can solve nonmonotone instances that require temporal relocation of some objects to access the next object to be sorted. Once a complete sorting sequence is found, the objects in the sequence are assigned to multiple mobile manipulators using a greedy allocation method. We develop four versions of the method with different search strategies. In the experiments, we show that our method can find a sorting sequence quickly (e.g., 4.6 sec with 20 objects sorted into five groups) even though the solved instances include hard nonmonotone ones. The extensive tests and the experiments in simulation show the ability of the method to solve the real-world sorting problem using multiple mobile manipulators.
Recent advances in robot-assisted surgery have resulted in progressively more precise, efficient, and minimally invasive procedures, sparking a new era of robotic surgical intervention. This enables doctors, in collaborative interaction with robots, to perform traditional or minimally invasive surgeries with improved outcomes through smaller incisions. Recent efforts are working toward making robotic surgery more autonomous which has the potential to reduce variability of surgical outcomes and reduce complication rates. Deep reinforcement learning methodologies offer scalable solutions for surgical automation, but their effectiveness relies on extensive data acquisition due to the absence of prior knowledge in successfully accomplishing tasks. Due to the intensive nature of simulated data collection, previous works have focused on making existing algorithms more efficient. In this work, we focus on making the simulator more efficient, making training data much more accessible than previously possible. We introduce Surgical Gym, an open-source high performance platform for surgical robot learning where both the physics simulation and reinforcement learning occur directly on the GPU. We demonstrate between 100-5000x faster training times compared with previous surgical learning platforms. The code is available at: //github.com/SamuelSchmidgall/SurgicalGym.
Application of deep learning methods to physical simulations such as CFD (Computational Fluid Dynamics), have been so far of limited industrial relevance. This paper demonstrates the development and application of a deep learning framework for real-time predictions of the impact of tip clearance variations on the aerodynamic performance of multi-stage axial compressors in gas turbines. The proposed C(NN)FD architecture is proven to be scalable to industrial applications, and achieves in real-time accuracy comparable to the CFD benchmark. The deployed model, is readily integrated within the manufacturing and build process of gas turbines, thus providing the opportunity to analytically assess the impact on performance and potentially reduce requirements for expensive physical tests.
Quantum Generative Modelling (QGM) relies on preparing quantum states and generating samples from these states as hidden - or known - probability distributions. As distributions from some classes of quantum states (circuits) are inherently hard to sample classically, QGM represents an excellent testbed for quantum supremacy experiments. Furthermore, generative tasks are increasingly relevant for industrial machine learning applications, and thus QGM is a strong candidate for demonstrating a practical quantum advantage. However, this requires that quantum circuits are trained to represent industrially relevant distributions, and the corresponding training stage has an extensive training cost for current quantum hardware in practice. In this work, we propose protocols for classical training of QGMs based on circuits of the specific type that admit an efficient gradient computation, while remaining hard to sample. In particular, we consider Instantaneous Quantum Polynomial (IQP) circuits and their extensions. Showing their classical simulability in terms of the time complexity, sparsity and anti-concentration properties, we develop a classically tractable way of simulating their output probability distributions, allowing classical training to a target probability distribution. The corresponding quantum sampling from IQPs can be performed efficiently, unlike when using classical sampling. We numerically demonstrate the end-to-end training of IQP circuits using probability distributions for up to 30 qubits on a regular desktop computer. When applied to industrially relevant distributions this combination of classical training with quantum sampling represents an avenue for reaching advantage in the NISQ era.
Research in high energy physics (HEP) requires huge amounts of computing and storage, putting strong constraints on the code speed and resource usage. To meet these requirements, a compiled high-performance language is typically used; while for physicists, who focus on the application when developing the code, better research productivity pleads for a high-level programming language. A popular approach consists of combining Python, used for the high-level interface, and C++, used for the computing intensive part of the code. A more convenient and efficient approach would be to use a language that provides both high-level programming and high-performance. The Julia programming language, developed at MIT especially to allow the use of a single language in research activities, has followed this path. In this paper the applicability of using the Julia language for HEP research is explored, covering the different aspects that are important for HEP code development: runtime performance, handling of large projects, interface with legacy code, distributed computing, training, and ease of programming. The study shows that the HEP community would benefit from a large scale adoption of this programming language. The HEP-specific foundation libraries that would need to be consolidated are identified
This paper addresses the problem of designing the {\it continuous-discrete} unscented Kalman filter (UKF) implementation methods. More precisely, the aim is to propose the MATLAB-based UKF algorithms for {\it accurate} and {\it robust} state estimation of stochastic dynamic systems. The accuracy of the {\it continuous-discrete} nonlinear filters heavily depends on how the implementation method manages the discretization error arisen at the filter prediction step. We suggest the elegant and accurate implementation framework for tracking the hidden states by utilizing the MATLAB built-in numerical integration schemes developed for solving ordinary differential equations (ODEs). The accuracy is boosted by the discretization error control involved in all MATLAB ODE solvers. This keeps the discretization error below the tolerance value provided by users, automatically. Meanwhile, the robustness of the UKF filtering methods is examined in terms of the stability to roundoff. In contrast to the pseudo-square-root UKF implementations established in engineering literature, which are based on the one-rank Cholesky updates, we derive the stable square-root methods by utilizing the $J$-orthogonal transformations for calculating the Cholesky square-root factors.
The estimation of rare event probabilities plays a pivotal role in diverse fields. Our aim is to determine the probability of a hazard or system failure occurring when a quantity of interest exceeds a critical value. In our approach, the distribution of the quantity of interest is represented by an energy density, characterized by a free energy function. To efficiently estimate the free energy, a bias potential is introduced. Using concepts from energy-based models (EBM), this bias potential is optimized such that the corresponding probability density function approximates a pre-defined distribution targeting the failure region of interest. Given the optimal bias potential, the free energy function and the rare event probability of interest can be determined. The approach is applicable not just in traditional rare event settings where the variable upon which the quantity of interest relies has a known distribution, but also in inversion settings where the variable follows a posterior distribution. By combining the EBM approach with a Stein discrepancy-based stopping criterion, we aim for a balanced accuracy-efficiency trade-off. Furthermore, we explore both parametric and non-parametric approaches for the bias potential, with the latter eliminating the need for choosing a particular parameterization, but depending strongly on the accuracy of the kernel density estimate used in the optimization process. Through three illustrative test cases encompassing both traditional and inversion settings, we show that the proposed EBM approach, when properly configured, (i) allows stable and efficient estimation of rare event probabilities and (ii) compares favorably against subset sampling approaches.
A myriad of approaches have been proposed to characterise the mesoscale structure of networks - most often as a partition based on patterns variously called communities, blocks, or clusters. Clearly, distinct methods designed to detect different types of patterns may provide a variety of answers to the network's mesoscale structure. Yet, even multiple runs of a given method can sometimes yield diverse and conflicting results, producing entire landscapes of partitions which potentially include multiple (locally optimal) mesoscale explanations of the network. Such ambiguity motivates a closer look at the ability of these methods to find multiple qualitatively different 'ground truth' partitions in a network. Here, we propose the stochastic cross-block model (SCBM), a generative model which allows for two distinct partitions to be built into the mesoscale structure of a single benchmark network. We demonstrate a use case of the benchmark model by appraising the power of stochastic block models (SBMs) to detect implicitly planted coexisting bi-community and core-periphery structures of different strengths. Given our model design and experimental set-up, we find that the ability to detect the two partitions individually varies by SBM variant and that coexistence of both partitions is recovered only in a very limited number of cases. Our findings suggest that in most instances only one - in some way dominating - structure can be detected, even in the presence of other partitions. They underline the need for considering entire landscapes of partitions when different competing explanations exist and motivate future research to advance partition coexistence detection methods. Our model also contributes to the field of benchmark networks more generally by enabling further exploration of the ability of new and existing methods to detect ambiguity in the mesoscale structure of networks.
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