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The present article proposes a partitioned Dirichlet-Neumann algorithm, that allows to address unique challenges arising from a novel mixed-dimensional coupling of very slender fibers embedded in fluid flow using a regularized mortar-type finite element discretization. The fibers are modeled via one-dimensional (1D) partial differential equations based on geometrically exact nonlinear beam theory, while the flow is described by the three-dimensional (3D) incompressible Navier-Stokes equations. The arising truly mixed-dimensional 1D-3D coupling scheme constitutes a novel approximate model and numerical strategy, that naturally necessitates specifically tailored solution schemes to ensure an accurate and efficient computational treatment. In particular, we present a strongly coupled partitioned solution algorithm based on a Quasi-Newton method for applications involving fibers with high slenderness ratios that usually present a challenge with regard to the well-known added mass effect. The influence of all employed algorithmic and numerical parameters, namely the applied acceleration technique, the employed constraint regularization parameter as well as shape functions, on efficiency and results of the solution procedure is studied through appropriate examples. Finally, the convergence of the two-way coupled mixed-dimensional problem solution under uniform mesh refinement is demonstrated, a comparison to a 3D reference solution is performed, and the method's capabilities in capturing flow phenomena at large geometric scale separation is illustrated by the example of a submersed vegetation canopy.

Multi-contrast magnetic resonance imaging is a significant and essential medical imaging technique.However, multi-contrast imaging has longer acquisition time and is easy to cause motion artifacts. In particular, the acquisition time for a T2-weighted image is prolonged due to its longer repetition time (TR). On the contrary, T1-weighted image has a shorter TR. Therefore,utilizing complementary information across T1 and T2-weighted image is a way to decrease the overall imaging time. Previous T1-assisted T2 reconstruction methods have mostly focused on image domain using whole-based image fusion approaches. The image domain reconstruction method has the defects of high computational complexity and limited flexibility. To address this issue, we propose a novel multi-contrast imaging method called partition-based k-space synthesis (PKS) which can achieve super reconstruction quality of T2-weighted image by feature fusion. Concretely, we first decompose fully-sampled T1 k-space data and under-sampled T2 k-space data into two sub-data, separately. Then two new objects are constructed by combining the two sub-T1/T2 data. After that, the two new objects as the whole data to realize the reconstruction of T2-weighted image. Finally, the objective T2 is synthesized by extracting the sub-T2 data of each part. Experimental results showed that our combined technique can achieve comparable or better results than using traditional k-space parallel imaging(SAKE) that processes each contrast independently.

Active feedback control in magnetic confinement fusion devices is desirable to mitigate plasma instabilities and enable robust operation. Optical high-speed cameras provide a powerful, non-invasive diagnostic and can be suitable for these applications. In this study, we process fast camera data, at rates exceeding 100kfps, on $\textit{in situ}$ Field Programmable Gate Array (FPGA) hardware to track magnetohydrodynamic (MHD) mode evolution and generate control signals in real-time. Our system utilizes a convolutional neural network (CNN) model which predicts the $n$=1 MHD mode amplitude and phase using camera images with better accuracy than other tested non-deep-learning-based methods. By implementing this model directly within the standard FPGA readout hardware of the high-speed camera diagnostic, our mode tracking system achieves a total trigger-to-output latency of 17.6$\mu$s and a throughput of up to 120kfps. This study at the High Beta Tokamak-Extended Pulse (HBT-EP) experiment demonstrates an FPGA-based high-speed camera data acquisition and processing system, enabling application in real-time machine-learning-based tokamak diagnostic and control as well as potential applications in other scientific domains.

The Gearhart-Koshy acceleration for the Kaczmarz method for linear systems is a line-search with the unusual property that it does not minimize the residual, but the error. Recently one of the authors generalized the this acceleration from a line-search to a search in affine subspaces. In this paper, we demonstrate that the affine search is a Krylov space method that is neither a CG-type nor a MINRES-type method, and we prove that it is mathematically equivalent with a more canonical Gram-Schmidt-based method. We also investigate what abstract property of the Kaczmarz method enables this type of algorithm, and we conclude with a simple numerical example.

Recently, Eldan, Koehler, and Zeitouni (2020) showed that Glauber dynamics mixes rapidly for general Ising models so long as the difference between the largest and smallest eigenvalues of the coupling matrix is at most $1 - \epsilon$ for any fixed $\epsilon > 0$. We give evidence that Glauber dynamics is in fact optimal for this "general-purpose sampling" task. Namely, we give an average-case reduction from hypothesis testing in a Wishart negatively-spiked matrix model to approximately sampling from the Gibbs measure of a general Ising model for which the difference between the largest and smallest eigenvalues of the coupling matrix is at most $1 + \epsilon$ for any fixed $\epsilon > 0$. Combined with results of Bandeira, Kunisky, and Wein (2019) that analyze low-degree polynomial algorithms to give evidence for the hardness of the former spiked matrix problem, our results in turn give evidence for the hardness of general-purpose sampling improving on Glauber dynamics. We also give a similar reduction to approximating the free energy of general Ising models, and again infer evidence that simulated annealing algorithms based on Glauber dynamics are optimal in the general-purpose setting.

Positron Emission Tomography (PET) enables functional imaging of deep brain structures, but the bulk and weight of current systems preclude their use during many natural human activities, such as locomotion. The proposed long-term solution is to construct a robotic system that can support an imaging system surrounding the subject's head, and then move the system to accommodate natural motion. This requires a system to measure the motion of the head with respect to the imaging ring, for use by both the robotic system and the image reconstruction software. We report here the design, calibration, and experimental evaluation of a parallel string encoder mechanism for sensing this motion. Our results indicate that with kinematic calibration, the measurement system can achieve accuracy within 0.5mm, especially for small motions.

Positron Emission Tomography (PET) enables functional imaging of deep brain structures, but the bulk and weight of current systems preclude their use during many natural human activities, such as locomotion. The proposed long-term solution is to construct a robotic system that can support an imaging system surrounding the subject's head, and then move the system to accommodate natural motion. This requires a system to measure the motion of the head with respect to the imaging ring, for use by both the robotic system and the image reconstruction software. We report here the design and experimental evaluation of a parallel string encoder mechanism for sensing this motion. Our preliminary results indicate that the measurement system may achieve accuracy within 0.5 mm, especially for small motions, with improved accuracy possible through kinematic calibration.

Embedding graphs in continous spaces is a key factor in designing and developing algorithms for automatic information extraction to be applied in diverse tasks (e.g., learning, inferring, predicting). The reliability of graph embeddings directly depends on how much the geometry of the continuous space matches the graph structure. Manifolds are mathematical structure that can enable to incorporate in their topological spaces the graph characteristics, and in particular nodes distances. State-of-the-art of manifold-based graph embedding algorithms take advantage of the assumption that the projection on a tangential space of each point in the manifold (corresponding to a node in the graph) would locally resemble a Euclidean space. Although this condition helps in achieving efficient analytical solutions to the embedding problem, it does not represent an adequate set-up to work with modern real life graphs, that are characterized by weighted connections across nodes often computed over sparse datasets with missing records. In this work, we introduce a new class of manifold, named soft manifold, that can solve this situation. In particular, soft manifolds are mathematical structures with spherical symmetry where the tangent spaces to each point are hypocycloids whose shape is defined according to the velocity of information propagation across the data points. Using soft manifolds for graph embedding, we can provide continuous spaces to pursue any task in data analysis over complex datasets. Experimental results on reconstruction tasks on synthetic and real datasets show how the proposed approach enable more accurate and reliable characterization of graphs in continuous spaces with respect to the state-of-the-art.

Background and Objective: Infra-red scanning laser ophthalmoscope (IRSLO) images are akin to colour fundus photographs in displaying the posterior pole and retinal vasculature fine detail. While there are many trained networks readily available for retinal vessel segmentation in colour fundus photographs, none cater to IRSLO images. Accordingly, we aimed to develop (and release as open source) a vessel segmentation algorithm tailored specifically to IRSLO images. Materials and Methods: We used 23 expertly annotated IRSLO images from the RAVIR dataset, combined with 7 additional images annotated in-house. We trained a U-Net (convolutional neural network) to label pixels as 'vessel' or 'background'. Results: On an unseen test set (4 images), our model achieved an AUC of 0.981, and an AUPRC of 0.815. Upon thresholding, it achieved a sensitivity of 0.844, a specificity of 0.983, and an F1 score of 0.857. Conclusion: We have made our automatic segmentation algorithm publicly available and easy to use. Researchers can use the generated vessel maps to compute metrics such as fractal dimension and vessel density.

We introduce Lineax, a library bringing linear solves and linear least-squares to the JAX+Equinox scientific computing ecosystem. Lineax uses general linear operators, and unifies linear solves and least-squares into a single, autodifferentiable API. Solvers and operators are user-extensible, without requiring the user to implement any custom derivative rules to get differentiability. Lineax is available at //github.com/google/lineax.