SCIENTIFIC COMPUTING AND IMAGING INSTITUTE
at the University of Utah

Purpose

Develop a framework to quantify the size, location and severity of femoral and acetabular-sided cartilage and labral damage observed in patients undergoing hip arthroscopy, and generate a database of individual defect parameters to facilitate future research and treatment efforts.

Methods

The size, location, and severity of cartilage and labral damage were prospectively collected using a custom, standardized post-operative template for 100 consecutive patients with femoroacetabular impingement syndrome. Chondrolabral junction damage, isolated intrasubstance labral damage, isolated acetabular cartilage damage and femoral cartilage damage were quantified and recorded using a combination of Beck and ICRS criteria. Radiographic measurements including alpha angle, head–neck offset, lateral centre edge angle and acetabular index were calculated and compared to the aforementioned chondral data using a multivariable logistic regression model and adjusted odd's ratio. Reliability among measurements were assessed using the kappa statistic and intraclass coefficients were used to evaluate continuous variables.

Results

Damage to the acetabular cartilage originating at the chondrolabral junction was the most common finding in 97 hips (97%) and was usually accompanied by labral damage in 65 hips (65%). The width (p = 0.003) and clock-face length (p = 0.016) of the damaged region both increased alpha angle on anteroposterior films. 10% of hips had femoral cartilage damage while only 2 (2%) of hips had isolated defects to either the acetabular cartilage or labrum. The adjusted odds of severe cartilage (p = 0.022) and labral damage (p = 0.046) increased with radiographic cam deformity but was not related to radiographic measures of acetabular coverage.

Conclusions

Damage at the chondrolabral junction was very common in this hip arthroscopy cohort, while isolated defects to the acetabular cartilage or labrum were rare. These data demonstrate that the severity of cam morphology, quantified through radiographic measurements, is a primary predictor of location and severity of chondral and labral damage and focal chondral defects may represent a unique subset of patients that deserve further study.

We present a systematic computational framework for generating positive quadrature rules in multiple dimensions on general geometries. A direct moment-matching formulation that enforces exact integration on polynomial subspaces yields nonlinear conditions and geometric constraints on nodes and weights. We use penalty methods to address the geometric constraints, and subsequently solve a quadratic minimization problem via the Gauss-Newton method. Our analysis provides guidance on requisite sizes of quadrature rules for a given polynomial subspace, and furnishes useful user-end stability bounds on error in the quadrature rule in the case when the polynomial moment conditions are violated by a small amount due to, e.g., finite precision limitations or stagnation of the optimization procedure. We present several numerical examples investigating optimal low-degree quadrature rules, Lebesgue constants, and 100-dimensional quadrature. Our capstone examples compare our quadrature approach to popular alternatives, such as sparse grids and quasi-Monte Carlo methods, for problems in linear elasticity and topology optimization.

Inspired by the works of Forman on discrete Morse theory, which is a combinatorial adaptation to cell complexes of classical Morse theory on manifolds, we introduce a discrete analogue of the stratified Morse theory of Goresky and MacPherson (1988). We describe the basics of this theory and prove fundamental theorems relating the topology of a general simplicial complex with the critical simplices of a discrete stratified Morse function on the complex. We also provide an algorithm that constructs a discrete stratified Morse function out of an arbitrary function defined on a finite simplicial complex; this is different from simply constructing a discrete Morse function on such a complex. We borrow Forman's idea of a "user's guide," where we give simple examples to convey the utility of our theory.

Given data, deep generative models, such as variational autoencoders (VAE) and generative adversarial networks (GAN), train a lower dimensional latent representation of the data space. The linear Euclidean geometry of data space pulls back to a nonlinear Riemannian geometry on the latent space. The latent space thus provides a low-dimensional nonlinear representation of data and classical linear statistical techniques are no longer applicable. In this paper we show how statistics of data in their latent space representation can be performed using techniques from the field of nonlinear manifold statistics. Nonlinear manifold statistics provide generalizations of Euclidean statistical notions including means, principal component analysis, and maximum likelihood fits of parametric probability distributions. We develop new techniques for maximum likelihood inference in latent space, and adress the computational complexity of using geometric algorithms with high-dimensional data by training a separate neural network to approximate the Riemannian metric and cometric tensor capturing the shape of the learned data manifold.

The need to scale next-generation industrial engineering problems to the largest computational platforms presents unique challenges. This paper focuses on data management related problems faced by the Uintah simulation framework at a production scale of 260K processes. Uintah provides a highly scalable asynchronous many-task runtime system, which in this work is used for the modeling of a 1000 megawatt electric (MWe) ultra-supercritical (USC) coal boiler. At 260K processes, we faced both parallel I/O and visualization related challenges, e.g., the default file-per-process I/O approach of Uintah did not scale on Mira. In this paper we present a simple to implement, restructuring based parallel I/O technique. We impose a restructuring step that alters the distribution of data among processes. The goal is to distribute the dataset such that each process holds a larger chunk of data, which is then written to a file independently. This approach finds a middle ground between two of the most common parallel I/O schemes--file per process I/O and shared file I/O--in terms of both the total number of generated files, and the extent of communication involved during the data aggregation phase. To address scalability issues when visualizing the simulation data, we developed a lightweight renderer using OSPRay, which allows scientists to visualize the data interactively at high quality and make production movies. Finally, this work presents a highly efficient and scalable radiation model based on the sweeping method, which significantly outperforms previous approaches in Uintah, like discrete ordinates. The integrated approach allowed the USC boiler problem to run on 260K CPU cores on Mira.

Traumatic brain injury (TBI) is a looming epidemic, growing most rapidly in the elderly population. Some of the most devastating sequelae of TBI are related to depressed levels of consciousness (e.g., coma, minimally conscious state) or deficits in executive function. To date, pharmacological and rehabilitative therapies to treat these sequelae are limited. Deep brain stimulation (DBS) has been used to treat a number of pathologies, including Parkinson disease, essential tremor, and epilepsy. Animal and clinical research shows that targets addressing depressed levels of consciousness include components of the ascending reticular activating system and areas of the thalamus. Targets for improving executive function are more varied and include areas that modulate attention and memory, such as the frontal and prefrontal cortex, fornix, nucleus accumbens, internal capsule, thalamus, and some brainstem nuclei. The authors review the literature addressing the use of DBS to treat higher-order cognitive dysfunction and disorders of consciousness in TBI patients, while also offering suggestions on directions for future research.

Constructing distributed representations for words through neural language models and using the resulting vector spaces for analysis has become a crucial component of natural language processing (NLP). However, despite their widespread application, little is known about the structure and properties of these spaces. To gain insights into the relationship between words, the NLP community has begun to adapt high-dimensional visualization techniques. In particular, researchers commonly use t-distributed stochastic neighbor embeddings (t-SNE) and principal component analysis (PCA) to create two-dimensional embeddings for assessing the overall structure and exploring linear relationships (e.g., word analogies), respectively. Unfortunately, these techniques often produce mediocre or even misleading results and cannot address domain-specific visualization challenges that are crucial for understanding semantic relationships in word embeddings. Here, we introduce new embedding techniques for visualizing semantic and syntactic analogies, and the corresponding tests to determine whether the resulting views capture salient structures. Additionally, we introduce two novel views for a comprehensive study of analogy relationships. Finally, we augment t-SNE embeddings to convey uncertainty information in order to allow a reliable interpretation. Combined, the different views address a number of domain-specific tasks difficult to solve with existing tools.

The use of appearance and shape priors in image segmentation is known to improve accuracy; however, existing techniques have several drawbacks. For instance, most active shape and appearance models require landmark points and assume unimodal shape and appearance distributions, and the level set representation does not support construction of local priors. In this paper, we present novel appearance and shape models for image segmentation based on a differentiable implicit parametric shape representation called a disjunctive normal shape model (DNSM). The DNSM is formed by the disjunction of polytopes, which themselves are formed by the conjunctions of half-spaces. The DNSM's parametric nature allows the use of powerful local prior statistics, and its implicit nature removes the need to use landmarks and easily handles topological changes. In a Bayesian inference framework, we model arbitrary shape and appearance distributions using nonparametric density estimations, at any local scale. The proposed local shape prior results in accurate segmentation even when very few training shapes are available, because the method generates a rich set of shape variations by locally combining training samples. We demonstrate the performance of the framework by applying it to both 2-D and 3-D data sets with emphasis on biomedical image segmentation applications.

Background
Neighbourhood quality has been connected with an array of health issues, but neighbourhood research has been limited by the lack of methods to characterise large geographical areas. This study uses innovative computer vision methods and a new big data source of street view images to automatically characterise neighbourhood built environments.

Methods
A total of 430 000 images were obtained using Google's Street View Image API for Salt Lake City, Chicago and Charleston. Convolutional neural networks were used to create indicators of street greenness, crosswalks and building type. We implemented log Poisson regression models to estimate associations between built environment features and individual prevalence of obesity and diabetes in Salt Lake City, controlling for individual-level and zip code-level predisposing characteristics.

Results
Computer vision models had an accuracy of 86%–93% compared with manual annotations. Charleston had the highest percentage of green streets (79%), while Chicago had the highest percentage of crosswalks (23%) and commercial buildings/apartments (59%). Built environment characteristics were categorised into tertiles, with the highest tertile serving as the referent group. Individuals living in zip codes with the most green streets, crosswalks and commercial buildings/apartments had relative obesity prevalences that were 25%–28% lower and relative diabetes prevalences that were 12%–18% lower than individuals living in zip codes with the least abundance of these neighbourhood features.

Conclusion
Neighbourhood conditions may influence chronic disease outcomes. Google Street View images represent an underused data resource for the construction of built environment features.

Analyzing large, multivariate graphs is an important problem in many domains, yet such graphs are challenging to visualize. In this paper, we introduce a novel, scalable, tree+table multivariate graph visualization technique, which makes many tasks related to multivariate graph analysis easier to achieve. The core principle we follow is to selectively query for nodes or subgraphs of interest and visualize these subgraphs as a spanning tree of the graph. The tree is laid out in a linear layout, which enables us to juxtapose the nodes with a table visualization where diverse attributes can be shown. We also use this table as an adjacency matrix, so that the resulting technique is a hybrid node-link/adjacency matrix technique. We implement this concept in Juniper, and complement it with a set of interaction techniques that enable analysts to dynamically grow, re-structure, and aggregate the tree, as well as change the layout or show paths between nodes. We demonstrate the utility of our tool in usage scenarios for different multivariate networks: a bipartite network of scholars, papers, and citation metrics, and a multitype network of story characters, places, books, etc.

Performance optimization in the petascale era and beyond in the exascale era has and will require modifications of legacy codes to take advantage of new architectures with large core counts and SIMD units. The Numerical Weather Prediction (NWP) physics codes considered here are optimized using thread-local structures of arrays (SOA). High-level and low-level optimization strategies are applied to the WRF Single-Moment 6-Class Microphysics Scheme (WSM6) and Global Forecast System (GFS) physics codes used in the NEPTUNE forecast code. By building on previous work optimizing WSM6 on the Intel Knights Landing (KNL), it is shown how to further optimize WMS6 and GFS physics, and GFS radiation on Intel KNL, Haswell, and potentially on future micro-architectures with many cores and SIMD vector units. The optimization techniques used herein employ thread-local structures of arrays (SOA), an OpenMP directive, OMP SIMD, and minor code transformations to enable better utilization of SIMD units, increase parallelism, improve locality, and reduce memory traffic. The optimized versions of WSM6, GFS physics, GFS radiation run 70, 27, and 23 faster (respectively) on KNL and 26, 18 and 30 faster (respectively) on Haswell than their respective original serial versions. Although this work targets WRF physics schemes, the findings are transferable to other performance optimization contexts and provide insight into the optimization of codes with complex physical models for present and near-future architectures with many core and vector units.

High performance computing frameworks utilizing CPUs, Nvidia GPUs, and/or Intel Xeon Phis necessitate portable and scalable solutions for application developers. Nvidia GPUs in particular present numerous portability challenges with a different programming model, additional memory hierarchies, and partitioned execution units among streaming multiprocessors. This work presents modifications to the Uintah asynchronous many-task runtime and the Kokkos portability library to enable one single codebase for complex multiphysics applications to run across different architectures. Scalability and performance results are shown on multiple architectures for a globally coupled radiation heat transfer simulation, ranging from a single node to 16384 Titan compute nodes.

The Uintah computational framework is used for the parallel solution of partial differential equations on adaptive mesh refinement grids using modern supercomputers. Uintah is structured with an application layer and a separate runtime system. Uintah is based on a distributed directed acyclic graph (DAG) of computational tasks, with a task scheduler that efficiently schedules and executes these tasks on both CPU cores and on-node accelerators. The runtime system identifies task dependencies, creates a task graph prior to the execution of these tasks, automatically generates MPI message tags, and automatically performs halo transfers for simulation variables. Automating halo transfers in a heterogeneous environment poses significant challenges when tasks compute within a few milliseconds, as runtime overhead affects wall time execution, or when simulation variables require large halos spanning most or all of the computational domain, as task dependencies become expensive to process. These challenges are magnified at production scale when application developers require each compute node perform thousands of different halo transfers among thousands simulation variables. The principal contribution of this work is to (1) identify and address inefficiencies that arise when mapping tasks onto the GPU in the presence of automated halo transfers, (2) implement new schemes to reduce runtime system overhead, (3) minimize application developer involvement with the runtime, and (4) show overhead reduction results from these improvements.

The proliferation of heterogeneous computing architectures in current and future supercomputing systems dramatically increases the complexity of software development and exacerbates the divergence of software stacks. Currently, task-based runtimes attempt to alleviate these impediments, however their effective use requires expertise and deep integration that does not facilitate reuse and portability. We propose to introduce a task-based abstraction layer that separates the definition of the algorithm from the runtime-specific implementation, while maintaining performance portability.

The proliferation of heterogeneous computing architectures in current and future supercomputing systems dramatically increases the complexity of software development and exacerbates the divergence of software stacks. Currently, task-based runtimes attempt to alleviate these impediments, however their effective use requires expertise and deep integration that does not facilitate reuse and portability. We propose to introduce a task-based abstraction layer that separates the definition of the algorithm from the runtime-specific implementation, while maintaining performance portability.

Ventricular tachycardia (VT), which can lead to sudden cardiac death, occurs frequently in patients with myocardial infarction. Catheter-based radio-frequency ablation of cardiac tissue has achieved only modest efficacy, owing to the inaccurate identification of ablation targets by current electrical mapping techniques, which can lead to extensive lesions and to a prolonged, poorly tolerated procedure. Here, we show that personalized virtual-heart technology based on cardiac imaging and computational modelling can identify optimal infarct-related VT ablation targets in retrospective animal (five swine) and human studies (21 patients), as well as in a prospective feasibility study (five patients). We first assessed, using retrospective studies (one of which included a proportion of clinical images with artefacts), the capability of the technology to determine the minimum-size ablation targets for eradicating all VTs. In the prospective study, VT sites predicted by the technology were targeted directly, without relying on prior electrical mapping. The approach could improve infarct-related VT ablation guidance, where accurate identification of patient-specific optimal targets could be achieved on a personalized virtual heart before the clinical procedure.

This paper discusses an algorithm for semi-supervised learning to predict cell division and motion in microscopy images. The cells for tracking are detected using extremal region selection and are depicted using a graphical representation. The supervised loss minimizes the error in predictions for the division and move classifiers. The unsupervised loss constrains the incoming links for every detection such that only one of the links is active. Similarly for the outgoing links, we enforce at-most two links to be active. The supervised and un-supervised losses are embedded in a Bayesian framework for probabilistic learning. The classifier predictions are used to model flow variables for every edge in the graph. The cell lineages are solved by formulating it as an energy minimization problem with constraints using integer linear programming. The unsupervised loss adds a significant improvement in the prediction of the division classifier.

In this paper we introduce a novel approach for enhancing the sampling convergence for properties predicted by molecular dynamics. The proposed approach is based upon the construction of a multi-fidelity surrogate model using computational models with different levels of accuracy. While low fidelity models produce result with a lower level of accuracy and computational cost, in this framework they can provide the basis for identification of the optimal sparse sampling pattern for high fidelity models to construct an accurate surrogate model. Such an approach can provide a significant computational saving for the estimation of the quantities of interest for the underlying physical/engineering systems. In the present work, this methodology is demonstrated for molecular dynamics simulations of a Lennard-Jones fluid. Levels of multi-fidelity are defined based upon the integration time step employed in the simulation. The proposed approach is applied to two different canonical problems including (i) single component fluid and (ii) binary glass-forming mixture. The results show about 70% computational saving for the estimation of averaged properties of the systems such as total energy, self diffusion coefficient, radial distribution function and mean squared displacements with a reasonable accuracy.

Introduction

Informal family caregivers (FCG) are an integral and crucial human component in the cancer care continuum. However, research and interventions to help alleviate documented anxiety and burden on this group is lacking. To address the absence of effective interventions, we developed the electronic Support Network Assessment Program (eSNAP) which aims to automate the capture and visualization of social support, an important target for overall FCG support. This study seeks to describe the preliminary efficacy and outcomes of the eSNAP intervention.

Methods

Forty FCGs were enrolled into a longitudinal, two-group randomized design to compare the eSNAP intervention in caregivers of patients with primary brain tumors against controls who did not receive the intervention. Participants were followed for six weeks with questionnaires to assess demographics, caregiver burden, anxiety, depression, and social support. Questionnaires given at baseline (T1) and then 3-weeks (T2), and 6-weeks (T3) post baseline questionnaire.

Results

FCGs reported high caregiver burden and distress at baseline, with burden remaining stable over the course of the study. The intervention group was significantly less depressed, but anxiety remained stable across groups.

Conclusions

With the lessons learned and feedback obtained from FCGs, this study is the first step to developing an effective social support intervention to support FCGs and healthcare providers in improving cancer care.

Preprocessing Framework for Electrograms Intermittently Fiducialized from Experimental Recordings (PFEIFER) is a MATLAB Graphical User Interface designed to process bioelectric signals acquired from experiments.

PFEIFER was specifically designed to process electrocardiographic recordings from electrodes placed on or around the heart or on the body surface. Specific steps included in PFEIFER allow the user to remove some forms of noise, correct for signal drift, and mark specific instants or intervals in time (fiducialize) within all of the time sampled channels. PFEIFER includes many unique features that allow the user to process electrical signals in a consistent and time efficient manner, with additional options for advanced user configurations and input. PFEIFER is structured as a consolidated framework that provides many standard processing pipelines but also has flexibility to allow the user to customize many of the steps. PFEIFER allows the user to import time aligned cardiac electrical signals, semi-automatically determine fiducial markings from those signals, and perform computational tasks that prepare the signals for subsequent display and analysis.