Research and Education in Computational Science and Engineering

Over the past two decades the field of computational science and engineering (CSE) has penetrated both basic and applied research in academia, industry, and laboratories to advance discovery, optimize systems, support decision-makers, and educate the scientific and engineering workforce. Informed by centuries of theory and experiment, CSE performs computational experiments to answer questions that neither theory nor experiment alone is equipped to answer. CSE provides scientists and engineers of all persuasions with algorithmic inventions and software systems that transcend disciplines and scales. Carried on a wave of digital technology, CSE brings the power of parallelism to bear on troves of data. Mathematics-based advanced computing has become a prevalent means of discovery and innovation in essentially all areas of science, engineering, technology, and society; and the CSE community is at the core of this transformation. However, a combination of disruptive developments---including the architectural complexity of extreme-scale computing, the data revolution that engulfs the planet, and the specialization required to follow the applications to new frontiers---is redefining the scope and reach of the CSE endeavor. This report describes the rapid expansion of CSE and the challenges to sustaining its bold advances. The report also presents strategies and directions for CSE research and education for the next decade.Comment: Major revision, to appear in SIAM Revie

Geometry Processing of Conventionally Produced Mouse Brain Slice Images

Brain mapping research in most neuroanatomical laboratories relies on conventional processing techniques, which often introduce histological artifacts such as tissue tears and tissue loss. In this paper we present techniques and algorithms for automatic registration and 3D reconstruction of conventionally produced mouse brain slices in a standardized atlas space. This is achieved first by constructing a virtual 3D mouse brain model from annotated slices of Allen Reference Atlas (ARA). Virtual re-slicing of the reconstructed model generates ARA-based slice images corresponding to the microscopic images of histological brain sections. These image pairs are aligned using a geometric approach through contour images. Histological artifacts in the microscopic images are detected and removed using Constrained Delaunay Triangulation before performing global alignment. Finally, non-linear registration is performed by solving Laplace's equation with Dirichlet boundary conditions. Our methods provide significant improvements over previously reported registration techniques for the tested slices in 3D space, especially on slices with significant histological artifacts. Further, as an application we count the number of neurons in various anatomical regions using a dataset of 51 microscopic slices from a single mouse brain. This work represents a significant contribution to this subfield of neuroscience as it provides tools to neuroanatomist for analyzing and processing histological data.Comment: 14 pages, 11 figure

Frequency Analysis of Gradient Estimators in Volume Rendering

Gradient information is used in volume rendering to classify and color samples along a ray. In this paper, we present an analysis of the theoretically ideal gradient estimator and compare it to some commonly used gradient estimators. A new method is presented to calculate the gradient at arbitrary sample positions, using the derivative of the interpolation filter as the basis for the new gradient filter. As an example, we will discuss the use of the derivative of the cubic spline. Comparisons with several other methods are demonstrated. Computational efficiency can be realized since parts of the interpolation computation can be leveraged in the gradient estimatio

Using computer simulation in operating room management: impacts of information quality on process performance

High quality information has a significant impact on improving operation performance and patient satisfaction, as well as resolving patient disputes. Based on the analysis of the perioperative process, information quality is considered as an important contributory factor in improving patient throughput. In this paper, we propose a conceptual framework to use computer simulations in modeling information flow of hospital process for operating room management (ORM). Additionally, we conduct simulation studies in different levels of the information quality for ORM. The results of our studies provide evidence that information quality can drive process performance in several phases of the ORM

Data Driven Surrogate Based Optimization in the Problem Solving Environment WBCSim

Large scale, multidisciplinary, engineering designs are always difficult due to the complexity and dimensionality of these problems. Direct coupling between the analysis codes and the optimization routines can be prohibitively time consuming due to the complexity of the underlying simulation codes. One way of tackling this problem is by constructing computationally cheap(er) approximations of the expensive simulations, that mimic the behavior of the simulation model as closely as possible. This paper presents a data driven, surrogate based optimization algorithm that uses a trust region based sequential approximate optimization (SAO) framework and a statistical sampling approach based on design of experiment (DOE) arrays. The algorithm is implemented using techniques from two packages—SURFPACK and SHEPPACK that provide a collection of approximation algorithms to build the surrogates and three different DOE techniques—full factorial (FF), Latin hypercube sampling (LHS), and central composite design (CCD)—are used to train the surrogates. The results are compared with the optimization results obtained by directly coupling an optimizer with the simulation code. The biggest concern in using the SAO framework based on statistical sampling is the generation of the required database. As the number of design variables grows, the computational cost of generating the required database grows rapidly. A data driven approach is proposed to tackle this situation, where the trick is to run the expensive simulation if and only if a nearby data point does not exist in the cumulatively growing database. Over time the database matures and is enriched as more and more optimizations are performed. Results show that the proposed methodology dramatically reduces the total number of calls to the expensive simulation runs during the optimization process

Scalable Interactive Volume Rendering Using Off-the-shelf Components

This paper describes an application of a second generation implementation of the Sepia architecture (Sepia-2) to interactive volu-metric visualization of large rectilinear scalar fields. By employingpipelined associative blending operators in a sort-last configuration a demonstration system with 8 rendering computers sustains 24 to 28 frames per second while interactively rendering large data volumes (1024x256x256 voxels, and 512x512x512 voxels). We believe interactive performance at these frame rates and data sizes is unprecedented. We also believe these results can be extended to other types of structured and unstructured grids and a variety of GL rendering techniques including surface rendering and shadow map-ping. We show how to extend our single-stage crossbar demonstration system to multi-stage networks in order to support much larger data sizes and higher image resolutions. This requires solving a dynamic mapping problem for a class of blending operators that includes Porter-Duff compositing operators