Démian Nave

BioWar: scalable agent-based model of bioattacks

While structured by social and institutional networks, disease outbreaks are modulated by physical, economical, technological, communication, health, and governmental infrastructures. To systematically reason about the nature of outbreaks, the potential outcomes of media, prophylaxis, and vaccination campaigns, and the relative value of various early warning devices, social context, and infrastructure, must be considered. Numerical models provide a cost-effective ethical system for reasoning about such events. BioWar, a scalable citywide multiagent network numerical model, is described in this paper. BioWar simulates individuals as agents who are embedded in social, health, and professional networks and tracks the incidence of background and maliciously introduced diseases. In addition to epidemiology, BioWar simulates health-care-seeking behaviors, absenteeism patterns, and pharmaceutical purchases, information useful for syndromic and behavioral surveillance algorithms.

Guaranteed: quality parallel delaunay refinement for restricted polyhedral domains

We describe a distributed memory parallel Delaunay refinement algorithm for polyhedral domains which can generate meshes containing tetrahedra with circumradius to shortest edge ratio less than 2, as long as the angle separating any two incident segments and/or facets is between 90° and 270° degrees. Input to our implementation is an element--wise partitioned, conforming Delaunay mesh of a restricted polyhedral domain which has been distributed to the processors of a parallel system. The submeshes of the distributed mesh are then independently refined by concurrently inserting new mesh vertices.Our algorithm allows a new mesh vertex to affect both the submesh tetrahedralizations and the submesh interfaces induced by the partitioning. This flexibility is crucial to ensure mesh quality, but it introduces unpredictable and variable latencies due to long delays in gathering remote data required for updating mesh data structures. In our experiments, more than 80% of this latency was masked with computation due to the fine--grained concurrency of our algorithm.Our experiments also show that the algorithm is efficient in practice, even for certain domains whose boundaries do not conform to the theoretical limits imposed by the algorithm. The algorithm we describe is the first step in the development of much more sophisticated guaranteed--quality parallel mesh generation algorithms.

Simultaneous mesh generation and partitioning for Delaunay meshes

In this paper, we present a new approach for the parallel generation and partitioning of unstructured 3D Delaunay meshes. The new approach couples the mesh generation and partitioning problems into a single optimization problem. Traditionally, these two problems are solved separately, first generating the mesh (usually sequentially) and then partitioning the mesh, either sequentially or in parallel. In the traditional approach, the overheads due to I/O and data movement exceed 50% of the total execution time. Even if parallel partitioning schemes are employed, data movement, synchronization, and data structure translation overheads are high; for applications which require frequent remeshing (e.g. crack growth simulations), these overheads are prohibitive. We present a method for solving the mesh partitioning and placement problem simultaneously with the mesh generation problem. By eliminating unnecessary and redundant cache, local, and remote memory accesses, we can speed up the generation and redistribution process, for very large meshes, by almost an order of magnitude compared to traditional approaches. Our results show that we can achieve nearly perfect equi-distribution of mesh elements over the processors, while maintaining reasonably good separator size, all while improving the quality of the mesh by eliminating many of the problems inherent in traditional parallel constrained mesh generation.

Mobile object layer: a runtime substrate for parallel adaptive and irregular computations

Abstract In this paper we present a parallel runtime substrate, the Mobile Object Layer (MOL), that supports data or object mobility and automatic message forwarding in order to ease the implementation of adaptive and irregular applications on distributed memory machines. The MOL implements a global logical name space for message passing and distributed directories to assist in the translation of logical to physical addresses. Our data show that the latency of the MOL primitives is within 10–14% of the latency of the underlying communication substrate. The MOL is a lightweight, portable library designed to minimize maintenance costs for very large-scale parallel adaptive applications.

Left ventricle volume measurements in cardiac micro-CT: The impact of radiation dose and contrast agent

Micro-CT-based cardiac function estimation in small animals requires measurement of left ventricle (LV) volume at multiple time points during the cardiac cycle. Measurement accuracy depends on the image resolution, its signal and noise properties, and the analysis procedure. This work compares the accuracy of the Otsu thresholding and a region sampled binary mixture approach, for live mouse LV volume measurement using 100 microm resolution datasets. We evaluate both analysis methods after varying the volume of injected contrast agent and the number of projections used for CT reconstruction with a goal of permitting reduced levels of both X-ray and contrast agent doses.

Date movement and control substrate for parallel adaptive applications

In this paper, we present the Data Movement and Control Substrate (DMCS), a library which implements low‐latency one‐sided communication primitives for use in parallel adaptive and irregular applications. DMCS is built on top of low‐level, vendor‐specific communication subsystems such as LAPI (Low‐level Application Programme Interface) for IBM SP machines, as well as on widely available message‐passing libraries like MPI for clusters of workstations and PCs. DMCS adds a small overhead to the communication operations provided by the lower communication system. In return, DMCS provides a flexible and easy to understand application program interface for one‐sided communication operations. Furthermore, DMCS is designed so that it can be easily ported and maintained by non‐experts. Copyright

Parallel FEM Simulation of Crack Propagation - Challenges, Status, and Perspectives

Understanding how fractures develop in materials is crucial to many disciplines, e.g., aeronautical engineering, material sciences, and geophysics. Fast and accurate computer simulation of crack propagation in realistic 3D structures would be a valuable tool for engineers and scien tists exploring the fracture process in materials. In the following, we will describe a next generation crack propagation simulation softw are that aims to make this potential a reality.

Photo-realistic representation of anatomical structures for medical education by fusion of volumetric and surface image data

We have produced improved photo-realistic views of anatomical structures for medical education combining data from photographic images of anatomical surfaces with optical, CT and MRI volumetric data such as provided by the NLM Visible Human Project. Volumetric data contains the information needed to construct 3D geometrical models of anatomical structures, but cannot provide a realistic appearance for surfaces. Nieder has captured high quality photographic sequences of anatomy specimens over a range of rotational angles. These have been assembled into QuickTime VR Object movies that can be viewed statically or dynamically. We reuse this surface imagery to produce textures and surface reflectance maps for 3D anatomy models to allow viewing from any orientation and lighting condition. Because the volumetric data comes from different individuals than the surface images, we have to warp these data into alignment. Currently we do not use structured lighting or other direct 3D surface information, so surface shape is recovered from rotational sequences using silhouettes and texture correlations. The results of this work improves the appearance and generality of models, used for anatomy instruction with the PSC Volume Browser.

Measurement and modeling of 4D live mouse heart volumes from CT time series

In vivo quantitative studies of cardiac function in mouse models provide information about cardiac pathophysiology in more detail than can be obtained in humans. Quantitative measurements of left ventricular (LV) volume at multiple contractile phases are particularly important. However, the mouse hearts small size and rapid motion present challenges for precise measurement in live animals. Researchers at Duke Universitys Center for In Vivo Microscopy (CIVM) have developed noninvasive time-gated microcomputed tomography (micro-CT) techniques providing the temporal and spatial resolutions required for in vivo characterization of cardiac structure and function. This paper describes analysis of the resulting reconstructions to produce volume measurements and corresponding models of heart motion. We believe these are the most precise noninvasive estimates of in vivo LV volume currently available. Our technique uses binary mixture models to directly recover volume estimates from reconstructed datasets. Unlike methods using segmentation followed by voxel counting, this approach provides statistical error estimates and maintains good precision at high noise levels. This is essential for long term multiple session experiments that must simultaneously minimize contrast agent and x-ray doses. The analysis tools are built into the Pittsburgh Supercomputing Centers Volume Browser (PSC-VB) that provides networked multi-site data sharing and collaboration including analysis and visualization functions.

A Model of Biological Attacks on a Realistic Population

The capability to assess the impacts of large-scale biological attacks and the efficacy of containment policies is critical and requires knowledge-intensive reasoning about social response and disease transmission within a complex social system. There is a close linkage among social networks, transportation networks, disease spread, and early detection. Spatial dimensions related to public gathering places such as hospitals, nursing homes, and restaurants, can play a major role in epidemics [Klovdahl et. al. 2001]. Like natural epidemics, bioterrorist attacks unfold within spatially defined, complex social systems, and the societal and networked response can have profound effects on their outcome. This paper focuses on bioterrorist attacks, but the model has been applied to emergent and familiar diseases as well.