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Sparse matrix problems are difficult to parallelize efficiently on message-passing machines, since they access data through multiple levels of indirection. Inspector/executor strategies, which are typically used to parallelize such problems impose significant preprocessing overheads. This paper describes the run-time support required by new compilation techniques for sparse matrices and evaluates...
Many parallel programs require run-time support to implement the communication caused by indirect data references. In previous work, we have developed the inspectorexecutor paradigm to handle these cases. This paper extends that work by developing a dataflow framework to aid in placing the executor communications calls. Our dataflow analysis determines when it is safe to combine communications statements,...
In this paper, we present a comprehensive framework to support classification of nuclei in digital microscopy images of diffuse gliomas. This system integrates multiple modules designed for convenient human annotations, standard-based data management, efficient data query and analysis. In our study, 2770 nuclei of six types are annotated by neuropathologists from 29 whole-slide images of glioma biopsies...
The segmentation of tissues in whole-slide histology images is a necessary step for the morphological analyses of tissues and cellular structures. Previous works have demonstrated the potential of two-point correlation functions (TPCF) as features for tissue segmentation, however the feature space is not yet well understood and computational methods are lacking. This paper illustrates several fundamental...
Spatial object association, also referred to as crossmatch of spatial datasets, is the problem of identifying and comparing objects in two or more datasets based on their positions in a common spatial coordinate system. In this work, we evaluate two crossmatch algorithms that are used for astronomical sky surveys, on the following database system architecture configurations: (1) Netezza Performance...
Data-intensive applications frequently transfer large amounts of data over wide-area networks. The performance achieved in such settings can often be improved by routing data via intermediate nodes chosen to increase aggregate bandwidth. We explore the benefits of overlay network approaches by designing and implementing a service-oriented architecture that incorporates two key optimizations - multi-hop...
Scheduling, in many application domains, involves the optimization of multiple performance metrics. For example, application workflows with real-time constraints have strict throughput requirements and also desire a low latency or response time. In this paper, we present a novel algorithm for the scheduling of workflows that act on a stream of input data. Our algorithm focuses on the two performance...
We present a novel use of GPUs (graphics processing units) for the analysis of histopathological images of neuroblastoma, a childhood cancer. Thanks to the advent of modern microscopy scanners, whole-slide histopathological images can now be acquired but the computational costs to analyze these images using sophisticated image analysis algorithms are usually high. In this study, we have implemented...
This paper describes our experience to date employing the systematic mapping and optimization of large- scale scientific application workflows to current and future parallel platforms. The overall goal of the project is to integrate a set of system layers - application program, compiler, run-time environment, knowledge representation, optimization framework, and workflow manager - and through a systematic...
Many scientific applications need to stage large volumes of files from one set of machines to another set of machines in a wide-area network. Efficient execution of such data transfers needs to take into account the heterogeneous nature of the environment and dynamic availability of shared resources. This paper proposes an algorithm that dynamically schedules a batch of data transfer requests with...
Design templates that involve discovery, analysis, and integration of information resources commonly occur in many scientific research projects. In this paper we present examples of design templates from the biomedical translational research domain and discuss the requirements imposed on Grid middleware infrastructures by them. Using caGrid, which is a Grid middleware system based on the model driven...
In this paper, a novel color texture classification approach is introduced and applied to computer-assisted grading of follicular lymphoma from whole-slide tissue samples. The digitized tissue samples of follicular lymphoma were classified into histological grades under a statistical framework. The proposed method classifies the image either into low or high grades based on the amount of cytological...
Developments in optical microscopy imaging have generated large high-resolution data sets that have spurred medical researchers to conduct investigations into mechanisms of disease, including cancer at cellular and subcellular levels. The work reported here demonstrates that a suitable methodology can be conceived that isolates modality-dependent effects from the larger segmentation task and that...
Translational research projects target a wide variety of diseases, test many different kinds of biomedical hypotheses, and employ a large assortment of experimental methodologies. Diverse data, complex execution environments, and demanding security and reliability requirements make the implementation of these projects extremely challenging and require novel e-Science technologies.
Neuroblastoma is one of the most malignant childhood cancers affecting infants mostly. The current prognosis is based on microscopic examination of slides by expert pathologists, a process that is error-prone, time consuming and may lead to inter- and intra-reader variations. Therefore, we are developing a Computer Aided Prognosis (CAP) system which provides computerized image analysis to assist pathologist...
The computational power and memory bandwidth of graphics processing units (GPUs) have turned them into attractive platforms for general-purpose applications. In this paper, we exploit this power in the context of biomedical image processing by establishing a cooperative environment between the CPU and the GPU. We deal with phenotype and color analysis on a wide variety of microscopic images from studies...
We propose strategies to efficiently execute a query workload, which consists of multiple related queries submitted against a scientific dataset, on a distributed-memory system in the presence of partial dataset replicas. Partial replication re-organizes and re-distributes one or more subsets of a dataset across the storage system to reduce I/O overheads and increase I/O parallelism. Our work targets...
In many data analysis applications, application-level parameters influence the execution time of the data analysis method or program. Some of these parameters also affect the accuracy of output of the analysis. In this work, we investigate execution strategies for adaptive data analysis applications where the user is willing to trade-off accuracy of output for performance gain and vice-versa. In order...
Peripheral neuroblastic tumors (pNTs) make the most commonly encountered tumor groups in children. Neuroblastoma, one of the categories in pNTs, is known to have unique biological behaviors with variable clinical prognoses of the patients. Part of the neuroblastoma prognosis is closely related with grade of neuroblastic differentiation. In this work, we present an automatic classification system that...
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