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A prediction method for multi-class systems based on limited data [clinical trials]

A prediction method for multi-class systems based on limited...

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Annual IEEE symposium on Computer-Based Medical Systems

作者： V.A. Kuznetsov G.D. Knott Laboratory Integrative and Medicine Biophysics National Institute of Child Health and Human Development Bethesda MD USA Civilized Software Inc. Silver Spring MD USA

In many clinical trials, the prediction of patient outcome following therapy requires the analysis of two or more small groups of responders having a large number of simultaneously measured covariates, some of whose values may be absent. Prediction of individual outcomes in these groups is a severe statistical problem. this has motivated us to develop a suitable approach for inference from such limited data. A new statistically-oriented prediction method, called optimized independent segment voting (OISV), is presented for constructing a class-membership prediction function for such data sets. this "voting" prediction function is constructed based on the most informative and robust discrete segments of all covariate ranges, which are thus discretized.

关键词： Prediction methods Voting Clinical trials Laboratories Biophysics Silver Springs Medical treatment Logistics Regression analysis

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An interoperable data architecture for data exchange in a biomedical research network

An interoperable data architecture for data exchange in a bi...

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Annual IEEE symposium on Computer-Based Medical Systems

作者： D. Crichton H. Kincaid G.J. Downing S. Srivastava J.S. Hughes NASA Jet Propulsion Laboratory California Institute of Technology USA Fred Hutchinson Cancer Research Center USA National Institutes of Health DHHS USA National Cancer Institute USA

Knowledge discovery and data correlation require a unified approach to basic data management. However, achieving such an approach is nearly impossible with hundreds of disparate data sources, legacy systems and data formats. this problem is pervasive in the biomedical research community, where data models, taxonomies and data management systems are locally implemented. these local implementations create an environment where interoperability and collaboration between researchers and research institutions are limited. the authors demonstrate how technology developed by NASA's Jet Propulsion Laboratory (JPL) for space science can be used to build an interoperable data architecture for bioinformatics. JPL has taken a novel approach towards solving this problem by exploiting Web technologies usually dedicated to e-commerce, combined with a rich, metadata-based environment. this paper discusses the approach taken to develop a prototype data architecture for the discovery and validation of disease biomarkers within a biomedical research network. Biomarkers are measured parameters of normal biological processes, pathogenic processes or pharmacological responses to a therapeutic intervention. Biomarkers are of growing importance in biomedical research for therapeutic discovery, disease prevention and detection. A bioinformatics infrastructure is crucial to support the integration and analysis of large, complex biological and epidemiological data sets.

关键词： Space technology Biomarkers Bioinformatics Diseases Knowledge management data models Taxonomy Collaboration Propulsion Prototypes

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Registration of time-series contrast enhanced magnetic resonance images for renography

Registration of time-series contrast enhanced magnetic reson...

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Annual IEEE symposium on Computer-Based Medical Systems

作者： P.J. Yim H.B. Marcos M. McAuliffe D. McGarry I. Heaton P.L. Choyke Warreti G. Magnuson Clinical Center National Institutes of Health DHHS USA Warren G. Magnuson Clinical Center National Institutes of Health Center for Information Technoloey National Institutes of Health Sensor Systems USA Sensor Systems Company

Renovascular disease is an important cause of hypertension. For assessing treatment options for renovascular disease, such as angioplasty or nephrectomy, it is important to characterize the renal tissue. Magnetic resonance (MR) renography is becoming a viable method for the characterization of the renal tissue. However, the analysis of MR renography is hampered by tissue motion. We investigate two automated image registration methods for minimizing the effects of tissue motion. the first is semi-automated registration using contours. the second is an adaptation of the automated image registration (AIR) algorithm that accommodates large-scale motion and tissue enhancement from a contrast agent. We compared the results of these methods with manual registration using image overlays. Semi-automated registration using contours accurately registered a 2D MR renography data set of 140 time frames with obvious errors in only seven slices. With correction in those slices, semi-automatic registration had equivalent quality to manual registration. the adaptation of the AIR algorithm produced better results on 3D MR renography in healthy kidneys than manual registration, but worse results in a diseased kidney. We conclude that automated registration of 2D and 3D MR renography is feasible.

关键词： Magnetic resonance Diseases Heart Mutual information Image registration Cost function Sensor systems Hypertension Computational Intelligence Society large-scale systems

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PaDDMAS: parallel and distributed data mining application suite

PaDDMAS: parallel and distributed data mining application su...

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International symposium on Parallel and Distributed Processing (IPDPS)

作者： O. Rana D. Walker Maozhen Li S. Lynden M. Ward Department of Computer Science University of Wales Cardiff UK

Discovering complex associations, anomalies and patterns in distributed data sets is gaining popularity in a range of scientific, medical and business applications. Various algorithms are employed to perform data analysis within a domain, and range from statistical to machine learning and AI based techniques. Several issues need to be addressed however to scale such approaches to large data sets, particularly when these are applied to data distributed at various sites. As new analysis techniques are identified, the core tool set must enable easy integration of such analytical components. Similarly, results from an analysis engines must be sharable, to enable storage, visualisation or further analysis of results. We describe the architecture of PaDDMAS, a component based system for developing distributed data mining applications. PaDDMAS provides a tool set for combining pre-developed or custom components using a dataflow approach, with components performing analysis, data extraction or data management and translation. Each component is wrapped as a Java/CORBA object, and has an interface defined in XML. Components can be serial or parallel objects, and may be binary or contain a more complex internal structure. We demonstrate a prototype using a neural network analysis algorithm.

关键词： data mining data analysis Machine learning algorithms Machine learning Artificial intelligence Engines visualization Performance analysis Java XML

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Optimizing retrieval and processing of multi-dimensional scientific datasets

Optimizing retrieval and processing of multi-dimensional sci...

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International symposium on Parallel and Distributed Processing (IPDPS)

作者： Chialin Chang T. Kurc A. Sussman J. Saltz Department of Computer Science University of Maryland College Park MD USA Department of Pathology Johns Hopkins Medical Institutions Baltimore MD USA

We have developed the Active data Repository (ADR), an infrastructure that integrates storage, retrieval, and processing of large multi-dimensional scientific datasets on distributed memory parallel machines with multiple disks attached to each node. In earlier work, we proposed three strategies for processing range queries within the ADR framework. Our experimental results show that the relative performance of the strategies changes under varying application characteristics and machine configurations. In this work we investigate approaches to guide and automate the selection of the best strategy for a given application and machine configuration. We describe analytical models to predict the relative performance of the strategies where input data elements are uniformly distributed in the attribute space of the output dataset, restricting the output dataset to be a regular d-dimensional array.

关键词： Information retrieval Computer science Educational institutions Pathology data analysis Area measurement Satellites Microscopy Microwave integrated circuits Tomography

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Efficient integration of compiler-directed cache coherence and data prefetching

Efficient integration of compiler-directed cache coherence a...

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International symposium on Parallel and Distributed Processing (IPDPS)

作者： Hock-Beng Lim Pen-Chung Yew Center for Supercomputing R & D University of Illinois Urbana IL USA Hewlett Packard Company Cupertino CA USA Department of Computer Science and Engineering University of Minnesota Minneapolis MN USA

Cache coherence enforcement and memory latency reduction and hiding are very important and challenging problems in the design of large-scale distributed shared-memory (DSM) multiprocessors. We propose an integrated framework to solve these problems through a compiler-directed cache coherence scheme called the Cache Coherence with data Prefetching (CCDP) scheme. the CCDP scheme enforces cache coherence by prefetching the potentially stale references in a parallel program. It also prefetches the nonstale references to hide their memory latencies. To optimize the performance of the CCDP scheme, some prefetch hardware support is provided to efficiently handle these two forms of data prefetching operations. We also developed the compiler techniques utilized by the CCDP scheme for stale reference detection, prefetch target analysis and prefetch scheduling. We evaluated the performance of the CCDP scheme via execution-driven simulations of several applications from the SPEC CFP95 and the Perfect benchmark suites. the simulation results show that the CCDP scheme provides significant performance improvements for the applications studied.

关键词： Prefetching Hardware Delay Random access memory Computer science data engineering Design engineering Read only memory large-scale systems Computer architecture

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Skiplist-based concurrent priority queues

Skiplist-based concurrent priority queues

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International symposium on Parallel and Distributed Processing (IPDPS)

作者： N. Shavit I. Lotan Sun MicroSystems Laboratories Inc. University of Stanford

this paper addresses the problem of designing scalable concurrent priority queues for large scale multiprocessors machines with up to several hundred processors. Priority queues are fundamental in the design of modern multiprocessor algorithms, with many classical applications ranging from numerical algorithms through discrete event simulation and expert systems. While highly scalable approaches have been introduced for the special case of queues with a fixed set of priorities, the most efficient designs for the general case are based on the parallelization of the heap data structure. though numerous intricate heap-based schemes have been suggested in the literature, their scalability seems to be limited to small machines in the range of ten to twenty processors. this paper proposes an alternative approach: to base the design of concurrent priority queues on the probabilistic skiplist data structure, rather than on a heap. To this end, we show that a concurrent skiplist structure, following a simple set of modifications, provides a concurrent priority queue with a higher level of parallelism and significantly less contention than the fastest known heap-based algorithms. Our initial empirical evidence, collected on a simulated 256 node shared memory multiprocessor architecture similar to the MIT Alewife, suggests that the new skiplist based priority queue algorithm scales significantly better than heap based schemes throughout most of the concurrency range. With 256 processors, they are about twice as fast in performing deletions and up to 8 times faster in performing insertions.

关键词： Algorithm design and analysis Electronic switching systems Expert systems Sun Laboratories Read only memory Concurrent computing Computer architecture Application software Discrete event simulation

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Intermediate variable encodings that enable multiplexor-based implementations of two operand addition

Intermediate variable encodings that enable multiplexor-base...

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Computer Arithmetic (ARIth)

作者： D.S. Phatak I. Koren Electrical Engineering Department State University of New York Binghamton NY USA Department of Electrical and Computer Engineering University of Massachusetts Amherst MA USA

In two operand addition, bit-wise intermediate variables such as the "propagate" and "generate" terms are defined/evaluated first. Basic carry propagation recursion is then expressed in terms of these variables and is "unrolled" to obtain a tree structure for fast execution. In CMOS VLSI technology, multiplexors are fast and efficient to implement. Hence, we investigate in this paper all possible two-bit encodings for the intermediate variables and identify the ones that enable multiplexor-based implementations. Some of these encodings enable further simplification of the multiplexor-based realizations. Our analysis also shows that adopting an intermediate signed-digit representation simply amounts to selecting one of the possible encodings. thus, there is no inherent advantage to the use of intermediate signed-digit representations in a two operand addition. Finally, we extend our analysis to the generalized look-ahead-recursions proposed by R.W. Doran (1988).

关键词： Encoding Chromium Tree data structures CMOS technology Birth disorders Very large scale integration Delay Signal synthesis Hardware

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visualization of radiation from a spiral antenna using EM-ANIMATE

Visualization of radiation from a spiral antenna using EM-AN...

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Proceedings of the 1998 14th Annual Review of Progress in Applied Computational Electromagnetics. Part 1 (of 2)

作者： Pearlman, R.A. Axe, M.R. Bornholdt, J.M. Roedder, J.M. Boeing Co St. Louis United States

A spiral antenna bent to conform with the leading edge of an aircraft wing was analyzed using a hybrid method of moments/high frequency technique. analysis of such a large problem would not have been possible without using a hybrid technique. Free space near field radiation generated by the antenna was used to calculate impressed currents on the aircraft and resulting reradiation. the results show excellent agreement with measured data. Animation was used to investigate the differences between flat and bent spiral performance. visualization was also used to locate which aircraft surface features perturb the antenna pattern. Such visualization allows a complex problem to be observed and provides clues for further study.

关键词： Directional patterns (antenna)

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Visual prompts and graphical design: a framework for exploring the design space of 2-D charts and graphs

Visual prompts and graphical design: a framework for explori...

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Proceedings of the 1997 14th National Conference on Artificial Intelligence, AAAI 97

作者： Mittal, Vibhu O. JPRC Pittsburgh United States

Graphical presentations can be very effective in communicating large datasets and patterns, trends and relationships in them. Charts and graphs used in reporting data usually tend to highlight certain aspects and suppress others. In fact, a recent study of several hundred annual reports found that more than 30% of charts in these reports were designed to facilitate inferences favorable to the companies while hindering others. Unfortunately, many of the techniques used to achieve these effects may not be obvious to the average user. One solution to this problem is to make design choices explicit to the user. this paper presents a data analysis interface that educates users by enabling them to explore the visualization space and modifying chart design parameters. this interface is based on an analysis of a corpus of charts and graphs and uses knowledge about a variety of techniques for emphasizing specific trends and/or values shown in 2-D charts and graphs.

关键词： data structures

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