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Current analysis approaches and performance needs for whole slide image processing in breast cancer diagnostics

Current analysis approaches and performance needs for whole ...

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international conference on embedded computer systems: architectures, modeling and simulation (IC-SAMOS)

作者： Irene Pöllänen Billy Braithwaite Keijo Haataja Tiia Ikonen Pekka Toivanen Ita-Suomen yliopisto Joensuu FI School of Computing University of Eastern Finland Kuopio Finland

In this paper, the current approaches and performance needs for whole slide image (WSI) analysis processing in breast cancer diagnostics are discussed. WSIs provide high resolution digital image data from the patient's diseased tissue. Digital whole slide images are typically very large and contain a high amount of information. Digitizing tissue specimen into the form of digital images allows the development and application of computational analysis algorithms. Biological tissues are complex with variance in tissue structures between healthy individuals as well as between patients with the same disease. Furthermore, the tissue preparation and digitization usually generates a lot of artifacts and more complexity, which causes classification challenges. This variance and also the large size of the images make creating an accurate and reliable automated breast cancer image analysis a challenge. In the ALMARVI project we aim at generating and implementing efficient histopathological image analysis algorithms in our breast cancer analysis scheme. This paper focuses on discussing relevant information concerning histopathological breast cancer diagnosis, and could also be considered as an introduction to the concept of WSI analysis to non-experts. Since the WSI sizes are very large (up to 40 GB with no compression) there are challenges on the computational analysis which requires computationally efficient tools and suitable approaches to relieve the problems caused by the large size of the images.

关键词： Breast cancer Image segmentation Computational modeling Feature extraction Analytical models Algorithm design and analysis Ducts

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Imposing coarse-grained reconfiguration to general purpose processors

Imposing coarse-grained reconfiguration to general purpose p...

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international conference on embedded computer systems: architectures, modeling and simulation (IC-SAMOS)

作者： M. Duric M. Stanic I. Ratkovic O. Palomar O. Unsal A. Cristal M. Valero A. Smith Centro Nacional de Supercomputacion Barcelona ES Barcelona Supercomputing Center Universitat Politecnica de catalunya IlIA -CSIC

Mobile devices execute applications with diverse compute and performance demands. This paper proposes a general purpose processor that adapts the underlying hardware to a given workload. Existing mobile processors need to utilize more complex heterogeneous substrates to deliver the demanded performance. They incorporate different cores and specialized accelerators. On the contrary, our processor utilizes only modest homogeneous cores and dynamically provides an execution substrate suitable to accelerate a particular workload. Instead of incorporating accelerators, the processor reconfigures one or more cores into accelerators on-the-fly. It improves performance with minimal hardware additions. The accelerators are made of general purpose ALUs reconfigured into a compute fabric and the general purpose pipeline that streams data through the fabric. To enable reconfiguration of ALUs into the fabric, the floorplan of a 4-core processor is changed to place the ALUs in close proximity on the chip. A configurable switched network is added to couple and dynamically reconfigure the ALUs to perform computation of frequently repeated regions, instead of executing general purpose instructions. Through this reconfiguration, the mobile processor specializes its substrate for a given workload and maximizes performance of the existing resources. Our results show that reconfiguration accelerates a set of selected compute intensive workloads by 1.56×, 2,39×, 3,51×, when configuring the accelerator of 1-, 2-, or 4- cores respectively.

关键词： Fabrics Program processors Registers Pipelines Switches computer architecture Mobile communication

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34th international conference on computer Safety, Reliability, and Security, SAFECOMP 2015

34th International Conference on Computer Safety, Reliabilit...

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34th international conference on computer Safety, Reliability, and Security, SAFECOMP 2015

ISBN: (纸本)9783319242545

The proceedings contain 34 papers. The special focus in this conference is on Flight systems, Automotive embedded systems, Automotive Software, Error Detection and Medical systems. The topics include: Medical devices, electronic health records and assuring patient safety;modeling guidelines and usage analysis towards applying hip-hops method to airborne electrical systems;the formal derivation of mode logic for autonomous satellite flight formation;simulation of automotive security threat warnings to analyze driver interpretations and emotional transitions;improving dependability of vision-based advanced driver assistance systems using navigation data and checkpoint recognition;model-based analysis for safety critical software;integrated safety analysis using systems-theoretic process analysis and software model checking;back-to-back fault injection testing in model-based development;understanding the effects of data corruption on application behaviour based on data characteristics;a multi-layer anomaly detector for dynamic service-based systems;safety case driven development for medical devices;towards an international security case framework for networked medical devices;systems-theoretic safety assessment of robotic telesurgical systems;risk classification of data transfer in medical systems;requirement engineering for functional alarm system for interoperable medical devices;the safety requirements decomposition pattern;automatic architecture hardening using safety patterns;a model for safety case confidence assessment;quantifying risks to data assets using formal metrics in embedded system design;barriers to the use of intrusion detection systems in safety-critical applications and organisational, political and technical barriers to the integration of safety and cyber-security incident reporting systems.

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4th international conference on Smart Cities, Green Technologies, and Intelligent Transport systems, SMARTGREENS 2015 and 1st international conference on Vehicle Technology and Intelligent Transport systems, VEHITS 2015

4th International Conference on Smart Cities, Green Technolo...

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4th international conference on Smart Cities, Green Technologies, and Intelligent Transport systems, SMARTGREENS 2015

ISBN: (纸本)9783319277523

The proceedings contain 17 papers. The special focus in this conference is on Smart Cities and Green ICT systems. The topics include: Chances and risks of energy efficient urban development;bases for the assessment of smart city projects;constructing human smart cities;an open platform for children’s independent mobility;architectures and requirements for the development of smart cities;daily practices in automated areas;introducing flexibility into data centers for smart cities;test suite for a pedestrian simulator based on different scenarios;voltage control in low voltage grids with distributed energy resources;a sensitivity based approach for efficient PMU deployment on smart grid;using flexibility information for planning the energy demand of households;laser scanner and camera fusion for automatic obstacle classification in ADAS application;vehicle routing to minimizing hybrid fleet fuel consumption;service oriented big data management for transport;an integrated architecture for simulation and modeling of smalland medium-sized transportation and communication networks;privacy endangerment from protocol data sets in VANETs and countermeasures.

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Puffin: An embedded domain-specific language for existing unstructured hydrodynamics codes 5

Puffin: An embedded domain-specific language for existing un...

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5th international Workshop on Domain-Specific Languages and High-Level Frameworks for High Performance Computing, WOLFHPC 2015

作者： Earl, Christopher Lawrence Livermore National Laboratory United States

ISBN: (纸本)9781450340168

In this paper, we present Puffin, a domain-specific language embedded in C++98 for incremental adoption in existing unstructured hydrodynamics codes. Because HPC systems with heterogeneous architectures (traditional CPUs, GPUS, Xeon Phis, etc.) are becoming increasingly common, developers of existing HPC software projects need performance across multiple architectures. While Puffin is not yet complete and only supports CPU execution so far, our aim for Puffin is to provide performance portability to existing un- structured hydrodynamics simulation projects. Our preliminary results focus on two topics. First, we show what the costs of using Puffin are. Adopting Puffin has a initial cost of rewriting existing code into Puffin. Using Puffin has the ongoing costs of increased compilation times (2-3X slower) and runtime overhead (0-11% slower). Second, we show the current benefits of using Puffin and mention the potential future benefits. We show how Puffin can gradually be adopted into an existing project, by doing so with the existing test application, LULESH 2.0. We show a reduction in code length by porting code to Puffin. © 2015 ACM.

关键词： Costs

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Statistical verification of dynamical systems using set oriented methods 18

Statistical verification of dynamical systems using set orie...

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18th ACM international conference on Hybrid systems: Computation and Control, HSCC 2015

作者： Wang, Yu Roohi, Nima West, Matthew Viswanathan, Mahesh Dullerud, Geir E. Coordinated Science Laboratory University of Illinois UrbanaChampaign United States Department of Computer Science University of Illinois UrbanaChampaign United States Department of Mechanical Science and Engineering University of Illinois UrbanaChampaign United States

ISBN: (纸本)9781450334334

modeling, analyzing and verifying real physical systems has long been a challenging task since the state space of the systems is usually infinite and the dynamics of the systems is generally nonlinear and stochastic. In this work, we employ an extension of linear temporal logic (LTL) to describe the behavior of discrete-time nonlinear stochastic systems;this extension is so-called linear inequality LTL (iLTL) which allows for atomic propositions that are linear inequalities on state spaces. To statistically verify iLTL formulas on the systems, we first reformulate discrete-time nonlinear stochastic dynamical systems into Markov processes on their continuous state spaces and then reduce them to discrete-time Markov chains (DTMC) using set-oriented methods. Furthermore, a statistical verification algorithm is proposed to verify iLTL formulas on the reduced systems. The correctness of this statistical verification algorithm is checked both by theoretical analysis and the simulation of a fluid problem. We will show in the successive work that the framework extends to hybrid systems, which is a significant motivation for the approach taken. © 2015 ACM.

关键词： Hybrid systems

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3rd international conference on Model-Driven Engineering and Software Development, MODELSWARD 2015

3rd International Conference on Model-Driven Engineering and...

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3rd international conference on Model-Driven Engineering and Software Development, MODELSWARD 2015

ISBN: (纸本)9783319278681

The proceedings contain 25 papers. The special focus in this conference is on modeling Languages, Tools and architectures. The topics include: Realizing a conceptual framework to integrate model-driven engineering, software product line engineering, and software configuration management;composition of heterogeneous modeling languages;a model-driven approach for the generation of customizable model migrations;parallel application development using architecture view driven model transformations;runtime translation of model-level queries to persistence-level;integration of handwritten and generated object-oriented code;a framework for metamodel composition and adaptation with conformance-preserving model migration;a textual domain-specific language based on the UML testing profile;metamodel and model composition by integration of operational semantics;computability assurance for UML Template Binding;current limitations and proposed improvements;an approach to define and apply collaboration process patterns for software development;an ontology-based process editor for generating model mapping in tool integration;using model driven engineering to support multi-paradigms security analysis;designing safe and secure embedded and cyber-physical systems with sysML-sec;methodologies, processes and platforms architecture optimization with sysML modeling;capturing semantics to bridge the gap between complex data models and object models;the interface-modular method for global system behaviour specification;a textual domain-specific language based on the UML testing profile;metamodel and model composition by integration of operational semantics;an approach to define and apply collaboration process patterns for software development and an ontology-based process editor for generating model mapping in tool integration.

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Rapid prototyping and Design Space Exploration methodologies for many-accelerator systems

Rapid prototyping and Design Space Exploration methodologies...

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international conference on Field Programmable Logic and Applications

作者： Efstathios Sotiriou-Xanthopoulos Sotirios Xydis Kostas Siozios George Economakos Dimitrios Soudris School of Electrical and Computer Engineering National Technical University of Athens Athens Greece

The ever-growing design complexity of modern embedded systems and the need for lower energy consumption have lead to design techniques which target to bridge the gap between the designer's productivity and the design complexity. In particular, Virtual Prototyping enables the system modeling and simulation in multiple abstraction levels, while the automated Design Space Exploration (DSE) targets to find optimized design solutions in a reasonable time. However, there is the need for more efficient techniques for prototyping and co-simulation, as the rapid simulation has become a stringent requirement. In addition, as emerging heterogeneous architectures expose even higher design complexity, typical DSE techniques may not achieve high-quality design solutions. Towards this direction, the proposed design flow introduces (a) a set of prototyping techniques which target to faster but accurate simulation, also supporting the system co-simulation with other environments, and (b) a number of DSE methodologies for high-complexity computation and communication architectures.

关键词： Hardware Three-dimensional displays Virtual prototyping Software computer architecture Computational modeling Complexity theory

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Agent-Based High-Performance simulation of Biological systems on the GPU

Agent-Based High-Performance Simulation of Biological System...

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IEEE international conference on High Performance Computing and Communications (HPCC)

作者： Savas Konur Mariam Kiran Marian Gheorghe Mark Burkitt Florentin Ipate School of Electrical Engineering and Computer Science University of Bradford UK Department of Computer Science University of Sheffield Sheffield UK Department of Computer Science University of Bucharest Bucharest Romania

simulation of biological systems are computationally demanding due to the large scale reaction networks of bacterial cells. This scalability issue escalates, in particular, when bacterial colonies, formed by many individual cells, are simulated. Agent-based modelling environments on parallel architectures, such as the FLAME (Flexible Large-scale Modelling Environment) framework, are good candidates to simulate such systems, but due to the complex nature of cellular systems more advance technology is needed. In this paper, we utilise FLAME GPU, extending FLAME with a high performance graphics processing unit, to simulate a pulse generator, a typical multicellular synthetic biology system. This system is specified using a membrane computing model. We also illustrate the performance improvement of FLAME GPU over FLAME.

关键词： Fires Graphics processing units Computational modeling Biological system modeling Microorganisms Biomembranes Pulse generation

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Proceedings of WOLFHPC 2015: 5th international Workshop on Domain-Specific Languages and High-Level Frameworks for High Performance Computing - Held in conjunction with SC 2015: The international conference for High Performance Computing, Networking, Storage and Analysis

Proceedings of WOLFHPC 2015: 5th International Workshop on D...

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5th international Workshop on Domain-Specific Languages and High-Level Frameworks for High Performance Computing, WOLFHPC 2015

ISBN: (纸本)9781450340168

The proceedings contain 7 papers. The topics discussed include: FDPS: a novel framework for developing high-performance particle simulation codes for distributed-memory systems;Puffin: an embedded domain-specific language for existing unstructured hydrodynamics codes;enhancing domain specific language implementations through ontology;reducing overhead in the Uintah framework to support short-lived tasks on GPU-heterogeneous architectures;optimizing the LULESH stencil code using concurrent collections;SDSLc: a multi-target domain-specific compiler for stencil computations;and from DSL to HPC component-based runtime: a multi-stencil DSL case study.

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