1,949 research outputs found

    Executable cancer models: successes and challenges

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    Making decisions on how best to treat cancer patients requires the integration of different data sets, including genomic profiles, tumour histopathology, radiological images, proteomic analysis and more. This wealth of biological information calls for novel strategies to integrate such information in a meaningful, predictive and experimentally verifiable way. In this Perspective we explain how executable computational models meet this need. Such models provide a means for comprehensive data integration, can be experimentally validated, are readily interpreted both biologically and clinically, and have the potential to predict effective therapies for different cancer types and subtypes. We explain what executable models are and how they can be used to represent the dynamic biological behaviours inherent in cancer, and demonstrate how such models, when coupled with automated reasoning, facilitate our understanding of the mechanisms by which oncogenic signalling pathways regulate tumours. We explore how executable models have impacted the field of cancer research and argue that extending them to represent a tumour in a specific patient (that is, an avatar) will pave the way for improved personalized treatments and precision medicine. Finally, we highlight some of the ongoing challenges in developing executable models and stress that effective cross-disciplinary efforts are key to forward progress in the field

    An investigation into the use of B-Nodes and state models for computer network technology and education

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    This thesis consists of a series of internationally published, peer reviewed, conference research papers and one journal paper. The papers evaluate and further develop two modelling methods for use in Information Technology (IT) design and for the educational and training needs of students within the area of computer and network technology. The IT age requires technical talent to fill positions such as network managers, web administrators, e-commerce consultants and network security experts as IT is changing rapidly, and this is placing considerable demands on higher educational institutions, both within Australia and internationally, to respond to these changes

    Adaptive heterogeneous parallelism for semi-empirical lattice dynamics in computational materials science.

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    With the variability in performance of the multitude of parallel environments available today, the conceptual overhead created by the need to anticipate runtime information to make design-time decisions has become overwhelming. Performance-critical applications and libraries carry implicit assumptions based on incidental metrics that are not portable to emerging computational platforms or even alternative contemporary architectures. Furthermore, the significance of runtime concerns such as makespan, energy efficiency and fault tolerance depends on the situational context. This thesis presents a case study in the application of both Mattsons prescriptive pattern-oriented approach and the more principled structured parallelism formalism to the computational simulation of inelastic neutron scattering spectra on hybrid CPU/GPU platforms. The original ad hoc implementation as well as new patternbased and structured implementations are evaluated for relative performance and scalability. Two new structural abstractions are introduced to facilitate adaptation by lazy optimisation and runtime feedback. A deferred-choice abstraction represents a unified space of alternative structural program variants, allowing static adaptation through model-specific exhaustive calibration with regards to the extrafunctional concerns of runtime, average instantaneous power and total energy usage. Instrumented queues serve as mechanism for structural composition and provide a representation of extrafunctional state that allows realisation of a market-based decentralised coordination heuristic for competitive resource allocation and the Lyapunov drift algorithm for cooperative scheduling

    Resiliency in numerical algorithm design for extreme scale simulations

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    This work is based on the seminar titled ‘Resiliency in Numerical Algorithm Design for Extreme Scale Simulations’ held March 1–6, 2020, at Schloss Dagstuhl, that was attended by all the authors. Advanced supercomputing is characterized by very high computation speeds at the cost of involving an enormous amount of resources and costs. A typical large-scale computation running for 48 h on a system consuming 20 MW, as predicted for exascale systems, would consume a million kWh, corresponding to about 100k Euro in energy cost for executing 1023 floating-point operations. It is clearly unacceptable to lose the whole computation if any of the several million parallel processes fails during the execution. Moreover, if a single operation suffers from a bit-flip error, should the whole computation be declared invalid? What about the notion of reproducibility itself: should this core paradigm of science be revised and refined for results that are obtained by large-scale simulation? Naive versions of conventional resilience techniques will not scale to the exascale regime: with a main memory footprint of tens of Petabytes, synchronously writing checkpoint data all the way to background storage at frequent intervals will create intolerable overheads in runtime and energy consumption. Forecasts show that the mean time between failures could be lower than the time to recover from such a checkpoint, so that large calculations at scale might not make any progress if robust alternatives are not investigated. More advanced resilience techniques must be devised. The key may lie in exploiting both advanced system features as well as specific application knowledge. Research will face two essential questions: (1) what are the reliability requirements for a particular computation and (2) how do we best design the algorithms and software to meet these requirements? While the analysis of use cases can help understand the particular reliability requirements, the construction of remedies is currently wide open. One avenue would be to refine and improve on system- or application-level checkpointing and rollback strategies in the case an error is detected. Developers might use fault notification interfaces and flexible runtime systems to respond to node failures in an application-dependent fashion. Novel numerical algorithms or more stochastic computational approaches may be required to meet accuracy requirements in the face of undetectable soft errors. These ideas constituted an essential topic of the seminar. The goal of this Dagstuhl Seminar was to bring together a diverse group of scientists with expertise in exascale computing to discuss novel ways to make applications resilient against detected and undetected faults. In particular, participants explored the role that algorithms and applications play in the holistic approach needed to tackle this challenge. This article gathers a broad range of perspectives on the role of algorithms, applications and systems in achieving resilience for extreme scale simulations. The ultimate goal is to spark novel ideas and encourage the development of concrete solutions for achieving such resilience holistically.Peer Reviewed"Article signat per 36 autors/es: Emmanuel Agullo, Mirco Altenbernd, Hartwig Anzt, Leonardo Bautista-Gomez, Tommaso Benacchio, Luca Bonaventura, Hans-Joachim Bungartz, Sanjay Chatterjee, Florina M. Ciorba, Nathan DeBardeleben, Daniel Drzisga, Sebastian Eibl, Christian Engelmann, Wilfried N. Gansterer, Luc Giraud, Dominik G ̈oddeke, Marco Heisig, Fabienne Jezequel, Nils Kohl, Xiaoye Sherry Li, Romain Lion, Miriam Mehl, Paul Mycek, Michael Obersteiner, Enrique S. Quintana-Ortiz, Francesco Rizzi, Ulrich Rude, Martin Schulz, Fred Fung, Robert Speck, Linda Stals, Keita Teranishi, Samuel Thibault, Dominik Thonnes, Andreas Wagner and Barbara Wohlmuth"Postprint (author's final draft

    Developing a distributed electronic health-record store for India

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    The DIGHT project is addressing the problem of building a scalable and highly available information store for the Electronic Health Records (EHRs) of the over one billion citizens of India

    Approximate Computing Survey, Part II: Application-Specific & Architectural Approximation Techniques and Applications

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    The challenging deployment of compute-intensive applications from domains such Artificial Intelligence (AI) and Digital Signal Processing (DSP), forces the community of computing systems to explore new design approaches. Approximate Computing appears as an emerging solution, allowing to tune the quality of results in the design of a system in order to improve the energy efficiency and/or performance. This radical paradigm shift has attracted interest from both academia and industry, resulting in significant research on approximation techniques and methodologies at different design layers (from system down to integrated circuits). Motivated by the wide appeal of Approximate Computing over the last 10 years, we conduct a two-part survey to cover key aspects (e.g., terminology and applications) and review the state-of-the art approximation techniques from all layers of the traditional computing stack. In Part II of our survey, we classify and present the technical details of application-specific and architectural approximation techniques, which both target the design of resource-efficient processors/accelerators & systems. Moreover, we present a detailed analysis of the application spectrum of Approximate Computing and discuss open challenges and future directions.Comment: Under Review at ACM Computing Survey

    Continuous maintenance and the future – Foundations and technological challenges

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    High value and long life products require continuous maintenance throughout their life cycle to achieve required performance with optimum through-life cost. This paper presents foundations and technologies required to offer the maintenance service. Component and system level degradation science, assessment and modelling along with life cycle ‘big data’ analytics are the two most important knowledge and skill base required for the continuous maintenance. Advanced computing and visualisation technologies will improve efficiency of the maintenance and reduce through-life cost of the product. Future of continuous maintenance within the Industry 4.0 context also identifies the role of IoT, standards and cyber security
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