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Primeur weekly 2016-06-27

Focus

Integration and co-design are key to reach capable exascale computing in the US ...

Sunway TaihuLight crunches its data near light-sparkling Lake Taihu ...

Exascale supercomputing

China's exascale supercomputer operational by 2020 ...

Quantum computing

Researchers refine method for detecting quantum entanglement ...

Focus on Europe

Crete becomes the Silicon-Island of high technology research and development ...

Bright Computing is debuting in France and unveils plans for the TERATEC Forum ...

Barcelona Supercomputing Center to issue new OmpSs release 16.06 ...

Quantum calculations broaden the understanding of crystal catalysts ...

Middleware

Jack Dongarra honoured with pair of prestigious supercomputing awards ...

Applications

McGill creates neuroscience research hub ...

Children's Mercy Kansas City accelerates major medical breakthroughs for critically ill children with powerful, scalable DDN storage ...

Real rocket science: How do hydrogen droplets behave when hydrogen-oxygen aerosol mixtures burn? ...

A better management of cerebrovascular accidents with supercomputing support ...

American Diabetes Association and IBM Watson Health join forces to reimagine how diabetes is prevented and managed ...

Illinois researchers part of the collaboration identifying a second gravitational wave event ...

Supercomputer changing genetic medicine in Africa ...

CWRU physicists deploy magnetic vortex to control electron spin ...

IBM Watson Health showcases progress tackling diabetes at American Diabetes Association's 76th Scientific Sessions ...

Medical imaging experts tap IBM and Watson to tackle cancer, diabetes, eye health, brain disease and heart disease ...

The Cloud

Mellanox enhances Cloud efficiency with 25Gb/s Ethernet connectivity ...

NetApp Flash accelerates Docker ecosystem with native storage integration ...

WorldQuant Ventures invests in Cycle Computing ...

NASA Johnson Space Center protects critical data with NetApp ...

JD.com and Mellanox join forces to drive e-commerce artificial intelligence ...

Local Motors debuts Olli, the first self-driving vehicle to tap the power of IBM Watson ...

VMware and IBM expand global Cloud partnership with desktop services ...

A better management of cerebrovascular accidents with supercomputing support


17 Jun 2016 Paris - Cerebrovascular accidents (CVA) are caused by a perturbation in the blood supply of the brain leading to a quick loss of cerebral functions, that is very often lethal. There are two categories of CVA: ischemic CVA (80% cases) resulting from the occlusion of a cerebral artery and haemorrhagic CVA (20% cases) provoked by a bleeding vessel. It is nowadays a major challenge in terms of public health care. In Western countries, one of 600 people suffers from a CVA each year and 120,000 cases are counted yearly in France. A project led by Frédéric Nataf, senior researcher at CNRS and INRIA, and his team addressed this problem and used amongst others the resources from GENCI and PRACE.

From a medical point of view, the detection and a fast characterisation of a CVA - ischemic or haemorrhagic, each having a specific and antinomian treatment - is crucial for patient survival. The faster the treatment is, the more brain damages are reversible and the chances of cure are high. If it is important to act promptly, it is just as crucial, once the urgent phase ended, to closely monitor the evolution of the CVA for adapting, if necessary, the treatment of the patient. But a continuous monitoring needs, theoretically, an image of the brain every fifteen minutes.

Yet, today, physicians can use two imaging systems of the brain: Magnetic resonance imaging (MRI) and cerebral tomogram (CT) scan. Even if these techniques are very precise - particularly MRI with a spatial resolution around a millimetre - and of high quality, their use is expensive, not well adapted to a prompt medical care as they need to be embedded in inside an ambulance, and indeed harmful in the case of a continuous monitoring with CT scan that measure the absorption of tissues by X rays.

This fully justifies the great interest of the project led by Frédéric Nataf, senior researcher at CNRS and INRIA, and his team. For the first time in the world, they have demonstrated on synthetic data the feasibility of a new imaging technique based on microwaves, allowing both the characterization of the CVA from the very first patient care in an ambulance and throughout his continuous monitoring during his hospitalisation. Winner of the 1st Bull Fourier 2015 award, the research team, gathering specialists of in Applied Mathematics from the Universities of Paris 6, Toulouse and Nice, and of in Electronics from Sophia Antipolis, has carried out its work in the context of an Agence Nationale de la Recherche (ANR) project in collaboration with an Austrian innovative SME, dedicated to biomedical imaging, EMTensor.

The electric properties of biological tissues are a great indicator of their functional and pathological conditions. Able to fully distinguish tissues, microwaves can image them, on the basis of differences in their dielectric properties. The principle of such a system is the following: The patient's head is equipped with a helmet consisting of electromagnetic antennas, that transmit data to a high performance computing centre for processing them and then sending the resulting images to doctors at the hospital where the patient will be treated. This type of imaging asks requires only a very reduced data acquisition phase - few milliseconds - with a satisfying spatial resolution and also with a level of harm lowest than that of a mobile phone. These characteristics make microwaves imaging very competitive even if a product for medicinal use doesn't exist yet.

It leverages several new technologies that are getting more and more common: Miniaturized antennas, mobile broadband technologies (4G, 5G, ...) and large-scale parallel computers with tens or hundreds of thousands of cores. From a computational point of view, it demands the fast solving of Maxwell equations with high contrasts in the coefficients in order to image the brain via the solving of an inverse problem.

For demonstrating the feasibility of such a technique, Frédéric Nataf and his team have developed a High Performance Computing approach which generates brain images before sending them back to the physician, all in less than 15 minutes.

In order to develop a numerically robust and precise methodology for microwaves imaging, three distinct research fields, must be controlled: optimisation, inverse problems and the simulation of the direct problem modelled using the Maxwell equations system. This last aspect implies mastering approximation and resolution methods - parallel solvers by domain decomposition, parallel computing. The precise simulation of a direct problem for a complex and highly heterogeneous medium in a frequency domain is a challenge in itself: EMTensor was led to develop its own simulation code for modelling the propagation of the electromagnetic field in a brain circled in a measurement chamber, not feasible with the existing commercial software.

The French team has capitalised on the tools developed by the researchers: The HPDDM library for domain decomposition and its interface with the FreeFem++ software (finite elements), that lead to a gain of several orders of magnitude in terms of development and execution time of the imaging algorithm. The core hours, firstly allocated by the computing centre of the Université Pierre et Marie Curie (UPMC) and then by Genci and PRACE on the massively parallel supercomputers, Turing at Idris (1,2 million hours in 2014) and Curie at TGCC (500,000 hours awarded by GENCI in 2015 and 3 million hours globally given through two PRACE allocations between 2012 and 2014), have been decisive to achieve the project.

EMTensor's experimental system consists in an electromagnetic reverberating chamber surrounded by five layers of 32 antennas each, able to work alternately as an emitter or a receptor.

The object to be reconstructed is introduced in the chamber. Alternately, each of the 160 antennas emits a signal at a fix frequency, typically 1 GHz. The electromagnetic field is propagated within the chamber and the object to be imaged regarding its properties. The other 159 antennas record the total field in the form of complex transmission coefficients traducing the amplitude and phase in each antenna. The electronic systems thus acquire the 160 measures in only around one millisecond. Each series of measures is represented in the form of a matrix of complex coefficients of 160x159 size. The inversion algorithm is aimed at reconstructing a brain image on the basis of these data.

For assessing the capacity of such a system to characterise a CVA and to monitor its evolution, a first step was to successfully compare the measure of data acquisition made with EMTensor's system with those numerically performed by the resolution of Maxwell equations on a 3D mesh (5 million degrees of freedom).

For the second step, researchers created synthetic data on a brain model coming from scan sections (362x434x362 voxels) and then simulated a haemorrhagic CVA. At last, they designed and tested an inversion algorithm for monitoring the evolution of the CVA, reconstructed by successive slices. Here, a slice corresponds to one layer of 32 antennas on the five equipping the experimental system.

Thanks to the use of parallelism, the reconstruction of each layer can be independently generated. Each reconstruction of a layer needs about thirty iterations.

An iteration asks several calculations, each one corresponding to the resolution of 32 3D Maxwell problems, that is one by emitting antenna. For each iteration, these 32 problems differ only by their right hand side. We can see here a second level of trivial parallelism, each resolution being independent.

Each Maxwell problem is solved by a domain decomposition method through the HPDDM library coupled to FreeFem++. The team has thus a third level of coarse grains parallelism well fitted to modern HPC architectures.

The different levels of parallelism and of arithmetic complexity involved in the inversion process make it a suitable candidate for generating images. The inversion algorithm helps reconstruct an image in 320 seconds on 2,048 computing cores of Curie. This restitution time, that can be further refined, already fits the physicians' objective to get an image every fifteen minutes for an efficient monitoring of the patient. It is only the case by using a massively parallel resource.

Frédéric Nataf and his team intend now to confirm their results with experimental data taken from twenty patients at the Département de neurologie of the University of Vienna, Austria between 2013 and 2014. They also want to improve the performance of their numerical methods for saving computing time: by accessing to very big decompositions - more than 10,000 subdomains, recycling information obtained during the convergence of the optimisation algorithm and exploring iterative methods by blocks in order to reduce the number of iterations.

The medical and industrial challenge of this work is very important. It is the first time that such a realistic study demonstrates the feasibility of microwaves imaging. Although it is less precise than RMI or CT scan, its low price, its reduced size and its lack of harm even in a continuous use could make microwaves imaging of the brain the equivalent of what echography (ultrasound imaging) brings to the exploration of other parts of the human body.

"This outstanding result is a new illustration, in one hand of the necessary complementarity of local, national and European resources and in the other, in a more general point of view, of the impact of numerical simulation and high performance computing on highly societal challenges such as health", Stéphane Requena, Chief Innovation Officer of Genci, concluded.

"Imaging CVAs with high performance computing" is authored by Frédéric Nataf, CNRS; Victorita Dolean, Université de Nice Sophia Antipolis and University of Strathclyde, UK; Frédéric Hecht, Université Pierre et Marie Curie; Pierre Jolivet, CNRS; and Pierre-Henri Tournier, Inria.

Source: PRACE

Back to Table of contents

Primeur weekly 2016-06-27

Focus

Integration and co-design are key to reach capable exascale computing in the US ...

Sunway TaihuLight crunches its data near light-sparkling Lake Taihu ...

Exascale supercomputing

China's exascale supercomputer operational by 2020 ...

Quantum computing

Researchers refine method for detecting quantum entanglement ...

Focus on Europe

Crete becomes the Silicon-Island of high technology research and development ...

Bright Computing is debuting in France and unveils plans for the TERATEC Forum ...

Barcelona Supercomputing Center to issue new OmpSs release 16.06 ...

Quantum calculations broaden the understanding of crystal catalysts ...

Middleware

Jack Dongarra honoured with pair of prestigious supercomputing awards ...

Applications

McGill creates neuroscience research hub ...

Children's Mercy Kansas City accelerates major medical breakthroughs for critically ill children with powerful, scalable DDN storage ...

Real rocket science: How do hydrogen droplets behave when hydrogen-oxygen aerosol mixtures burn? ...

A better management of cerebrovascular accidents with supercomputing support ...

American Diabetes Association and IBM Watson Health join forces to reimagine how diabetes is prevented and managed ...

Illinois researchers part of the collaboration identifying a second gravitational wave event ...

Supercomputer changing genetic medicine in Africa ...

CWRU physicists deploy magnetic vortex to control electron spin ...

IBM Watson Health showcases progress tackling diabetes at American Diabetes Association's 76th Scientific Sessions ...

Medical imaging experts tap IBM and Watson to tackle cancer, diabetes, eye health, brain disease and heart disease ...

The Cloud

Mellanox enhances Cloud efficiency with 25Gb/s Ethernet connectivity ...

NetApp Flash accelerates Docker ecosystem with native storage integration ...

WorldQuant Ventures invests in Cycle Computing ...

NASA Johnson Space Center protects critical data with NetApp ...

JD.com and Mellanox join forces to drive e-commerce artificial intelligence ...

Local Motors debuts Olli, the first self-driving vehicle to tap the power of IBM Watson ...

VMware and IBM expand global Cloud partnership with desktop services ...