Democratization of HPC Part 2: HPC in Personalized Non-invasive Clinical Treatment of Schizophrenia and Parkinson’s

By Wolfgang Gentzsch

October 4, 2018

This is the second in a series of articles demonstrating the growing acceptance of high-performance computing (HPC) in new user communities and application areas. In this article we present UberCloud use case #200 on how India’s National Institute of Health was able for schizophrenia – and potentially Parkinson’s disease, depression, and other brain disorders – to replace the current highly risky procedure of brain-invasive operations with an innovative technique of non-invasive low-risk treatment based on HPC that is also significantly more affordable.

This UberCloud Experiment #200 is based on computer simulations of non-invasive transcranial electro-stimulation of the human brain in schizophrenia, a serious mental illness characterized by illogical thoughts, bizarre behavior and speech, and delusions or hallucinations. This work represents an initial effort to demonstrate the high value of computational modeling and simulation in improving the clinical application of non-invasive electro-stimulation of the human brain in schizophrenia and other neuropsychiatric disorders. With the addition of HPC, clinicians can now precisely and non-invasively target regions of the brain without affecting major parts of the healthy brain. The HPC simulations have been collaboratively performed by NIMHANS National Institute of Mental Health & Neuro Sciences in India, Dassault SIMULIA, Advania Data Centers, and UberCloud, with sponsorship from Hewlett Packard Enterprise and Intel.

Figure 1: Schematic of electrical stimulation modalities.

The Problem

Neuromodulation refers to neural activity via an artificial stimulus such as an electrical current or a chemical agent. It may involve (highly risky) invasive approaches such as spinal cord stimulation or deep brain stimulation wherein electrodes are implanted directly on the nerves to be stimulated. It may also be performed non-invasively using methods such as electrical stimulation wherein external electrodes induce the required neural activity changes without the need for surgical implantation, but in which low intensity (mA) electrical currents are applied to the head via scalp-mounted electrodes, as shown in Figure 1 [Yavari 2017]. Stimulation with the negative pole (cathode) placed over a selected cortical region will decrease neuronal activity under the electrode, whereas stimulation with the positive pole (anode) will increase neuronal activity under the electrode. Therefore, this method may be used to increase cortical brain activity in specific brain areas that are under aroused, or alternatively decrease activity in areas that are overexcited. This procedure is simple, affordable, and portable, and the human is fully conscious and experiences minimal discomfort.

HPC Brain Simulation in the Advania Cloud

The power of multi-physics technology on the Advania Data Centers Cloud Platform allowed us to simulate deep brain stimulation by placing two sets of electrodes on the scalp to generate temporal interference deep inside the grey matter of the brain. However, a basic level of customization in post processing was required in making this methodology available to the clinician in real time and also reduce overall computational effort, where doctors can choose two pre-computed electrical fields of an electrode pair to generate temporal interference at specific regions of the grey matter of the brain.

After a satisfactory 3D head/brain model was developed, electrode placement was performed with Synopsys Simpleware ScanIP and CAD modules using the 10/10 international convention with the anode at AF3 and the cathode at CP5 (Figure 2). Finally, a high-resolution tetrahedral FE mesh (element size = 1mm3) was generated using the ScanIP and ScanFE modules.

Figure 2: International 10/10 convention (left) showing anode AF3 (red) and cathode CP5 (blue); subject-specific model (right).

A high-fidelity finite element human head model was considered including skin, skull, CSF, sinus grey & white matter, which demanded high computing resources to try various electrode configurations. Access to the HPE cluster at Advania and SIMULIA’s Abaqus 2017 code in an UberCloud HPC container empowered us to simulate numerous configurations of electrode placements and sizes. This also allowed us to study the sensitivity of electrode placements and sizes which was not possible before on our inhouse workstations and HPC systems.

During the final production phase, we have run 26 different SIMULIA Abaqus jobs – each representing a different electrode configuration – on the Advania/UberCloud HPC cluster of HPE ProLiant servers XL230 Gen9 with 2x Intel Broadwell E5-2683 v4 and Intel OmniPath interconnect. Each job contained 1.8M finite elements. On our own cluster with 16 cores, a single run took about 75 minutes, whereas on the UberCloud cluster a single run took about 28 minutes on 24 cores. Thus, we got a significant speedup running on UberCloud/Advania.

Figure 3 results are for two sets of electrical fields superimposed to produce temporal interference. Left: Electrical fields generated from electrodes placed on the left and right side of pre-temporal region of the scalp. Right: Electrical fields generated from electrodes placed on the left of the pre-temporal and rear region of the scalp.

Figure 3: The results show the sensitivity of the temporal interference region deep inside the brain based on two different electrode placements on the scalp.

Conclusion

The HPC application discussed in this case study demonstrates a breakthrough for deep brain stimulation in a non-invasive way which has the potential to replace the more painful/high risk brain surgeries such as in schizophrenia and Parkinson’s. The huge benefits of these HPC simulations are that (i) they predict the electrical current distribution with high resolution; (ii) allow for personalized and quantifiable treatment; (iii) facilitate electrode montage variations; and (iv) clinicians can devise the most effective treatment for a specific patient. HPCwire readers can download UberCloud Case Study #200 by Ganesh Venkatasubramanian from NIMHANS, Umashankar Gunasheker and Karl D’Souza from Dassault Systemes, and Wolfgang Gentzsch from UberCloud.

Subscribe to HPCwire's Weekly Update!

Be the most informed person in the room! Stay ahead of the tech trends with industy updates delivered to you every week!

Is Data Science the Fourth Pillar of the Scientific Method?

April 18, 2019

Nvidia CEO Jensen Huang revived a decade-old debate last month when he said that modern data science (AI plus HPC) has become the fourth pillar of the scientific method. While some disagree with the notion that statistic Read more…

By Alex Woodie

At ASF 2019: The Virtuous Circle of Big Data, AI and HPC

April 18, 2019

We've entered a new phase in IT -- in the world, really -- where the combination of big data, artificial intelligence, and high performance computing is pushing the bounds of what's possible in business and science, in w Read more…

By Alex Woodie with Doug Black and Tiffany Trader

Google Open Sources TensorFlow Version of MorphNet DL Tool

April 18, 2019

Designing optimum deep neural networks remains a non-trivial exercise. “Given the large search space of possible architectures, designing a network from scratch for your specific application can be prohibitively expens Read more…

By John Russell

HPE Extreme Performance Solutions

HPE and Intel® Omni-Path Architecture: How to Power a Cloud

Learn how HPE and Intel® Omni-Path Architecture provide critical infrastructure for leading Nordic HPC provider’s HPCFLOW cloud service.

powercloud_blog.jpgFor decades, HPE has been at the forefront of high-performance computing, and we’ve powered some of the fastest and most robust supercomputers in the world. Read more…

IBM Accelerated Insights

Bridging HPC and Cloud Native Development with Kubernetes

The HPC community has historically developed its own specialized software stack including schedulers, filesystems, developer tools, container technologies tuned for performance and large-scale on-premises deployments. Read more…

Interview with 2019 Person to Watch Michela Taufer

April 18, 2019

Today, as part of our ongoing HPCwire People to Watch focus series, we are highlighting our interview with 2019 Person to Watch Michela Taufer. Michela -- the General Chair of SC19 -- is an ACM Distinguished Scientist. Read more…

By HPCwire Editorial Team

At ASF 2019: The Virtuous Circle of Big Data, AI and HPC

April 18, 2019

We've entered a new phase in IT -- in the world, really -- where the combination of big data, artificial intelligence, and high performance computing is pushing Read more…

By Alex Woodie with Doug Black and Tiffany Trader

Interview with 2019 Person to Watch Michela Taufer

April 18, 2019

Today, as part of our ongoing HPCwire People to Watch focus series, we are highlighting our interview with 2019 Person to Watch Michela Taufer. Michela -- the Read more…

By HPCwire Editorial Team

Intel Gold U-Series SKUs Reveal Single Socket Intentions

April 18, 2019

Intel plans to jump into the single socket market with a portion of its just announced Cascade Lake microprocessor line according to one media report. This isn Read more…

By John Russell

BSC Researchers Shrink Floating Point Formats to Accelerate Deep Neural Network Training

April 15, 2019

Sometimes calculating solutions as precisely as a computer can wastes more CPU resources than is necessary. A case in point is with deep learning. In early stag Read more…

By Ken Strandberg

Intel Extends FPGA Ecosystem with 10nm Agilex

April 11, 2019

The insatiable appetite for higher throughput and lower latency – particularly where edge analytics and AI, network functions, or for a range of datacenter ac Read more…

By Doug Black

Nvidia Doubles Down on Medical AI

April 9, 2019

Nvidia is collaborating with medical groups to push GPU-powered AI tools into clinical settings, including radiology and drug discovery. The GPU leader said Monday it will collaborate with the American College of Radiology (ACR) to provide clinicians with its Clara AI tool kit. The partnership would allow radiologists to leverage AI techniques for diagnostic imaging using their own clinical data. Read more…

By George Leopold

Digging into MLPerf Benchmark Suite to Inform AI Infrastructure Decisions

April 9, 2019

With machine learning and deep learning storming into the datacenter, the new challenge is optimizing infrastructure choices to support diverse ML and DL workfl Read more…

By John Russell

AI and Enterprise Datacenters Boost HPC Server Revenues Past Expectations – Hyperion

April 9, 2019

Building on the big year of 2017 and spurred in part by the convergence of AI and HPC, global revenue for high performance servers jumped 15.6 percent last year Read more…

By Doug Black

The Case Against ‘The Case Against Quantum Computing’

January 9, 2019

It’s not easy to be a physicist. Richard Feynman (basically the Jimi Hendrix of physicists) once said: “The first principle is that you must not fool yourse Read more…

By Ben Criger

Why Nvidia Bought Mellanox: ‘Future Datacenters Will Be…Like High Performance Computers’

March 14, 2019

“Future datacenters of all kinds will be built like high performance computers,” said Nvidia CEO Jensen Huang during a phone briefing on Monday after Nvidia revealed scooping up the high performance networking company Mellanox for $6.9 billion. Read more…

By Tiffany Trader

ClusterVision in Bankruptcy, Fate Uncertain

February 13, 2019

ClusterVision, European HPC specialists that have built and installed over 20 Top500-ranked systems in their nearly 17-year history, appear to be in the midst o Read more…

By Tiffany Trader

Intel Reportedly in $6B Bid for Mellanox

January 30, 2019

The latest rumors and reports around an acquisition of Mellanox focus on Intel, which has reportedly offered a $6 billion bid for the high performance interconn Read more…

By Doug Black

It’s Official: Aurora on Track to Be First US Exascale Computer in 2021

March 18, 2019

The U.S. Department of Energy along with Intel and Cray confirmed today that an Intel/Cray supercomputer, "Aurora," capable of sustained performance of one exaf Read more…

By Tiffany Trader

Looking for Light Reading? NSF-backed ‘Comic Books’ Tackle Quantum Computing

January 28, 2019

Still baffled by quantum computing? How about turning to comic books (graphic novels for the well-read among you) for some clarity and a little humor on QC. The Read more…

By John Russell

IBM Quantum Update: Q System One Launch, New Collaborators, and QC Center Plans

January 10, 2019

IBM made three significant quantum computing announcements at CES this week. One was introduction of IBM Q System One; it’s really the integration of IBM’s Read more…

By John Russell

Deep500: ETH Researchers Introduce New Deep Learning Benchmark for HPC

February 5, 2019

ETH researchers have developed a new deep learning benchmarking environment – Deep500 – they say is “the first distributed and reproducible benchmarking s Read more…

By John Russell

Leading Solution Providers

SC 18 Virtual Booth Video Tour

Advania @ SC18 AMD @ SC18
ASRock Rack @ SC18
DDN Storage @ SC18
HPE @ SC18
IBM @ SC18
Lenovo @ SC18 Mellanox Technologies @ SC18
NVIDIA @ SC18
One Stop Systems @ SC18
Oracle @ SC18 Panasas @ SC18
Supermicro @ SC18 SUSE @ SC18 TYAN @ SC18
Verne Global @ SC18

IBM Bets $2B Seeking 1000X AI Hardware Performance Boost

February 7, 2019

For now, AI systems are mostly machine learning-based and “narrow” – powerful as they are by today's standards, they're limited to performing a few, narro Read more…

By Doug Black

The Deep500 – Researchers Tackle an HPC Benchmark for Deep Learning

January 7, 2019

How do you know if an HPC system, particularly a larger-scale system, is well-suited for deep learning workloads? Today, that’s not an easy question to answer Read more…

By John Russell

Arm Unveils Neoverse N1 Platform with up to 128-Cores

February 20, 2019

Following on its Neoverse roadmap announcement last October, Arm today revealed its next-gen Neoverse microarchitecture with compute and throughput-optimized si Read more…

By Tiffany Trader

France to Deploy AI-Focused Supercomputer: Jean Zay

January 22, 2019

HPE announced today that it won the contract to build a supercomputer that will drive France’s AI and HPC efforts. The computer will be part of GENCI, the Fre Read more…

By Tiffany Trader

Intel Launches Cascade Lake Xeons with Up to 56 Cores

April 2, 2019

At Intel's Data-Centric Innovation Day in San Francisco (April 2), the company unveiled its second-generation Xeon Scalable (Cascade Lake) family and debuted it Read more…

By Tiffany Trader

Oil and Gas Supercloud Clears Out Remaining Knights Landing Inventory: All 38,000 Wafers

March 13, 2019

The McCloud HPC service being built by Australia’s DownUnder GeoSolutions (DUG) outside Houston is set to become the largest oil and gas cloud in the world th Read more…

By Tiffany Trader

Intel Extends FPGA Ecosystem with 10nm Agilex

April 11, 2019

The insatiable appetite for higher throughput and lower latency – particularly where edge analytics and AI, network functions, or for a range of datacenter ac Read more…

By Doug Black

UC Berkeley Paper Heralds Rise of Serverless Computing in the Cloud – Do You Agree?

February 13, 2019

Almost exactly ten years to the day from publishing of their widely-read, seminal paper on cloud computing, UC Berkeley researchers have issued another ambitious examination of cloud computing - Cloud Programming Simplified: A Berkeley View on Serverless Computing. The new work heralds the rise of ‘serverless computing’ as the next dominant phase of cloud computing. Read more…

By John Russell

  • arrow
  • Click Here for More Headlines
  • arrow
Do NOT follow this link or you will be banned from the site!
Share This