Kyoto University Chooses Intel Machine and Deep Learning Tech to Tackle Drug Discovery, Medicine and Healthcare Challenges

Kyoto University Graduate School of Medicine*, one of Asia’s leading research-oriented institutions, has recently chosen Intel® Xeon® Scalable processors to power its clinical genome analysis cluster and its molecular simulation cluster. These clusters will aid in Kyoto’s search for new drug discoveries and help reduce research and development costs.

The Intel Xeon Scalable platform offers potent performance for all types of artificial intelligence (AI). Intel’s optimizations for popular deep learning frameworks have produced up to 127 times1 performance gains for deep learning training and 198 times2 performance gains for deep learning inference for AI workloads running on Intel Xeon Scalable processors. Kyoto is one of many leading healthcare providers and research institutions that are working with Intel and using Intel artificial intelligence technology to tackle some of the biggest challenges in healthcare.

More: One Simple Truth about Artificial Intelligence in Healthcare: It’s Already Here (Navin Shenoy Editorial) | Shaping the Future of Healthcare through Artificial Intelligence (Event Video Replay) | Artificial Intelligence (Press Kit) | Advancing Data-Driven Healthcare Solutions (Press Kit)

“We are only at the beginning of solving these problems. We are continuing to push forward and work with industry-leading entities to solve even more,” said Arjun Bansal, vice president of the Artificial Intelligence Products Group and general manager of Artificial Intelligence Labs and Software at Intel Corporation. “For example, I’m happy to announce that Kyoto University has recently chosen Intel to power their clinical genome analysis cluster and their molecular simulation cluster. These clusters are to aid in their drug discovery efforts and should help reduce the R&D costs of testing different compounds and accelerate precision medicine by adopting Deep Learning techniques.”

It can take up to 15 years – and billions of dollars – to translate a drug discovery idea from initial inception to a market-ready product. Identifying the right protein to manipulate in a disease, proving the concept, optimizing the molecule for delivery to the patient, carrying out pre-clinical and clinical safety and efficacy testing are all essential, but ultimately the process takes far too long today.

Dramatic shifts are needed to meet the needs of society and a future generation of patients. Artificial intelligence presents researchers with an opportunity to do R&D differently – driving down the resources and costs to develop drugs and bringing the potential for a substantial increase in new treatments for serious diseases.

1 Performance estimates were obtained prior to implementation of recent software patches and firmware updates intended to address exploits referred to as “Spectre” and “Meltdown.”  Implementation of these updates may make these results inapplicable to your device or system.

Software and workloads used in performance tests may have been optimized for performance only on Intel microprocessors.  Performance tests, such as SYSmark and MobileMark, are measured using specific computer systems, components, software, operations and functions.  Any change to any of those factors may cause the results to vary.  You should consult other information and performance tests to assist you in fully evaluating your contemplated purchases, including the performance of that product when combined with other products. For more complete information visit http://www.intel.com/benchmarks

Source: Intel measured as of June 2017 Optimization Notice: Intel’s compilers may or may not optimize to the same degree for non-Intel microprocessors for optimizations that are not unique to Intel microprocessors. These optimizations include SSE2, SSE3, and SSSE3 instruction sets and other optimizations. Intel does not guarantee the availability, functionality, or effectiveness of any optimization on microprocessors not manufactured by Intel. Microprocessor-dependent optimizations in this product are intended for use with Intel microprocessors. Certain optimizations not specific to Intel microarchitecture are reserved for Intel microprocessors. Please refer to the applicable product User and Reference Guides for more information regarding the specific instruction sets covered by this notice.

Configurations for Inference throughput

Processor :2 socket Intel(R) Xeon(R) Platinum 8180 CPU @ 2.50GHz / 28 cores HT ON , Turbo ON Total Memory 376.46GB (12slots / 32 GB / 2666 MHz).CentOS Linux-7.3.1611-Core , SSD sda RS3WC080 HDD 744.1GB,sdb RS3WC080 HDD 1.5TB,sdc RS3WC080 HDD 5.5TB , Deep Learning Framework caffe version: f6d01efbe93f70726ea3796a4b89c612365a6341 Topology :googlenet_v1 BIOS:SE5C620.86B.00.01.0004.071220170215 MKLDNN: version: ae00102be506ed0fe2099c6557df2aa88ad57ec1 NoDataLayer. Measured: 1190 imgs/sec vs Platform: 2S Intel® Xeon® CPU E5-2699 v3 @ 2.30GHz (18 cores), HT enabled, turbo disabled, scaling governor set to “performance” via intel_pstate driver, 256GB DDR4-2133 ECC RAM. CentOS Linux release 7.3.1611 (Core), Linux kernel 3.10.0-514.el7.x86_64. OS drive: Seagate* Enterprise ST2000NX0253 2 TB 2.5″ Internal Hard Drive. Performance measured with: Environment variables: KMP_AFFINITY=’granularity=fine, compact,1,0‘, OMP_NUM_THREADS=36, CPU Freq set with cpupower frequency-set -d 2.3G -u 2.3G -g performance. Deep Learning Frameworks: Intel Caffe: (http://github.com/intel/caffe/), revision b0ef3236528a2c7d2988f249d347d5fdae831236. Inference measured with “caffe time –forward_only” command, training measured with “caffe time” command. For “ConvNet” topologies, dummy dataset was used. For other topologies, data was stored on local storage and cached in memory before training. Topology specs from https://github.com/intel/caffe/tree/master/models/intel_optimized_models (GoogLeNet, AlexNet, and ResNet-50), https://github.com/intel/caffe/tree/master/models/default_vgg_19 (VGG-19), and https://github.com/soumith/convnet-benchmarks/tree/master/caffe/imagenet_winners (ConvNet benchmarks; files were updated to use newer Caffe prototxt format but are functionally equivalent). GCC 4.8.5, MKLML version 2017.0.2.20170110. BVLC-Caffe: https://github.com/BVLC/caffe, Inference & Training measured with “caffe time” command.  For “ConvNet” topologies, dummy dataset was used. For other topologies, data was st ored on local storage and cached in memory before training  BVLC Caffe (http://github.com/BVLC/caffe), revision 91b09280f5233cafc62954c98ce8bc4c204e7475 (commit date 5/14/2017). BLAS: atlas ver. 3.10.1.

2Configuration for training throughput:

Processor :2 socket Intel(R) Xeon(R) Platinum 8180 CPU @ 2.50GHz / 28 cores HT ON , Turbo ON Total Memory 376.28GB (12slots / 32 GB / 2666 MHz).CentOS Linux-7.3.1611-Core , SSD sda RS3WC080 HDD 744.1GB,sdb RS3WC080 HDD 1.5TB,sdc RS3WC080 HDD 5.5TB , Deep Learning Framework caffe version: f6d01efbe93f70726ea3796a4b89c612365a6341 Topology :alexnet BIOS:SE5C620.86B.00.01.0009.101920170742 MKLDNN: version: ae00102be506ed0fe2099c6557df2aa88ad57ec1 NoDataLayer. Measured: 1023 imgs/sec vs Platform: 2S Intel® Xeon® CPU E5-2699 v3 @ 2.30GHz (18 cores), HT enabled, turbo disabled, scaling governor set to “performance” via intel_pstate driver, 256GB DDR4-2133 ECC RAM. CentOS Linux release 7.3.1611 (Core), Linux kernel 3.10.0-514.el7.x86_64. OS drive: Seagate* Enterprise ST2000NX0253 2 TB 2.5″ Internal Hard Drive. Performance measured with: Environment variables: KMP_AFFINITY=’granularity=fine, compact,1,0‘, OMP_NUM_THREADS=36, CPU Freq set with cpupower frequency-set -d 2.3G -u 2.3G -g performance. Deep Learning Frameworks: Intel Caffe: (http://github.com/intel/caffe/), revision b0ef3236528a2c7d2988f249d347d5fdae831236. Inference measured with “caffe time –forward_only” command, training measured with “caffe time” command. For “ConvNet” topologies, dummy dataset was used. For other topologies, data was stored on local storage and cached in memory before training. Topology specs from https://github.com/intel/caffe/tree/master/models/intel_optimized_models (GoogLeNet, AlexNet, and ResNet-50), https://github.com/intel/caffe/tree/master/models/default_vgg_19 (VGG-19), and https://github.com/soumith/convnet-benchmarks/tree/master/caffe/imagenet_winners (ConvNet benchmarks; files were updated to use newer Caffe prototxt format but are functionally equivalent). GCC 4.8.5, MKLML version 2017.0.2.20170110. BVLC-Caffe: https://github.com/BVLC/caffe, Inference & Training measured with “caffe time” command.  For “ConvNet” topologies, dummy dataset was used. For other topologies, data was st ored on local storage and cached in memory before training  BVLC Caffe (http://github.com/BVLC/caffe), revision 91b09280f5233cafc62954c98ce8bc4c204e7475 (commit date 5/14/2017). BLAS: atlas ver. 3.10.1.

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