Accelerating Epistasis Detection - How oneAPI Supports Genetics Researchers

Advancements in genomics have accelerated significantly over the past few decades as compute technology has grown exponentially.  Professor Alessandra Ilic and Ricardo Nobre join Tony to talk about their research and how oneAPI is helping them accelerate research in the area of epistasis detection, which in genetics is when the effect of a gene or set of genes is affected by the presences or absence of another set of genes.

Guests:

Aleksandar Ilic is an Assistant Professor at the IST, University of Lisbon, and a Researcher of INESC-ID, Portugal. His research interests include high-performance and energy-efficient computing and modeling of parallel heterogeneous systems.

Ricardo Nobre is a PostDoc researcher at the INESC-ID R&D center in Lisbon/Portugal, as part of the High-Performance Computing Architectures and Systems (HPCAS) research area. His interests include high-performance computing, parallel programming, compilers and machine learning.

Aleksandar Ilic

Ricardo Nobre

 

Resources:

INESC-ID Achieves 9x Acceleration for Epistasis Disease Detection using oneAPI Tools and Intel Hardware

https://www.intel.com/content/www/us/en/developer/articles/case-study/inesc-id-9x-acceleration-for-disease-detection-app.html?wapkw=inesc

 

Source Code

https://github.com/hiperbio

 

Intel® Advisor

https://www.intel.com/content/www/us/en/developer/tools/oneapi/advisor.html

 

Intel® VTune™ Profiler

https://www.intel.com/content/www/us/en/developer/tools/oneapi/vtune-profiler.html

 

oneAPI

https://oneapi.io

https://www.intel.com/content/www/us/en/developer/tools/oneapi/overview.html

 

4th Gen Intel® Xeon® Scalable processors

Intel® Data Center GPU Max Series

 

References:

D. Marques, R. Campos, S. Santander-Jiménez, Z. Matveev, L. Sousa and A. Ilic. Unlocking Personalized Healthcare on Modern CPUs/GPUs: Three-way Gene Interaction Study. Paper presented in the 36th IEEE International Parallel & Distributed Processing Symposium (IPDPS) Lyon, France, 2022. DOI: 10.1109/IPDPS53621.2022.00023

R. Nobre, A. Ilic, S. Santander-Jiménez and L. Sousa. Fourth-Order Exhaustive Epistasis Detection for the xPU Era. Paper presented in the 50th International Conference on Parallel Processing (ICPP), Chicago, USA, 2021. DOI: 10.1145/3472456.3472509

D. Marques, A. Ilic, Z. A. Matveev, and L. Sousa. Application-driven Cache-aware Roofline Model. Future Generation Computer Systems 107 (2020): 257-273. DOI: 10.1016/j.future.2020.01.044

Ilic, F. Pratas, and L. Sousa. Cache-aware roofline model: Upgrading the loft. IEEE Computer Architecture Letters 13.1 (2013): 21-24. DOI: 10.1109/L-CA.2013.6

 

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