Profile

Kento Aoyama (M.Sc.) is a Ph.D. Student at Department of Computer Science, School of Computing, Tokyo Institute of Technology. His research interests include High Performance Computing, Parallel/Distributed/Cloud Computing, and Bioinformatics.
His research theme focuses on parallel/distributed performance of Container Virtualization in Bioinformatics application field.

Affiliation

Experiences

Ph.D. Student

2016 - present
Tokyo Institute of Techonology

Software Developer

2015 - 2016
Fujitsu Ltd.

M.Sc. in Computer Science

2013 - 2015
Tokyo Institute of Techonology

B.Sc. in Computer Science

2011 - 2013
The University of Electro-Communications

Relevant Skills

  • Software Development: My experience as a developer of enterprise products gave me skills as object oriented design pattern programming, Continuous Integration(CI), etc.
  • Infrastructure Engineering: Management of computing cluster and cloud computing environment, and deployment of application containers (e.g. Docker).
  • C, C++: High-performance programming skills as CUDA, OpenMP, MPI, etc. and algebra libraries(e.g. BLAS).
  • Java: Android Applications and other general object oriented programming.
  • Python, R, MATLAB: Statistical Analytics, Machine Learning, Computing Simulation.
  • UNIX system administration.

Projects

MEGADOCK - An ultra-high-performance protein-protein docking for heterogeneous supercomputers, which is a structural bioinformatics software for FFT-grid-based protein-protein docking. It supports multi-node GPU/MIC acceralations. (C++/CUDA/OpenMP/MPI)

MEGADOCK-Azure - MEGADOCK for general cloud computing environment (e.g. Microsoft Azure). It provides massively parallel protein-protein docking system for every reseachers.

GHOST-MP - A massively parallel sequence similarity search tool, searches for similar sequences among nucleotide query sequences and amino acid sequence database like BLASTX. (C++/OpenMP/MPI)

Publications

Peer-reviewed Domestic Journal Papers

Kento Aoyama, Masanori Kakuta, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama, "Development of Exome Analysis Pipeline on the K Computer", IPSJ Transactions on Advanced Computing System(ACS), No.9, Vol.2, pp.15-33, 2016. [IPSJ], [PDF]

Domestic Conferences (without peer review)

Kento Aoyama, Yuki Yamamoto, Masahito Ohue, Yutaka Akiyama, "Evaluation of Container Virtualized MEGADOCK System in Distributed Computing Environment", IPSJ SIG Technical Report, 2017-BIO-49(3), pp.1–8. 2017. [Slide]
Kento Aoyama, Masanori Kakuta, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama, "Large-scale Parallelization of Exome Analysis Pipeline on K-computer", IPSJ SIG Technical Report, 2014-BIO-38(33), pp.1–7. 2014.
Kento Aoyama, Kyouhei Akai, Junichi Akita, Akira Tsukada. "ヒト視覚系におけるマッハバンド発生機構の役割について", IEEJ Hokuriku Branch, B-5, 2010.

Poster Presentations

Kento Aoyama, Yuki Yamamoto, Masahito Ohue, Yutaka Akiyama, "High-Performance Protein-Protein Interaction Predictions on Distributed Containerized Environment", High Performance Computing Symposium 2017 (HPCS 2017), Jun. 2017.
Kento Aoyama, Masanori Kakuta, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama, "Large-scale Parallelization of Exome Analysis Pipeline on K-computer", ACLS International Summer School 2014, Aug. 2014.

Awards

Outstanding Student Award, IPSJ Hokuriku Branch, 2010.

Graduation Thesis

"エクソーム解析パイプラインのスーパーコンピュータ「京」による大規模並列化", Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, M.Sc.
"FoxアルゴリズムによるGPUクラスタ向け4倍精度行列-行列積計算", Department of Computer Science, The University of Electro-Communications, B.Sc.
"ヒト視覚系におけるマッハバンド発生機構の役割について", National Institute of Technology, Toyama College, A.Sc.