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-revied 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.
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, Masanori Kakuta, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama, "Large-scale Parallelization of Exome Analysis Pipeline on K-computer", ACLS International Summer School 2014, 2014/08 (poster session).

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, Associate degree.