Profile

Kento Aoyama (M.Sc.) is a Ph.D. Student at Department of Computer Science, School of Computing, Tokyo Institute of Technology. Research interests include High Performance Computing, Parallel/Distributed/Cloud Computing, Container Virtualization, and Bioinformatics.

Affiliation

Experiences

Ph.D. Student

2016 - present
Tokyo Institute of Techonology

Research Internship

2017.9 - 2017.12
Swiss National Supercomputing Centre (CSCS), ETH Zurich

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: Agile Programming, Object Oriented Programming, Continuous Integration(CI), etc.
  • Infrastructure Engineering: Management of computing cluster and cloud computing environment, and deployment of linux containers (e.g. Docker, Shifter).
  • 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, a structural bioinformatics software for FFT-grid-based protein-protein docking. (C++/OpenMP/MPI/GPU)

MEGADOCK-Azure - MEGADOCK for general cloud computing environment (e.g. Azure) that provides massively parallel protein-protein docking system for every reseachers. (C++/OpenMP/MPI/GPU)

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]

Domestic Conferences (without peer review)

Kento Aoyama, Masahito Ohue, Yutaka Akiyama, "Survey and Performance Comparison of Container Technologies in Bioinformatics Field, IPSJ SIG Technical Report, 2017-BIO-54(47), pp.1–7. 2018.
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, "Improvements of the GPU accelerated Simulation for Mach Bands Generation Mechanism in Human Visual System Model", IEEJ Hokuriku Branch, B-5, 2010.

Poster Presentations

Kento Aoyama, Masahito Ohue, Yutaka Akiyama, "Comparison of the HPC Container Technologies for Bioinformatics Application", Real World Big-Data Computation Open Innovation Laboratory (RWBC-OIL) 1st Workshop, May. 2018.
Kento Aoyama, Yuki Yamamoto, Masahito Ohue, Yutaka Akiyama, "Large-Scale Parallelization of Cloud Native PPI-System using Container Virtualization", ACLS International Summer School 2017, Sep. 2017.
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

Runner-Up Award, ACLS International Summer School 2017 Group Work, 2017.
Outstanding Student Award, IPSJ Hokuriku Branch, 2010.

Graduation Thesis

Large-scale Parallelization of Exome Analysis Pipeline on K-computer
Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, M.Sc.
Large-scale Parallelization of Matrix-matrix Product in Double-double Precision using Fox Algorithm on GPU Cluster
Department of Computer Science, The University of Electro-Communications, B.Sc.
Improvements of the GPU accelerated Simulation for Mach Bands Generation Mechanism in Human Visual System Model
National Institute of Technology, Toyama College, A.Sc.