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IMOTO, Yusuke

IMOTO, Yusuke

IMOTO, Yusuke

Affiliation: Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University Institute for Advanced Study(KUIAS), Kyoto University, Japan

Position: Associate Professor

Degree: Ph.D (mathematics)

Research keywords: Applied mathematics, Numerical analysis for partial differential equations, Computational fluid dynamics, Hyper-dual numbers, Topological data analysis, High-dimensional statistics, Statistical causal discovery.

e-mail：imoto.yusuke.4e * kyoto-u.ac.jp (change * to ＠)

Curriculum Vitae / GitHub / X (Twitter)

JAPANESE

Recent Topics / News

[Pless release] Detecting topology and flow of cell differentiation

[Pless release] Clearing the mist hiding the genome

[Poster] Landscape Data Analysis; from Life Science to Meteorology

Research Topics

  1. Numerical Analysis of Particle Methods and Application into Engineering and Disaster Science.
  2. Theoretical Study of Hyper-Dual Numbers and Application to Material Science.
  3. Data Science for Single-cell Biology.
  4. Data Science for Meteorology and Earth Science.
Dam-break simulation by a particle method.
Dam-break simulation by a particle method [PM1, PM2, PM3, PM4, PM5, PM6, PM7, PM8]
 
Image of dual number [HDN1, HDN2] 
Image of dual number [HDN1, HDN2]
Noise reduction of single-cell data [RECODE1, RECODE2]
Noise reduction of single-cell data [RECODE1, RECODE2]

Single-cell data analysis by topological data analysis [TDA1, TDA2, TDA3]
Single-cell data analysis by topological data analysis [TDA1, TDA2, TDA3]

Publications

  1. Topological Node2vec: Enhanced Graph Embedding via Persistent Homology. [ journal ]
    Y. Hiraoka, Y Imoto, K. Meehan*, T. Lacombe, T. Yachimura.
    Journal of Machine Learning Research, Vol. 25, 134, pp.1–26, 2024.
  2. V-Mapper: topological data analysis for high-dimensional data with velocity. [ journal ]
    Y Imoto*, Y Hiraoka.
    Nonlinear Theory and Its Applications (NOLTA), Vol.E14-N (2), pp. 92–105, 2023.
  3. Resolution of the curse of dimensionality in single-cell RNA sequencing data analysis.[preprint/journal]
    Y Imoto, T Nakamura, E G Escolar, M Yoshiwaki, Y Kojima, Y Yabuta, Y Katou, T Yamamoto, Y Hiraoka*, M Saitou*.
    Life Science Alliance, Vol. 5 (12), 2022.
  4. Nucleome programming for the foundation of totipotency in mammalian germline development.[ journal ]
    M Nagano, B Hu, S Yokobayashi, A Yamamura, F Umemura, M Coradin, H Ohta, Y Yabuta, Y Ishikura, I Okamoto, H Ikeda, N Kawahira, Y Nosaka, S Shimizu, Y Kojima, K Mizuta, T Kasahara, Y Imoto, K Meehan, R Stocsits, G Wutz, Y Hiraoka, Y Murakawa, T Yamamoto, K Tachibana, J-M Peters, L A Mirny, B A Garcia, J Majewski, M Saitou*. The EMBO Journal, e110600, 2022.
  5. Difference between smoothed particle hydrodynamics and moving particle semi-implicit operators[ journal(open access) ]
    Y Imoto*.
    Computer Methods in Applied Mechanics and Engineering, Vol. 395, 115012, 2022.
  6. Hyper-dual number-based numerical differentiation of eigensystems. [ journal ]
    M Fujikawa*, M Tanaka, N Mitsume, Y Imoto*.
    Computer Methods in Applied Mechanics and Engineering, Vol. 390, 114452, 2022.
  7. Fundamental theorem of matrix representations of hyper-dual numbers for computing higher-order derivatives. [ journal ]
    Y Imoto*, N Yamanaka, T Uramoto, M Tanaka, M Fujikawa, N Mitsume.
    JSIAM Letters, Vol. 12, pp. 29–32, 2020.
  8. Truncation error estimates of approximate operators in a generalized particle method.[ journal / preprint ]
    Y Imoto*.
    Japan Journal of Industrial and Applied Mathematics, Vol. 37, pp. 565–598, 2020.
  9. Convergence study and optimal weight functions of an explicit particle method for the incompressible Navier–Stokes equations. [ journal / preprint ]
    Y Imoto, S Tsuzuki, D Nishiura.
    Computational Particle Mechanics, Vol. 6 (4), pp. 671–694, 2019.
  10. Improvements in highly viscous fluid simulation using a fully implicit SPH method.[ journal ]
    D Morikawa*, M Asai, N Idris, Y Imoto, M Isshiki.
    Computational Particle Mechanics, Vol. 6 (4), pp. 529–544, 2019.
  11. Unique solvability and stability analysis for incompressible smoothed particle hydrodynamics method.[ journal / preprint ]
    Y Imoto*.
    Computational Particle Mechanics, Vol. 6 (2), pp. 297–309, 2019.
  12. Unique solvability and stability of a generalized particle method for a Poisson equation in discrete Sobolev norms.[ journal / preprint ]
    Y Imoto*.
    Applications of Mathematics, Vol. 64 (1), pp. 33–43, 2019.
  13. Truncation error estimates of approximate differential operators of a particle method based on the Voronoi decomposition.[ journal ]
    Y Imoto*, D Tagami.
    JSIAM Letters, Vol. 9, pp. 69–72, 2017.
  14. A truncation error estimate of the interpolant of a particle method based on the Voronoi decomposition.[ journal ]
    Y Imoto*, D Tagami. JSIAM Letters, Vol. 8, pp. 29–32, 2016.

*corresponding author(s)

Preprints

  1. Curse of Dimensionality on Persistence Diagrams [ link ]
    Y Hiraoka, Y Imoto, S Kanazawa, E Liu*.
    arXiv:2404.18194, submitted April 28, 2024.
  2. Comprehensive Noise Reduction in Single-Cell Data with the RECODE Platform. [link]
    Y Imoto*.
    bioRxiv:20.1101/2024.04.18.590054, submitted April 18, 2024.
  3. scEGOT: Single-cell trajectory inference framework based on entropic Gaussian mixture optimal transport. [link]
    T Yachimura, H Wang, Y Imoto, M Yoshida, S Tasaki, Y Kojima, Y Yabuta, M Saitou, Y Hiraoka.
    bioRxiv:2023.09.11.557102, 2023.

*corresponding author(s)

Research Grants & Projects

Principal Investigator

  1. FOREST（創発） in Japan science and technology agency (JST), 4/2024–3/2032, total amount: 50,000K JPY.
  2. PRESTO（さきがけ） in Japan science and technology agency (JST), Multi-resolution structural analysis system for cell differentiation, JPMJPR2021, 11/2020–3/2024, total amount: 40,000K JPY. [ link ]
  3. Grant-in-Aid for Young Scientists (B) in Japan Society for the Promotion of Science (JSPS)
    , A development of a particle method with high accuracy for flow problems and its mathematical justification (No. 17K17585), 4/2017–3/2021, total amount: 4,420K JPY. [ link ]
  4. General Joint Research Projects in Joint Usage/Research Center for Interdisciplinary Large-scale Information Infrastructures (JHPCN), Constructions of fundamental theory in particle methods and their expansion to a large-scale simulator, 4/2018–3/2019. [ link ]
  5. General Joint Research Projects in Joint Usage/Research Center for Interdisciplinary Large-scale Information Infrastructures (JHPCN), Developments of particle methods with high accuracy and their applications to large-scale computational fluid dynamics, 4/2017–3/2018. [ link ]

Co-Investigator / collaborator

  1. Moonshot Goal8 Feasibility Study in Japan science and technology agency(JST), Quantifying Weather Controllability and Mitigatable Flood Damage Based on Ensemble Weather Forecast, PI: Shunji Kotsuki, 06/2022–03/2025, total amount: 2,250K JPY.
  2. General Joint Research Projects in Joint Usage/Research Center for Interdisciplinary Large-scale Information Infrastructures (JHPCN), Development of a Powerful Tool for the Effective Particle Simulations of Debris Flows Using Dynamic Load Balance on a GPU Supercomputer., PI: Dr. Satori Tsuzuki, 4/2016–3/2017. [ link ]
  3. General Joint Research Projects in Joint Usage/Research Center for Interdisciplinary Large-scale Information Infrastructures (JHPCN), Large-scale Particle Simulations using Dynamic Load Balance on a GPU Supercomputer II — Application to Fluid-Structure Interaction, PI: Takayuki Aoki, 4/2015–3/2016. [ link ]
  4. JST CREST “Development of a Numerical Library based on Hierarchical Domain Decomposition for Post Petascale Simulation”, PI: Prof. Ryuji Shioya, 4/2012–3/2017. [ link ]

Awards

  1. JSIAM best paper award (JSIAM Letters).
    Y Imoto, D Tagami.
    The Japan society for industrial and applied mathematics (JSIAM), September 10, 2020.
  2. The 2018 MSJ Prize for Excellent Applied Mathematicians.</strong >
    Y Imoto.
    The Mathematical Society of Japan (MSJ), March 18, 2019. [ link ]
  3. Presentation award on JSIAM Spring meeting 2018.
    Y Imoto.
    The Japan society for industrial and applied mathematics (JSIAM), June 2018[ link ]
  4. Kyushu University student award (research).
    Y Imoto.
    Kyushu University, March 25, 2016.
  5. resentation award on applied mechanics symposium 2015.</strong >
    Y Imoto.
    Applied mechanics committee of Japan society of civil engineers (JSCE), December 1, 2015. [ link ]
  6. Best CFD graphics award.
    S Tsuzuki, T Aoki, Y Imoto, D Tagami.
    The Japan society of fluid mechanics, December 10, 2014.
  7. Best poster award at JSIAM annual meeting 2013,
    Y Imoto, D Tagami.
    The Japan society for industrial and applied mathematics (JSIAM), September 10, 2013.
  8. IMI director’s award.
    Y Imoto.
    Institute of Mathematics for Industry, Kyushu University, October 10, 2012.