Basic Information

Professional Memberships

• The Japan Society for Computational Engineering and Science
• The Japan Society for Industrial and Applied Mathematics
• The Mathematical Society of Japan

Academic Degree

• 修士（数理学）(九州大学)
• 博士（数理学）(九州大学)

Research History

• From Apr. 2024, To Mar. 2025

  Kyoto University, FOREST Principal Investigator
• From Sep. 2022, To Present

  Kyoto University, Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University Institute for Advanced Study (KUIAS), Associate Professor
• From Nov. 2020, To Mar. 2024

  Japan Science and Technology Agency, PRESTO Researcher
• From Feb. 2019, To Aug. 2022

  Kyoto University, Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University Institute for Advanced Study (KUIAS), Assistant professor
• From Apr. 2016, To Jan. 2019

  Tohoku University, Tohoku Forum for Creativity, Assistant professor

Profile

• Profile

  数値解析と高次元データ解析が専門です。

ID,URL

• J-Global ID

  201601013589839798

• External link

  https://ashbi.kyoto-u.ac.jp/y-imoto/en/

researchmap URL

• https://researchmap.jp/7000017823

Research

Research Interests

• High-dimensional statistics
• Statistical Causal Discovery
• Topological Data Analysis
• Hyper-Dual Numbers
• Applied mathematics
• Computational Fluid Dynamics
• Numerical Analysis

Research Areas

• Informatics, Computational science, Computational Mechanics
• Natural sciences, Applied mathematics and statistics, Applied Mathematics
• Natural sciences, Basic mathematics, Applied Mathematics

Papers

• Geometric inference of cross-species transcriptome correspondence using Gromov-Wasserstein optimal transport

  Yuya Tokuta; Tomonori Nakamura; Kohei Fujiwara; Masanori Imamura; Masahiro Nagano; Mitinori Saitou; Yusuke Imoto; Yasuaki Hiraoka

  bioRxiv, 24 Oct. 2025, Corresponding author

  
• Accurate highly variable gene selection using RECODE in scRNA-seq data analysis

  Yusuke Imoto

  bioRxiv, 27 Jun. 2025, Lead author, Last author, Corresponding author

  
• Filtrations Indexed by Attracting Levels and their Applications

  Yusuke Imoto; Tomoo Yokoyama

  arXiv, 23 Jun. 2025

  
• Meteorological Landscape of Tropical Cyclone

  Pascal Oettli; Keita Tokuda; Yusuke Imoto; Shunji Kotsuki

  EGUsphere, 14 Apr. 2025, Corresponding author

  
• Single-cell multiomic analysis revealed the differentiation, localization, and heterogeneity of IL10+ Foxp3– follicular T cells in humans

  Shusei Fujioka; Mayu Fujioka; Yusuke Imoto; Yasuyo Harada; Hiroyuki Yoshitomi; Masato Kubo; Yasuaki Hiraoka; Hideki Ueno

  International Immunology, 21 Mar. 2025, Peer-reviewed

  
• The balance between IFN-γ and ERK/MAPK signaling activities ensures lifelong maintenance of intestinal stem cells

  May Nakajima-Koyama; Mio Kabata; Joonseong Lee; Yuko Sogabe; Satoko Sakurai; Akira Hirota; Mizuki Kimura; Tomonori Nakamura; Yusuke Imoto; Kohei Kometani; Yoko Hamazaki; Yasuaki Hiraoka; Mitinori Saitou; Eisuke Nishida; Takuya Yamamoto

  Cell Reports, Mar. 2025, Peer-reviewed

  Access this paper :

  
• Hyper-Dual Number-Based Numerical Differentiation —Theory and Application—

  Yusuke Imoto

  Bulletin of the Japan Society for Industrial and Applied Mathematics, Dec. 2024, Invited, Lead author, Last author, Corresponding author

  
• Numerical Computation of High Reynolds Number Cavity Flow Using SPH Method with Stream Function and Vorticity Formulation

  Yusuke Imoto

  arXiv, Aug. 2024, Lead author, Last author, Corresponding author

  
• Curse of dimensionality on persistence diagrams

  Yasuaki Hiraoka; Yusuke Imoto; Shu Kanazawa; Enhao Liu

  Foundations of Data Science, Mar. 2026, Peer-reviewed

  
• Comprehensive noise reduction in single-cell data with the RECODE platform

  Yusuke Imoto

  Cell Reports Methods, 21 Oct. 2025, Peer-reviewed, Lead author, Last author, Corresponding author

  
• Topological Node2vec: Enhanced Graph Embedding via Persistent Homology

  Yasuaki Hiraoka; Yusuke Imoto; Killian Meehan; Théo Lacombe; Toshiaki Yachimura

  Journal of Machine Learning Research, Apr. 2024, Peer-reviewed

  
• scEGOT: single-cell trajectory inference framework based on entropic Gaussian mixture optimal transport

  Toshiaki Yachimura; Hanbo Wang; Yusuke Imoto; Momoko Yoshida; Sohei Tasaki; Yoji Kojima; Yukihiro Yabuta; Mitinori Saitou; Yasuaki Hiraoka

  BMC Bioinformatics, 23 Dec. 2024, Peer-reviewed

  
• V-Mapper: topological data analysis for high-dimensional data with velocity

  Yusuke Imoto; Yasuaki Hiraoka

  Nonlinear Theory and Its Applications, IEICE, 01 Apr. 2023, Peer-reviewed, Lead author, Corresponding author

  
• Nucleome programming is required for the foundation of totipotency in mammalian germline development.

  Masahiro Nagano; Bo Hu; Shihori Yokobayashi; Akitoshi Yamamura; Fumiya Umemura; Mariel Coradin; Hiroshi Ohta; Yukihiro Yabuta; Yukiko Ishikura; Ikuhiro Okamoto; Hiroki Ikeda; Naofumi Kawahira; Yoshiaki Nosaka; Sakura Shimizu; Yoji Kojima; Ken Mizuta; Tomoko Kasahara; Yusuke Imoto; Killian Meehan; Roman Stocsits; Gordana Wutz; Yasuaki Hiraoka; Yasuhiro Murakawa; Takuya Yamamoto; Kikue Tachibana; Jan-Michel Peters; Leonid A Mirny; Benjamin A Garcia; Jacek Majewski; Mitinori Saitou

  The EMBO journal, 15 Jun. 2022, Peer-reviewed

  
• Difference between smoothed particle hydrodynamics and moving particle semi-implicit operators

  Yusuke Imoto

  Computer Methods in Applied Mechanics and Engineering, 15 May 2022, Peer-reviewed, Lead author, Last author, Corresponding author

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• Resolution of the curse of dimensionality in single-cell RNA sequencing data analysis

  Yusuke Imoto; Tomonori Nakamura; Emerson G Escolar; Michio Yoshiwaki; Yoji Kojima; Yukihiro Yabuta; Yoshitaka Katou; Takuya Yamamoto; Yasuaki Hiraoka; Mitinori Saitou

  Life Science Alliance, Aug. 2022, Peer-reviewed, Lead author

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• Hyper-dual number-based numerical differentiation of eigensystems

  Masaki Fujikawa; Masato Tanaka; Naoto Mitsume; Yusuke Imoto

  Computer Methods in Applied Mechanics and Engineering, 15 Feb. 2022, Peer-reviewed, Last author, Corresponding author

  
• Development of Bottom Boundary-Fitted MPS Method

  Kyuya MATSUMOTO; Yusuke IMOTO; Mitsuteru ASAI; Naoto MITSUME

  Transactions of the Japan Society for Computational Engineering and Science, 29 Oct. 2021, Peer-reviewed

  
• A SELECTIVE DUAL VELOCITY ISPH METHOD DIVIDING INTO PHYSICAL AND TRANSPORT VELOCITY FOR FLUID-SOLID PARTICLE MULTIPHASE SIMULATIONS

  Takehiro FUJII; Mitsuteru ASAI; Yusuke IMOTO

  Journal of Japan Society of Civil Engineers, Ser. A2 (Applied Mechanics (AM)), 01 Feb. 2021, Peer-reviewed, Corresponding author

  
• Fundamental theorem of matrix representations of hyper-dual numbers for computing higher-order derivatives

  Yusuke Imoto; Naoya Yamanaka; Takeo Uramoto; Masato Tanaka; Masaki Fujikawa; Naoto Mitsume

  JSIAM Letters, 01 Jun. 2020, Peer-reviewed, Lead author, Corresponding author

  
• Truncation error estimates of approximate operators in a generalized particle method

  Yusuke Imoto

  Japan Journal of Industrial and Applied Mathematics (JJIAM), 03 May 2020, Peer-reviewed, Lead author, Corresponding author

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• A RATIONALE OF THE STABILIZED ISPH METHOD II –AN OPTIMIZATION OF RELAXATION COEFFICIENT BASED ON ERROR ESTIMATES–

  IMOTO Yusuke; ASAI Mitsuteru; FUJII Takehiro

  Journal of Japan Society of Civil Engineers, Ser. A2 (Applied Mechanics (AM)), 06 Feb. 2020, Peer-reviewed, Lead author, Corresponding author

  
• Formulation for an Ogden-type hyperelastic analysis with hyper dual numbers and its performance evaluation

  Masaki FUJIKAWA; Masato TANAKA; Yusuke IMOTO; Naoto MITSUME; Takeo URAMOTO; Naoya YAMANAKA

  Transactions of the JSME (in Japanese), 25 Jan. 2020, Peer-reviewed

  
• Convergence study and optimal weight functions of an explicit particle method for the incompressible Navier–Stokes equations

  Yusuke Imoto; Satori Tsuzuki; Daisuke Nishiura

  Computational Particle Mechanics, 23 Oct. 2019, Peer-reviewed, Lead author, Corresponding author

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• Improvements in highly viscous fluid simulation using a fully implicit SPH method

  Daniel Morikawa; Mitsuteru Asai; Nur Ain Idris; Yusuke Imoto; Masaharu Isshiki

  Computational Particle Mechanics, 01 Oct. 2019, Peer-reviewed

  
• Bingham flow model by fully implicit SPH and its application to reinforce underground caves

  Daniel Morikawa; Mitsuteru Asai; Nur’Ain Idris; Yusuke Imoto; Masaharu Isshiki

  Proceedings of the 2019 Rock Dynamics Summit (RDS 2019), 07 May 2019

  
• Unique solvability and stability analysis for incompressible smoothed particle hydrodynamics method

  Yusuke Imoto

  Computational Particle Mechanics, 17 Apr. 2019, Peer-reviewed, Lead author, Last author, Corresponding author

  
• Unique solvability and stability analysis of a generalized particle method for a Poisson equation in discrete Sobolev norms

  Yusuke Imoto

  Applications of Mathematics, 14 Feb. 2019, Peer-reviewed, Lead author, Last author, Corresponding author

  
• A rationale of the stabilized ISPH method - a derivation of a stabilization term from an energy minimization problem -

  Yusuke IMOTO; Mitsuteru ASAI

  Journal of Applied Mechanics, 31 Jan. 2019, Peer-reviewed, Lead author, Corresponding author

  
• Truncation error estimates of approximate differential operators of a particle method based on the Voronoi decomposition

  Yusuke Imoto; Daisuke Tagami

  JSIAM Letters, 2017, Peer-reviewed

  
• Error Estimates of Generalized Particle Methods for the Poisson and Heat Equations

  Yusuke Imoto

  Kyushu University, Mar. 2016, Peer-reviewed

  
• A truncation error estimate of the interpolant of a particle method based on the Voronoi decomposition

  Yusuke Imoto; Daisuke Tagami

  JSIAM Letters, 2016, Peer-reviewed

  
• A Parallel Computation for Voronoi Diagram and its Applications to SPH method.

  IMOTO Yusuke

  COMPSAFE2014 Proceedings, IASM & APACM, Apr. 2014

  
• UNIFIED NUMERICAL ANAYSIS BETWEEN THE EXTENDED DARCY'S LAW AND NAVIER-STOKES EQUATION BY USING STABILIZED ISPH METHOD

  MORIMOTO Toshihiro; ASAI Mitsuteru; KASAMA Kiyonobu; FUJISAWA Kazunori; IMOTO Yusuke

  Journal of Japan Society of Civil Engineers, Ser. A2 (Applied Mechanics (AM)), 2014, Peer-reviewed

  
• SPH法で用いられる近似差分作用素の打ち切り誤差解析

  Yusuke Imoto

  Kyushu University, Mar. 2013, Peer-reviewed

  

Misc.

• Voronoi分割に基づくSPH法の近似差分作用素の打ち切り誤差解析—Truncation Error Analysis of Difference Operators in SPH Method Based on Voronoi Division

  井元 佑介; 田上 大助

  計算工学講演会論文集 = Proceedings of the Conference on Computational Engineering and Science / 日本計算工学会 編, Jun. 2013

  
• 選択型デュアル流速ISPH法を用いた固液混相流解析の精度検証

  藤井孟大; 浅井光輝; 井元佑介

  土木学会年次学術講演会講演概要集(CD-ROM), 2020

  
• Development of Bottom Boundary-Fitted Particle Methods Based on Coordinate Transformation

  松本久也; 井元佑介; 浅井光輝; 三目直登

  計算工学講演会論文集(CD-ROM), 2021

  
• A stabilized ISPH method with dual physical and transport velocity for fluid flow analysis including density variations

  藤井孟大; 浅井光輝; 井元佑介

  計算工学講演会論文集(CD-ROM), 2020

  
• 非圧縮性Navier‐Stokes方程式に対する粒子法における安定化項の考察

  井元佑介; 浅井光輝

  日本応用数理学会年会講演予稿集(CD-ROM), 21 Aug. 2019

  
• 2D‐3D片方向連成波モデルによる津波再現水槽実験の並列解析

  三目直登; TOMICZEK Tori; DONAHUE Aaron; 井元佑介; WESTERINK Joannes; 山田知典; 吉村忍

  日本機械学会計算力学講演会論文集(CD-ROM), 15 Sep. 2017

  
• 非斉次Neumann境界条件を含むPoisson方程式に対する粒子法の誤差評価とその応用

  井元佑介; 三目直登

  日本機械学会計算力学講演会論文集(CD-ROM), 21 Sep. 2016

  
• Truncation error analysis of approximation operators used in generalized particle based methods and its applications

  Imoto Yusuke; Tagami Daisuke

  The Computational Mechanics Conference, 22 Nov. 2014

  

Presentations

• Single-cell trajectory analysis with V-Mapper

  Yusuke Imoto

  AATRN Applied Topology Seminar, 07 Aug. 2024, Invited

  
• シングルセルデータ前処理の共通基盤を目指して

  井元佑介

  Single-cell Meets Data, 31 Jul. 2024

  
• ビッグデータのランドスケープ解析: 生命科学から気象学まで

  井元 佑介

  MfIP連携探索ワークショップ 数学を軸とする新たな価値創造に向けて, 27 Apr. 2024

  
• RNA landscape in single cells

  IMOTO,Yusuke

  Differential Equations for Data Science 2025, 12 Feb. 2025

  
• 高次元粒子法とデータ解析

  井元 佑介

  2024年度応用数学合同研究集会, 07 Dec. 2024

  
• Comprehensive Noise Reduction of Single-Cell Data with RECODE

  IMOTO,Yusuke

  1st Asia & Pacific Bioinformatics Joint Conference, 23 Oct. 2024

  
• 高次元遺伝子発現ダイナミクスのランドスケープ解析

  井元佑介; 平岡 裕章; 谷地村 敏明; 前原 一満

  第66回 システム制御情報学会 研究発表講演会, 19 May 2022, Invited

  
• Statistical Estimation of Gene Regulatory Network

  Yusuke Imoto; Yasuaki Hiraoka; Shohei Shimizu; Takashi Nicolas Maeda; Yoji Kojima; Mitinori Saitou

  JSPS Core-to-Core Program “Establishing International Research Network of Mathematical Oncology”, 27 Oct. 2020, Invited

  
• Statistical causal discovery for gene regulatory network

  Y. Imoto; Y. Hiraoka

  1st ASHBi Mathematical Biology Workshop, 23 Aug. 2019, Invited

  
• Initial particle placement based on the centroidal Voronoi tessellation for two-dimensional flow simulation by the particle method

  M. Ogino; H. Hasegawa; Y. Imoto

  The 10th International Conference on Computational Methods (ICCM), 11 Jul. 2019

  
• Verified Algorithm for High Order Differentiation Based on Hyper-dual Numbers

  N. Yamanaka; Y. Imoto; T. Uramoto; M. Fujikawa; N. Mitsume

  2019 SIAM Conference on Computational Science and Engineering, 15 Feb. 2019

  
• Numerical error evaluations of the incompressible Navier--Stokes equations by a time-explicit generalized particle method

  D. Tagami; Y. Imoto

  13th International SPHERIC SPH Workshop, Jul. 2018

  
• Some investigations of a time-explicit generalized particle method for the incompressible Navier--Stokes equations

  D. Tagami; Y. Imoto

  ECCM--ECFD2018, Jun. 2018

  
• Numerical analysis of tsunami open flume experiment using parallel solver of 2D-3D coupled wave model.

  N. Mitsume; T. Tomiczek; Y. Imoto; A. S. Donahue; J. J. Westerink; T. Yamada; S. Yoshimura

  The 2nd International Conference on Computational Engineering and Science for Safety and Environmental Problems (COMPSAFE 2017), Oct. 2017

  
• An error estimate of particle methods for Poisson equation with Neumann boundary conditions.

  Y. Imoto; D. Tagami

  International Conference on Mathematical Analysis of Continuum Mechanics, 20 Sep. 2017, Invited

  
• Error estimates of a characteristic particle method for convection-diffusion equations.

  D. Tagami; Y. Imoto

  A3 Workshop on Computational Fluid Dynamics and Numerical Analysis, 20 Feb. 2017

  
• Error estimates of a generalized particle method for the Poisson equation with Neumann boundary conditions

  Y. Imoto; D. Tagami

  A3 Workshop on Computational Fluid Dynamics and Numerical Analysis, 20 Feb. 2017

  
• Recent study and possibility of applications of particle methods for interface problems.

  Y. Imoto

  Workshop on interface motions and free boundary problems, Jul. 2016

  
• Some Investigations of a Generalized Particle Method for Convection-Diffusion Equations

  D. Tagami; Y. Imoto

  European Congress on Computational Methods in Applied Sciences and Engineering Congress 2016 (ECCOMAS Congress 2016), Jun. 2016

  
• Mathematical Analysis of Generalized Particle Methods for Poisson equations and heat equations.

  D. Tagami; Y. Imoto

  the 11 International SPHERIC Workshop (SPHERIC2016), Jun. 2016

  
• Some Investigations of Stability Conditions on a Generalized Particle Method for the Heat Equation.

  Y. Imoto; D. Tagami

  Second Joint Workshop of China-Japan-Korea A3 Foresight Program., Nov. 2015

  
• Error estimates of a generalized particle method for partial differential equations.

  Y. Imoto; D. Tagami

  International Workshops on Advances in Computational Mechanics III (IWACOM III), Oct. 2015, Invited

  
• Error estimates of a particle-based method for partial differential equations.

  Y. Imoto; D. Tagami

  the Fourth Conference on Particle-Based Method (PARTICLES2015), Sep. 2015

  
• Regularity and Connectivity Conditions of a Generalized Particle-Based Method for Partial Differential Equations

  D. Tagami; Y. Imoto

  13th US National Congress on Computational Mechanics (USNCCN13), Jul. 2015

  
• Error estimates of a generalized particle-based method for partial differential equations.

  Y. Imoto; D. Tagami

  A3 joint Workshop, Feb. 2015

  
• Truncation Error Analysis of SPH Method and its Applications to Numerical Simulations of Flow Problem.

  Y. Imoto; D. Tagami

  MEIS2013, Oct. 2014

  
• Truncation Error Analysis of Approximation Operators on Particle Methods.

  Y. Imoto

  FMI2013, Oct. 2014

  
• Error estimates of SPH methods for Poisson equations.

  Y. Imoto; D. Tagami

  SIAM: East Asian Section Conference 2016 (EASIAM2014), Jun. 2014

  
• A Parallel Computation for Voronoi Diagram and its Applications to SPH methods.

  Y. Imoto; D. Tagami

  COMPSAFE 2014, Apr. 2014

  
• Truncation Error Analysis of Finite Difference Operators in SPH Method Based on Voronoi Decomposition.

  D. Tagami; Y. Imoto

  the Fourth Conference on Particle-Based Method (PARTICLES2013), Sep. 2013

  
• シングルセルデータ科学への招待

  井元佑介

  日本数学会 2022年度年会, 30 Mar. 2022, Invited

  
• Resolution of the curse of dimensionality in single-cell analysis

  Y Imoto

  2nd ASHBi SignAC Workshop: Integrating Single-cell Analysis and Mathematics, 10 Dec. 2021, Invited

  
• Topological Trajectory Inference for Single-cell RNA Sequencing Data

  Y Imoto; T Nakamura; Y Kojima; H Natsukawa; Y Hiraoka; M Saitou

  Society for Mathematical Biology Annual Meeting 2021 (SMB2021), 16 Jun. 2021

  
• Single-cell-differentiation inference based on a topological data analysis

  Y Imoto; T Nakamura; Y Kojima; H Natsukawa; Y Hiraoka; M Saitou

  SIAM Conference on Applications of Dynamical Systems (DS21), 25 May 2021

  

Books and Other Publications

• 数学セミナー 2024年12月号：ノイズを知り，呪いを祓う - 高次元統計解析に基づく1細胞データのノイズ削減法の開発

  井元 佑介, Single work

  日本評論社, Nov. 2024

  
• 数理科学2023年6月号 高次元データの 「かたち」 を可視化する: トポロジカルデータ解析手法 Mapper の理論・応用

  井元佑介, Single work

  サイエンス社, May 2023

  
• いまさら聞けない計算力学の定石

  応用力学委員会 計算力学小委員会(編集), Contributor, 第13 話 「粒子法のいま」

  丸善出版, 21 Mar. 2020

  
• RIMS共同研究 (公開型)「次世代の科学技術を支える数値解析学の基盤整備と応用展開」開催報告

  IMOTO Yusuke, Single work

  JSIAM Online Magazine, 02 Feb. 2019, Not refereed

  
• 東北大学 知のフォーラムの活動と今後の展開

  IMOTO Yusuke, Single work

  JSIAM Online Magazine, Mar. 2018, Not refereed

  

Industrial Property Rights

• 特許7672160, 特願2022-531772, データ処理方法、データ処理装置およびデータ処理プログラム

  井元佑介; 中村友紀; 平岡裕章; 斎藤通紀

  

External funds: Kakenhi

• A development of a particle method with high accuracy for flow problems and its mathematical justification

  Grant-in-Aid for Young Scientists (B)

  Kyoto University;Tohoku University

  Yusuke Imoto

  From 01 Apr. 2017, To 31 Mar. 2021, Project Closed

  偏微分方程式の数値解析;数値流体力学;粒子法;数値解析;安定性;収束性;非圧縮性Navier-Stokes方程式;誤差評価;数値計算手法;最小二乗法

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-17K17585/
• 超双対数に基づく微分計算の基盤理論構築とその応用

  Grant-in-Aid for Early-Career Scientists

  Basic Section 12040:Applied mathematics and statistics-related

  Kyoto University

  井元 佑介

  From 01 Apr. 2023, To 31 Mar. 2028, Declined

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-23K13014/

Academic, Social Contribution

Committee Memberships

• From Apr. 2023, To Present

  Committee, Research activity `Young Reseachers', Japan Society for Industrial and Applied Mathematics (JSIAM)
• From Apr. 2021, To Present

  Committee, Research activity `Topological Data Analysis', Japan Society for Industrial and Applied Mathematics (JSIAM)
• From Apr. 2020, To Mar. 2024

  Secretary Editors in JSIAM Letters, The Japan Society for Industrial and Applied Mathematics
• From Jul. 2019, To Mar. 2023

  Committee, Research activity `Young Reseachers', Japan Society for Industrial and Applied Mathematics (JSIAM)
• From Apr. 2019, To Present

  Committee, Research activity `Mathematical Aspects on Continuum Mechanics', Japan Society for Industrial and Applied Mathematics (JSIAM)
• From Apr. 2019, To Mar. 2022

  Editorial committee of JSIAM flagship journal, Japan Society for Industrial and Applied Mathematics (JSIAM)