Updated on 2025/07/16

写真a

 
HAYAMIZU, Momoko
 
Affiliation
Faculty of Science and Engineering, School of Fundamental Science and Engineering
Job title
Associate Professor
Degree
M.D. ( 2017.03 総合研究大学院大学 )
Ph.D. ( 2010.03 東京大学 )
Homepage URL
https://www.youtube.com/c/hayamizu-lab
Profile

I went to medical school with the intention of becoming a researcher in basic medicine and worked as a clinician for several years after graduation. However, I ended up becoming an applied mathematician because I was keenly aware of the importance of methods for extracting information from data since my student days, and I wanted to contribute to medicine through theoretical research on methods for analysing biological data.

My research is therefore related to mathematical science, information science, statistical science and life science, but my specialisation is in discrete mathematics (combinatorics, graph theory, discrete geometry, discrete algorithms), which deals with problems related to graphs and networks. I believe that my strength and originality lie in formulating important biological problems into mathematical problems and creating new theorems and algorithms to solve them.

I am currently particularly interested in the mathematical and computational aspects of phylogenetic trees and networks and their applications. Studying them can help elucidate many important biological processes, such as cell differentiation and bacterial or viral evolution.

I am also active in education and outreach activities. For more information, please visit my laboratory's YouTube channel.

 

Research Experience

  • 2024.06
    -
    Now

    Waseda University   Department of Applied Mathematics, Faculty of Science and Engineering   Associate Professor

  • 2019.10
    -
    Now

    Japan Science and Technology Agency (JST)   PRESTO Researcher

  • 2022.04
    -
    2024.06

    Waseda University   Faculty of Science and Engineering   Associate Professor

  • 2020.04
    -
    2022.03

    Waseda University   Faculty of Science and Engineering   Assistant Professor

  • 2017.04
    -
    2020.03

    Department of Statistical Science, School of Multidisciplinary Sciences, The Graduate University for Advanced Studies   Assistant Professor

  • 2017.04
    -
    2020.03

    The Institute of Statistical Mathematics   Assistant Professor

  • 2016.10
    -
    2020.03

    Japan Science and Technology Agency (JST)   PRESTO Researcher

  • 2014.04
    -
    2017.03

    Research Center for Statistical Machine Learning, The Institute of Statistical Mathematics   Research Assistant

  • 2013.11
    -
    2014.03

    Research Center for Statistical Machine Learning, The Institute of Statistical Mathematics   Technical assistant

  • 2012.04
    -
    2013.10

    Department of Radiology, The University of Tokyo Hospital   Radiologist

  • 2010.04
    -
    2012.03

    Kohnodai Hospital, National Center for Global Health and Medicine   Resident

▼display all

Education Background

  • 2014.04
    -
    2017.03

    The Graduate University for Advanced Studies   School of Multidisciplinary Sciences   Department of Statistical Science  

  • 2006.04
    -
    2010.03

    The University of Tokyo   Faculty of Medicine  

  • 2004.04
    -
    2006.03

    The University of Tokyo   College of Arts and Sciences  

Committee Memberships

  • 2019.03
    -
    2020.02

    The Mathematical Society of Japan  Local Delegate

Professional Memberships

  • 　
    　
    　

    Society for Mathematical Biology

  • 　
    　
    　

    THE JAPAN SOCIETY FOR INDUSTRIAL AND APPLIED MATHEMATICS

  • 　
    　
    　

    Mathematical Society of Japan

Research Areas

  • Statistical science / Applied mathematics and statistics / Basic mathematics / Theory of informatics

Research Interests

  • computational biology

  • theoretical biology

  • discrete mathematics

Awards

  • 日本応用数理学会・年会優秀ポスター賞(2022年度)

    2022.09   日本応用数理学会   横断歩道における歩行者対向流の組合せ論的考察

    Winner： 村田 悠, 早水 桃子

  • The Young Scientists’ Prize of the Commendation for Science and Technology

    2022.04   The Minister of Education, Culture, Sports, Science and Technology, Japan   Research of discrete mathematical problems related to the data analysis of life sciences

    Winner： Momoko Hayamizu

  • The 10th WASEDA e-Teaching Award

    2022.03   Waseda University   Introduction to Discrete Mathematics

    Winner： Momoko Hayamizu

  • 2020 9th Waseda e-Teaching Award Grand Award

    2021.05   Waseda University  

    Winner： Momoko Hayamizu, Manabu Machida, Kenji Nakamura

  • Best presentation award at the 2019 Joint Meeting of JSIAM Activity Groups

    2019.06   The Japan Society for Industrial and Applied Mathematics (JSIAM)  

    　View Summary

    'A structure theorem for tree-based networks and its application to phylogenetic tree inference'

  • Student Prize

    2017.03   The Institute of Statistical Mathematics  

  • Anita Borg Scholarship Asia Pacific (APAC)

    2015.07   Google  

▼display all

Media Coverage

▼display all

 

Papers

  • Machine learning approaches to explore important features behind bird flight modes

    Yukino Kawai, Tatsuya Hisada, Kozue Shiomi, Momoko Hayamizu

    IPSJ Transactions on Bioinformatics (TBIO)   18  2025.04  [Refereed]  [International journal]

    Authorship：Last author, Corresponding author

  • Orientability of undirected phylogenetic networks to a desired class: Practical algorithms and application to tree-child orientation

    Tsuyoshi Urata, Manato Yokoyama, Momoko Hayamizu

    The Workshop on Algorithms in Bioinformatics (WABI 2024)    2024.07  [Refereed]  [International journal]

    Authorship：Last author, Corresponding author

    DOI

    Scopus

  • Bridging Between Deviation Indices for Non-Tree-Based Phylogenetic Networks

    Takatora Suzuki, Han Guo, Momoko Hayamizu

    IEEE/ACM Transactions on Computational Biology and Bioinformatics   21 ( 6 ) 2226 - 2234  2024  [Refereed]

    Authorship：Last author, Corresponding author

    DOI

    Scopus

  • Orienting undirected phylogenetic networks to tree-child network

    Shunsuke Maeda, Yusuke Kaneko, Hideaki Muramatsu, Yukihiro Murakami, Momoko Hayamizu

    Preprint    2023.05  [International coauthorship]

    Authorship：Last author, Corresponding author

    DOI

  • Ranking top-k trees in tree-based phylogenetic networks

    Momoko Hayamizu, Kazuhisa Makino

    IEEE/ACM Transactions on Computational Biology and Bioinformatics    2022.12

    Authorship：Lead author, Corresponding author

    DOI

    Scopus

    1
    Citation
    (Scopus)

  • A Structure Theorem for Rooted Binary Phylogenetic Networks and Its Implications for Tree-Based Networks

    Momoko Hayamizu

    SIAM Journal on Discrete Mathematics   35 ( 4 ) 2490 - 2516  2021.01  [Refereed]

    Authorship：Lead author, Last author, Corresponding author

    DOI

  • Recognizing and realizing cactus metrics

    Momoko Hayamizu, Katharina T. Huber, Vincent Moulton, Yukihiro Murakami

    Information Processing Letters   157 ( 105916 ) 1 - 5  2020.05  [Refereed]  [International journal]  [International coauthorship]

    Authorship：Lead author

    DOI

    Scopus

    6
    Citation
    (Scopus)

  • Ranking top-k trees in tree-based phylogenetic networks

    Momoko Hayamizu, Kazuhisa Makino

       2019.11

    DOI

  • On minimum spanning tree-like metric spaces

    Momoko Hayamizu, Kenji Fukumizu

    Discrete Applied Mathematics   226   51 - 57  2017.07  [Refereed]  [International journal]

    Authorship：Lead author, Corresponding author

    　View Summary

    We attempt to shed new light on the notion of 'tree-like' metric spaces by focusing on an approach that does not use the four-point condition. Our key question is: Given metric space M on n points, when does a fully labelled positive-weighted tree T exist on the same n vertices that precisely realises M using its shortest path metric? We prove that if a spanning tree representation, T, of M exists, then it is isomorphic to the unique minimum spanning tree in the weighted complete graph associated with M, and we introduce a fourth-point condition that is necessary and sufficient to ensure the existence of T whenever each distance in M is unique. In other words, a finite median graph, in which each geodesic distance is distinct, is simply a tree. Provided that the tie-breaking assumption holds, the fourth-point condition serves as a criterion for measuring the goodness-of-fit of the minimum spanning tree to M, i.e., the spanning tree-likeness of M. It is also possible to evaluate the spanning path-likeness of M. These quantities can be measured in O(n(4)) and O(n(3)) time, respectively. (C) 2017 The Authors. Published by Elsevier B.V.

    DOI

    Scopus

    6
    Citation
    (Scopus)

  • A Characterization of Minimum Spanning Tree-Like Metric Spaces

    Momoko Hayamizu, Hiroshi Endo, Kenji Fukumizu

    IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)   14 ( 2 ) 468 - 471  2017.03  [Refereed]  [International journal]

    Authorship：Lead author, Corresponding author

    　View Summary

    Recent years have witnessed a surge of biological interest in the minimum spanning tree (MST) problem for its relevance to automatic model construction using the distances between data points. Despite the increasing use of MST algorithms for this purpose, the goodness-of-fit of an MST to the data is often elusive because no quantitative criteria have been developed to measure it. Motivated by this, we provide a necessary and sufficient condition to ensure that a metric space on n points can be represented by a fully labeled tree on n vertices, and thereby determine when an MST preserves all pairwise distances between points in a finite metric space.

    DOI

    Scopus

    1
    Citation
    (Scopus)

  • On the existence of infinitely many universal tree-based networks

    Momoko Hayamizu

    Journal of Theoretical Biology   396   204 - 206  2016.05  [Refereed]

    Authorship：Lead author, Last author, Corresponding author

    DOI

    Scopus

    15
    Citation
    (Scopus)

▼display all

Works

  • Treefit - The first software for quantitative trajectory inference

    Momoko Hayamizu, Kouhei Sutou, Ryohei Suzuki, Hiromi Ishii  Software 

    2020.02
    -
    Now

    　View Summary

    Treefit is a novel data analysis toolkit that helps you perform two types of quantitative analysis of single-cell RNA-seq data: 1) measuring the goodness-of-fit between your single-cell RNA-seq data and esimated tree trajectories; and 2) discovering novel cell types or detecting contaminating cell types by predicting the number of principal paths in the best-fit tree trajectory. Treefit can be used to analyze either row counts or normalized expression data.

    Treefit is implemented in both R and Python languages and can be used in conjunction with other popular software packages, such as Seurat and dynverse. User-friendly tutorials of Treefit are available on the website.

  • Introduction to Discrete Mathematics (YouTube - Public lecture series)

    Momoko Hayamizu  Educational material 

    2021.04
    -
    Now

Presentations

  • Combinatorics of evolutionary trees and networks

    Momoko Hayamizu  [Invited]

    The Mathematical Society of Japan Autumn Meeting 2022  (Hokkaido University)  The Mathematical Society of Japan

    Presentation date： 2022.09

    Event date：
    2022.09
    　
    　

  • Treefit: a method to measure the robustness of differentiation trajectories inferred from single-cell RNA-seq data

    Momoko Hayamizu  [Invited]

    The 55th Annual Meeting of the Japanese Society of Developmental Biologists Symposium 4：Novel insights into cellular plasticity in development, regeneration, and aging  (Kanazawa / Zoom)  Japanese Society of Developmental Biologists

    Presentation date： 2022.06

  • How to reconstruct a cell differentiation trajectory using scRNA-seq snapshot data

    Momoko Hayamizu  [Invited]

    The 1st International Symposium on Human InformatiX X-Dimensional Human Informatics and Biology  (Kyoto)  Advanced Telecommunications Research Institute International (ATR)

    Presentation date： 2020.02

  • Characterising fully labelled tree-like metric spaces without using the four-point condition

    Momoko Hayamizu  [Invited]

    mini-symposium Combinatorial Phylogenetics 1, SIAM Conference on Applied Algebraic Geometry (AG'15)  (KAIST, Daejeon (Korea))  SIAM

    Presentation date： 2015.08

  • An introduction to discrete mathematics of phylogenetic networks: from basic concepts to recent advances

    Momoko Hayamizu  [Invited]

    Math and Biology in the Age of Huge Date and Computation/The 130th Annual Meeting of the Japanese Association of Anatomists(JAA)・The 102nd Annual Meeting of the Physiological Society of Japan(PSJ)・The 98th Annual Meeting of the Japanese Pharmacological Society(JPS)（APPW2025） 

    Presentation date： 2025.03

    Event date：
    2025.03
    　
    　

  • Neighbor-Net法の距離制約と複雑な進化史の表現に対する適用限界

    伊藤綾香, 早水桃子

    日本応用数理学会第21回研究部会連合発表会 離散システム  (岡山大学)  日本応用数理学会

    Presentation date： 2025.03

  • 系統樹におけるクラスタ分離度を評価する定量的尺度の開発

    河井雪野, 森田航太郎, 早水桃子

    日本応用数理学会 第21回 研究部会連合発表会 離散システム  (岡山大学)  日本応用数理学会

    Presentation date： 2025.03

  • HIV ゲノムの組み換え検出における Neighbor-Net 法の性能評価

    伊藤 綾香, 早水 桃子

    バーチャル学会2024  (Cluster) 

    Presentation date： 2024.12

  • Converting undirected graphs into directed phylogenetic networks in a desired class: Novel FPT and heuristic algorithms and their application

    Tsuyoshi Urata, Manato Yokoyama, Momoko Hayamizu

    2024 8th International Conference on Computational Biology and Bioinformatics (ICCBB 2024)  (Kyoto University) 

    Presentation date： 2024.11

  • Clustering Bird Species by Averaging Genetic Distances: A Neighbor-Net Approach to Flight Mode Evolution

    Yukino Kawai, Tatsuya Hisada, Kozue Shiomi, Momoko Hayamizu

    2024 8th International Conference on Computational Biology and Bioinformatics (ICCBB 2024)  (Kyoto University) 

    Presentation date： 2024.11

  • Exploring Phenotypic Factors behind Avian Flight Styles: Neighbor-Joining Clustering with ML-based Distances

    Yukino Kawai, Tatsuya Hisada, Kozue Shiomi, Momoko Hayamizu

    1st Asia & Pacific Bioinformatics Joint Conference (APBJC2024)  (NAHA Cultural Arts Theater NAHArt) 

    Presentation date： 2024.10

  • Practical algorithms for orienting undirected phylogenetic networks into a desired class

    Momoko Hayamizu  [Invited]

    ICERM Semester Program: Theory, Methods, and Applications of Quantitative Phylogenomics  (Providence)  ICERM, Brown University

    Presentation date： 2024.09

    Event date：
    2024.09
    　
    　

  • 距離行列から系統ネットワークを作る NJ-like ヒューリスティックスの開発

    横山 慎人, 菊地 祐太, 早水桃子

    日本応用数理学会2024年度年会 離散システム(2)  (京都大学)  日本応用数理学会

    Presentation date： 2024.09

  • Tree-child networkに向きづけ可能かを判定できる無向グラフについて

    前田隼佑, 浦田剛志, 早水桃子

    日本応用数理学会2024年度年会 離散システム(2)  (京都大学)  日本応用数理学会

    Presentation date： 2024.09

  • 無向系統ネットワークの向き付け問題に対する実用的なFPTアルゴリズムの開発

    浦田 剛志, 横山 慎人, 早水 桃子

    日本応用数理学会2024年度年会 離散システム(2)  (京都大学)  日本応用数理学会

    Presentation date： 2024.09

  • Terminal planar network の禁止部分グラフによる特徴づけ

    宮地 晴希, 野口 友暉, 渡邉 慶大, 鈴木 尭虎, Liu Hexuan, Wu Taoyang, 早水 桃子[International coauthorship]

    (Kyoto University)  JSIAM

    Presentation date： 2024.09

  • Boltzmann Samplerを用いた重み付きカクタスグラフのランダムサンプリング

    鈴木 尭虎, 小堤 幹太, 早水 桃子

    日本応用数理学会2024年度年会 離散システム(2)  (京都大学)  日本応用数理学会

    Presentation date： 2024.09

  • Bipartition距離の部分木分解による系統樹の局所構造比較：進化系統解析における遺伝子樹評価への応用

    森田航太郎, 早水桃子

    早大京大合同若手研究交流会  (京都大学)  SIAM Student Chapter

    Presentation date： 2024.09

  • 系統ネットワークで見るコムギの進化

    徳江圭吾, 早水桃子

    早大京大合同若手研究交流会  (京都大学)  SIAM Student Chapter

    Presentation date： 2024.09

  • 重み付きカクタスグラフを一様ランダムに生成するBoltzmann Samplerの構成と実装

    小堤 幹太, 鈴木 尭虎, 早水 桃子

    早大京大合同若手研究交流会  (京都大学)  SIAM Student Chapter

    Presentation date： 2024.09

  • Beyond the Majority Rule Consensus Tree

    Yuki Takazawa, Atsushi Takeda, Momoko Hayamizu, Olivier Gascuel[International coauthorship]

    Mathematical and Computational Evolutionary Biology (MCEB 2024)  (Hameau de l'Etoile) 

    Presentation date： 2024.06

    Event date：
    2024.06
    　
    　

  • Measuring the robustness of cell differentiation trajectories inferred from single-cell RNA-seq data

    Momoko Hayamizu, Ryohei Suzuki, Hiromi Ishii, Kohei Sutou

    Mathematical and Computational Evolutionary Biology (MCEB 2024)  (Hameau de l'Etoile) 

    Presentation date： 2024.06

    Event date：
    2024.06
    　
    　

  • Tree-based networkからの逸脱度評価法をめぐる考察

    鈴木 尭虎, 早水桃子

    日本応用数理学会第20回研究部会連合発表会 離散システム（２）  (長岡技術科学大学)  日本応用数理学会

    Presentation date： 2024.03

  • 系統ネットワークを用いたHIVのDNA配列組み換えの解明と地理的影響の分析

    伊藤綾香

    バーチャル学会2023  (Cluster) 

    Presentation date： 2023.12

  • 距離行列からグラフを構築するアルゴリズムを用いた鳥の飛行スタイルに関する系統解析

    久田 竜也

    バーチャル学会2023  (Cluster)  バーチャル学会

    Presentation date： 2023.12

  • The structure of rooted binary phylogenetic networks and implications for trees in a network

    Momoko Hayamizu  [Invited]

    iTHEMS Graph-Theory meeting 2023  (RIKEN) 

    Presentation date： 2023.11

    Event date：
    2023.11
    　
    　

  • ネットワークの中にひそむ ネットワークを探る

    早水桃子  [Invited]

    数理×神経科学ワークショップ  (Zoom) 

    Presentation date： 2023.10

  • The structure theorem for rooted binary phylogenetic networks: theory, applications, and challenges

    Momoko Hayamizu  [Invited]

    Workshop 2: Algorithms and Software in Phylogenetics, Mathematics of Evolution-Phylogenetic Trees and Networks  (IMS Auditorium, Institute for Mathematical Sciences, National University of Singapore) 

    Presentation date： 2023.09

    Event date：
    2023.09
    　
    　

  • Mathematical methods and software for inferring differentiation trajectories from single-cell RNA-seq data

    Momoko Hayamizu  [Invited]

    Skin Research Society Seminar  (Matrix Building, Biopolis, Singapore) 

    Presentation date： 2023.09

    　View Summary

    The development of high-throughput single-cell RNA-seq has provided unprecedented opportunities for a better understanding of cell differentiation. Although many practical software packages have been developed to infer cell differentiation trajectories, there are still many mathematical, statistical and computational challenges to overcome to gain meaningful insights from such data. For example, methods for inferring cell differentiation trees need to be further explored. It is also important to establish quantitative methods for assessing the reliability of inferred trees. In this talk, we will explain several mathematical approaches, including our software Treefit, that may be useful for stem cell biologists. We will present some results of analyses using these approaches. The development of Treefit is a joint work with Ryohei Suzuki, Hiromi Ishii and Kohei Sutou. https://hayamizu-lab.github.io/treefit/

  • Orienting undirected phylogenetic networks to tree-child networks

    Shunsuke Maeda, Yusuke Kaneko, Hideaki Muramatsu, Yukihiro Murakami, Momoko Hayamizu[International coauthorship]

    WABI 2023 

    Presentation date： 2023.09

    Event date：
    2023.09
    　
    　

  • A Phylogenetic Analysis of Migratory and Resident Birds

    Yukino Kawai, Tatsuya Hisada, Momoko Hayamizu

    ICIAM 2023  (Waseda University) 

    Presentation date： 2023.08

  • Counting the trees inside a phylogenetic network: an analytic combinatorial approach

    Hiroaki Kojima, Momoko Hayamizu

    ICIAM 2023  (Waseda University) 

    Presentation date： 2023.08

  • Constructing a Phylogenetic X-cactus from a Distance Matrix

    Keita Watanabe, Momoko Hayamizu

    ICIAM 2023  (Waseda University) 

    Presentation date： 2023.08

  • Phylogenetic Analysis of Flapping and Soaring in Birds: Uncovering Evolutionary Differences

    Tatsuya Hisada, Yukino Kawai, Momoko Hayamizu

    ICIAM 2023  (Waseda University) 

    Presentation date： 2023.08

  • Navigating the Frontiers of Phylogenetic Research: Challenges and Applications

    Momoko Hayamizu

    Mini-symposium Challenges and Recent Advances in Phylogenetics, ICIAM 2023  (Waseda University)  Organizer(s) : Momoko Hayamizu, Yuki Murakami, Koyo Hayashi, Hiroshi Hirai

    Presentation date： 2023.08

    　View Summary

    This talk serves as an introduction to our mini-symposium on phylogenetic research. It emphasizes key challenges and applications in this rapidly evolving field from both theoretical and biological perspectives. After providing a brief overview of the symposium topics and presentations, I will discuss some of the recent results and open problems related to phylogenetic trees and networks, with a focus on combinatorial and algorithmic approaches.

  • Inferring the maturation trajectory of human iPS cell-derived megakaryocytes: single-cell gene expression data analysis using Mapper

    Takumu Maehashi, Momoko Hayamizu

    TDA Week 2023 (satellite conference of ICIAM 2023)  (Kyoto University) 

    Presentation date： 2023.07

  • Part 1: Exploring the interface of discrete mathematics and life science, Part 2: YouTube as the intersection of research, education and social media

    Momoko Hayamizu  [Invited]

    Catch-all Mathematical Colloquium of Japan 

    Presentation date： 2023.05

  • 生物進化と細胞分化の系統解析：様々な未解決問題と将来展望

    Momoko Hayamizu  [Invited]

    Presentation date： 2023.04

  • Mapperを用いたシングルセル遺伝子発現データ解析

    Presentation date： 2023.03

  • 距離行列から系統カクタスグラフを構築する単純で効率的なアルゴリズム

    JSIAM 

    Presentation date： 2023.03

  • 横断歩道における歩行者対交流の組合せ論的考察

    JSIAM 

    Presentation date： 2023.03

  • Tree-childな有向系統ネットワークを作るための無向グラフの向きづけについて

    村松 秀晃, 金子 祐輔, 前田 隼佑, Yukihiro Murakami, 早水 桃子[International coauthorship]

    科研費・学術変⾰領域研究(B)「組合せ遷移の展開に向けた計算機科学・⼯学・数学によるアプローチの融合」2022年度「組合せ遷移」の学⽣シンポジウム 

    Presentation date： 2023.02

    　View Summary

    系統ネットワークは系統樹の概念を⼀般化した有向⾮巡回グラフで，ツリーでは記述できない複雑な進化史を表すのに使われる．⽣物種間の距離 (⾮類似度) から無向系統ネットワークを構築する⽅法はあるが，⽣物学的なゴールは進化の流れを再構築することなので無向グラフを所望の性質を持つ有向系統ネットワークにしたいという需要があり，無向系統ネットワークの向きづけに関する組み合せ論的研究がなされている．本発表では，系統ネットワークのサブクラスの中で特によく研究されているtree-childというクラスに注⽬し，根の挿⼊と辺の向きづけという2つの操作によって与えられた無向グラフをtree-childにできるかを判定する問題 (Tree-child Orientability) を考察した結果を紹介する．

  • 複雑なネットワークにひそむ進化の系統樹を探るための組合せ論

    早水桃子

    Virtual Conference 2022 

    Presentation date： 2022.12

    Event date：
    2022.12
    　
    　

  • 距離行列からグラフを構築するアルゴリズムを用いた鳥の飛行スタイルの予測

    久田 竜也, 河井 雪野, 前橋 拓歩, 早水 桃子

    Virtual Conference 2022 

    Presentation date： 2022.12

  • 木の数え上げに現れる特殊な分割数 ～再帰式と母関数およびその近似式～

    小嶋大瑛, 早水桃子

    Virtual Conference 2022 

    Presentation date： 2022.12

  • 距離行列から系統カクタスグラフを構成する単純かつ高速なアルゴリズム

    渡邉慶大, 金子祐輔, 河井雪野, 中山真吾, 村松秀晃, 小嶋大瑛, 久田竜也, 早水桃子

    Virtual Conference 2022 

    Presentation date： 2022.12

  • 横断歩道における歩行者対向流の組合せ論的考察

    Virtual Conference 2022 

    Presentation date： 2022.12

  • 木の数え上げに現れる特殊な分割数〜再帰式と母関数およびその解析学的な解釈〜

    Presentation date： 2022.09

  • 系統ネットワークに含まれる全域系統樹とベース系統樹の数え上げ問題

    Presentation date： 2022.09

  • 横断歩道における歩行者対向流の組合せ論的考察

    Presentation date： 2022.09

  • 進化の系統樹と系統ネットワークに関する組合せ論への招待

    Momoko Hayamizu  [Invited]

    FRIS/TI-FRIS Life Science Seminar  東北大学・学際科学フロンティア研究所

    Presentation date： 2022.07

  • 細胞分化の軌跡推定に関するソフトウェアTreefitの概要 @ Bio”Pack”athon2022#4

    早水桃子  [Invited]

    Bio”Pack”athon2022#4 

    Presentation date： 2022.04

  • YouTubeを本格的に活用したe-Teachingへの挑戦 「離散数学入門」

    早水桃子  [Invited]

    第10回WASEDA e-Teaching Award講演会  早稲田大学

    Presentation date： 2022.03

  • Treefit: measuring the tree-likeness of point clouds and application to the analysis of single-cell gene expression data

    Momoko Hayamizu  [Invited]

    Waseda International Symposium Topological Data Science, Causality, Analysis of Variance, & Time Series 

    Presentation date： 2022.03

    Event date：
    2022.03
    　
    　

  • 進化の系統樹と系統ネットワークにまつわる組合せ論

    早水桃子  [Invited]

    ネットワーク科学研究会2021 

    Presentation date： 2021.12

    Event date：
    2021.12
    　
    　

  • １細胞の遺伝子発現データを用いた細胞分化の軌跡推定

    早水桃子  [Invited]

    AI・データ利活用研究会 第25回 

    Presentation date： 2021.12

  • Combinatorial problems on phylogenetic trees and networks (in Japanese)

    Momoko Hayamizu  [Invited]

    Presentation date： 2021.11

  • Mathematical methods and software for the inference of cell differentiation trajectories using single-cell RNA-Seq data (in Japanese)

    Momoko Hayamizu  [Invited]

    IIBMP2021 

    Presentation date： 2021.09

    Event date：
    2021.09
    　
    　

  • The structure of rooted binary phylogenetic networks and its applications to various computational problems in evolutionary analysis

    Momoko Hayamizu  [Invited]

    Toward an integration of fluids, ecology, and evolution in Biofluids 2021  (Zoom) 

    Presentation date： 2021.07

    Event date：
    2021.07
    　
    　

    　View Summary

    Evolutionary processes are commonly represented using phylogenetic trees, but more general models called phylogenetic networks are needed in order to accurately represent the complicated information in real data or complex evolutionary histories such as hybridisation of plants and horizontal gene transfer in bacterial evolution. However, because of the many computational difficulties involved in using phylogenetic networks, it is still a major challenge to recognise biologically meaningful problems that are solvable in polynomial time and to clarify how such networks can be actually useful in the analysis of evolutionary data. In this talk, I will first provide the necessary background in the field of combinatorial phylogenetics, and then present a 'structure theorem for rooted binary phylogenetic networks' and show how it yields a series of fast algorithms for solving various interesting problems in a unified manner.

  • A structure theorem for tree-based phylogenetic networks: from theory to algorithms

    Momoko Hayamizu  [Invited]

    Waseda Cherry Blossom Workshop on Topological Data Science  (Nishi-Waseda Campus, Waseda University / Zoom) 

    Presentation date： 2021.03

    　View Summary

    While phylogenetic networks are useful to visualise nontreelike data or complex evolutionary histories, there are many computationally hard problems regarding them. Therefore, it is important to define nice subclasses of phylogenetic networks that are mathematically tractable and biologically meaningful. In view of this, the concept of "tree-based" phylogenetic networks, which was originally introduced by Francis and Steel in 2015, has attracted great attention and given rise to various interesting research problems in combinatorial phylogenetics. In this talk, I provide the necessary background and explain how to solve those different problems in a unified manner. The talk is mainly based on arXiv:1811.05849 [math.CO]. I also mention more recent advancement that is joint work with Kazuhisa Makino (arXiv:1904.12432 [math.CO])

  • 細胞分化の軌跡推定への深層学習によるアプローチ

    平井 広志, 早水 桃子, 二反田 篤史

    第3回JSTさきがけ数理構造活用領域会議 

    Presentation date： 2021.02

  • 離散幾何学が拓く計算系統学の新展開

    早水桃子

    第2回JSTさきがけ数理構造活用領域会議  (Zoom) 

    Presentation date： 2020.10

  • Treefit: Software for quantitative trajectory inference using single-cell gene expression data

    Momoko Hayamizu  [Invited]

    The Institute of Statistical Mathematics

    Presentation date： 2020.07

  • Support trees and tree-based phylogenetic networks: from theory to algorithms

    Momoko Hayamizu  [Invited]

    第2090回 Biological symposium  (Mishima)  National Institute of Genetics

    Presentation date： 2020.02

  • 基礎医学と社会医学をつなぐ離散幾何学的モデリング

    早水桃子  [Invited]

    CREST・さきがけ・AIMaP合同シンポジウム「数学パワーが世界を変える2020」  (秋葉原コンベンションホール) 

    Presentation date： 2020.02

  • 系統ネットワークの構造定理と全域系統樹に関する諸問題への応用

    早水桃子  [Invited]

    組合せ数学セミナー (COMA SEMI)  (東京大学 駒場キャンパス) 

    Presentation date： 2019.12

  • 「進化」のシナリオを探る数学

    早水桃子  [Invited]

    広がる数学X～第32回数学キャラバン～  (岡山大学) 

    Presentation date： 2019.11

  • 次世代のデータ解析技術をつくる離散数学

    Momoko Hayamizu  [Invited]

    Math for Innovation Symposium, Kyushu University  (Kyushu University (Ito campus))  IMI, Kyushu University

    Presentation date： 2019.06

  • A structure theorem for tree-based phylogenetic networks and its algorithmic applications

    Momoko Hayamizu  [Invited]

    Combinatorics Seminar, Institute of Mathematics, Academia Sinica  (Institute of Mathematics, Academia Sinica (National Taiwan University campus))  Institute of Mathematics, Academia Sinica

    Presentation date： 2019.04

  • Tree-based network の構造定理と系統樹推定に関する諸問題への応用

    Momoko Hayamizu  [Invited]

    2019 Joint Meeting of JSIAM Activity Groups, The Japan Society for Industrial and Applied Mathematics (JSIAM)  (Tsukuba University)  JSIAM

    Presentation date： 2019.03

  • A structure theorem for tree-based phylogenetic networks and its applications

    Momoko Hayamizu  [Invited]

    The 17th Japan-Korea Workshop on Algebra and Combinatorics  (Tsukuba University (Tokyo campus)) 

    Presentation date： 2019.01

  • 二分系統ネットワークの構造定理と細分系統樹の数え上げ

    Momoko Hayamizu

    応用数学合同研究集会2018  (Ryukoku University (Seta campus)) 

    Presentation date： 2018.12

  • 系統ネットワークにおけるサブディビジョンツリーの数え上げと列挙

    Momoko Hayamizu  [Invited]

    RIMS Discrete Optimization Seminar  (RIMS, Kyoto University)  RIMS, Kyoto University

    Presentation date： 2018.10

  • Enumeration of phylogenetic trees inside phylogenetic networks

    Momoko Hayamizu  [Invited]

    The 3rd IMI-ISM-ZIB Modal Workshop on Challenges in Real World Data Analytics and High-Performance Optimization  (National Graduate Institute for Policy Studies (GRIPS))  九州大学IMI, 統計数理研究所, Zuse Institute Berlin

    Presentation date： 2018.09

  • A linear time algorithm for counting the number of support trees for a binary phylogenetic network

    Momoko Hayamizu

    The 22nd Annual New Zealand Phylogenomics Meeting (Portobello 2018) - The Interface of Mathematics and Biology  (Portobello, New Zealand) 

    Presentation date： 2018.02

  • 離散数学と幹細胞生物学のコラボレーション

    Momoko Hayamizu  [Invited]

    AIMaP公開シンポジウム「数学と産業の協働ケーススタディ」  (Nihon-bashi, Tokyo)  AIMaP

    Presentation date： 2018.01

  • A generalisation of the fundamental theorem of phylogenetics

    Momoko Hayamizu

    Phylomania 2017 The Ninth UTAS Theoretical Phylogenetics Meeting  (University of Tasmania (Sandy Bay campus), Australia) 

    Presentation date： 2017.12

  • Discrete mathematical approaches in phylogenetics

    Momoko Hayamizu  [Invited]

    Workshop on Topological Data Analysis  (Meiji University (Nakano campus)) 

    Presentation date： 2017.11

  • 生物系統学における離散幾何学

    Momoko Hayamizu  [Invited]

    Colloquium, Shibaura Institute of Techinology  (Shibaura Institute of Technology (Omiya campus)) 

    Presentation date： 2017.11

  • 四点条件から広がるcombinatorial phylogeneticsの世界

    Momoko Hayamizu  [Invited]

    IMI Colloquium, Kyushu University  (Kyushu University (Ito campus))  IMI, Kyushu University

    Presentation date： 2017.10

  • Universal tree-based networkとその最小サイズについて

    Momoko Hayamizu, Speaker, Shizuo Kaji, Satoru Fujishige

    日本数学会 2017年度秋季総合分科会  (Yamagata University) 

    Presentation date： 2017.09

  • Universal tree-based networkとその最小サイズについて

    Momoko Hayamizu, Speaker, Shizuo Kaji, Satoru Fujishige  [Invited]

    日本応用数理学会 2017年度 年会 離散システム研究部会  (Musashino University (Ariake campus))  JSIAM

    Presentation date： 2017.09

  • Bounding the size of universal tree-based networks

    Momoko Hayamizu

    Algebraic and Combinatorial Phylogenetics  (Universitat Polit_cnica de Catalunya (UPC), Barcelona) 

    Presentation date： 2017.06

  • 進化系統樹の拡張をめぐる離散数学の諸問題

    Momoko Hayamizu  [Invited]

    RIMS Discrete Optimization Seminar, Kyoto University  (RIMS, Kyoto University)  RIMS, Kyoto University

    Presentation date： 2017.05

  • Universal tree-based network に関する研究の最近の展開

    Momoko Hayamizu  [Invited]

    Combinatorial mathematics seminar (COMA SEMI)  (The University of Tokyo (Komaba campus)) 

    Presentation date： 2017.04

  • Tree metricの拡張による進化系統樹の一般化

    Momoko Hayamizu  [Invited]

    早稲田大学数学若手異分野交流会  (Waseda University (Nishi-Waseda campus)) 

    Presentation date： 2017.03

  • X-cactuses and cactus metrics

    Momoko Hayamizu  [Invited]

    Seminar, Centre for Research in Mathematics, Western Sydney University (Parramatta Campus)  (Centre for Research in Mathematics, Western Sydney University (Parramatta Campus)) 

    Presentation date： 2017.03

  • X-cactus trees and cactus tree metrics

    Momoko Hayamizu

    The 21st Annual New Zealand Phylogenomics Meeting (Waiheke 2017) - The Interface of Mathematics and Biology [abstract]  (The Venue Waiheke, New Zealand) 

    Presentation date： 2017.02

  • 系統学の基本定理の一般化

    Momoko Hayamizu

    2016年度応用数学合同研究集会  (Ryukoku University (Seta campus)) 

    Presentation date： 2016.12

  • 距離空間と最小全域木のフィッティングの良さをはかる尺度の構築にむけて

    Momoko Hayamizu  [Invited]

    2016 Annual Meeting of the Japan Society for Industrial and Applied Mathematics (JSIAM)  (Kita-Kyushu)  JSIAM

    Presentation date： 2016.09

  • 重みなしブロックグラフが導く距離行列の余因子と行列式

    Momoko Hayamizu

    組合せ論サマースクール 2016 (COS2016) 未解決問題セッション  (Gero, Gifu) 

    Presentation date： 2016.08

  • 木ではないメディアングラフが導く距離空間について

    Momoko Hayamizu

    組合せ論サマースクール 2016 (COS2016) 一般講演セッション  (Gero, Gifu) 

    Presentation date： 2016.08

  • Universal tree-based networkについて

    Momoko Hayamizu  [Invited]

    グレブナー若手集会  (Tokai University (Shonan campus)) 

    Presentation date： 2016.02

  • Universal tree-based networks が無数に存在することの証明／Tree-like metric spacesの特殊化と一般化

    Momoko Hayamizu  [Invited]

    Combinatorial mathematics seminar (COMA SEMI)  (The University of Tokyo (Komaba campus)) 

    Presentation date： 2016.01

  • 重みつき木で表現可能な距離空間の特徴づけ

    Momoko Hayamizu

    日本数学会2015年度秋季総合分科会 一般講演 (応用数学分科会)  (Kyoto Sangyo University) 

    Presentation date： 2015.09

▼display all

Research Projects

  • 離散数学と統計科学の融合による生命科学データ解析の技術革新

    JST (Japan Science and Technology Agency)  FOREST

    Project Year :

    2023.04
    -
    2030.03
     

    Momoko Hayamizu

  • 離散幾何学が拓く計算系統学の新展開

    科学技術振興機構 (JST)  戦略的基礎研究推進事業 さきがけ研究

    Project Year :

    2019.10
    -
    2023.03
     

    早水 桃子

  • Discrete geometrical modelling of biological processes and its medical applications

    Japan Science and Technology Agency (JST)  PRESTO

    Project Year :

    2016.10
    -
    2020.03
     

    Momoko Hayamizu

  • 細胞系譜を解明する新しい系統解析技術の創出

    早稲田大学  PI飛躍支援プログラム

    Project Year :

    2023.04
    -
    2026.03
     

    早水桃子

  • 上皮幹細胞可塑性を利用した新しい再生医療のための非侵襲的幹細胞同定法の開発

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Fund for the Promotion of Joint International Research (Fostering Joint International Research (B))

    Project Year :

    2021.10
    -
    2024.03
     

  • 顔画像の特徴量変化解析の研究

    民間企業からの受託研究

    Project Year :

    2021.06
    -
    2022.05
     

  • Discrete mathematical research for building a novel model of evolution

    Research Organization of Information and Systems  Challenging Exploratory Research Projects for the Future

    Project Year :

    2019.07
    -
    2020.03
     

  • 生物系統学に関するグラフ理論と離散最適化の研究

    2019年度 統計数理研究所 公募型共同利用  一般研究2

    Project Year :

    2019.07
    -
    2019.08
     

    早水 桃子

  • Collaborative research on phylogenetic networks

    London Mathematical Society  Financial Support for in Pairs - Scheme 4 Grants

    Project Year :

    2019.07
    -
    2019.08
     

    Katharina Huber

  • 系統ネットワークにおける離散構造 （訪問滞在型研究計画）

    京都大学数理解析研究所  RIMS共同研究（グループ型B）

    Project Year :

    2019.07
    　
    　
     

    牧野 和久

▼display all

Other

  • Visitor

    2019.04
    　
    　

    　View Summary

    Institute of Statistical Science, Academia Sinica (Hosted by Prof. Hsien-Kuei Hwang)

  • Visiting Fellow

    2017.03
    　
    　

    　View Summary

    School of Computing, Engineering and Mathematics at Western Sydney University (Hosted by Prof. Andrew Francis)

  • Involvement in other research projects

    2016.09
    　
    　

    　View Summary

    Member of Statistics Group, JST CREST Project 'Topological data analysis for new descriptors on soft matters' (Director: Yasuaki Hiraoka)

 

Syllabus

▼display all

Teaching Experience

  • 生命科学のための離散数学

    Waseda University  

    2021.09
    -
    Now
     

  • 離散数学入門

    Waseda University  

    2021.04
    -
    Now
     

  • Advanced Topic in Modern Mathematical Sciences 1, 2

    Waseda University  

    2020.04
    -
    Now
     

  • 数学B1（微分積分）生医・建築(1)

    Waseda University  

    2020.04
    -
    2021.03
     

  • Seminar on Applied Dsicrete Mathematics A, B, C, D

    Waseda University  

    2022.04
    -
    Now
     

  • Research on Applied Discrete Mathematics

    Waseda University  

    2022.04
    -
    Now
     

  • 数学講究・応用数理講究

    Waseda University  

    2021.04
    -
    Now
     

  • 応用数理概論

    Waseda University  

    2020.04
    -
    Now
     

  • Statistical science

    The Graduate University for Advanced Studies (SOKENDAI)  

  • Multivariable calculus

    Hitotsubashi University  

  • 統計数理セミナー

    総合研究大学院大学 統計科学専攻  

  • 微分積分 II

    一橋大学  

▼display all

 

Social Activities

  • 教員の授業見学受入れ（対象科目：「離散数学入門」）

    Center for Higher Education Studies, Waseda University 

    2022.04
    -
    Now

  • プレゼンテーション徹底入門 –プロの考え方と伝え方–

    国立国会図書館  調査員向けセミナー  （国立国会図書館） 

    2024.07
    -
    　

    　View Summary

    プレゼンテーション徹底入門：プロの考え方と伝え方
    プレゼンテーションの準備にあたり、多くのプレゼンターはスライド作成と格闘し、さらに当日は制限時間以内にうまく喋れるか、アドリブで適切な質疑応答ができるだろうかといった不安やプレッシャーを感じている。本講義では、全てのプレゼンターが知っておくべき基本原則と、プレゼンテーションのトーク本体および質疑応答を成功させる正しい準備方法を解説する。また、複雑な情報を正しく伝えるために不可欠なスライド作成の基本テクニックについても紹介する。

  • フォントスイッチプロジェクトYouTube スライド添削動画シリーズ（全4回）

    株式会社モリサワ  フォントスイッチプロジェクト 

    2023.12
    -
    2024.03

  • YouTubeを気楽に始めよう／よくある10の質問と私の答え

    日本評論社  『数学セミナー』2024年3月号 通巻 749号  （数学を伝える） 

    2024.02
    -
    　

  • フォントとレイアウトでできる！ 研究発表ポスターデザイン改善術

    株式会社モリサワ  Zoomウェビナー 

    2023.12
    -
    　

  • 巻頭エッセイ「令和の研究者と博士課程」

    岩波書店  『科学』2024年1月号 

    2023.12
    -
    　

  • 系統ネットワークの数理とアルゴリズム

    サイエンス社  『数理科学』2023年9月号 (発売日2023年08月19日) 

    2023.08
    -
    　

  • 組合せ論的系統学入門

    開成学園  2023年度特別講義  （東京） 

    2023.06
    -
    　

  • JST／CRDS俯瞰ワークショップ（WS）

    日本評論社  社会に最先端の数学が求められるワケ(2) データ分析と数学の可能性  （座談会 数学と産業界のこれから） 

    2022.03
    　
    　

  • Waseda University 2023 Admission Brochure

    Admissions Center  Waseda University 2023 Admission Brochure  （Faculty of Science and Engineering p.134） 

    2022
    　
    　

  • 早稲田大学基幹理工学部模擬授業

    （早稲田実業学校高等部） 

    2021.02
    　
    　

  • 早稲田大学基幹理工学部模擬授業

    （サレジオ学院高等学校） 

    2020.11
    　
    　

  • 早稲田大学基幹理工学部模擬授業

    （大妻多摩高等学校） 

    2020.10
    　
    　

  • 進化の系統樹とデータ解析／ (2) 系統ネットワークの構造定理といろいろなデータ解析への応用

    日本評論社  数学セミナー2020年2月号 通巻 700号  （数理のクロスロード） 

    2020.02
    -
    　

  • 進化の系統樹とデータ解析／ (1) 系統樹と系統ネットワークの離散数学

    日本評論社  数学セミナー2020年1月号 通巻 699号  （数理のクロスロード） 

    2020.01
    -
    　

  • 響き合う人とデータ 統数研プロジェクト紹介 第19回「基礎医学と社会医学をつなぐ離散幾何学的モデリング」

    統計数理研究所  統数研ニュース No.146 

    2019.11
    -
    　

  • AIMaP公開シンポジウム「数学と産業の協働ケーススタディ」パネルディスカッション

    AIMaP  AIMaP公開シンポジウム「数学と産業の協働ケーススタディ」 

    2018.01
    -
    　

  • 平成29年度科学人材育成事業 マスフェスタ

    2017.08
    -
    　

    　View Summary

    SSH高校生の数学研究に対する指導助言と，アウトリーチ活動（高校生・高校教員を対象とするポスター発表による研究紹介）．
    （開催場所：関西学院大学上ケ原キャンパス）

▼display all

Academic Activities

  • ICIAM 2023 Mini-symposium "Challenges and Recent Advances in Phylogenetics" (4 sessions)

    Competition, symposium, etc.

    ICIAM (International Council for Industrial and Applied Mathematics)   Waseda University (+Zoom)

    2023.08
    　
    　

    　View Summary

    Phylogenetic trees and networks are used to elucidate the evolutionary history of genes or species. Data proliferation due to recent technological advancements has led to the pursuit of more efficient algorithms and novel approaches. Advances in the area can lead to breakthroughs in various disciplines of biology and life sciences, including genetics, cell biology, zoology, botany, microbiology, epidemiology, drug discovery, and biodiversity conservation, to name a few. This mini-symposium will cover recent topics related to phylogenetic research, from both theoretical and practical viewpoints, with results from algebra, algorithms, bioinformatics, combinatorics, computational complexity, geometry, statistics, and software development.

  • バイオインフォマティクスセミナー

    Academic society, research group, etc.

    早水桃子  

    2023.05
    -
    　

  • ICIAM 2023

    Peer review

    ICIAM (International Council for Industrial and Applied Mathematics)  

    2023.02
    -
    2023.05

  • CAT(0) festival

    Academic society, research group, etc.

    Momoko Hayamizu   Waseda University

    2022.03
    -
    　

  • 第2回 JST数学領域 未解決問題ワークショップ（オーガナイザー・出題者）

    Academic society, research group, etc.

    2018.09
    　
    　

  • 日本応用数理学会 2017年度 年会 機械学習一般講演セッション 座長

    Academic society, research group, etc.

    日本応用数理学会  

    2017.09
    　
    　

  • 第1回 JST数学領域 未解決問題ワークショップ（企画立案・オーガナイザー代表・問題選定委員・出題者）

    Academic society, research group, etc.

    2017.09
    　
    　

  • Journal of Combinatorial Optimization

    Peer review

  • Journal of Mathematical Biology

  • IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences

  • Advances in Applied Mathematics

  • Algorithmica

▼display all

Sub-affiliation

  • Faculty of Science and Engineering   Graduate School of Fundamental Science and Engineering

Research Institute

  • 2025
    -
    2026

    Center for Data Science   Concurrent Researcher

  • 2024
    -
    2026

    Waseda Research Institute for Science and Engineering   Concurrent Researcher