Updated on 2022/05/25

写真a

 
HAYAMIZU, Momoko
 
Affiliation
Faculty of Science and Engineering, School of Fundamental Science and Engineering
Job title
Associate Professor
Profile
My research interest lies in the field of combinatorics and its application. I am particularly interested in the interface between discrete mathematics and biology. In the past few years I have been working on biological issues, such as evolution and cellular differentiation, from a mathematical perspective.

Concurrent Post

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

Research Institute

  • 2021
    -
    2022

    データ科学センター   兼任センター員

  • 2020
    -
    2022

    理工学術院総合研究所   兼任研究員

Education

  • 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  

Degree

  • 2017.03   M.D.

  • 2010.03   Ph.D.

Research Experience

  • 2022.04
    -
    Now

    Waseda University   Faculty of Science and Engineering   Associate Professor

  • 2019.10
    -
    Now

    Japan Science and Technology Agency (JST)   PRESTO Researcher

  • 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

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Professional Memberships

  •  
     
     

    Society for Mathematical Biology

  •  
     
     

    THE JAPAN SOCIETY FOR INDUSTRIAL AND APPLIED MATHEMATICS

  •  
     
     

    Mathematical Society of Japan

 

Research Areas

  • Basic mathematics

  • Theory of informatics

  • Applied mathematics and statistics

  • Statistical science

Research Interests

  • computational biology

  • theoretical biology

  • discrete mathematics

Papers

  • 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

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

    Momoko Hayamizu, Kazuhisa Makino

    arXiv:1904.12432 [math.CO]    2019.04

     View Summary

    &#039;Tree-based&#039; phylogenetic networks provide a mathematically-tractable model for representing reticulate evolution in biology. Such networks consist of an underlying &#039;support tree&#039; together with arcs between the edges of this tree. However, a tree-based network can have several such support trees, and this leads to a variety of algorithmic problems that are relevant to the analysis of biological data.<br />
    Recently, Hayamizu (arXiv:1811.05849 [math.CO]) proved a structure theorem for tree-based phylogenetic networks and obtained linear-time and linear-delay algorithms for many basic problems on support trees, such as counting, optimisation, and enumeration. In the present paper, we consider the following fundamental problem in statistical data analysis: given a tree-based phylogenetic network $N$ whose arcs are associated with probability, create the top-$k$ support tree ranking for $N$ by their likelihood values. We provide a linear-delay (and hence optimal) algorithm for the problem and thus reveal the interesting property of tree-based phylogenetic networks that ranking top-$k$ support trees is as computationally easy as picking $k$ arbitrary support trees.

    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

  • 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

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

    Momoko Hayamizu

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

    DOI

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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.

Other

  • Visitor

    2019.04
     
     

     View Summary

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

  • Organiser

    2018.09
     
     
  • 座長

    2017.09
     
     

     View Summary

    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

  • Organiser-in-Chief

    2017.09
     
     

     View Summary

    The 1st JST Workshop on Mathematical Open Problems

  • 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)

  • Reviewer

     View Summary

    Advances in Applied Mathematics

  • Reviewer

     View Summary

    IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences

  • Reviewer

     View Summary

    Journal of Mathematical Biology

  • Reviewer

     View Summary

    Journal of Combinatorial Optimization

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Awards

  • 令和4年度 科学技術分野の文部科学大臣表彰 若手科学者賞(令和4年4月20日)

    2022.04   文部科学省   生命科学のデータ解析に関わる離散数学の諸問題の研究

    Winner: 早水桃子

  • 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  

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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

    Project Year :

    2023.04
    -
    2030.03
     

  • 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

  • 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
     

  • 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

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Presentations

  • 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

  • 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

  • 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

  • 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

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Syllabus

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Teaching Experience

  • 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  

 

Committee Memberships

  • 2019.03
    -
    2020.02

    The Mathematical Society of Japan  Local Delegate

  • 2019.03
    -
    2020.02

    日本数学会  地方区代議員

Social Activities

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Media Coverage

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