Updated on 2024/07/10

写真a

 
Ohkubo Yusaku
 
Organization
Faculty of Environmental, Life, Natural Science and Technology Lecturer
Position
Lecturer
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Degree

  • Ph.D. ( 2019.9   Hokkaido University )

Research Areas

  • Humanities & Social Sciences / Philosophy and ethics  / 科学哲学、統計学の哲学、モデルの哲学

  • Life Science / Ecology and environment  / Ecostatistics

Education

  • Hokkaido University   環境科学院  

    2017.4 - 2019.9

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Research History

  • The Institute of Statistical Mathematics   学際統計数理研究系   Visiting Lecturer

    2024.4

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  • Okayama University   Faculty of Engineering   Senior Assistant Professor

    2023.4

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  • The Institute of Statistical Mathematics   統計思考院

    2022.7 - 2023.3

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  • Joint Support-Center for Data Science Research   Center for Data Assimilation Research and Applications   Specially Appointed Researcher

    2020.5 - 2023.4

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    Country:Japan

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  • The Institute of Statistical Mathematics   Modeling Research Group   Specially Appointed Researcher

    2020.5 - 2023.3

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    Country:Japan

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  • Hokkaido University   Center for Human Nature, Artificial Intelligence, and Neuroscience   Doctoral Researcher

    2019.11 - 2020.4

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    Country:Japan

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  • CHOWA GIKEN Corporation   Researcher

    2019.2 - 2019.10

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    Country:Japan

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Professional Memberships

 

Papers

  • Hereditary nature of death-feigning frequency in a parasitoid wasp Heterospilus prosopidis using sib analysis

    Haruna Fujioka, Takahisa Miyatake, Yusaku Ohkubo, Masakazu Shimada

    Journal of Evolutionary Biology   2024.6

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    Publishing type:Research paper (scientific journal)   Publisher:Oxford University Press (OUP)  

    Abstract

    Death feigning, a state of immobility observed in many animals in response to external stimuli, is an anti-predator behaviour. Although previous studies showed that death-feigning behaviours are quantitative genetic traits, the knowledge of the heritable basis of death-feigning behaviour is lacking. To investigate the heritable basis of death-feigning behaviour, we used 3 laboratory strains of a braconid parasitoid wasp, Heterospilus prosopidis. The heritable basis using half-sib analysis, and the effects of different geographical backgrounds, rearing conditions in the laboratory, and host age were evaluated. The results of the half-sib analysis showed that the frequency of death feigning varied among sires, suggesting a certain extent of additive genetic variance. Also, the frequency of death feigning varied between geographical backgrounds and among strains. Death-feigning frequency was not affected by the age of the host. Our findings highlight the importance of genetic factors underlying the basis of the death-feigning behaviour and provide support for the genetic alterations of traits from the perspective of evolution in various animal species.

    DOI: 10.1093/jeb/voae079

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  • Foraging predicts the evolution of warning coloration and mimicry in snakes Reviewed

    Yosuke Kojima, Ryosuke K. Ito, Ibuki Fukuyama, Yusaku Ohkubo, Andrew M. Durso

    Proceedings of the National Academy of Sciences   2024.3

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    Publishing type:Research paper (scientific journal)  

    DOI: 10.1073/pnas.2318857121

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  • Heritable effects on caste determination and colony-level sex allocation in termites under field conditions Reviewed

    Mamoru Takata, Shuya Nagai, Tatsuya Inagaki, Yusaku Ohkubo, Eisuke Tasaki, Kenji Matsuura

    iScience   26 ( 3 )   106207 - 106207   2023.3

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Elsevier BV  

    DOI: 10.1016/j.isci.2023.106207

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  • A novel phylogenetic comparative method for evaluating the strength of branch-specific directional selection Reviewed

    Yusaku Ohkubo, Nobuyuki Kutsukake, Itsuro Koizumi

    Evolution   77 ( 1 )   63 - 82   2022.12

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    Authorship:Lead author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:Oxford University Press (OUP)  

    Abstract

    Phylogenetic comparative methods (PCMs) have played a central role in studying the evolution of phenotypic traits. However, when a trait experienced directional selection, previous PCMs have faced a dilemma between mathematically tractable but restrictive models (i.e., simple Gaussian process models) and flexible but intractable approaches (i.e., a simulation-based process model of phenotype evolution built on population genetics frameworks). This paper proposes a novel Gaussian process macroevolutionary model, called the “branch-specific directional selection (BSDS),” for evaluating the strength of directional selection to reconcile these two approaches. This model is based on a second-order approximation of a previous simulation-based process model but has a closed-form likelihood function. This can also be extended to incorporate intraspecies variations and to linear mixed models, which are necessary for meta-analysis. We conduct numerical experiments to validate the proposed method and apply it to the brain volume of Hominidae species. The results show that the proposed methods yield statistically more reliable inferences and computational time is about hundred thousand times faster than the previous simulation-based methods. Further extensions of the BSDS model are expected to provide a clearer picture of the connection of microevolutionary processes and macroevolutionary patterns.

    DOI: 10.1093/evolut/qpac015

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  • Spillover and spillback risks of ectoparasites by an invasive squirrel Callosciurus erythraeus in Kanto region of Japan Reviewed

    Hirotaka Katahira, Yuya Eguchi, Saki Hirose, Yukino Ohtani, Azusa Banzai, Yusaku Ohkubo, Tatsuki Shimamoto

    International Journal for Parasitology: Parasites and Wildlife   19   1 - 8   2022.12

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    Publishing type:Research paper (scientific journal)   Publisher:Elsevier BV  

    DOI: 10.1016/j.ijppaw.2022.07.006

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  • The habitat use and trophic niche comparisons among closely related land snails in Northeast Asia Reviewed

    Yuta Morii, Yusaku Ohkubo, Gen Kanaya, Larisa Prozorova

    Population Ecology   64 ( 4 )   282 - 299   2022.10

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    Publishing type:Research paper (scientific journal)   Publisher:Wiley  

    DOI: 10.1002/1438-390X.12127

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    Other Link: https://onlinelibrary.wiley.com/doi/full-xml/10.1002/1438-390X.12127

  • Revisiting the Two Predominant Statistical Problems: The Stopping-rule Problem and the Catch-all Hypothesis Problem Invited Reviewed

    Yusaku OHKUBO

    Annals of the Japan Association for Philosophy of Science   30   23 - 41   2021.9

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    Authorship:Lead author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:The Japan Association for Philosophy of Science  

    DOI: 10.4288/jafpos.30.0_23

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  • Do green park characteristics influence human-wildlife distance in arboreal squirrels? Reviewed

    Kenta Uchida, Takahiro Yamazaki, Yusaku Ohkubo, Hisashi Yanagawa

    Urban Forestry & Urban Greening   58   126952 - 126952   2021.3

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    Publishing type:Research paper (scientific journal)   Publisher:Elsevier BV  

    DOI: 10.1016/j.ufug.2020.126952

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  • p 値とは何だったのか (Fisher の有意性検定と Neyman-Pearson の仮説検定を超えるために) Reviewed

    Yusaku Ohkubo

    生物科学   70 ( 4 )   238 - 251   2019.3

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    Authorship:Lead author, Corresponding author   Language:Japanese   Publishing type:Research paper (scientific journal)  

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  • The benefits of grouping as a main driver of social evolution in a halictine bee Reviewed

    Yusaku Ohkubo, Tatsuhiro Yamamoto, Natsuki Ogusu, Saori Watanabe, Yuuka Murakami, Norihiro Yagi, Eisuke Hasegawa

    Science Advances   4 ( 10 )   2018.10

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    Authorship:Lead author   Publishing type:Research paper (scientific journal)   Publisher:American Association for the Advancement of Science ({AAAS})  

    DOI: 10.1126/sciadv.1700741

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  • Cricket mate selection as a spatial discounting phenomenon without learning Reviewed

    Yusaku Ohkubo, Jin Yoshimura, Eisuke Hasegawa

    Journal of Ethology   36 ( 3 )   229 - 233   2018.6

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    Authorship:Lead author, Corresponding author   Publishing type:Research paper (scientific journal)   Publisher:Springer Nature America, Inc  

    DOI: 10.1007/s10164-018-0552-1

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  • Activity of invasive slug Limax maximus in relation to climate conditions based on citizen's observations and novel regularization based statistical approaches Reviewed

    Morii, Y., Ohkubo, Y., Watanabe, S.

    Science of the Total Environment   637-638   1061 - 1068   2018

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    Authorship:Lead author   Publishing type:Research paper (scientific journal)  

    DOI: 10.1016/j.scitotenv.2018.04.403

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  • Morph-Specific weapon-correlated traits in a male dimorphic stag beetle prosopocoilus inclinatus, (Coleoptera: Lucanidae) Reviewed

    Ito, J., Ohkubo, Y., Hasegawa, E.

    Annals of the Entomological Society of America   110 ( 3 )   2017

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    Publishing type:Research paper (scientific journal)  

    DOI: 10.1093/aesa/saw096

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  • Male guppies change courtship behaviour in response to their own quality relative to that of a rival male Reviewed

    Yoshikawa, T., Ohkubo, Y., Karino, K., Hasegawa, E.

    Animal Behaviour   118   2016.8

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    Publishing type:Research paper (scientific journal)  

    DOI: 10.1016/j.anbehav.2016.05.022

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  • Difference in evolutionary patterns of strongly or weakly selected characters among ant populations Reviewed

    Imai, S., Kobayashi, K., Ohkubo, Y., Yagi, N., Hasegawa, E.

    Scientific Reports   6   39451 - 39451   2016

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Nature Publishing Group  

    DOI: 10.1038/srep39451

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Books

  • 生物学者のための科学哲学

    鈴木 大地, 森元 良太, 三中 信宏, 大久保 祐作, 吉田 善哉( Role: Joint translator ,  第2章、第3章、第4章)

    勁草書房  2023.2  ( ISBN:9784326103195

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MISC

  • On the “expectation” of Bayesian methods: how the prior is chosen in “objective” manner in practices of statistics. Invited

    Ohkubo Yusaku

    Linkage   1 ( 1 )   9 - 14   2021.4

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    Authorship:Lead author   Language:English   Publishing type:Rapid communication, short report, research note, etc. (bulletin of university, research institution)  

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  • マクロ進化の大規模種間比較研究における枝特異的方向性淘汰モデルの提案

    大久保祐作

    2020 年度科学研究費シンポジウム「大規模複雑データの理論と方法論:最前線の動向と新たな展開」予稿集   2020.12

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    Authorship:Lead author   Publishing type:Internal/External technical report, pre-print, etc.  

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Presentations

  • The status of the statistical predictionalism on the philosophy of scientific model representations Invited

    Ohkubo Yusaku

    the 17th edition of the International Congress on Logic, Methodology and Philosophy of Science and Technology.  2023.7.28 

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    Event date: 2023.7.25

    Language:English   Presentation type:Symposium, workshop panel (public)  

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  • マクロ進化の大規模種間比較研究における枝特異的方向性淘汰モデルの提案

    大久保祐作

    2020 年度科学研究費シンポジウム 「大規模複雑データの理論と方法論:最前線の動向と新たな展開」  2020.12.5 

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    Event date: 2020.12.4 - 2020.12.5

    Language:Japanese   Presentation type:Symposium, workshop panel (public)  

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  • Recent advances in the Phylogenetic Comparative Methods Invited

    CMStatistics 2023  2023.12.18 

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    Language:English   Presentation type:Oral presentation (invited, special)  

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  • Frequentist predictionalism: the role of model selection criterion and its ontology

    Ohkubo Yusaku, Otsuka Jun

    Philosophy of Science around the world  2023.11.11 

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    Language:English   Presentation type:Oral presentation (general)  

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  • ベイズモデルを用いたマクロ進化の種間比較研究とBSDSモデルによる祖先形質の推定

    大久保祐作

    統計関連連合大会  2022.9 

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    Presentation type:Oral presentation (general)  

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  • なぜ私はフィールドワーカーから聞かれた質問に応えられないのか Invited

    大久保祐作

    第69回日本生態学会年次大会  2022.3.18 

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    Language:Japanese   Presentation type:Symposium, workshop panel (nominated)  

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  • Recent advancements of phylogenetic method Invited

    OHKUBO Yusaku

    2021.11.22 

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    Presentation type:Oral presentation (invited, special)  

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  • ミクロ進化とマクロ進化を結ぶ統計モデリング:連続形質の系統比較法 Invited

    大久保祐作

    統計物理と統計科学のセミナー  2021.6.15 

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    Language:Japanese  

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  • 枝特異的な方向性淘汰の推定について

    大久保祐作, 沓掛展之, 小泉逸郎

    日本生態学会  2021.3 

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    Presentation type:Oral presentation (general)  

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  • ランダム効果×ベイズ推定 Invited

    大久保祐作

    日本比較生理学会若手の会オンライン勉強会  2020.5.14 

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    Language:Japanese   Presentation type:Public lecture, seminar, tutorial, course, or other speech  

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  • データ生成過程という考え方:近似ベイズ 計算による 系統比較法 Invited

    大久保祐作

    統計数理研究所共同利用研究集会「生態データ統計モデルの包括的推進:個体群・群集・行動」  2020.1.10 

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    Language:Japanese   Presentation type:Public lecture, seminar, tutorial, course, or other speech  

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  • Revisiting the two major statistical problems, stopping-rule and the catch-all hypothesis, from the viewpoint of neo-Bayesian statistics.

    Ohkubo Yusaku

    16th Congress of Logic, Methodology and Philosophy of Science and Technology  2019.8.10 

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    Language:English   Presentation type:Oral presentation (general)  

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  • p値とはなんだったのか Invited

    大久保祐作

    日本生態学会  2018.3 

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    Presentation type:Symposium, workshop panel (nominated)  

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Research Projects

  • The role of scientific modeling and the representation theory in the Data Science.

    Grant number:2023-ISMCRP-4202  2023.04

    the Institute of Statistical Mathematics  公募型共同利用研究 

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    Authorship:Principal investigator 

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  • データ同化による数理モデリングと統計モデリングの融合

    Grant number:21K15170  2021.04 - 2026.03

    日本学術振興会  科学研究費助成事業 若手研究  若手研究

    大久保 祐作

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    Authorship:Principal investigator 

    Grant amount:\3510000 ( Direct expense: \2700000 、 Indirect expense:\810000 )

    生態学のあつかう自然現象を説明するには、主に二つのアプローチが考えられる。ひとつはロトカ=ヴォルテラモデルに代表される数理モデルで、もうひとつは階層ベイズモデルに代表される統計モデルである。いずれも生態学を支える礎で同じ「数学」という道具に基づいているにも関わらず、両者には著しい溝がある。
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    異なる2つの数理アプローチを「融合」させることは、生態学がフィールドの複雑な現象を理解する上で不可欠である。特に数理モデルの知見を近年発達の著しい統計モデルに組み込むことは、分析結果の解釈性や一般性を高めるために有効な戦略であると考えられる。本研究では、近年の生態学研究で大きな役割を果たしている二つの手法に注目し、2つのアプローチの融合へ向けた新たな手法の確立を目指す。

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  • Construction of scientific inference program based on philosophy of science and of statistics

    Grant number:20H01736  2020.04 - 2024.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)  Grant-in-Aid for Scientific Research (B)

    松王 政浩, 島谷 健一郎, 森元 良太, 川本 思心, 大久保 祐作

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    Authorship:Coinvestigator(s) 

    Grant amount:\9620000 ( Direct expense: \7400000 、 Indirect expense:\2220000 )

    本研究は、これまで科学哲学で議論されてきた科学の方法論に、数理的および統計学的な視点をプラスして、最終的に科学教育に応用することを目的とする。この目的を果たす上で、二つの大きな課題がある。一つは科学哲学の概念的な議論の中に、科学における数理モデル、統計モデルとの接点を見出すこと。もう一つは、逆に数理・統計モデルに関してその概念的意味を明らかにして科学哲学で扱う問題に接続することである。
    本年は、特に後者に関して重要な成果を上げることができた。これまで本研究のメンバーで研究会等で議論してきた内容を、科学基礎論学会の英文誌 Annalsに、Special Edition: Philosophy of Statistics として5本の論文を掲載した(いずれも査読付き論文)。島谷は科学における統計モデルの位置づけについて、松王は尤度主義の概念的問題について、森元は頻度主義における根本的対立の意味について、また大久保はベイズ主義と頻度主義の対立解消の糸口について、そして尾崎はベイズ主義の実践科学における意味について、それぞれ論じた。このような統計学の哲学的解題は、これまで日本ではほとんど例がなく、画期的である。
    上記成果に加え、代表者の松王は、科学哲学教育の試行の一環として、最高裁判所下の司法研修所における講演を請け負った。講演では、科学哲学の伝統的な問題の一つである、「科学者が科学的判断において価値判断を行うことは適切か」という問題をめぐって、これが実際の科学においていかに問題になりうるかを、統計的な視点を交えつつ、イタリアの「ラクイラ地震裁判」を例として論じた。参加した裁判官の方々に、司法の場で「科学者の価値判断」の可否、是非について考察するよい機会になったものと考える。

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Other research activities

  • Suntory Foundation Grant for the Groundbreaking Young Researchersun

    2019.04
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    2020.03

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Class subject in charge

  • Multivariate Data Analysis B (2023academic year) Second semester  - 月3~4,木5~6

  • Advanced Mathematical Science in Liberal Arts (2023academic year) Third semester  - 水3~4

  • Seminar in Spatio-Temporal Statistics (2023academic year) Year-round  - その他

  • Seminar in Spatio-Temporal Statistics (2023academic year) Year-round  - その他

  • Seminar in Computational Statistics (2023academic year) Year-round  - その他

  • Seminar in Computational Statistics (2023academic year) Year-round  - その他

  • Computational Statistics A-1 (2023academic year) Second semester  - 月3,木5

  • Computational Statistics A-2 (2023academic year) Second semester  - 月4,木6

  • Computational Statistics A (2023academic year) Third semester  - 火1~2,金1~2

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Media Coverage

  • ヘビの警告色・擬態の進化は目立つコストで予測できる Internet

    時事ドットコムニュース  PR TIMES  2024.3

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  • ヘビの警告色・擬態の進化は目立つコストで予測できる Internet

    岡山大学プレスリリース  2024.3

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