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From artisanship to amateur: the challenge to identify large fossils using deep learning

Research Project

Project/Area Number 21K14031
Research Category

Grant-in-Aid for Early-Career Scientists

Allocation TypeMulti-year Fund
Review Section Basic Section 17050:Biogeosciences-related
Research InstitutionKyushu University

Principal Investigator

Matsui Kumiko  九州大学, 総合研究博物館, 特別研究員(CPD) (80816207)

Project Period (FY) 2021-04-01 – 2024-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Fiscal Year 2023: ¥520,000 (Direct Cost: ¥400,000、Indirect Cost: ¥120,000)
Fiscal Year 2022: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2021: ¥3,120,000 (Direct Cost: ¥2,400,000、Indirect Cost: ¥720,000)
Keywords化石 / 種同定 / 軟体動物 / 深層学習 / 自動化
Outline of Research at the Start

本研究計画は化石生物の種同定の自動化を試みるものである.化石の種同定は古生物学の基本であり,地質年代の決定や古環境・堆積環境の推定のために欠かせない技術である.化石種は形態情報に基づく種記載と同定が行われるが,多くの場合で,それらは定性的指標に基づいて主観的に行われて来た.この作業を正確に行うには,長年の経験を要し,古生物学研究の作業効率を低下させている.そこで,本研究ではまず化石を3Dデジタルデータ化する. そして,得られたデータを,深層学習技術を用いて処理,化石の種分類の自動化を実現する事によって古生物学における同定作業の大幅な簡略化を目指す.

Outline of Final Research Achievements

This research project attempts to automate the identification of fossil species. Species identification of fossils is fundamental in paleontology and is an essential technique for determining geological ages and estimating paleo and sedimentary environments. Fossil species are identified based on morphological descriptions, but in many cases, these identifications have been made subjectively based on qualitative indicators. Accurate identification requires years of experience and has reduced the efficiency of paleontological research. Therefore, this study first digitizes fossils into 3D digital data. Then, by processing the obtained data using deep learning technologies, the project aims to automate fossil species classification, significantly simplifying the identification process in paleontology.

Academic Significance and Societal Importance of the Research Achievements

現生生物においてはDNA情報を用いる種同定自動化技術は現在盛んに研究されているものの,形態データにディープラーニングといった人工知能技術を用いた例は非常に限られており,かつ大型化石を種レベルで同定しようという試みは少ない.本研究で使用したイノセラムス類化石は複雑な立体形状を持ち、かつ変形しているなど,形態情報が多い分類群であり,分類のために利用できる情報が限定的で深層学習技術を導入するには比較的悪い条件の対象群であった.これまで「職人技」であった形態種の同定技術をこれまでよりも確実に多くの人が同一の基準を持って実施できるような技術へと変換する技術を提供するものである.

Report

(4 results)
  • 2023 Annual Research Report   Final Research Report ( PDF )
  • 2022 Research-status Report
  • 2021 Research-status Report
  • Research Products

    (27 results)

All 2023 2022 2021 Other

All Int'l Joint Research (3 results) Journal Article (10 results) (of which Int'l Joint Research: 5 results,  Peer Reviewed: 7 results,  Open Access: 9 results) Presentation (14 results) (of which Int'l Joint Research: 9 results)

  • [Int'l Joint Research] Smithsonian Institution/University of California, Santa Cruz/University of Washington(米国)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] Smithsonian Institution/University California, Santa Cruz/University of Washington(米国)

    • Related Report
      2022 Research-status Report
  • [Int'l Joint Research] Smithsonian Institution/University California, Santa Cruz(米国)

    • Related Report
      2021 Research-status Report
  • [Journal Article] New evidence for the antiquity of Desmostylus (Desmostylia) from the Skooner Gulch Formation of California2023

    • Author(s)
      Matsui Kumiko、Pyenson Nicholas D.
    • Journal Title

      Royal Society Open Science

      Volume: 10 Issue: 6 Pages: 221648-221648

    • DOI

      10.1098/rsos.221648

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] 淡水から深海まで:海棲哺乳類の進化と海棲適応2023

    • Author(s)
      松井久美子
    • Journal Title

      細胞

      Volume: 55 Pages: 1173-1176

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A new program of the hands-on research activity workshop using mammalian teeth.2023

    • Author(s)
      Kumiko Matsui
    • Journal Title

      The Bulletin of the Hobetsu Museum

      Volume: 38 Pages: 1-10

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] New data from the first discovered paleoparadoxiid (Desmostylia) specimen shed light into the morphological variation of the genus Neoparadoxia2022

    • Author(s)
      Matsui Kumiko、Valenzuela-Toro Ana M.、Pyenson Nicholas D.
    • Journal Title

      Scientific Reports

      Volume: 12 Issue: 1 Pages: 14246-14246

    • DOI

      10.1038/s41598-022-18295-5

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Museum Exhibitions of Fossil Specimens Into Commercial Products: Unexpected Outflow of 3D Models due to Unwritten Image Policies2022

    • Author(s)
      Matsui Kumiko、Kimura Yuri
    • Journal Title

      Frontiers in Earth Science

      Volume: 10 Pages: 874736-874736

    • DOI

      10.3389/feart.2022.874736

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] New data from the first discovered paleoparadoxiid (Desmostylia) specimen shed light into the morphological variation of the genus Neoparadoxia2022

    • Author(s)
      Kumiko Matsui, Ana M. Valenzuela-Toro, Nicholas D. Pyenson
    • Journal Title

      Research Square

      Volume: 10.21203/rs.3.rs-1094164/

    • Related Report
      2022 Research-status Report
    • Open Access / Int'l Joint Research
  • [Journal Article] A “mammalian-like” pycnodont fish: Independent acquisition of thecodont implantation, true vertical replacement, and carnassial dentitions in carnivorous mammals and a peculiar group of pycnodont fish2022

    • Author(s)
      Matsui, K. and Y. Kimura
    • Journal Title

      Life

      Volume: 12 Issue: 2 Pages: 250-250

    • DOI

      10.3390/life12020250

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Museum exhibitions of fossils into commercial products: Unexpected outflow of 3D models due to unwritten image policies into commercial products2022

    • Author(s)
      Matsui Kumiko、Kimura Yuri
    • Journal Title

      EarthArXiv

      Volume: -

    • DOI

      10.31223/x5zw5z

    • Related Report
      2021 Research-status Report
    • Open Access
  • [Journal Article] New record of a rostrum of waterbird (Aves, Suliformes) from the Oligocene of Ashiya Group in Ainoshima Island, Kyushu, Japan2021

    • Author(s)
      Soichiro Kawabe, Yusuke Ando, Shigenori Kawano, Kumiko Matsui
    • Journal Title

      Bulletin of the Kitakyushu Museum of Natural History

      Volume: 19 Pages: 35-39

    • NAID

      130008029553

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Independent Acquisition of Carnassial Teeth in Fishes and Mammals2021

    • Author(s)
      Matsui Kumiko、Kimura Yuri
    • Journal Title

      Research Square

      Volume: -

    • DOI

      10.21203/rs.3.rs-1094239/v1

    • Related Report
      2021 Research-status Report
    • Open Access
  • [Presentation] Fossil baleen whales (Cetacea, Mysticeti) show that brain shapes achieved modern before baleen evolved2023

    • Author(s)
      Kumiko Matsui, Nicholas D. Pyenson, Takanobu Tsuihiji, Hiroshi Sawamura, Tatsuro Ando
    • Organizer
      SVP 83rd Annual Meeting
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] New discoveries from the museum's classic fossil collections2023

    • Author(s)
      Kumiko Matsui, Ana Valenzuela-Toro, Nicholas Pyenson
    • Organizer
      APC2
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] A specimen of Menabites (Collignoniceratidae, Ammonitida) with pathological deformations found from the Campanian Toyajo Formation, Wakayama Prefecture, Japan.2023

    • Author(s)
      Tomoki Karasawa, Akihiro Misaki, Kumiko Matsui
    • Organizer
      The 172nd Regular Meeting, the Palaeontological Society of Japan.
    • Related Report
      2022 Research-status Report
  • [Presentation] “Outbreak”: Walking with a smartphone or camera sets a new risk for the museums2022

    • Author(s)
      Kumiko Matsui, Yuri Kimura
    • Organizer
      GSA Connects 2022
    • Related Report
      2022 Research-status Report
    • Int'l Joint Research
  • [Presentation] The same Pathological deformation patterns were recognized in Japanese ammonoids from different age and different taxa2022

    • Author(s)
      Tomoki Karasawa, Kumiko Matsui, Akihiro Misaki, Shigehiro Uchida
    • Organizer
      GSA Connects 2022
    • Related Report
      2022 Research-status Report
    • Int'l Joint Research
  • [Presentation] Fossil Baleen whales (Mysticeti) show that cerebrum size achieved modern size before baleen evolved2022

    • Author(s)
      Kumiko Matsui, Nicholas D. Pyenson, Takanobu Tsuihiji, Hiroshi Sawamura, Tatsuro Ando
    • Organizer
      GSA Connects 2022
    • Related Report
      2022 Research-status Report
    • Int'l Joint Research
  • [Presentation] Museums at risk by leaving 3D image policies unwritten2022

    • Author(s)
      Kumiko Matsui, Yuri Kimura
    • Organizer
      AVICOM in ICOM 2022
    • Related Report
      2022 Research-status Report
    • Int'l Joint Research
  • [Presentation] Reexamination of Neostrachanognathus feeding organ reconstruction based on natural conodont assemblages from Olenekian (Late Early Triassic) whetstone-type siliceous claystone in the Itsuki area, Kumamoto Prefecture, Japan2022

    • Author(s)
      Yuichi Fukushima, Sachiko Agematsu, Kumiko Matsui, Kaneyoshi Fujiwara, Teruyuki Maruoka
    • Organizer
      The 129th Annual Meeting of the Geological Society of Japan
    • Related Report
      2022 Research-status Report
  • [Presentation] Mammalian fossils from Senjo-jiki, Wakamatsu, Kitakyushu, Japan.2022

    • Author(s)
      Kumiko Matsui, Nicholas D. Pyenson, Kohta Shimazoe, Tomoyuki Ohashi
    • Organizer
      The 2022 Annual Meeting, the Palaeontological Society of Japan
    • Related Report
      2022 Research-status Report
  • [Presentation] Walking with a smartphone makes new risks: unwritten photo policies in museums cause an unexpected outbreak.2022

    • Author(s)
      Kimura Yuri, Kumiko Matsui
    • Organizer
      The 2022 Annual Meeting, the Palaeontological Society of Japan
    • Related Report
      2022 Research-status Report
  • [Presentation] ”Newly” discovered desmostylians from Unalaska, Alaska, USA.2022

    • Author(s)
      松井久美子, Nicholas D. Pyenson
    • Organizer
      The 171st Regular Meeting, the Palaeontological Society of Japan
    • Related Report
      2021 Research-status Report
  • [Presentation] Are internal structures preserved in vertebrates’ fossils useful for finite element analyses?; a pilot analysis using multiple preservation fossils2021

    • Author(s)
      Kumiko Matsui
    • Organizer
      MECHANICAL FINDER User Meeting 2021
    • Related Report
      2021 Research-status Report
    • Int'l Joint Research
  • [Presentation] Mammalian-like tooth replacement in a Pycnodont fish jaw.2021

    • Author(s)
      Kumiko Matsui, Yuri Kimura.
    • Organizer
      The Society of Vertebrate Paleontology 81st Annual Meeting Virtual 2021
    • Related Report
      2021 Research-status Report
    • Int'l Joint Research
  • [Presentation] The digital cranial endocast of Dusisiren dewana: the implication for paleoecological changes of hydrodamalinae2021

    • Author(s)
      Kumiko Matsui, Tohru Kobayashi
    • Organizer
      The 9th SECAD. Online
    • Related Report
      2021 Research-status Report
    • Int'l Joint Research

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Published: 2021-04-28   Modified: 2025-01-30  

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