• Search Research Projects
  • Search Researchers
  • How to Use
  1. Back to previous page

Applications of modern coding theory to DNA storage

Research Project

Project/Area Number 21K14160
Research Category

Grant-in-Aid for Early-Career Scientists

Allocation TypeMulti-year Fund
Review Section Basic Section 21020:Communication and network engineering-related
Research InstitutionShinshu University (2023)
Tokyo University of Science (2021-2022)

Principal Investigator

Shibata Ryo  信州大学, 工学部, 助教 (60898401)

Project Period (FY) 2021-04-01 – 2024-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2023: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2022: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Fiscal Year 2021: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
KeywordsLDPC符号 / 空間結合符号 / 挿入削除誤り / DNAストレージ / 次世代ストレージ / 連接符号 / 同期誤り訂正 / 確率推論 / DNA / 挿入/削除誤り / 確率伝搬法 / 次世代ストレージ技術
Outline of Research at the Start

近年、DNAを使ってデジタルデータを記録しようという挑戦が世界中の研究機関や企業でなされている。DNAストレージは、数百年単位の記録寿命かつ1グラムあたり数百ペタバイトのデータ保存を実現できると期待されているが、データの重複・損失・置換による誤りが発生し、信頼性の低下が懸念される。本研究では、シャノン限界に近い性能を達成するLDPC符号と確率推論に基づく復号法に代表される現代的な符号理論の枠組みで、それらの誤りの訂正方法の提案、より高い効率性・信頼性・安定性の実現方法の提案、および訂正能力を評価しその有効性を示すことを目的とする。

Outline of Final Research Achievements

In this study, we propose a new coding and decoding scheme based on Low-Density Parity-Check (LDPC) codes and probabilistic inference to correct insertion, deletion, and substitution (IDS) errors, which are known to occur in DNA storage. Specifically, we developed a design method for irregular LDPC codes for ID+noise errors, a sliding window-based error correction method, and a nonbinary LDPC coding method to correct position errors in racetrack memory (RM). These methods have improved the reliability and efficiency of IDS error correction codes, taking a step toward practical application. Additionally, the delayed coding (DC) scheme enables high performance while reducing computational costs.

Academic Significance and Societal Importance of the Research Achievements

本研究は,DNAストレージ技術の信頼性,効率性,安定性を向上させるための新しい基礎理論を提供するものである.学術的には,IDS誤りの数理モデルと通信路容量の計算を通じて理論的限界を明らかにし,LDPC符号と確率推論に基づく革新的な符号化および復号法を提案した.社会的には,次世代ストレージ技術 (DNAストレージ,レーストラックメモリ等) の発展とデータ保存の信頼性向上に貢献するものである.これにより,重要なデータの長期保存がより安全かつ確実に行えるようになる.

Report

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

    (14 results)

All 2024 2023 2022 2021

All Journal Article (5 results) (of which Peer Reviewed: 4 results,  Open Access: 1 results) Presentation (9 results) (of which Int'l Joint Research: 4 results,  Invited: 1 results)

  • [Journal Article] Shift-Interleave Coding for DNA-Based Storage: Correction of IDS Errors and Sequence Losses2024

    • Author(s)
      R. Shibata and H. Kaneko
    • Journal Title

      arXiv [cs.IT]

      Volume: Jan. 26 Pages: 1-6

    • Related Report
      2023 Annual Research Report
  • [Journal Article] Symbol-Level Detection With Matched Non-Binary LDPC Codes for Position Errors in Racetrack Memories2023

    • Author(s)
      Shibata Ryo、Yashima Hiroyuki
    • Journal Title

      IEEE Transactions on Magnetics

      Volume: 59 Issue: 2 Pages: 1-9

    • DOI

      10.1109/tmag.2022.3214932

    • Related Report
      2022 Research-status Report
    • Peer Reviewed
  • [Journal Article] Windowed-based synchronization error-correction for spatially coupled codes2022

    • Author(s)
      Shibata Ryo、Yashima Hiroyuki
    • Journal Title

      IEICE Communications Express

      Volume: 11 Issue: 11 Pages: 697-702

    • DOI

      10.1587/comex.2022XBL0121

    • ISSN
      2187-0136
    • Year and Date
      2022-11-01
    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Deep-learning-aided design of LDPC coding scheme for two-user Gaussian multiple access channels2022

    • Author(s)
      Usui Jumpei、Shibata Ryo、Yashima Hiroyuki
    • Journal Title

      IEICE Communications Express

      Volume: 11 Issue: 2 Pages: 111-116

    • DOI

      10.1587/comex.2021XBL0200

    • NAID

      130008150682

    • ISSN
      2187-0136
    • Year and Date
      2022-02-01
    • Related Report
      2021 Research-status Report
    • Peer Reviewed
  • [Journal Article] Design and Performance of Low-Density Parity-Check Codes for Noisy Channels with Synchronization Errors2022

    • Author(s)
      SHIBATA Ryo、YASHIMA Hiroyuki
    • Journal Title

      IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences

      Volume: E105.A Issue: 1 Pages: 63-67

    • DOI

      10.1587/transfun.2021EAL2013

    • NAID

      130008138750

    • ISSN
      0916-8508, 1745-1337
    • Year and Date
      2022-01-01
    • Related Report
      2021 Research-status Report
    • Peer Reviewed
  • [Presentation] LDPC coded DBICM system for multiple access channels2024

    • Author(s)
      M. Kawasumi, H. Yashima, R. Shibata
    • Organizer
      in Proc. International Workshop on Nonlinear Circuits, Communications and Signal Processing (NCSP)
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] A novel energy efficient clustering using a sleep awake algorithm for energy harvesting wireless sensor networks2023

    • Author(s)
      S. Takie, R. Shibata, and H. Yashima
    • Organizer
      in Proc. International Workshop on Nonlinear Circuits, Communications and Signal Processing (NCSP)
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] マルチアクセス通信路に対するLDPC符号化DBICMシステムの設計と解析2023

    • Author(s)
      川隅匡登,柴田 凌,八嶋弘幸
    • Organizer
      第46回情報理論とその応用シンポジウム
    • Related Report
      2023 Annual Research Report
  • [Presentation] Improved HICR scheme for noisy insertion and deletion channels: dynamic scheduling and unequal error protection2023

    • Author(s)
      R. Shibata
    • Organizer
      The 46th Symposium on Information Theory and its Applications
    • Related Report
      2023 Annual Research Report
  • [Presentation] マルチアクセス通信路に対するLDPC符号化DBICMシステム2023

    • Author(s)
      川隅匡登,柴田 凌,八嶋弘幸
    • Organizer
      電子情報通信学会情報理論研究会
    • Related Report
      2023 Annual Research Report
  • [Presentation] Modern Channel Coding for Synchronization Errors2022

    • Author(s)
      Shibata Ryo
    • Organizer
      2022 International Conference on Emerging Technologies for Communications
    • Related Report
      2022 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Delayed Coding Scheme for Channels with Insertion, Deletion, and Substitution Errors2022

    • Author(s)
      Shibata Ryo, Yashima Hiroyuki
    • Organizer
      2022 IEEE Global Communications Conference
    • Related Report
      2022 Research-status Report
    • Int'l Joint Research
  • [Presentation] FSK信号を入出力としたAND/OR切替可能な全光論理回路2022

    • Author(s)
      平川竜之, 柴田 凌, 八嶋 弘幸
    • Organizer
      2022年電子情報通信学会総合大会
    • Related Report
      2021 Research-status Report
  • [Presentation] 非正則Multi-Kernel Polar符号の提案と性能調査2021

    • Author(s)
      樋口 智大, 柴田 凌, 八嶋 弘幸
    • Organizer
      第44回情報理論とその応用シンポジウム
    • Related Report
      2021 Research-status Report

URL: 

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

Information User Guide FAQ News Terms of Use Attribution of KAKENHI

Powered by NII kakenhi