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Theory design and implementation of practical optimization and enumeration algorithms over graph structure

Research Project

Project/Area Number 20K11691
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Review Section Basic Section 60020:Mathematical informatics-related
Research InstitutionKyoto University

Principal Investigator

NAGAMOCHI Hiroshi  京都大学, 情報学研究科, 教授 (70202231)

Co-Investigator(Kenkyū-buntansha) Shurbevski A  京都大学, 情報学研究科, 助教 (70750230)
Project Period (FY) 2020-04-01 – 2023-03-31
Project Status Completed (Fiscal Year 2022)
Budget Amount *help
¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
Fiscal Year 2022: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2021: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2020: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Keywords離散最適化 / グラフ理論 / アルゴリズム / 整数計画法 / 動的計画法 / ケモインフォマティックス / グラフ・ネットワーク / 計算量
Outline of Research at the Start

情報工学的諸問題の多くは離散構造を有しており、これらを離散最適化問題として定式化することで数学的に高度な議論の適用が可能になる。しかし一般に、分枝限定法、動的計画法や整数計画法などの汎用的手法を原理的に適用するだけでは、効率の良いアルゴリズムを得ることは期待できない。本研究では、広範な現実問題が共有する数学的な構造としてグラフ・ネットワーク構造などを抽出し、構造特性を利用したアルゴリズムを設計することを目指す。

Outline of Final Research Achievements

We have obtained a common generalization of straight-line and upward drawings; a theory of 1-plane re-embeddable drawings; a polynomial-delay algorithm for generating all induced connected subgraphs with maximal common item sets in a graph with items on vertices; and a method of finding all PCGs based on an integer programming formulation and an alternative theorem of linear programming. We have also formulated an integer program based method that infers a chemical graph with a desired chemical property using a trained artificial neural network and designed an algorithm for enumerating isomers of the solution of the integer program.

Academic Significance and Societal Importance of the Research Achievements

オペレーションズ・リサーチ(OR)の手法である数理計画法(線形計画法・整数計画法など)とコンピュータサイエンス(CS)の離散構造列挙アルゴリズムを組み合わせることで,グラフ構造の数学的問題を解き,化学グラフ列挙決システムを構築した.本研究で示した方法論は,学術的には新しい研究分野の創成につながる可能性がある点で重要である.また,計算機で化合物の分子構造を自動設計するシステムは実装・公開しており,今後利用が広まれば社会的にも大きな影響を与えると考えられる.

Report

(4 results)
  • 2022 Annual Research Report   Final Research Report ( PDF )
  • 2021 Research-status Report
  • 2020 Research-status Report
  • Research Products

    (33 results)

All 2023 2022 2021 2020 Other

All Int'l Joint Research (3 results) Journal Article (14 results) (of which Int'l Joint Research: 5 results,  Peer Reviewed: 14 results,  Open Access: 9 results) Presentation (11 results) (of which Int'l Joint Research: 11 results) Book (1 results) Remarks (4 results)

  • [Int'l Joint Research] シドニー大学(オーストラリア)

    • Related Report
      2021 Research-status Report
  • [Int'l Joint Research] シドニー大学(オーストラリア)

    • Related Report
      2020 Research-status Report
  • [Int'l Joint Research] 電子科学技術大学(中国)

    • Related Report
      2020 Research-status Report
  • [Journal Article] Enumeration of Support-Closed Subsets in Confluent Systems2022

    • Author(s)
      Haraguchi Kazuya、Nagamochi Hiroshi
    • Journal Title

      Algorithmica

      Volume: - Issue: 5 Pages: 1279-1315

    • DOI

      10.1007/s00453-022-00927-x

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A New Approach to the Design of Acyclic Chemical Compounds Using Skeleton Trees and Integer Linear Programming2022

    • Author(s)
      F. Zhang, J. Zhu, R. Chiewvanichakorn, A. Shurbevski, H. Nagamochi, T. Akutsu
    • Journal Title

      Applied Intelligence

      Volume: - Issue: 15 Pages: 17058-17072

    • DOI

      10.1007/s10489-021-03088-6

    • Related Report
      2022 Annual Research Report 2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] On the enumeration of minimal non-pairwise compatibility graphs2022

    • Author(s)
      Naveed Ahmed Azam, Aleksandar Shurbevski, Hiroshi Nagamochi
    • Journal Title

      Journal of Combinatorial Optimization

      Volume: 44 Issue: 4 Pages: 2871-2892

    • DOI

      10.1007/s10878-021-00799-x

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A Novel Method for Inferring Chemical Compounds with Prescribed Topological Substructures Based on Integer Programming2021

    • Author(s)
      J. Zhu, N. A. Azam, F. Zhang, A. Shurbevski, K. Haraguchi, L. Zhao, H. Nagamochi, T. Akutsu
    • Journal Title

      Transaction on Computational Biology and Bioinformatics

      Volume: - Issue: 6 Pages: 3233-3245

    • DOI

      10.1109/tcbb.2021.3112598

    • Related Report
      2022 Annual Research Report 2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Re-embedding a 1-Plane Graph for a Straight-line Drawing in Linear Time2021

    • Author(s)
      S. Hong, H. Nagamochi
    • Journal Title

      Theoretical Computer Science

      Volume: 892 Pages: 132-154

    • DOI

      10.1016/j.tcs.2021.09.015

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] A novel method for inference of acyclic chemical compounds with bounded branch-height based on artificial neural networks and integer programming2021

    • Author(s)
      Azam Naveed Ahmed、Zhu Jianshen、Sun Yanming、Shi Yu、Shurbevski Aleksandar、Zhao Liang、Nagamochi Hiroshi、Akutsu Tatsuya
    • Journal Title

      Algorithms for Molecular Biology

      Volume: 16 Issue: 1 Pages: 18-18

    • DOI

      10.1186/s13015-021-00197-2

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] A Method for Enumerating Pairwise Compatibility Graphs with a Given Number of Vertices2021

    • Author(s)
      N. A. Azam, Aleksandar Shurbevski, H. Nagamochi
    • Journal Title

      Discrete Applied Mathematics

      Volume: 303 Pages: 171-185

    • DOI

      10.1016/j.dam.2020.08.016

    • Related Report
      2021 Research-status Report
    • Peer Reviewed
  • [Journal Article] 機械学習QSARの整数計画法に基づく逆解析法2021

    • Author(s)
      NAGAMOCHI Hiroshi、ZHU Jianshen、AZAM Naveed Ahmed、HARAGUCHI Kazuya、ZHAO Liang、AKUTSU Tatsuya
    • Journal Title

      Journal of Computer Chemistry, Japan

      Volume: 20 Issue: 3 Pages: 106-111

    • DOI

      10.2477/jccj.2021-0030

    • NAID

      130008130265

    • ISSN
      1347-1767, 1347-3824
    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] An Inverse QSAR Method Based on a Two-Layered Model and Integer Programming2021

    • Author(s)
      Shi Yu、Zhu Jianshen、Azam Naveed Ahmed、Haraguchi Kazuya、Zhao Liang、Nagamochi Hiroshi、Akutsu Tatsuya
    • Journal Title

      International Journal of Molecular Sciences

      Volume: 22 Issue: 6 Pages: 2847-2847

    • DOI

      10.3390/ijms22062847

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Group Strategy-proof Mechanisms for Shuttle Facility Games2020

    • Author(s)
      Yuhei Fukui, Aleksandar Shurbevski, Hiroshi Nagamochi
    • Journal Title

      Journal of Information Processing

      Volume: 28 Issue: 0 Pages: 976-986

    • DOI

      10.2197/ipsjjip.28.976

    • NAID

      130007956357

    • ISSN
      1882-6652
    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Enumerating tree-like graphs and polymer topologies with a given cycle rank2020

    • Author(s)
      Naveed Ahmed Azam, Aleksandar Shurbevski, Hiroshi Nagamochi
    • Journal Title

      Entropy

      Volume: 22 Issue: 11 Pages: 1295-1295

    • DOI

      10.3390/e22111295

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Characterizing star-PCGs2020

    • Author(s)
      Mingyu Xiao, Hiroshi Nagamochi
    • Journal Title

      Algorithmica

      Volume: 82 Issue: 10 Pages: 3066-3090

    • DOI

      10.1007/s00453-020-00712-8

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] An efficient algorithm to count tree-like graphs with a given number of vertices and self-loops2020

    • Author(s)
      Naveed Ahmed Azam, Aleksandar Shurbevski, Hiroshi Nagamochi
    • Journal Title

      Entropy

      Volume: 22 Issue: 9 Pages: 923-923

    • DOI

      10.3390/e22090923

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A novel method for inference of chemical compounds of cycle index two with desired properties based on artificial neural networks and integer programming2020

    • Author(s)
      Jianshen Zhu, Chenxi Wang, Aleksandar Shurbevski, Hiroshi Nagamochi,Tatsuya Akutsu
    • Journal Title

      Algorithms

      Volume: 13 Issue: 5 Pages: 124-124

    • DOI

      10.3390/a13050124

    • NAID

      120006993972

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] Adjustive linear regression and its application to the inverse QSAR2022

    • Author(s)
      Jianshen Zhu, Kazuya Haraguchi, Hiroshi Nagamochi, Tatsuya Akutsu
    • Organizer
      13th International Conference on Bioinformatics Models, Methods and Algorithms
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Molecular design based on integer programming and quadratic descriptors in a two-layered model2022

    • Author(s)
      Jianshen Zhu, Naveed Ahmed Azam, Shengjuan Cao, Ryota Ido, Kazuya Haraguchi, Liang Zhao, Hiroshi Nagamochi and Tatsuya Akutsu
    • Organizer
      The 21st International Conference on Bioinformatics
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Adjustive Linear Regression and Its Application to the Inverse QSAR2022

    • Author(s)
      J. Zhu, K. Haraguchi, H. Nagamochi, T. Akutsu
    • Organizer
      The 13th International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS 2022)
    • Related Report
      2021 Research-status Report
    • Int'l Joint Research
  • [Presentation] Molecular Design Based on Artificial Neural Networks, Integer Programming and Grid Neighbor Search2021

    • Author(s)
      N. A. Azam, J. Zhu, K. Haraguchi, L. Zhao, H. Nagamochi, T. Akutsu
    • Organizer
      The IEEE International Conference on Bioinformatics and Biomedicine (BIBM2021)
    • Related Report
      2021 Research-status Report
    • Int'l Joint Research
  • [Presentation] An Inverse QSAR Method Based on Decision Tree and Integer Programming2021

    • Author(s)
      K. Tanaka, J. Zhu, N. A. Azam, K. Haraguchi, L. Zhao, H. Nagamochi, T. Akutsu
    • Organizer
      The 17th International Conference on Intelligent Computing
    • Related Report
      2021 Research-status Report
    • Int'l Joint Research
  • [Presentation] An Improved Integer Programming Formulation for Inferring Chemical Compounds with Prescribed Topological Structures2021

    • Author(s)
      J. Zhu, N. A. Azam, K. Haraguchi, L. Zhao, H. Nagamochi, T. Akutsu
    • Organizer
      The 34th International Conference on Industrial, Engineering & Other Applications of Applied Intelligent Systems (IEA/AIE 2021)
    • Related Report
      2021 Research-status Report
    • Int'l Joint Research
  • [Presentation] Experimental results of a dynamic programming algorithm for generating chemical isomers based on frequency vectors2020

    • Author(s)
      Naveed Ahmed Azam, Jianshen Zhu, Ryota Ido, Hiroshi Nagamochi,Tatsuya Akutsu
    • Organizer
      The Fourth International Workshop on Enumeration Problems and Applications
    • Related Report
      2020 Research-status Report
    • Int'l Joint Research
  • [Presentation] Path-monotonic upward drawings of plane graphs2020

    • Author(s)
      Seok-Hee Hong, Hiroshi Nagamochi
    • Organizer
      The 26th International Computing and Combinatorics Conference
    • Related Report
      2020 Research-status Report
    • Int'l Joint Research
  • [Presentation] On the enumeration of minimal non-pairwise compatibility graphs2020

    • Author(s)
      Naveed Ahmed Azam, Aleksandar Shurbevski, Hiroshi Nagamochi
    • Organizer
      The 26th International Computing and Combinatorics Conference
    • Related Report
      2020 Research-status Report
    • Int'l Joint Research
  • [Presentation] A novel method for the inverse QSAR/QSPR to monocyclic chemical compounds based on artificial neural networks and integer programming2020

    • Author(s)
      Ren Ito, Naveed Ahmed Azam, Chenxi Wang, Aleksandar Shurbevski,Hiroshi Nagamochi, Tatsuya Akutsu
    • Organizer
      The 21st International Conference on Bioinformatics & Computational Biology
    • Related Report
      2020 Research-status Report
    • Int'l Joint Research
  • [Presentation] A new integer linear programming formulation to the inverse QSAR/QSPR for acyclic chemical compounds using skeleton trees2020

    • Author(s)
      F. Zhang, J. Zhu, R. Chiewvanichakorn, A. Shurbevski, H. Nagamochi,T. Akutsu
    • Organizer
      The 33rd International Conference on Industrial, Engineering and Other Applications of Applied Intelligent Systems
    • Related Report
      2020 Research-status Report
    • Int'l Joint Research
  • [Book] ケモインフォマティクスにおけるデータ解析の進め方と具体的応用法2023

    • Author(s)
      永持仁(分担執筆)
    • Publisher
      技術情報協会
    • Related Report
      2022 Annual Research Report
  • [Remarks] 京都大学情報学研究科離散数理分野ホームページ

    • URL

      https://www-or.amp.i.kyoto-u.ac.jp/index.html

    • Related Report
      2022 Annual Research Report
  • [Remarks] 化学グラフの構造推定を行う計算プログラムのサイト

    • URL

      https://github.com/ku-dml/mol-infer

    • Related Report
      2022 Annual Research Report
  • [Remarks] 分子構造設計アルゴリズムに開発したプログラムコードの公開サイトGitHub

    • URL

      https://github.com/ku-dml/mol-Infer

    • Related Report
      2021 Research-status Report
  • [Remarks] 分子構造設計アルゴリズムに開発したプログラムコードの公開サイト

    • Related Report
      2020 Research-status Report

URL: 

Published: 2020-04-28   Modified: 2024-01-30  

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