Development of versatile techniques for computing similarity between tree-structured data

• Project/Area Number: 21700178
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Single-year Grants
• Research Field: Intelligent informatics
• Research Institution: Doshisha University (2010-2012); National Institute of Informatics (2009)
• Principal Investigator: FUKAGAWA Daiji 同志社大学, 文化情報学部, 助教 (10442518)
• Project Period (FY): 2009 – 2012
• Project Status: Completed (Fiscal Year 2012)
• Budget Amount: ¥2,990,000 (Direct Cost: ¥2,300,000、Indirect Cost: ¥690,000); Fiscal Year 2012: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000); Fiscal Year 2011: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000); Fiscal Year 2010: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000); Fiscal Year 2009: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
• Keywords: 木構造 / 類似度 / 近似パターン照合 / アルゴリズム / 類似度計算

Research Abstract

In this project, we developed several methods which computes distance between tree structured data and gives an approximate matching between them. As a result, we obtained fast approximate algorithms which computes edit distance between ordered/unordered trees, fixed parameter algorithm to compute the proper tree edit distance, fast exact algorithm to compute an optimal tree matching via maximum clique problem, a probabilistic model to measure similarity of trees and a learning algorithm for the model.

Research Products

• [Journal Article] Approximation and parameterized algorithms for common subtrees and edit distance between unordered trees (2013)
  • Author(s): Tatsuya Akutsu, Daiji Fukagawa, Magnus M. Halldorsson, Atsuhiro Takasu, Keisuke Tanaka
  • Journal Title: Theoretical Computer Science Volume: 470 Pages: 10-22
  • NAID: 120005241356
  • Peer Reviewed
• [Journal Article] A Clique-Based Method Using Dynamic Programming for Computing Edit Distance Between Unordered Trees (2012)
  • Author(s): Tomoya Mori, Takeyuki Tamura, Daiji Fukagawa, Atsuhiro Takasu, Etsuji Tomita, Tatsuya Akutsu
  • Journal Title: Journal of Computational Biology Volume: 19(10) Issue: 10 Pages: 1089-1104
  • DOI: 10.1089/cmb.2012.0133
  • NAID: 120004920413
  • Peer Reviewed
• [Journal Article] A clique-based method for the edit distance between unordered trees and its application to analysis of glycan structures (2011)
  • Author(s): Daiji Fukagawa, Takeyuki Tamura, Atsuhiro Takasu, Etsuji Tomita, Tatsuya Akutsu
  • Journal Title: BMC Bioinformatics Volume: 12(S-1): S13 Issue: S1
  • DOI: 10.1186/1471-2105-12-s1-s13
  • NAID: 120003517915
  • Peer Reviewed
• [Journal Article] Exact algorithms for computing the tree edit distance between unordered trees (2011)
  • Author(s): Tatsuya Akutsu, Daiji Fukagawa, Atsuhiro Takasu, Takeyuki Tamura
  • Journal Title: Theoretical Computer Science Volume: 412(4-5) Issue: 4-5 Pages: 352-364
  • DOI: 10.1016/j.tcs.2010.10.002
  • NAID: 120003517914
  • Peer Reviewed
• [Journal Article] A clique-based method for the edit distance between unordered trees and its application to analysis of glycan structures. (2011)
  • Author(s): D.Fukagawa, T.Tamura, A.Takasu, E.Tomita, T.Akutsu
  • Journal Title: BMC Bioinformatics (Suppl.for APBC 2011) Volume: 12, Suppl 1
  • NAID: 120003517915
  • Peer Reviewed
• [Journal Article] Exact algorithms for computing tree edit distance between unordered trees. (2011)
  • Author(s): T.Akutsu, D.Fukagawa, A.Takasu, T.Tamura
  • Journal Title: Theoretical Computer Science Volume: 421 Pages: 352-364
  • NAID: 120003517914
  • Peer Reviewed
• [Journal Article] Approximating Tree Edit Distance through String Edit Distance (2010)
  • Author(s): Tatsuya Akutsu, Daiji Fukagawa, Atsuhiro Takasu
  • Journal Title: Algorithmica Volume: 57(2) Issue: 2 Pages: 325-348
  • DOI: 10.1007/s00453-008-9213-z
  • NAID: 120002141662
  • Peer Reviewed
• [Journal Article] Approximating tree edit distance through string edit distance. (2010)
  • Author(s): T.Akutsu, D.Fukagawa, A.Takasu
  • Journal Title: Algorithmica Volume: 57 Pages: 325-348
  • NAID: 120002141662
  • Peer Reviewed
• [Journal Article] Approximating tree edit distance through string edit distance (2010)
  • Author(s): T.Akutsu, D.Fukagawa, A.Takasu
  • Journal Title: Algorithmica 57 Pages: 325-348
  • NAID: 120002141662
  • Peer Reviewed
• [Presentation] 無順序木の編集距離の指数時間厳密アルゴリズム (2012)
  • Author(s): 阿久津達也, 田村武幸, 深川大路, 高須淳宏
  • Organizer: 電子情報通信学会コンピュテーション研究会
  • Place of Presentation: 北海道大学
  • Year and Date: 2012-06-21
• [Presentation] Efficient Exponential Time Algorithms for Edit Distance between Unordered Trees. Proc. (2012)
  • Author(s): Tatsuya Akutsu, Takeyuki Tamura, Daiji Fukagawa, Atsuhiro Takasu
  • Organizer: 23rd Annual Symposium on Combinatorial Pattern Matching (CPM 2012)
  • Place of Presentation: Helsinki, Finland
• [Presentation] Efficient Exponential Time Algorithms for Edit Distance between Unordered Trees (2012)
  • Author(s): Tatsuya Akutsu, Takeyuki Tamura, Daiji Fukagawa, Atsuhiro Takasu
  • Organizer: 23rd Annual Symposium on Combinatorial Pattern Matching (CPM 2012)
  • Place of Presentation: Helsinki, Finland
• [Presentation] An Improved Clique-Based Method for Computing Edit Distance between Rooted Unordered Trees (2011)
  • Author(s): Tomoya Mori, Takeyuki Tamura, Daiji Fukagawa, Atsuhiro Takasu, Etsuji Tomita, Tatsuya Akutsu
  • Organizer: 情報処理学会第26回バイオ情報学研究発表会
  • Place of Presentation: 神戸大学
  • Year and Date: 2011-09-13
• [Presentation] An Improved Clique-Based Method for Computing Edit Distance between Rooted Unordered Trees",研究報告.SIG-BIO,バイオ情報学2011(3)pp.1-6 2011年9月 (2011)
  • Author(s): T.Mori, T.Tamura, D.Fukagawa, A.Takasu, E.Tomita, T.Akutsu
  • Organizer: 情報処理学会第26回バイオ情報学研究発表会
  • Place of Presentation: 神戸大学・自然科学総合研究棟(兵庫県)
  • Year and Date: 2011-09-13
• [Presentation] An improved clique-based method for computing edit distance between unordered trees and its application to comparison of glycan structures (2011)
  • Author(s): T.Akutsu, T.Mori, T.Tamura, D.Fukagawa, A.Takasu, E.Tomita
  • Organizer: 4th International Workshop on Intelligent Informatics in Biology and Medicine (IIBM 2011)
  • Place of Presentation: Korean Bible University (Seoul, Korea)
  • Year and Date: 2011-06-30
• [Presentation] An Improved Clique-Based Method for Computing Edit Distance between Unordered Trees and Its Application to Comparison of Glycan Structures (2011)
  • Author(s): Tatsuya Akutsu, Tomoya Mori, Takeyuki Tamura, Daiji Fukagawa, Atsuhiro Takasu, Etsuji Tomita
  • Organizer: International Conference on Complex, Intelligent and Software Intensive Systems (CISIS 2011)
  • Place of Presentation: Korean Bible University (Seoul, Korea)
• [Presentation] A variational Bayesian EM algorithm for tree similarity (2010)
  • Author(s): A.Takasu, D.Fukagawa, T.Akutsu
  • Organizer: Proc.20th International Conference on Pattern Recognition (ICPR 2010)
  • Place of Presentation: Istanbul Convention & Exhibition Centre, Istanbul, Turkey
  • Year and Date: 2010-08-24
• [Presentation] 無順序木の編集距離を計算する実用的アルゴリズムについて (2010)
  • Author(s): 深川大路, 田村武幸, 高須淳宏
  • Organizer: 人工知能学会 第78回 人工知能基本問題研究会
  • Place of Presentation: 兵庫県立大学(神戸キャンパス)
  • Year and Date: 2010-08-01
• [Presentation] 高さ制約付き無順序木の高速類似検索アルゴリズムについて (2010)
  • Author(s): 深川大路, 阿久津達也, 高須淳宏, 安達淳
  • Organizer: 情報処理学会第72回全国大会
  • Place of Presentation: 東京大学
  • Year and Date: 2010-03-09
• [Presentation] 無順序木の編集距離計算のための厳密アルゴリズム (2010)
  • Author(s): 阿久津達也, 深川大路, 高須淳宏, 田村武幸
  • Organizer: 情報処理学会アルゴリズム研究会
  • Place of Presentation: 東芝科学館(東京)
  • Year and Date: 2010-03-05
• [Presentation] 無順序木の編集距離計算のための厳密アルゴリズム (2010)
  • Author(s): 阿久津達也, 深川大路, 高須淳宏, 田村武幸
  • Organizer: 情報処理学会研究報告ALアルゴリズム研究会
  • Place of Presentation: 東芝科学館(東京)
  • Year and Date: 2010-03-05
• [Presentation] A Variational Bayesian EM Algorithm for Tree Similarity. Proc. (2010)
  • Author(s): Atsuhiro Takasu, Daiji Fukagawa, Tatsuya Akutsu
  • Organizer: 20th International Conference on Pattern Recognition (ICPR 2010)
  • Place of Presentation: Istanbul, Turkey
• [Presentation] Constant factor approximation of edit distance of bounded height unordered trees (2009)
  • Author(s): 深川大路, 阿久津達也, 高須淳宏
  • Organizer: Proc.16th International Symposium on String Processing and Information Retrieval(SPIRE 2009)
  • Place of Presentation: Saariselka, Finland
  • Year and Date: 2009-08-25
• [Presentation] 高さの制限された無順序木の編集距離問題に対する近似アルゴリズム (2009)
  • Author(s): 深川大路, 阿久津達也, 高須淳宏
  • Organizer: 電子情報通信学会コンピュテーション研究会
  • Place of Presentation: 北海道大学
  • Year and Date: 2009-06-29
• [Presentation] Constant Factor Approximation of Edit Distance of Bounded Height Unordered Trees (2009)
  • Author(s): Daiji Fukagawa, Tatsuya Akutsu, Atsuhiro Takasu
  • Organizer: 16th International Symposium on String Processing and Information Retrieval (SPIRE 2009)
  • Place of Presentation: Saariselka, Finland