About Me

About Me

Tetsuji KUBOYAMA, Ph.D.
Professor,

Computer Centre, &
Archival Science, Graduate School of Humanities,
Gakushuin University
1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, JAPAN [MAP]
E-mail: tkuboyama-atmark-tk-dot-cc-dot-gakushuin-dot-ac-dot-jp
Researchmap / ORCID / Scopus / ResearcherID

Academic Appointments

Professor at Computer Centre / Graduate School of Humanities, Department of Archival Science, Gakushuin University
Visiting Professor at Research Institute for Artificial Intelligence, Tokyo Denki University
Project Researcher at Institute of Industrial Science / Computer Center, The University of Tokyo

Research Interests

Approximate pattern matching, similarity measure design, and edit distance calculation for discrete data structures (strings, trees, graphs, etc.)
Machine learning and data mining for discrete data structures
Bioinformatics (glycan structure analysis, genetic mutation analysis of influenza viruses)
Bid data analysis / PC operation log analysis
Computational archival science

Academic Career

1992: Bachelor of Engineering, Department of Computer Science and Communication Engineering, Kyushu University
1994: Master of Engineering, Department of Information Systems, Graduate School of Information Science and Electrical Engineering, Kyushu University
1997: Completed doctoral course without dissertation, Department of Information Systems, Graduate School of Information Science and Electrical Engineering, Kyushu University
1997: Research Associate at Center for Collaborative Research, The University of Tokyo
2007: Assistant Professor at Center for Collaborative Research, The University of Tokyo
2008-2013: Associate Professor at Computer Centre, Gakushuin University
- 2008-present: Collaborative Researcher at Kitsuregawa Lab., Institute of Industrial Science, The University of Tokyo
- 2008-2014: Researcher at Yasuda Lab., School of Science and Technology for Future Life, Tokyo Denki University
- 2008-2009: Collaborative Researcher at Watanabe Lab., Research Center for Advanced Science and Technology, The University of Tokyo
- Jul.-Sep. 2009: Visiting Researcher at Institute of Applied Mathematics (IAM), University of Bern, Switzerland (JSPS-SNSF Short-term Exchange Program)
2013-present: Professor at Computer Centre, Gakushuin University
2019-present: Professor at Graduate School of Humanities, Department of Archival Science, Gakushuin University (concurrent with Computer Centre)
- Dec. 2019-present: Visiting Professor at Research Institute for Artificial Intelligence, Tokyo Denki University
- 2021-2023: Chair of the Research Committee, Research Institute of Oriental Culture, Gakushuin University
- 2024-2026: Organizer of the Data Science Minor Program, Gakushuin University
Apr. 2025: Director of Computer Centre, Gakushuin University

Grants

Grants-in-Aid for Scientific Research (KAKENHI)

External Collaborative Research Projects

2017-2019: Art Research Center Collaborative Research Project (Resource Utilization Type), Ritsumeikan University (Principal Investigator)
- “Automation of Pattern Image Classification Using Machine Learning”
2015: National Institute of Informatics Collaborative Research/Research Meeting Project (Principal Investigator)
- “Development of Pattern Discovery Methods for Legal Expression Paraphrasing”
2013: Research Center for Zoonosis Control, Hokkaido University Collaborative Research (Co-Investigator)
2012: Research Center for Zoonosis Control, Hokkaido University Collaborative Research (Principal Investigator)
- “Analysis of Antigenic Variation in Influenza Virus Using Matrix Decomposition Techniques”
2011: Research Center for Zoonosis Control, Hokkaido University Collaborative Research (Principal Investigator)
- “Trend Analysis of Antigenic Variation in Influenza Virus Using Dimension Reduction Methods”
2010: Research Center for Zoonosis Control, Hokkaido University Collaborative Research (Principal Investigator)
- “Prediction of Antigenic Variation in Influenza Virus Using High-Dimensional Encoding of Amino Acids”
2009: JSPS-SNSF Short-term Exchange Program
- “Graph Edit Distance and Kernel Learning”

Internal Competitive Funding

Research Institute of Oriental Culture, Gakushuin University, General Research Project
- 2021-2022: “Quantitative Linguistic Study of Tang and Song Eight Masters’ Prose”
Computer Centre Special Research Projects, Gakushuin University
- 2025: “Structural Analysis of Archival Description Standards EAD and EAC-CPF”
- 2024: “Context Structure Extraction and Characterization from Archival Descriptions”
- 2023: “Feature Extraction and Quantitative Analysis from Classical Chinese Texts”
- 2022: “Visualization and Quantification of Fonds Structure in Digital Archives Description”
- 2021: “Supporting Understanding of Phenomena in Multi-person Meal Conversations”
- 2020: “Metadata Creation Support for Ise Pattern Images”
- 2019: “Survey on Environment Construction for Hands-on Data Analysis Classes”
- 2018: “Enumeration and Editing-based Extraction Method for Bipartite Communities”
- 2017: “Comparative Experiments of Clustering Methods for Bipartite Graphs”
- 2016: “Characterization of High-Dimensional Data Using Ultra-High-Speed Categorical Feature Selection Methods”
- 2016: “Development of New Research Methods Using Court Case Databases” (Co-Investigator)
- 2015: “Investigation and Construction of Static Website Generation CMS”
- 2015: “Research on Student Assignment Methods for Classes” (Co-Investigator)
- 2014: “Research on Paperless Processing of Internal Documents”
- 2013: “Analysis of Wireless LAN Usage Patterns”
- 2012: “Non-commutative Polynomial Ring Processing for Milnor Invariant Calculation”
- 2011: “User Behavior Analysis from Campus Website Logs”
- 2010: “Qualitative Analysis of Campus Communication Structure Using Email Transmission Logs”
- 2009: “Implementation of Fast Document Similarity Calculation Methods and Application to Report Plagiarism Detection”
- 2008: “Machine Learning Approach to Patent Quality Evaluation”

Selected Publications

Awards

2016: The Best Paper Award at The 15th IFIP I3E conference
- E. Hashimoto, M. Ichino, T. Kuboyama, I. Echizen, H. Yoshiura: Breaking Anonymity of Social Network Accounts by Using Coordinated and Extensible Classifiers based on Machine Learning, 15th IFIP I3E, LNCS 9844, pp.455-470, 2016.
2009: The Best Invited Session Award (Chair with Prof. Sebastian Rios in the University of Chile), The 13th International Conference on Knowledge-Based and Intelligent Information & Engineering Systems (KES 2009)
2007: SIG Research Excellence Award, Japanese Society for Artificial Intelligence, “Generalization of Convolution Kernels and Polynomial Kernels”
2006: Best Presentation Award, The 17th Data Engineering Workshop & 4th Annual Meeting of the Database Society of Japan (DEWS)

Academic Service

Committee Memberships

2018-present: Editorial Committee Member, Transactions on Mathematical Modeling and its Applications, Information Processing Society of Japan
2012-2014: Chair, Special Interest Group on Fundamental Problems in Artificial Intelligence (SIG-FPAI), Japanese Society for Artificial Intelligence
2010-2012: Chief Secretary, Special Interest Group on Fundamental Problems in Artificial Intelligence (SIG-FPAI), Japanese Society for Artificial Intelligence
2008-2010: Secretary, Special Interest Group on Fundamental Problems in Artificial Intelligence (SIG-FPAI), Japanese Society for Artificial Intelligence
2012-2016: Editorial Committee Member, Transactions on Mathematical Modeling and its Applications, Information Processing Society of Japan
2011-2012: Guest Editorial Committee Member, Transactions on Mathematical Modeling and its Applications, Information Processing Society of Japan
2007-2011: Editorial Committee Member, Transactions on Mathematical Modeling and its Applications, Information Processing Society of Japan
Other roles: Session Chair and Reviewer for the Annual Conference of the Japanese Society for Artificial Intelligence, Commentator for the Forum on Data Engineering and Information Management (DEIM), etc.

Conference Service

2018-2025: Program Committee Member, Asian Conference on Intelligent Information and Database Systems (ACIIDS2018-2025)
- Program Committee Member, Special Session ICxS2018 (Intelligent and Contextual Systems)
2023: Program Committee Member, Discovery Science (DS2023)
2017: Program Committee Member, 29th IEEE International Conference on Tools with Artificial Intelligence (ICTAI)
2017: PC Co-Chair, 20th International Conference on Discovery Science (DS2017)
2017: Program Committee Member, 20th International Conference on Discovery Science
2016: Program Committee Member, 28th IEEE International Conference on Tools with Artificial Intelligence (ICTAI)
2016: Organizer, Special Session on High Dimensional Data Summarization for Discrete Structures, International Workshop on Smart Info-Media Systems in Asia (SISA2016)
2015: Co-Chair, Workshop on Time Series Data Analysis and its Applications (TSDAA2015) in the 7th JSAI International Symposia on AI (isAI2015)
2014: Co-Chair, Workshop on Graph-based Algorithms for Big Data and its Applications (GABA2014) in the 6th JSAI International Symposia on AI (isAI2014)
2013: Co-Chair, Workshop on Data Discretization and Segmentation for Knowledge Discovery (DDS13) in the 5th JSAI International Symposia on AI (isAI2013)
2013: Program Committee Member, 9th IAPR-TC-15 Workshop on Graph-based Representations in Pattern Recognition (GbR 2013)
2012: Chair of Organized Session on Machine Learning and its Application to Bioinformatics (with Prof. Kilho Shin), SCIS-ISIS 2012
2012: Program Committee Member, The 7th IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB2012)
2012: Program Committee Member, IEEE World Congress on Computational Intelligence (WCCI 2012) Special Session on Computational Intelligence in Social Media Analysis and Mining
2011: Program Committee Member, 2nd Workshop on Algorithms for Large-Scale Information Processing in Knowledge Discovery (ALSIP 2011)
2011: Program Committee Member, The 3rd Asian Conference on Machine Learning (ACML 2011)
2011: Program Committee Member, 8th IAPR-TC-15 Workshop on Graph-based Representations in Pattern Recognition (GbR 2011)
2010: Program Committee Member, The 2nd Asian Conference on Machine Learning (ACML 2010)
2009: Chair of Invited Session on Social Networks (with Prof. Sebastian Rios, University of Chile), The 13th International Conference on Knowledge-Based and Intelligent Information & Engineering Systems (KES 2009)
2009: Program Committee Member, The 1st Asian Conference on Machine Learning (ACML 2009)

Academic Memberships

Teaching Experience

Apr. 2023-present: Gakushuin University
- Introduction to Computer Science
- Introduction to Information Theory
- Introduction to Artificial Intelligence
- Intermediate Programming
- Digital Archives Practical
2018-present: National Institute of Japanese Literature
- Archives College Long-term Course: Archives Information Systems
2023-present: School of Commerce, Waseda University
- Computer Architecture
2022-present: Intensive Course, Graduate School, Kyushu Institute of Technology
- Issues in Artificial Intelligence
Apr. 2008-Mar. 2022: Gakushuin University
- Elementary Information Processing 1, 2
- Information Processing 1A, 1B
  - Computer operating principles and overview of computer science
  - Introduction to data processing using lightweight programming languages
- Information Processing 2A, 2B
  - Principles of the Internet
  - Introduction to network analysis (PageRank, community detection)
- Introduction to Information Mathematical Analysis 1, 2 (until 2009)
Jul. 25-26, 2017: Intensive Course, Graduate School of Simulation Studies/Graduate School of Applied Informatics, University of Hyogo
- Artificial Intelligence and Big Data Analysis
Apr. 2010-2014: Tokyo Denki University, Supervision of Bachelor’s, Master’s, and Doctoral theses
- 2013: 1 Master’s student (2nd year), 1 corporate researcher — Feature selection, PC operation log analysis
- 2012: 1 undergraduate student (4th year), 1 Master’s student (1st year), 1 corporate researcher — Feature selection, PC operation log analysis
- 2011: 1 undergraduate student (4th year), 1 Master’s student (2nd year), 1 corporate researcher — Web/PC operation log analysis
- 2010: 1 undergraduate student (4th year), 1 Master’s student (1st year) — Web/PC operation log analysis
First semester, 2009: Part-time Lecturer, Graduate School of Information Science and Engineering, Tokyo Institute of Technology
- Similarity measure design for discrete data structures and its application to machine learning
2008: Summer Project Reader (Advisor Prof. Shin), Carnegie Mellon University Japan
- Supervision of summer projects related to information security and machine learning
Apr. 2007-Mar. 2008: Part-time Lecturer, Tokyo Gakugei University
- Mathematics and Information Processing (for 1st and 2nd-year mathematics majors)
- Document creation with LaTeX and document processing with Ruby
Apr. 1999-Mar. 2002: Part-time Lecturer, Tokyo Gakugei University
- Information Mathematics II (for 3rd and 4th-year mathematics/information majors)
  - Graph theory, language theory, combinatorial optimization problems, etc.
- Mathematical Logic (for 3rd and 4th-year mathematics/information majors)
  - First-order predicate logic (tableau method, completeness proofs, etc.), propositional modal logic
2003-2007: Center for Collaborative Research Technology Liaison Fellow Lectures, The University of Tokyo
- Information security, data mining, etc.
2002-2003: Center for Collaborative Research Information Education Security Project, The University of Tokyo
- Security education for senior local government managers

External Committees

2014-2021: External Evaluation Committee Member, International Cyber Security Course, Tokyo Denki University
2014-2016: PhD Student Advisory Committee Member, Hirokawa Laboratory, Kyushu University
2014: External Deputy Examiner, Thesis Examination Committee, Sakamoto Laboratory, Kyushu Institute of Technology

Previous Research Projects

Apr. 2006-Mar. 2009: Information Security Community Committee Member, Center for Collaborative Research, The University of Tokyo
2003: Development of “Security Education Curriculum” for Technology Management (MOT) Program Development Project (Ministry of Economy, Trade and Industry: compiled by Mitsubishi Research Institute)
Apr. 2002-Mar. 2006: Information/Education Security Project Committee Member, Center for Collaborative Research, The University of Tokyo
Apr. 1994-Mar. 1996: Committee Member, Parallel Theorem Proving Task Group, Institute for New Generation Computer Technology (ICOT)

Industry-Academia Collaboration

Apr. 2000-Mar. 2008: University of Tokyo Industry-Academia Collaboration Proposal (former CCR-DB)
- Establishment, specification design, and system management
- This was a web database of research themes proposed by each faculty member of the University of Tokyo through interviews for industry-academia collaboration.
- The system included comprehensive management from interview scheduling and interviewer assignment to external inquiries and industry-academia liaison activities.
Apr. 1998-Mar. 2000: Construction of patent information database

Network Administration

Apr. 1997-Mar. 2008: Network Department Administrator, Center for Collaborative Research, The University of Tokyo
- Since the initial establishment of the network environment, served as the only administrator in the department, responsible for CCR network specification design and all network infrastructure operations (router, switch, server management including mail, DNS, DHCP, Web, databases, etc.)
Apr. 1997-Mar. 2008: Staff member, Computer Room, Institute of Industrial Science, The University of Tokyo
- Creation of web applications for network equipment and user registration, construction of billing systems, and security diagnostics within the institute

PhD Thesis

Matching and Learning in Trees (PDF 2.7MB)

Ph.D. in Engineering, The University of Tokyo, April 2007

This thesis organizes various approximate matching algorithms for tree structures based on tree edit distance from a unified perspective and applies the results to classification learning using kernel methods. By formalizing the exact meaning of approximate matching of tree structures using ordered algebra, it resolves various errors and problems contained in existing research and clarifies the relationships between existing approximate matching algorithms. As a result, it became clear that tree approximate matching algorithms have a clean class hierarchy according to the sensitivity (degree of approximation) of structural comparison, that there is a close relationship between computational complexity and structural comparison sensitivity, and that multiple algorithms that were thought to be separate algorithms are actually the same algorithm.

Using these results, various similarity measures between tree structures were designed, and kernels were designed for classification learning of tree structures. It also includes a new kernel design framework that goes beyond the conventional convolution kernel framework. Furthermore, by using the concept of tree q-grams, which extends string q-grams, a fast tree kernel was designed and applied to classification learning of glycan structures.

This thesis includes a comprehensive survey of tree edit distance. For an overview of tree edit distance, please refer to Chapter 2 and the last section (summary) of Chapter 4.

Keywords: tree edit distance, alignment of trees, tree kernels, glycans