Details of the Researcher

PHOTO

Yoshifumi Sakai
Section
Graduate School of Agricultural Science
Job title
Associate Professor
Degree

  • 博士（情報科学） (Tohoku University)

  • 修士（工学） (Tohoku University)

Professional Memberships 2

  • Information Processing Society of Japan

  • The Institute of Electronics, Information and Communication Engineers

Research Interests 2

  • アルゴリズム

  • 計算機科学

Research Areas 1

  • Informatics / Information theory /

Papers 74

  1. Development of prediction equations for immunoglobulin A, immunoglobulin G, and immunoglobulin M concentrations in mature milk from Holstein cows using milk infrared spectral data

    Yuri Satake, Teppei Katsura, Tao Zhuang, Megumi Urakawa, Yugo Mineshima, Toshimi Baba, Gaku Yoshida, Haruki Kitazawa, Hitoshi Shirakawa, Takehiko Nakamura, Tomonori Nochi, Yoshifumi Sakai, Masahiro Satoh, Satoshi Haga, Hisashi Aso, Yoshinobu Uemoto

    Journal of Dairy Science　108　(7)　7354-7369　2025/07

    Publisher: American Dairy Science Association

    DOI： 10.3168/jds.2024-25991 　

    ISSN： 0022-0302

  2. Freeze-dried fecal microorganisms as an effective biomaterial for the treatment of calves suffering from diarrhea

    Jahidul Islam, Natsuki Ohtani, Yu Shimizu, Masae Tanimizu, Yoshiaki Goto, Masumi Sato, Eiji Makino, Toru Shimada, Chise Ueda, Ayumi Matsuo, Yoshihisa Suyama, Yoshifumi Sakai, Niel A. Karrow, Hiroshi Yoneyama, Ryota Hirakawa, Mutsumi Furukawa, Hidekazu Tanaka, Tomonori Nochi

    Scientific Reports　14　(1)　2024/11/14

    Publisher: Springer Science and Business Media LLC

    DOI： 10.1038/s41598-024-79267-5 　

    eISSN： 2045-2322

  3. Formation of the junctions between lymph follicles in the Peyer's patches even before postweaning activation

    Anri Teshigahara, Yuri Banba, Hiromi Yoshida, Mitsuji Kaji, Zhou Zhou, Nao Koyama, Yoshifumi Sakai, Niel A. Karrow, Kouetsu Ogasawara, Ryota Hirakawa, Jahidul Islam, Mutsumi Furukawa, Tomonori Nochi

    Scientific Reports　14　(1)　2024/07/09

    Publisher: Springer Science and Business Media LLC

    DOI： 10.1038/s41598-024-65984-4 　

    eISSN： 2045-2322

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    Abstract Peyer’s patches (PPs), which contain an abundance of B and T cells, play a key role in inducing pivotal immune responses in the intestinal tract. PPs are defined as aggregated lymph follicles, which consist of multiple lymph follicles (LFs) that may interact with each other in a synergistic manner. LFs are thought to be spherical in shape; however, the characteristics of their structure are not fully understood. To elucidate changes in the structure of PPs as individuals grow, we generated serial 2D sections from entire PPs harvested from mice at 2, 4, and 10 weeks of age and performed a 3D analysis using a software, Amira. Although the number of LFs in PPs was not changed throughout the experiment, the volume and surface area of LFs increased significantly, indicating that LFs in PPs develop continuously by recruiting immune cells, even after weaning. In response to the dramatic changes in the intestinal environment after weaning, the development of germinal centers (GCs) in LFs was observed at 4 and 10 weeks (but not 2 weeks) of age. In addition, GCs gradually began to form away from the center of LFs and close to the muscle layer where export lymphatic vessels develop. Importantly, each LF was joined to the adjacent LF; this feature was observed even in preweaning nonactivated PPs. These results suggest that PPs may have a unique organization and structure that enhance immune functions, allowing cells in LFs to have free access to adjacent LFs and egress smoothly from PPs to the periphery upon stimulation after weaning.

  4. A Faster Reduction of the Dynamic Time Warping Distance to the Longest Increasing Subsequence Length Peer-reviewed

    Yoshifumi Sakai, Shunsuke Inenaga

    Algorithmica　84　(9)　2581-2596　2022/05/11

    Publisher: Springer Science and Business Media LLC

    DOI： 10.1007/s00453-022-00968-2 　

    ISSN： 0178-4617

    eISSN： 1432-0541

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    Abstract The similarity between a pair of time series, i.e., sequences of indexed values in time order, is often estimated by the dynamic time warping (DTW) distance, instead of any in the well-studied family of measures including the longest common subsequence (LCS) length and the edit distance. Although it may seem as if the DTW and the LCS(-like) measures are essentially different, we reveal that the DTW distance can be represented by the longest increasing subsequence (LIS) length of a sequence of integers, which is the LCS length between the integer sequence and itself sorted. For a given pair of time series of length n such that the dissimilarity between any elements is an integer between zero and c, we propose an integer sequence that represents any substring-substring DTW distance as its band-substring LIS length. The length of the produced integer sequence is $$O(c n^2)$$, which can be translated to $$O(n^2)$$ for constant dissimilarity functions. To demonstrate that techniques developed under the LCS(-like) measures are directly applicable to analysis of time series via our reduction of DTW to LIS, we present time-efficient algorithms for DTW-related problems utilizing the semi-local sequence comparison technique developed for LCS-related problems.

  5. A data structure for substring-substring LCS length queries

    Yoshifumi Sakai

    Theoretical Computer Science　911　41-54　2022/04

    Publisher: Elsevier BV

    DOI： 10.1016/j.tcs.2022.02.004 　

    ISSN： 0304-3975

  6. Development of a rational framework for the therapeutic efficacy of fecal microbiota transplantation for calf diarrhea treatment

    Jahidul Islam, Masae Tanimizu, Yu Shimizu, Yoshiaki Goto, Natsuki Ohtani, Kentaro Sugiyama, Eriko Tatezaki, Masumi Sato, Eiji Makino, Toru Shimada, Chise Ueda, Ayumi Matsuo, Yoshihisa Suyama, Yoshifumi Sakai, Mutsumi Furukawa, Katsuki Usami, Hiroshi Yoneyama, Hisashi Aso, Hidekazu Tanaka, Tomonori Nochi

    Microbiome　10　(1)　2022/02

    Publisher: Springer Science and Business Media LLC

    DOI： 10.1186/s40168-021-01217-4 　

    eISSN： 2049-2618

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    <title>Abstract</title><sec> <title>Background</title> Establishing fecal microbiota transplantation (FMT) to prevent multifactorial diarrhea in calves is challenging because of the differences in farm management practices, the lack of optimal donors, and recipient selection. In this study, the underlying factors of successful and unsuccessful FMT treatment cases are elucidated, and the potential markers for predicting successful FMT are identified using fecal metagenomics via 16S rRNA gene sequencing, fecal metabolomics via capillary electrophoresis time-of-flight mass spectrometry, and machine learning approaches. </sec><sec> <title>Results</title> Specifically, 20 FMT treatment cases, in which feces from healthy donors were intrarectally transferred into recipient diarrheal calves, were conducted with a success rate of 70%. <italic>Selenomonas</italic> was identified as a microorganism genus that showed significant donor–recipient compatibility in successful FMT treatments. A strong positive correlation between the microbiome and metabolome data, which is a prerequisite factor for FMT success, was confirmed by Procrustes analysis in successful FMT (<italic>r</italic> = 0.7439, <italic>P</italic> = 0.0001). Additionally, weighted gene correlation network analysis confirmed the positively or negatively correlated pairs of bacterial taxa (family <italic>Veillonellaceae</italic>) and metabolomic features (i.e., amino acids and short-chain fatty acids) responsible for FMT success. Further analysis aimed at establishing criteria for donor selection identified the genus <italic>Sporobacter</italic> as a potential biomarker in successful donor selection. Low levels of metabolites, such as glycerol 3-phosphate, dihydroxyacetone phosphate, and isoamylamine, in the donor or recipients prior to FMT, are predicted to facilitate FMT. </sec><sec> <title>Conclusions</title> Overall, we provide the first substantial evidence of the factors related to FMT success or failure; these findings could improve the design of future microbial therapeutics for treating diarrhea in calves. </sec>

  7. The gut microbiota induces Peyer’s-patch-dependent secretion of maternal IgA into milk

    Katsuki Usami, Kanae Niimi, Ayumi Matsuo, Yoshihisa Suyama, Yoshifumi Sakai, Shintaro Sato, Kohtaro Fujihashi, Hiroshi Kiyono, Saeka Uchino, Mutsumi Furukawa, Jahidul Islam, Kaori Ito, Taiki Moriya, Yutaka Kusumoto, Michio Tomura, Russell C. Hovey, Junichi Sugawara, Hiroshi Yoneyama, Haruki Kitazawa, Kouichi Watanabe, Hisashi Aso, Tomonori Nochi

    Cell Reports　36　(10)　109655-109655　2021/09

    Publisher: Elsevier BV

    DOI： 10.1016/j.celrep.2021.109655 　

    ISSN： 2211-1247

  8. A Reduction of the Dynamic Time Warping Distance to the Longest Increasing Subsequence Length Peer-reviewed

    Yoshifumi Sakai, Shunsuke Inenaga

    31st International Symposium on Algorithms and Computation (ISAAC 2020), Leibniz International Proceedings in Informatics (LIPIcs)　181　6:1-6:16　2020/12

    Publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik

    DOI： 10.4230/LIPIcs.ISAAC.2020.6 　

  9. Elucidation of the Effects of a Current X-SCID Therapy on Intestinal Lymphoid Organogenesis Using an In Vivo Animal Model. International-journal Peer-reviewed

    Tomonori Nochi, Shunichi Suzuki, Shun Ito, Shotaro Morita, Mutsumi Furukawa, Daiichiro Fuchimoto, Yoji Sasahara, Katsuki Usami, Kanae Niimi, Osamu Itano, Minoru Kitago, Sachiko Matsuda, Ayumi Matsuo, Yoshihisa Suyama, Yoshifumi Sakai, Guoyao Wu, Fuller W Bazer, Kouichi Watanabe, Akira Onishi, Hisashi Aso

    Cellular and molecular gastroenterology and hepatology　10　(1)　83-100　2020/02/01

    DOI： 10.1016/j.jcmgh.2020.01.011 　

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    BACKGROUND & AIMS: Organ-level research using an animal model lacking Il2rg, the gene responsible for X-linked severe combined immunodeficiency (X-SCID), is clinically unavailable and would be a powerful tool to gain deeper insights into the symptoms of patients with X-SCID. METHODS: We used an X-SCID animal model, which was first established in our group by the deletion of Il2rg gene in pigs, to understand the clinical signs from multiple perspectives based on pathology, immunology, microbiology, and nutrition. We also treated the X-SCID pigs with bone marrow transplantation (BMT) for mimicking a current therapeutic treatment for patients with X-SCID and investigated the effect at the organ-level. Moreover, the results were confirmed using serum and fecal samples collected from patients with X-SCID. RESULTS: We demonstrated that X-SCID pigs completely lacked Peyer's patches (PPs) and IgA production in the small intestine, but possessed some dysfunctional intestinal T and B cells. Another novel discovery was that X-SCID pigs developed a heterogeneous intestinal microflora and possessed abnormal plasma metabolites, indicating that X-SCID could be an immune disorder that affects various in vivo functions. Importantly, the organogenesis of PPs in X-SCID pigs was not promoted by BMT. Although a few isolated lymphoid follicles developed in the small intestine of BMT-treated X-SCID pigs, there was no evidence that they contributed to IgA production and microflora formation. Consistently, most patients with X-SCID who received BMT possessed abnormal intestinal immune and microbial environments regardless of the presence of sufficient serum IgG. CONCLUSIONS: These results indicate that the current BMT therapies for patients with X-SCID may be insufficient to induce the organogenesis of intestinal lymphoid tissues that are associated with numerous functions in vivo.

  10. A substring–substring LCS data structure Peer-reviewed

    Yoshifumi Sakai

    Theoretical Computer Science　753　16-34　2019/01

    Publisher: Elsevier BV

    DOI： 10.1016/j.tcs.2018.06.034 　

    ISSN： 0304-3975

  11. A maximal local maximum-sum segment data structure Peer-reviewed

    SAKAI Yoshifumi

    IEICE TRANSACTIONS on Fundamentals of Electronics, Communications and Computer Sciences　E101-A　(9)　1541-1542　2018/09

  12. Maximal common subsequence algorithms Peer-reviewed

    SAKAI Yoshifumi

    Leibniz International Proceedings in Informatics (29th Annual Symposium on Combinatorial Pattern Matching)　105　1:1-1:10　2018/07

  13. Development of immune and microbial environments is independently regulated in the mammary gland Peer-reviewed

    K. Niimi, K. Usami, Y. Fujita, M. Abe, M. Furukawa, Y. Suyama, Y. Sakai, M. Kamioka, N. Shibata, E. J. Park, S. Sato, H. Kiyono, H. Yoneyama, H. Kitazawa, K. Watanabe, T. Nochi, H. Aso

    Mucosal Immunology　11　(3)　643-653　2018/05/01

    Publisher: Nature Publishing Group

    DOI： 10.1038/mi.2017.90 　

    ISSN： 1935-3456 1933-0219

    eISSN： 1935-3456

  14. A Linear-Space Algorithm for the Substring Constrained Alignment Problem Peer-reviewed

    Yoshifumi Sakai

    STRING PROCESSING AND INFORMATION RETRIEVAL, SPIRE 2016　9954　15-21　2016

    DOI： 10.1007/978-3-319-46049-9_2 　

    ISSN： 0302-9743

  15. A Fast On-Line Algorithm for the Longest Common Subsequence Problem with Constant Alphabet Peer-reviewed

    Yoshifumi Sakai

    IEICE TRANSACTIONS ON FUNDAMENTALS OF ELECTRONICS COMMUNICATIONS AND COMPUTER SCIENCES　E95A　(1)　354-361　2012/01

    DOI： 10.1587/transfun.E95.A.354 　

    ISSN： 1745-1337

  16. Computing the Longest Common Subsequence of Two Run-Length Encoded Strings Peer-reviewed

    Yoshifumi Sakai

    ALGORITHMS AND COMPUTATION, ISAAC 2012　7676　197-206　2012

    DOI： 10.1007/978-3-642-35261-4_23 　

    ISSN： 0302-9743

  17. A fast algorithm for multiplying min-sum permutations Peer-reviewed

    Yoshifumi Sakai

    DISCRETE APPLIED MATHEMATICS　159　(17)　2175-2183　2011/10

    DOI： 10.1016/j.dam.2011.06.022 　

    ISSN： 0166-218X

  18. In silico Analysis of 3 &apos;-End-Processing Signals in Aspergillus oryzae Using Expressed Sequence Tags and Genomic Sequencing Data Peer-reviewed

    Mizuki Tanaka, Yoshifumi Sakai, Osamu Yamada, Takahiro Shintani, Katsuya Gomi

    DNA RESEARCH　18　(3)　189-200　2011/06

    DOI： 10.1093/dnares/dsr011 　

    ISSN： 1340-2838

  19. A New Algorithm for the Characteristic String Problem under Loose Similarity Criteria Peer-reviewed

    Yoshifumi Sakai

    ALGORITHMS AND COMPUTATION　7074　663-672　2011

    DOI： 10.1007/978-3-642-25591-5_68 　

    ISSN： 0302-9743

  20. An Almost Quadratic Time Algorithm for Sparse Spliced Alignment Peer-reviewed

    Yoshifumi Sakai

    THEORY OF COMPUTING SYSTEMS　48　(1)　189-210　2011/01

    DOI： 10.1007/s00224-009-9239-x 　

    ISSN： 1432-4350

  21. Flexible computation of the longest common subsequence of run-length encoded strings Peer-reviewed

    Yoshifumi Sakai

    The 13th Japan-Korea Joint Workshop on Algorithms and Computation　72-79　2010/07/23

  22. Redundant architecture in Cooperative Search Engine Peer-reviewed

    上原 稔, Nobuyoshi Sato, Yoshifumi Sakai, Hideki Mori

    Int. J. Applied Systemic Studies　3　(1)　73-88　2010/01

    DOI： 10.1504/IJASS.2010.031555 　

  23. Computing the longest topological common subsequence of a symbol-wise totally ordered directed acyclic graph and a sequence Peer-reviewed

    Yoshifumi Sakai

    THEORETICAL COMPUTER SCIENCE　410　(27-29)　2759-2766　2009/06

    DOI： 10.1016/j.tcs.2009.03.027 　

    ISSN： 0304-3975

  24. When should throwaway contents be renewed? Peer-reviewed

    Yoshifumi Sakai, Minoru Uehara, Nobuyoshi Sato

    電子情報通信学会論文誌　J89-D　(9)　1913-1922　2006/09/01

    Publisher: The Institute of Electronics, Information and Communication Engineers

    ISSN： 1880-4535

  25. A linear space algorithm for computing a longest common increasing subsequence Peer-reviewed

    Yoshifumi Sakai

    INFORMATION PROCESSING LETTERS　99　(5)　203-207　2006/09

    DOI： 10.1016/j.ipl.2006.05.005 　

    ISSN： 0020-0190

  26. Evaluation of freshness considering scoring on fresh information retrieval Peer-reviewed

    Nobuyoshi Sato, Minoru Uehara, Yoshifumi Sakai

    Journal of Interconnection Networks　6　(3)　265-281　2005/09/01

    DOI： 10.1142/S0219265905001423 　

  27. The weakly constrained longest common subsequence problem Peer-reviewed

    Yoshifumi Sakai

    電子情報通信学会論文誌　J88-D-I　(8)　1261-1263　2005/08/01

    Publisher: The Institute of Electronics, Information and Communication Engineers

    ISSN： 0915-1915

  28. Adaptive scoring method based on freshness for fresh information retrieval Peer-reviewed

    Minoru Uehara, Nobuyoshi Sato, Yoshifumi Sakai

    Proceedings - International Workshop on Challenges in Web Information Retrieval and Integration, WIRI'05　2005　226-231　2005

    DOI： 10.1109/WIRI.2005.5 　

  29. The evaluations of FTF-IDF scoring for fresh information retrieval Peer-reviewed

    Nobuyoshi Sato, Minoru Uehara, Yoshifumi Sakai

    Proceedings - International Conference on Advanced Information Networking and Applications, AINA　1　635-640　2005

    DOI： 10.1109/AINA.2005.326 　

    ISSN： 1550-445X

  30. Adaptive calculation of scores for fresh information retrieval Peer-reviewed

    Minoru Uehara, Nobuyoshi Sato, Yoshifumi Sakai

    Proceedings of the International Conference on Parallel and Distributed Systems - ICPADS　1　750-755　2005

    DOI： 10.1109/ICPADS.2005.65 　

    ISSN： 1521-9097

  31. Redundant Architecture in Cooperative Search Engine Peer-reviewed

    Nobuyoshi Sato, Minoru Udagawa, Minoru Uehara, Yoshifumi Sakai, Hideki Mori

    Journal of Applied Systems Studies　5　(2)　157-168　2004/07

  32. Searching restricted documents in a cooperative search engine Peer-reviewed

    N Sato, M Udagawa, M Uehara, Y Sakai

    24TH INTERNATIONAL CONFERENCE ON DISTRIBUTED COMPUTING SYSTEMS WORKSHOPS, PROCEEDINGS　44-49　2004

  33. Distributed index updating method for Intranet infortnation retrieval Peer-reviewed

    M Udagawa, N Sato, M Uehara, Y Sakai

    24TH INTERNATIONAL CONFERENCE ON DISTRIBUTED COMPUTING SYSTEMS WORKSHOPS, PROCEEDINGS　56-61　2004

  34. FTY center dot IDF scoring for fresh information retrieval Peer-reviewed

    N Sato, M Uehara, Y Sakai

    18TH INTERNATIONAL CONFERENCE ON ADVANCED INFORMATION NETWORKING AND APPLICATIONS, VOL 1 (LONG PAPERS), PROCEEDINGS　165-170　2004

    DOI： 10.1109/AINA.2004.1283905 　

  35. Distributed pipelining processing for index updating method Peer-reviewed

    M Udagawa, N Sato, M Uehara, Y Sakai

    18TH INTERNATIONAL CONFERENCE ON ADVANCED INFORMATION NETWORKING AND APPLICATIONS, VOL 2 (REGULAR PAPERS), PROCEEDINGS　489-492　2004

    DOI： 10.1109/AINA.2004.1283850 　

  36. A case study on freshness based scoring for fresh information retrieval Peer-reviewed

    N Sato, M Uehara, Y Sakai

    IEEE INTERNATIONAL SYMPOSIUM ON COMMUNICATIONS AND INFORMATION TECHNOLOGIES 2004 (ISCIT 2004), PROCEEDINGS, VOLS 1 AND 2　210-215　2004

  37. A Scalable Distributed Search Engine for Fresh Information Retrieval Peer-reviewed

    Nobuyoshi Sato, Minoru Uehara, Yoshifumi Sakai

    Proceedings on IADIS International Conference on WWW/Internet 2003(ICWI2003)　877-880　2003/11/05

  38. Tempral Ranking for Fresh Information Retrieval Peer-reviewed

    Nobuyoshi Sato, Minoru Uehara, Yoshifumi Sakai

    Proceedings of the 6th International Workshop on Information Retrieval with Asian Language　116-123　2003/07

  39. Pruning Boolean formulas of subformulas without changing the minimal monotone functions Peer-reviewed

    Yoshifumi Sakai, Nobuyoshi Sato, Minoru Uehara, Hideki Mori

    電子情報通信学会論文誌D-I　J86-D-I　(6)　367-374　2003/06

    Publisher: The Institute of Electronics, Information and Communication Engineers

    ISSN： 0915-1915

  40. A Scalable Distributed Search Engine for Intranet Information Retrieval Peer-reviewed

    Nobuyoshi Sato, Minoru Udagawa, Minoru Uehara, Yoshifumi Sakai, Hideki Mori

    Proceedings of 5th International Conference on Enterprise Information Systems(ICEIS 2003)　1　562-565　2003/04/24

  41. Reliable Information Retrieval in a Distributed Search Engine Peer-reviewed

    Nobuyoshi Sato, Minoru Udagawa, Minoru Uehara, Yoshifumi Sakai

    Proceedings of 1st International Forum on Information and Computer Techonology (IFICT 2003)　185-190　2003/01/10

  42. Redundancy of meta search servers in a distributed search engine Peer-reviewed

    N Sato, M Udagawa, M Uehara, Y Sakai, H Mori

    AINA 2003: 17TH INTERNATIONAL CONFERENCE ON ADVANCED INFORMATION NETWORKING AND APPLICATIONS　400-407　2003

    DOI： 10.1109/AINA.2003.1192912 　

  43. Reliability of a distributed search engine for fresh information retrieval in large-scale Intranet Peer-reviewed

    N Sato, M Udagawa, M Uehara, Y Sakai

    PARALLEL AND DISTRIBUTED PROCESSING AND APPLICATIONS, PROCEEDINGS　2745　14-27　2003

    ISSN： 0302-9743

  44. Temporal information retrieval in cooperative search engine Peer-reviewed

    N Sato, M Uehara, Y Sakai

    14TH INTERNATIONAL WORKSHOP ON DATABASE AND EXPERT SYSTEMS APPLICATIONS, PROCEEDINGS　215-220　2003

    DOI： 10.1109/DEXA.2003.1232026 　

  45. Improving Reliability of a Distributed Search Engine by Group Communication Peer-reviewed

    Nobuyoshi Sato, Minoru Udagawa, Minoru Uehara, Yoshifumi Sakai, Hideki Mori

    Proceedings of the IASTED International Conference on Networks, Parallel and Distributed Processing, and Applications(NPDPA02)　277-282　2002/10/02

  46. A Fresh Information Retrieval System based on Distributed Architecture Peer-reviewed

    Nobuyoshi Sato, Minoru Uehara, Yoshifumi Sakai, Hideki Mori

    Proceedings of the 3rd International Conference on Parallel and Distributed Computing, Applications and Technologies(PDCAT2002)　204-211　2002/09/03

  47. The learnability of decision lists on cellular automata by counterexamples Peer-reviewed

    Yoshifumi Sakai

    The Transactions of the Institute of Electronics, Information and Communication Engineers D-I　J85-D-I　(4)　342-349　2002/04

    Publisher: The Institute of Electronics, Information and Communication Engineers

    ISSN： 0915-1915

  48. Fresh Information Retrieval using Distributed Search Engines Peer-reviewed

    Nobuyoshi Sato, Minoru Uehara, Yoshifumi Sakai, Hideki Mori

    IPSJ Pan-Yellow-Sea International Workshop on Information Technologies for Network Era(PYIWIT'02)　321-328　2002/03/07

  49. A distributed search engine for fresh information retrieval Peer-reviewed

    Nobuyoshi Sato, Minoru Uehara, Yoshifumi Sakai, Hideki Mori

    IPSJ Journal　43　(2)　321-331　2002/02

  50. Fresh Information Retrieval using Cooperative Meta Search Engines Peer-reviewed

    Nobuyoshi Sato, Minoru Uehara, Yoshifumi Sakai, Hideki Mori

    Proceedins of Proceedings of the 16th International Conference on Information Networking (ICOIN-16)　2　(7A-2)　1-7　2002/01/31

  51. Fresh information retrieval using cooperative meta search engines

    Nobuyoshi Sato, Minoru Uehara, Yoshifumi Sakai, Hideki Mori

    Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)　2344　656-670　2002

    Publisher: Springer Verlag

    DOI： 10.1007/3-540-45801-8_62 　

    ISSN： 1611-3349 0302-9743

  52. On updating in very short time by distributed search engines Peer-reviewed

    N Sato, M Uehara, Y Sakai, H Mori

    2002 SYMPOSIUM ON APPLICATIONS AND THE INTERNET (SAINT 2002), PROCEEDINGS　176-183　2002

    DOI： 10.1109/SAINT.2002.994475 　

  53. Persistent cache in Cooperative Search Engine Peer-reviewed

    N Sato, M Uehara, Y Sakai, Mori, I

    22ND INTERNATIONAL CONFERENCE ON DISTRIBUTED COMPUTING SYSTEMS WORKSHOP, PROCEEDINGS　182-187　2002

    DOI： 10.1109/ICDCSW.2002.1030767 　

  54. Persistent cache in a Distributed Search Engine Peer-reviewed

    N Sato, M Uehara, Y Sakai, H Mori

    13TH INTERNATIONAL WORKSHOP ON DATABASE AND EXPERT SYSTEMS APPLICATIONS, PROCEEDINGS　54-58　2002

    DOI： 10.1109/DEXA.2002.1045876 　

  55. Reliable distributed search engine based on multiple meta servers Peer-reviewed

    N Sato, M Udagawa, M Uehara, Y Sakai, H Mori

    FIRST INTERNATIONAL SYMPOSIUM ON CYBER WORLDS, PROCEEDINGS　79-84　2002

    DOI： 10.1109/CW.2002.1180863 　

  56. Scalability and reliability in a distributed search engine Peer-reviewed

    N Sato, M Udagawa, M Uehara, Y Sakai, H Mori

    NINTH INTERNATIONAL CONFERENCE ON PARALLEL AND DISTRIBUTED SYSTEMS, PROCEEDINGS　57-62　2002

    DOI： 10.1109/ICPADS.2002.1183378 　

  57. Query based site selection for distributed search engines Peer-reviewed

    N Sato, M Udagawa, M Uehara, Y Sakai, H Mori

    23RD INTERNATIONAL CONFERENCE ON DISTRIBUTED COMPUTING SYSTEMS WORKSHOPS　556-561　2002

    DOI： 10.1109/ICDCSW.2003.1203612 　

  58. Fresh Information Retrieval in Cooperative Search Engine Peer-reviewed

    Nobuyoshi Sato, Minoru Uehara, Yoshifumi Sakai, Hideki Mori

    Proceedings of the ACIS 2nd International Conference on Software Engineering, Artificial Intelligence, Networking & Parallel/Distributed Computing(SNPD'01)　104-111　2001/08/20

  59. A sufficient hypothesis class for weak PAC learning using difference gaining Peer-reviewed

    Yoshifumi Sakai

    The Transactions of the Institute of Electronics, Information and Communication Engineers D-I　J84-D-I　(5)　505-507　2001/05

    Publisher: The Institute of Electronics, Information and Communication Engineers

    ISSN： 0915-1915

  60. A naive boosting algorithm using DNF formulas Peer-reviewed

    Yoshifumi Sakai

    The Transactions of the Institute of Electronics, Information and Communication Engineers D-I　J84-D-I　(1)　62-68　2001/01

    Publisher: The Institute of Electronics, Information and Communication Engineers

    ISSN： 0915-1915

  61. Distributed Information Retrieval by using Cooperative Meta Search Engines Peer-reviewed

    N Sato, M Uehara, Y Sakai, H Mori

    21ST INTERNATIONAL CONFERENCE ON DISTRIBUTED COMPUTING SYSTEMS WORKSHOPS, PROCEEDINGS　345-350　2001

    DOI： 10.1109/CDCS.2001.918728 　

  62. A distributed search engine for fresh information retrieval Peer-reviewed

    N Sato, M Uehara, Y Sakai, H Mori

    12TH INTERNATIONAL WORKSHOP ON DATABASE AND EXPERT SYSTEMS APPLICATIONS, PROCEEDINGS　211-216　2001

    DOI： 10.1109/DEXA.2001.953065 　

  63. The learnability of exclusive-or expansions based on monotone DNF formulas Peer-reviewed

    E Takimoto, Y Sakai, A Maruoka

    THEORETICAL COMPUTER SCIENCE　241　(1-2)　37-50　2000/06

    ISSN： 0304-3975

    eISSN： 1879-2294

  64. Difference gaining under PAC learning Peer-reviewed

    Yoshifumi Sakai

    The Transactions of the Institute of Electronics, Information and Communication Engineers D-I　J83-D-I　(5)　508-509　2000/05

  65. Learning monotone log-term DNF formulas under the uniform distribution Peer-reviewed

    Y Sakai, A Maruoka

    THEORY OF COMPUTING SYSTEMS　33　(1)　17-33　2000/01

    ISSN： 1432-4350

  66. Proper learning algorithm for functions of k terms under smooth distributions Peer-reviewed

    Y Sakai, E Takimoto, A Maruoka

    INFORMATION AND COMPUTATION　152　(2)　188-204　1999/08

    DOI： 10.1006/inco.1998.2785 　

    ISSN： 0890-5401

  67. Learning orthogonal F-Horn formulas Peer-reviewed

    E Takimoto, A Miyashiro, A Maruoka, Y Sakai

    THEORETICAL COMPUTER SCIENCE　185　(1)　177-190　1997/10

    DOI： 10.1016/S0304-3975(97)00020-0 　

    ISSN： 0304-3975

    eISSN： 1879-2294

  68. Learning k-term monotone Boolean formulae Peer-reviewed

    Yoshifumi Sakai, Akira Maruoka

    Interdisciplinary Information Sciences (Graduate School of Infromation Sciences, Tohoku University)　3　(2)　71-80　1997

    Publisher: Tohoku University

    DOI： 10.4036/iis.1997.71 　

    ISSN： 1340-9050

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    Valiant introduced a computational model of learning by examples, and gave the precise definition of polynominal time learnability based on the model. Since then, much effort has been devoted to characterize learnable classes of concepts on this model. Among such learnable classes is the one, denoted monotone k -term DNF, consisting of monotone disjunctive normal form formulae with at most k terms. So far it has been shown [6], [8] that for fixed k, monotone k -term DNF is learnable under the assumption that positive examples are drawn according to the uniform distribution. In this paper we introduce a class of probabilistic distributions, called smooth distributions, which is generalization of all the distribution classes which appeared in literature as the ones for specific distributiion setting: A smooth distribution is the one such that a ratio of the probabilities of any two examples with Hamming distance 1 is bounded from below by the inverse of some polynomial. It is proved that monotone k -term DNF is learnable even if positive examples are drawn according to smooth distributions. From this result it follows the learnability of monotone k -term DNF under specific distribution dealt with in literature such as product distributions [7] and q -bounded distributions [2].

  69. Learnability of Exclusive-Or Expansion Based on Monotone DNF Formulas. Peer-reviewed

    Eiji Takimoto, Yoshifumi Sakai, Akira Maruoka

    Algorithmic Learning Theory, 7th International Workshop, ALT '96, Sydney, Australia, October 23-25, 1996, Proceedings　12-25　1996

    Publisher: Springer

    DOI： 10.1007/3-540-61863-5_30 　

  70. Proper Learning Algorithm for Functions of k Terms Under Smooth Distributions. Peer-reviewed

    Yoshifumi Sakai, Eiji Takimoto, Akira Maruoka

    Proceedings of the Eigth Annual Conference on Computational Learning Theory, COLT 1995, Santa Cruz, California, USA, July 5-8, 1995　906　206-213　1995

    Publisher: ACM

    DOI： 10.1145/225298.225323 　

    ISSN： 1880-2818

  71. Learning Orthogonal F-Horn Formulas. Peer-reviewed

    Akira Miyashiro, Eiji Takimoto, Yoshifumi Sakai, Akira Maruoka

    Algorithmic Learning Theory, 6th International Conference, ALT '95, Fukuoka, Japan, October 18-20, 1995, Proceedings　110-122　1995

    Publisher: Springer

    DOI： 10.1007/3-540-60454-5_32 　

  72. Learning monotone log-term DNF formulas Peer-reviewed

    Yoshifumi Sakai, Akira Maruoka

    Proceedings of the Annual ACM Conference on Computational Learning Theory　129415　165-172　1994/07/16

    Publisher: Association for Computing Machinery

    DOI： 10.1145/180139.181095 　

  73. Learning k-term monotone boolean formulae

    Yoshifumi Sakai, Akira Maruoka

    Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)　743　197-207　1993

    Publisher: Springer Verlag

    DOI： 10.1007/3-540-57369-0_39 　

    ISSN： 1611-3349 0302-9743

  74. Studies on the Composite Materials of High Characteristic Properties Mode from SiC Whisker

    SAKAI Yoshifumi

    Transactions of the Japan Society of Mechanical Engineers Series B　50　(449)　8-14　1984

    Publisher: The Japan Society of Mechanical Engineers

    DOI： 10.1299/kikaia.50.8 　

    ISSN： 0387-5008

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Misc. 16

  1. Indexing maximum densities of characters in substrings of a sparse string (New Trends in Theoretical Computer Science)

    Sakai Yoshifumi

    RIMS Kokyuroku　1849　18-21　2013/08

    Publisher: Kyoto University

    ISSN： 1880-2818

  2. 海草全単射の漸減構築 (アルゴリズムと計算理論の新展開)

    酒井 義文

    数理解析研究所講究録　1799　60-64　2012/06

    Publisher: 京都大学

    ISSN： 1880-2818

  3. 最長共通部分配列計算における run 長の対数時間寄与 (計算機科学とアルゴリズムの数理的基礎とその応用)

    酒井 義文

    数理解析研究所講究録　1744　107-114　2011/06

    Publisher: 京都大学

    ISSN： 1880-2818

  4. Reliability of a Distributed Search Engine for Fresh Information Retrieval Peer-reviewed

    上原 稔, Nnobuyoshi Sato, Minoru Udagawa, Yoshifumi Sakai, 森 秀樹

    NEW HORIZONS OF PARALLEL AND DISTRIBUTED COMPUTING, Springer　203-216　2005/01

    DOI： 10.1007/0-387-28967-4_14 　

  5. Freshness based Scoring in Fresh Information Retreiva

    2004　(15)　239-244　2004/11/24

  6. Security of Restricted Documents in Cooperative Search Engine

    2003　(19)　281-286　2003/12/10

  7. Ranking Documents for Repeated Retrieval in Search Engines

    2003　(19)　151-156　2003/12/10

  8. Research of the Concept Model of a Problem in a Distance Learning System

    2003　(19)　221-226　2003/12/10

  9. Distributed Index Updating Method in Cooperative Search Engine

    2003　(19)　299-304　2003/12/10

  10. A Pipeline Processing Method for Index Update

    2002　(15)　147-152　2002/10/16

  11. A Reliable Distributed Search Engine by Redundant Meta Servers

    2002　(15)　153-158　2002/10/16

  12. L-14 The Pipelined Web Robot for High Throughput Update

    Udagawa Minoru, Sato Nobuyoshi, Uehara Minoru, Sakai Yoshifumi, Mori Hideki

    2002　(4)　29-30　2002/09/13

    Publisher: Forum on Information Technology

  13. M-19 Implementation of Persistent Cache in Cooperative Search Engine

    Sato Nobuyoshi, Udagawa Minoru, Uehara Minoru, Sakai Yoshifumi, Mori Hideki

    2002　(4)　71-72　2002/09/13

    Publisher: Forum on Information Technology

  14. Persistent Cache for Cooperative Search Engine

    SATO Nobuyoshi, UEHARA Minoru, SAKAI Yoshifumi, MORI Hideki

    IEICE technical report. Computer systems　102　(276)　35-40　2002/08/16

    Publisher: The Institute of Electronics, Information and Communication Engineers

    ISSN： 0913-5685

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    Cooperative Search Engine (CSE) is a distributed search engine we developped, which can update indexes in very short time for the purpose of fresh information retrieval in a intranet. CSE can reduce the update interval time because CSE gathers documents and makes indexes in bottom up. However, CSE had a problem that CSE retrieval was slow because many communications occur. Now, this problem was solved by caching retrieval results, look ahead caching on background. In the other hand, however, the cache becomes invalid as soon as indexes are updated. Therefore, we need persistent cache that can hold valid cache contents before and after updating. In this paper, we describe the principal and evaluations of persistent cache of CSE.

  15. 協調サーチエンジン:最新情報の検索に適した分散型サーチエンジン

    上原 稔, 森 秀樹, 酒井 義文

    東洋大学工学部研究報告　(36)　21-27　2000

    Publisher: 東洋大学工学部

    ISSN： 0285-8304

  16. LEARNING MONOTONE LOG-TERM DNF FORMULAS

    Sakai Yoshifumi, Maruoka Akira

    RIMS Kokyuroku　871　204-211　1994/05

    Publisher: Kyoto University

    ISSN： 1880-2818

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Presentations 10

  1. 部分文字列最大密度索引

    2012年冬のLAシンポジウム　2013/01/28

  2. run長符号化文字列の最強共通部分列計算

    2012年夏のLAシンポジウム　2012/07/17

  3. 海藻全単射の漸減構築

    2011年冬のLAシンポジウム　2012/01/30

  4. 緩い類似税判定基準のもとでの特徴文字列問題アルゴリズム

    2011年夏のLAシンポジウム　2011/07/19

  5. 最長共通部分も配列計算におけるrun長の対数時間寄与

    2010年冬のLAシンポジウム　2011/02/01

  6. 可能な最長部分パターンの文字列照合問題

    2010年夏のLAシンポジウム　2010/07/20

  7. 最長共通部分配列のオンライン計算

    2009年冬のLAシンポジウム　2010/02/01

  8. 二値配列の空白位置が柔軟な累進多重整列

    2009年夏のLAシンポジウム　2009/07/22

  9. 重なりのない逆位操作後の配列からの類似配列の復元

    2008年夏のLAシンポジウム　2008/07/22

  10. 記号毎に全順序付けられた有向非循環グラフのトポロジカルソート配列と配列の最長共通部分配列アルゴリズム

    2007年夏のLAシンポジウム　2007/07/18

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Research Projects 7

  1. 多重文字列の極大共通部分列列挙に関する研究

    酒井 義文

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 基盤研究(C)

    Institution: 東北大学

    2023/04/01 - 2026/03/31

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    多重文字列の極大共通部分列を効率よく列挙するためのアルゴリズムの設計を目指す一環として、系列データを効率よく処理するための線形領域アルゴリズムに採用し得る手法の開発を意図し、以下の成果を得た。 （１）２本の文字列の極大共通部分列を列挙するアルゴリズムとして、２乗領域を用いて動作する既存のアルゴリズムを、従来用いられていたデータ構造が常時保持するデータを必要なもののみに限定するように変更することで、線形領域で動作するアルゴリズムへと改良した。また、線形領域ではなく３乗領域を要するものの、既存のアルゴリズムとは異なるアプローチを採用することで、すべての極大共通部分列を効率よく表現する新規に提案したデータ構造を用いるアルゴリズムを設計した。後者のアルゴリズムは、条件の課された特別な極大共通部分列を効率よく探索することにも利用できる。残念ながら、どちらのアルゴリズムに用いられた手法も、多重文字列の極大共通部分列の列挙をするためにそのまま適用すると、文字列の本数に関する指数関数的な大きさの領域を要する。 （２）任意に指定されるオフセットを伴う数値列における最大和断片を効率よく求めるためのデータ構造を提案し、これを効率よく構築する線形領域アルゴリズムを設計した。ここで、オフセットを伴う数値列とは、数値列の各要素の値からオフセットとして指定された値を減ずることで結果として得られる数値列のことである。文字列の極大共通部分列と数値列の最大和断片は異なる計算対象であるが、線形領域を実現するために採用した手法は、多重文字列の極大共通部分列の列挙において用いる領域の大きさを指数関数ではなく多項式に抑えるための手法の開発の一助となる可能性がある。

  2. 変態発生制御のシグナル回路と形態異常感受性に関する研究

    鈴木 徹, 酒井 義文, 田川 正朋, 横井 勇人

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 基盤研究(B)

    Institution: 東北大学

    2017/04/01 - 2021/03/31

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    私達は，これまで異体類の発生とその内分泌調節について検討し，変態に伴う眼球移動や左右非対称な体色形成、骨形成はレチノイン酸(RA)，甲状腺ホルモン，コルチゾル等の内分泌シグナルにより制御され，種苗の形態異常(眼位や体色異常，骨異常)は，これらシグナル回路の攪乱によって発生することを示唆している。本研究では，飼育技術と育種の両面から健苗育成に貢献することを目的として、これまでの研究を発展し，変態を調節するシグナル回路を解明した上で，種苗で頻発する無眼側黒化の発生原因となるシグナル回路の乱れを究明し、さらに無眼側黒化のリスク遺伝子を特定することをめざす。本年度は、ヒラメ・カレイ類の変態期に起こる有眼側限定的な色素胞の分化の発生制御機構を解明することに成功した。すなわち色素胞の前駆細胞は、変態期初期に幹細胞に近い状態で脊髄周辺に発生する。この時、幹細胞は、神経堤細胞のマーカー遺伝子であるSox10を発現し、このSox10の発現誘導にWntシグナルが働くことが明らかになった。脊髄周辺で分化したSox10陽性幹細胞は、脊髄から伸びる神経軸索に沿って背鰭基部に到達し、さらにそこから伸びる神経に沿って左右の皮膚に移動する。幹細胞から色素胞への分化はRA依存的であり、無眼側ではRAの分解酵素であるcyp26bが強発現して色素胞の分化が抑制され、有眼側のみ着色することを明らかにした。RA合成酵素は変態期に腸管上皮で強発現することから、腸管で合成されたRAは血流を介して体全体に拡散して色素胞の分化を誘導するが、無眼側ではcyp26bにより分解されることで色素分化に左右差が発生することが示唆された。 無眼側黒化のリスク遺伝子を特定するための基盤整備として、ヒラメのほぼ全遺伝子について、cDNAの塩基配列を解読し、塩基配列の一塩基多型の情報を得るために複数個体のcDNA塩基配列を取得した。

  3. Approach to molecular system controlling left-right asymmetry of flatfish body color using next generation techniques

    SUZUKI Tohru

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (B)

    Institution: Tohoku University

    2014/04/01 - 2017/03/31

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    Flounder larvae are externally symmetric commonly to general fishes, but they transform to left-right (L-R) asymmetric body by migrating one eye to the other side of body and then differentiating chromatophores at ocular side skin. In the hatcheries for aquaculture, since abnormal pigmentation, including pigmentation of ocular side and pseudo-albinism of blind side, often appears, elucidation of the mechanism to induce abnormal pigmentation is required. This research revealed cellular and molecular systems that control L-R asymmetric skin color development in flounder, and also abnormal pigmentation

  4. The genetic effect of long period expose of radioactive materials on fishes

    Nakajima Masamichi

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (A)

    Institution: Tohoku University

    2013/04/01 - 2017/03/31

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    The radioactive Cesium released by the accident of Fukushima Daiichi Nuclear Power Station destribute to Abukuma Mountains in Fukushima. The effects of expose of radiocesium on masu salmon were examined.Following results were obtained. 1)Positive corelation was observed betaeen the concentration of 137Cs in muscle and meranomacrophage in spleen. The histrogical deformities were also observed in gill. 2)the hemogrobin concentration decreased according to the increase of 137Cs concentration in muscle. This phenomenon also observed in rearing experiment. 3)Point mutations were observed in mitochondria DNA in the offspring obtained from the females which were collected from Mano River. These were not observed in the offspring obtained from the female which was rearing in Fukushima Prefectural Inland Water experimental Station. 4)Decrease of expression level in the gene which affecting to the apoptosis was observed. These results are plobably caused by exposition to radioactive materials.

  5. Trial to identify genes related with fish characters using bioinformatics and genome database

    Suzuki Tohru, SAKAI Yoshifumi, YOKOI Hayato

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Challenging Exploratory Research

    Institution: Tohoku University

    2013/04/01 - 2016/03/31

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    One of representative genetic traits required for aquaculture is fish character adequate for breeding, such as non-nervousness. In mammals, polymorphism of single amino acid repeat and microsatellites in promoter region that evolved in the genes related with brain function cause variation of character among strains. Medaka strains of d-rR and HNI-II have opposing character; the former being tame, while the latter being nervous. Using these two strains, this study aimed at searching the genes correlated with characters of fish strains by using bioinformatics and genome databases. Serotonin receptor, androgen receptor and dopamine receptor were selected as candidate genes. Since polymorphism in repetitive sequences were detected among two strains and wild medaka, it is highly possible that selected three genes are actually correlated with character of strains.

  6. A study on preprocessing for time-efficiently aligning sequences

    SAKAI Yoshifumi

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (C)

    Institution: Tohoku University

    2010 - 2012

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    Problems of finding a ‘good' alignment of two strings have many applications in computing the similarity between strings. This study proposed algorithms for some of such problems. By exploiting information obtained from preprocessing, these algorithms can perform faster than the previous algorithms. The problems for which the algorithms were proposed include the problem in which only one of two strings is allowed to be preprocessed because of an one-line environment, and the problem in which strings to be aligned are compressed in a certain manner.

  7. オンライン予測の手法を用いた意思決定モデルに関する研究

    瀧本 英二, 酒井 義文, 天野 一幸

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 特定領域研究

    Institution: 東北大学

    2004 - 2007

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    1.オンライン最適化問題に関する成果 あるルーティングの問題を零和型行列ゲームとして定式化し,オンライン予測の手法を用いてその最適戦略を効率よく求めるアルゴリズムを与えた.また,広いオンライン問題のクラスであるメトリカルタスクシステム問題に対する新しいアルゴリズムを提案し,その性能評価を与えた. 2.新しい評価基準に基づく問題のモデル化に関する成果 脳の計算機構をモデル化した閾値回路のエネルギー消費量を表す尺度として,エネルギー複雑度とパターン複雑度の概念を導入し,エネルギー複雑度やパターン複雑度が制限された回路の計算能力に一定の限界があることを示した.複数の文字配列の多重アラインメントを求める問題を,あるトポロジカルソートが表す複数の文字配列と,別に与えられた1つの文字配列同士のすべての組み合わせにおいて,最も長い共通部分列を求める問題として定式化し,効率の良いアルゴリズムを与えた.ブール関数に対するフィルタの概念を定式化し,そのノイズ除去効果を表す公式を与えた. 3.知識表現の複雑さに関する成果 乗算を計算するほぼ最適な順序付二部決定グラフを設計した.方形描画の符号化に必要な符号長の限界値を求める問題を,超大規模行列の第一固有値を求める問題に帰着することにより,符号長の下界を与えた.回路計算量の下界を導出する従来手法は,k乱雑性と呼ばれる論理関数の組み合わせ論的な性質に基づいていることを指摘し,その性質のみを利用するだけでは,従来の下界を改良できないことを示した.

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