Dr. Yasuo Tabei

[English | Japanese]

Profile

Name
Yasuo Tabei
Affiliation
        Unit leader at succinct information processing unit in the RIKEN Center for Advanced Intelligence Project
E-mail
        yasuo.tabei (at)riken.jp
Blog
English Japanese
Employment
        2013-2016 Researcher at PRESTO, Japan Science and Technology Agency
2010-2013 Posdoc researcher at ERATO Minato Project, Japan Science and Technology Agency
2009-2010 JSPS Research Fellow (PD)
2008-2009 JSPS Research Fellow (DC2)
2006-2008 AIST Research Staff
Intern
2009 Preferred Infrastructure, Inc
2008 Max Planck Institute for Biological Cybernetics
Link
Google Scholar
DBLP
SlideShare
arXiv
github

News

  • Our paper about predictions of drug-target interactions and metabolic pathways has been accepted. (Apr. 4, 2017) 
  • I promoted to the unit leader of succinct information processing unit at the RIKEN Center for Advanced Intelligence Project. (Apr. 1, 2017) 

Old News

Future Event

Research Topic
Succinct data structure
Wavelet tree
Grammar compression
Lempel-ziv compression
FM-index
Machine Learning 
All Pairs Similarity Search
Nearest Neighbor Search
Conditional Random Fields(CRFs)
Boosting
Data Mining
Graph Similarity Search
Graph Mining
Frequent Pattern Mining
Bioinformatics
Chemical fingerprint search
Drug-target interaction prediction
Metabolic pathway prediction
Structural alignment algorithm for RNA sequences

Journal Paper

  • (new) Yoshihiro Yamanishi, Yasuo Tabei, Masaaki Kotera: Statistical machine learning for agriculture and human healthcare based on biomedical big data, to be appeared in the Proceedings of Forum "Math-for-Industry" 2017.
  • Yasuo Tabei, Yoshihiro Yamanishi and Massaki Kotera: Simultaneous prediction of enzyme orthologs from chemical transformation patterns for de novo metabolic pathway reconstruction, accepted to Bioinformatics. Link to the paper
  • Yoshimasa Takabatake, Kenta Nakashima, Yasuo Tabei, Hiroshi Sakamoto: siEDM: an efficient string index and search algorithm for edit distance with moves, Algorithms, 9, 26. Link to the paper
  • Yoshihiro Yamanishi*, Yasuo Tabei*, Masaaki Kotera:  Metabolome-scale de novo pathway reconstruction using regioisomer-sensitive graph alignments, Bioinformatics, 31, i161-i170, 2015. (*joint first author) Link to the paper
  • Masaaki Kotera*, Yasuo Tabei*, Yoshihiro Yamanishi*, Ai Muto, Yuki Moriya, Toshiaki Tokimatsu, Susumu Goto: Metabolome-scale prediction of intermediate compounds in multi-step metabolic pathways with a recursive supervised approach, Bioinformatics, 30(12), i165-i174, 2014. (*joint first author) Link to the paper
  • Masaaki Kotera*, Yasuo Tabei*, Yoshihiro Yamanishi*, Toshiaki Tokimatsu, Susumu Goto: Supervised de novo reconstruction of metabolic pathways from metabolome-scale compound sets, Bioinformatics, 29(13), i135-i144, 2013. (*joint first author) Link to the paper
  • Yasuo Tabei, Edouard Pauwels, Veronique Stoven, Kazuhiro Takemoto, Yoshihiro Yamanishi: Identification of chemogenomic features from drug-target interaction networks using interpretable classifiers, Bioinformatics, 28(18), i487-i494, 2012. Link to the paper
  • Junichi Ito, Yasuo Tabei, Kana Shimizu, Koji Tsuda and Kentaro Tomii: PoSSuM: a database of similar protein–ligand binding and putative pockets, Nucl. Acids Res., DB issue 2012;40:D541-8. Link to the paper
  • Junichi Ito, Yasuo Tabei, Kana Shimizu, Kentaro Tomii and Koji Tsuda: PDB-scale analysis of known and putative ligand binding sites with structural sketches, Proteins, 80, 747-763, 2012. Link to the paper
  • Yasuo Tabei and Koji Tsuda: SketchSort: Fast all pairs similarity search for large databases of molecular fingerprints, Molecular Informatics, 30(9), 801-807, 2011. Link to the paper
  • Yasuo Tabei and Kiyoshi Asai: A local multiple alignment method for detection of non-coding RNA sequences, Bioinformatics, 25(12), 1498-1505, 2009. Link to the paper
  • Kiyoshi Asai, Hisanori Kiryu, Michiaki Hamada, Yasuo Tabei, Kengo Sato, Hiroshi Matsui, Yasubumi Sakakibara, Goro Terai and Totai Mituyama: Software.ncrna.org: web servers for analyses of RNA sequences, Nucl. Acids Res., 36, W75-W78, 2008. Link to the paper
  • Yasuo Tabei, Hisanori Kiryu, Taishin Kin and Kiyoshi Asai: A fast structural multiple alignment method for long RNA sequences, BMC Bioinformatics, 9(33), 2008. Link to the paper
  • Hisanori Kiryu, Yasuo Tabei, Taishin Kin, and Kiyoshi Asai: Murlet: A practical multiple alignment tool for structural RNA sequences, Bioinformatics, 23(13), 1588-1598, 2007. Link to the paper
  • Yasuo Tabei, Koji Tsuda, Taishin Kin, and Kiyoshi Asai: SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments, Bioinformatics, 22(14), 1723-1729, 2006. Link to the paper

Conference Paper (refereed)

  • Yasuo Tabei, Hiroto Saigo, Yoshihiro Yamanishi, Simon J. Puglisi: Scalable partial least squares regression on grammar-compressed data matrices, 22nd ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD), 2016. (acceptance rate:(142/784=)18%) Link to the paper
  • Yasuo Tabei, Yoshihiro Yamanishi, Massaki Kotera: Simultaneous prediction of enzyme orthologs from chemical transformation patterns for de novo metabolic pathway reconstruction, 23rd International Conference on Intelligent Systems for Molecular Biology (ISMB), 2016. (acceptance rate: (41/187)=21%) Link to the paper
  • Yoshimasa Takabatake, Yasuo Tabei, Hiroshi Sakamoto: Online self-indexed grammar compression, 22nd edition of the International Symposium on String Processing and Information Retrieval (SPIRE), 2015. 
  • Djamal Belazzougui, Patrick Cording, Simon J. Puglisi, Yasuo Tabei: Access, rank, and select in grammar-compressed strings, 23rd European Symposium on Algorithms (ESA), 2015. (acceptance rate: (85/320=)26%)
  • Yoshihiro Yamanishi*, Yasuo Tabei*, Masaaki Kotera: Metabolome-scale de novo pathway reconstruction using regioisomer-sensitive graph alignments, ISMB/ECCB, 2015. (*joint first author) (acceptance rate: (43/241=)18%) Link to the paper
  • Djamal Belazzougui, Travis Gagie, Paweł Gawrychowski, Juha Kärkkäinen, Alberto Ordóñez, Simon J. Puglisi, Yasuo Tabei: Queries on LZ-Bounded Encodings, Data Compression Conference (DCC), 2015. (selected as a full paper and an oral presentation) full-version(arXiv)
  • Yoshimasa Takabatake, Yasuo Tabei, Hiroshi Sakamoto: Online pattern matching for string edit distance with moves, 21st International Symposium on String Processing and Information Retrieval (SPIRE), 2014. full-version(arXiv)
  • Masaaki Kotera*, Yasuo Tabei*, Yoshihiro Yamanishi*, Ai Muto, Yuki Moriya, Toshiaki Tokimatsu, Susumu Goto: Metabolome-scale prediction of intermediate compounds in multi-step metabolic pathways with a recursive supervised approach, 22nd Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), 2014. (*joint first author) (acceptance rate:(37/191=)19%) Link to the paper
  • Yoshimasa Takabatake, Yasuo Tabei, Hiroshi Sakamoto: Improved ESP-index: a practical self-index for highly repetitive texts, 13th International Symposium on Experimental Algorithms (SEA), 2014. full-version(arXiv) proceeding(pdf)
  • Shirou Maruyama and Yasuo Tabei: Fully Online Grammar Compression in Constant Space, Data Compression Conference (DCC), 2014. (selected as a full paper and an oral presentation) full-version(arXiv) proceeding(pdf)  
  • Yasuo Tabei and Yoshihiro Yamanishi: Scalable prediction of compound-protein interactions using minwise hashing, 24th International Conference on Genome Informatics (GIW), 2013.
  • Masaaki Kotera, Yasuo Tabei, Yoshihiro Yamanishi, Yuki Moriya, Toshiaki Tokimatsu, Minoru Kanehisa and Susumu Goto: KCF-S: KEGG Chemical Function and Substructure for improved interpretability and prediction in chemical bioinformatics, 24th International Conference on Genome Informatics (GIW), 2013.
  • Hiroaki Iwata, Sayaka Mizutani, Yasuo Tabei, Masaaki Kotera, Susumu Goto and Yoshihiro Yamanishi: Inferring protein domains associated with drug side effects based on drug-target interaction network, 24th International Conference on Genome Informatics (GIW), 2013.
  • Shirou Maruyama, Yasuo Tabei, Hiroshi Sakamoto, Kunihiko Sadakane: Fully-Online Grammar Compression, 20th String Processing and Information Retrieval Symposium (SPIRE), 2013. paper(pdf)
  • Yasuo Tabei, Akihiro Kishimoto, Masaaki Kotera, Yoshihiro Yamanishi: Succinct Interval-Splitting Tree for Scalable Similarity Search of Compound-Protein Pairs with Property Constraints, 19th ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD), 2013. (acceptance rate:(126/726=)17%) paper(pdf)
  • Masaaki Kotera*, Yasuo Tabei*, Yoshihiro Yamanishi*, Toshiaki Tokimatsu, Susumu Goto: Supervised de novo reconstruction of metabolic pathways from metabolome-scale compound sets, ISMB/ECCB2013 (*joint first author) (acceptance rate:(40/247=)16%) Link to the paper
  • Yasuo Tabei, Yoshimasa Takabatake, Hiroshi Sakamoto: A Succinct Grammar Compression, 24th Annual Symposium on Combinatorial Pattern Matching (CPM), 2013. paper(pdf) slide(slideshare)
  • Yoshimasa Takabatake, Yasuo Tabei, Hiroshi Sakamoto: Variable-Length Codes for Space-Efficient Grammar-Based Compression, 19th International Symposium on String Processing and Information Retrieval (SPIRE), Cartagena, Colombia, 2012. paper(pdf)
  • Yasuo Tabei: Succinct Multibit Tree: Compact Representation of Multibit Trees by Using Succinct Data Structures in Chemical Fingerprint Searches, 12th Workshop on Algorithms in Bioinformatics (WABI) ALGO, Ljubljana, Slovenia, 2012. paper(pdf) slide(slideshare)
  • Yasuo Tabei, Edouard Pauwels, Veronique Stoven, Kazuhiro Takemoto, Yoshihiro Yamanishi: Identification of chemogenomic features from drug-target interaction networks using interpretable classifiers, 11th European Conference on Computational Biology (ECCB), Basel, Switzerland, 2012. (acceptance rate:(48/341=)14%) Link to the paper
  • Yasuo Tabei, Daisuke Okanohara, Shuichi Hirose, Koji Tsuda: LGM: Mining Frequent Subgraphs from Linear Graphs, The 15th Pacific-Asia Conference on Knowledge Discovery and Data Mining(PAKDD), Shenzhen, China, 2011. (acceptance rate:(90/331=)27%) paper(pdf) slide(pdf)
  • Yasuo Tabei and Koji Tsuda: Kernel-based Similarity Search in Massive Graph Databases with Wavelet Trees, Eleventh SIAM International Conference on Data Mining (SDM), Arizona, USA, 2011. (acceptance rate:(86/343=)25%) paper(pdf) slide(pdf)
  • Yasuo Tabei, Takeaki Uno, Masashi Sugiyama, Koji Tsuda: Single Versus Multiple Sorting in All Pairs Similarity Search, The 2nd Asian Conference on Machine Learning (ACML), Tokyo, Japan, 2010. (acceptance rate:(23/74=)31%) paper(pdf) slide(pdf) slide(pptx)
  • Yasuo Tabei, Kiyoshi Asai: A local multiple alignment method for detection of non-coding RNA sequences, RNA meeting 2009, 27--29 July, Niigata, Japan, 2009.
  • Yasuo Tabei, Daisuke Okanohara, Koji Tsuda: Mining Frequent Patterns from Linear Graphs, The Fourth International Workshop on Data-mining Statistical Science(DMSS), July, 7-8 2009, Kyoto, Japan.

Invited Talk

  • Theory and Practice of Grammar Compression, The 27th RAMP Symposium (RAMP2015), Oct. 15th, 2015, Shizuoka University, Japan
  • Large-scale machine learning using compact data representation, Tutorial session, FIT2015, Sep. 17th, 2015, Ehime University, Japan
  • Dictionary based compression for processing massive genome sequences, committee on genome technology164, Hosted by Prof. Tetsuo Shibuya, Dec. 12, 2014
  • Kernel-based Similarity Search in Massive Graph Databases with Wavelet Trees, The 5th DMSS Workshop, Mar. 29-30, 2011, Osaka University Nakanoshima Center, Osaka, Japan

Talk

  • Succinct Data Structure for Scalable Knowledge Discoveries, tutorial session, 20th Pacific Asia Conference on Knowledge Discovery and Data Mining (PAKDD), Apr. 19, 2016 (Tue.)
  • Fast Similarity Search by Wavelet Tree, Similarity Search Seminar, IT University of Copenhagen, Hosted by Prof. Rasmus Pagh, Dec. 5, 2014 (Fri.)
  • Fast Graph Search by Wavelet Tree, University of Leister, Hosted by Prof. Rajeev Raman, Sep. 6, 2012 (Thr.)
  • Fast similarity search of massive graph databases by wavelet trees, NTT Communication Science Laboratories, Hosted by Dr. Akisato Kimura, Mar. 5, 2012 (Mon.)
  • Kernel-based Similarity Search in Massive Graph Databases with Wavelet Trees, Curie Institute Paris France, Hosted by Dr. Yoshihiro Yamanishi, Sep. 19, 2011 (Mon.)
  • Kernel-based Similarity Search in Massive Graph Databases with Wavelet Trees, Max Planck Institute for Intelligent Systems Tübingen Germany, Hosted by Prof. Karsten Borgwardt, Sep. 14, 2011 (Wed.)
  • Fast similarity search for locality sensitive binary code with wavelet tree, 5th Information-Based Inductive Sciences and Machine Learning(IBISML), Jun. 20-21, 2011, University of Tokyo, Tokyo, Japan
  • SketchSort: Fast All Pairs Similarity Search Method, Tokyo Institute of Technology, Hosted by Prof. Masashi Sugiyama, Octorber 26, 2010 (Thu.) slide(pdf)
  • SketchSort: Fast All Pairs Similarity Search Method, Ochanomizu University, Hosted by Prof. Sese, October 14, 2010 (Thu.) slide(pdf)
  • Mining Frequent Subgraphs from Linear Graphs, Max Planck Institute for Informatics Germany, Hosted by Dr. Hiroto Saigo, February 26, 2010 (Fri.)
  • Mining Frequent Subgraphs from Linear Graphs, Max Planck Institute for Biological Cybernetics Germany, Hosted by Philipp Drewe, February 25, 2010 (Thr.)
  • SketchSort: An Efficient Method for All Pairs Similarity Search, Max Planck Institute for Informatics Germany, Hosted by Dr. Hiroto Saigo, February 23, 2010 (Tue.)
  • Mining Frequent Subgraphs from Linear Graphs, Curie Institute Paris France, Hosted by Dr. Yoshihiro Yamanishi, February 22, 2010 (Mon.)
  • Mining Frequent Subgraphs from Linear Graphs, Computational Biology Research Center (CBRC) Japan, Feb 12, 2010 (Fri.)
  • Mining Frequent Subgraphs from Linear Graphs, Hokkaido University Japan, Hosted by Prof. Shinichi Minato, January 7, 2010 (Thr.)
  • Mining Structured Patterns from Linear Graphs, IBM Tokyo Research Laboratory, Hosted by Dr. Hisashi Kashima, January 7, 2009 (Wed.)
  • A fast structural multiple alignment method for long RNA sequeces, Max Planck Institute for Informatics, Hosted by Dr. Hiroto Saigo, September 11, 2008 (Thr.) pdf
  • A local alignment model for non-coding RNA sequences and its application of local multiple alignment, Computational Biology Research Center (CBRC), July 11, 2008 (Fri.) pdf

Research Grants

  • Grand-in-Aid for Scientific Research by Japan Society for the Promotion of Science (JSPS) 
    • Grant-in-Aid for Young Scientists (B) (Apr. 2012 - Mar. 2015) 
    • Grant-in-Aid for JSPS Fellows (Apr. 2008 - Mar. 2010)

Software

Machine Learning and Data Mining
  • SMBT (Succinct multibit tree for fast similarity searches of large-scale fingerprints)
  • gWT (Fast graph similarity search for massive graph databases)
  • SketchSort (Fast all pairs similarity search for cosine distance)
  • SketchSortE (Fast all pairs similarity search for Euclidean distance)
  • SketchSortJ (Fast all pairs similarity search for Jaccard-Tanimoto distance)
  • SACHICA++ (Scalable Algorithm for Characteristic/Homogeneous Interval Calculation)
  • LCM (Linear time Closed itemset Miner)
  • PrefixSpan (Frequent Sequential Pattern Miner)
  • iboost (Itemset Boosting)
  • Data structure
  • FM-index++ (c++ implementation of FM-index)
  • olca++ (c++ implementation of online grammar-based compression)
  • Bioinformatics
  • PACHA (Pairwise Chemical Aligner)
  • SCARNA (fast and accurate structural pairwise alignment software for RNA sequences)
  • MXSCARNA (Multiple alignment software for RNA sequences)
  • SCARNA_LM (Local multiple alignment software for RNA sequences)