出版物
ジャーナル論文
Takaaki Nishimoto, Yasuo Tabei: LZRR: LZ77 parsing with right reference, Information and Computation, 2022
Shunsuke Kanda, Yasuo Tabei : DyFT: a dynamic similarity search method on integer sketches, Knowledge and Information Systems, 2021.
Mirai Takayanagi, Yasuo Tabei, Einoshin Suzuki, Hiroto Saigo: Sparse Nonnegative Interaction Models, IEEE Access, 2021.
Djamal Belazzougui, Manuel Cáceres, Travis Gagie, Pawel Gawrychowski, Juha Kärkkäinen, Gonzalo Navarro, Alberto Ordóñez, Simon J. Puglisi, and Yasuo Tabei: Block Trees, Journal of Computer and System Sciences 117:1-22, 2021.
Shunsuke Kanda, Dominik Köppl, Yasuo Tabei, Kazuhiro Morita, Masao Fuketa: Dynamic Path-decomposed Tries, ACM Journal of Experimental Algorithmics, 2020.Yasuo Tabei, Yoshihiro Yamanishi, Rasmus Pagh: Space-efficient Feature Maps for String Alignment Kernels, Data Science and Engineering, 2020.
Takaaki Nishimoto, Yoshimasa Takabatake, Yasuo Tabei: A compressed dynamic self-index for highly repetitive text collections, Information and Computation, 104518, 2020.
Yasuo Tabei: Scalable prediction of compound‐protein interaction on compressed molecular fingerprints, Molecular Informatics, 2020.
Yoshitaka Yamamoto, Yasuo Tabei, Koji Iwanuma: PARASOL: a hybrid approximation approach for scalable frequent itemset mining in streaming data, Journal of Intelligent Information Systems, 2019.
Ryusuke Sawada, Michio Iwata, Yasuo Tabei, Haruka Yamato, Yoshihiro Yamanishi: Predicting inhibitory and activatory drug targets by chemically and genetically perturbed transcriptome signatures, Nature Scientific Reports, 2018. Link to the paper
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, Masaaki Kotera: Simultaneous prediction of enzyme orthologs from chemical transformation patterns for de novo metabolic pathway reconstruction, Bioinformatics, 32, i278-i287, 2016. Link to the paper
Yoshimasa Takabatake, Kenta Nakashima, Yasuo Tabei and 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
国際会議/ワークショップ論文(すべて査読あり)
Kotaro Ii, Hiroto Saigo, Yasuo Tabei: A Branch-and-Bound Approach to Efficient Classification and Retrieval of Documents. 13th International Conference on Pattern Recognition Applications and Methods, 2024.
Takaaki Nishimoto, Shunsuke Kanda, Yasuo Tabei: Optimal-Time RLBWT Construction in BWT-runs Bounded Space, 49th International Colloquium on Automata, Languages, and Programming(ICALP), 2022
Koh Takeuchi, Masaaki Imaizumi, Shunsuke Kanda, Keisuke Fujii, Masakazu Ishihata, Yasuo Tabei, Frechet and Hausdorff Kernels for Trajectory Data Analysis, 29th ACM SIGSPATIAL International Conference on Advances in Geographic Information Systems, 2021.
Takaaki Nishimoto and Yasuo Tabei: Optimal-Time Queries on BWT-runs Compressed Indexes, 48th International Colloquium on Automata, Languages, and Programming (ICALP), 2021.
Takaaki Nishimoto and Yasuo Tabei: Enumeration of Characteristic Substrings in BWT-runs Bounded Space, 32nd International Conference on Combinatorial Pattern Matching (CPM), 2021.
Ryoichiro Yafune, Daisuke Sakuma, Yasuo Tabei, Noritaka Saito, Hiroto Saigo: Automatically Mining Relevant Variable Interactions via Sparse Bayesian Learning, International Conference on Pattern Recognition (ICPR), 2020.
Shunsuke Kanda and Yasuo Tabei: Dynamic Similarity Search on Integer Sketches, IEEE International Conference on Data Mining (ICDM), 2020.
Shunsuke Kanda, Koh Takeuchi, Keisuke Fujii, Yasuo Tabei: Succinct Trit-array Trie for Scalable Trajectory Similarity Search, 28th ACM SIGSPATIAL International Conference on Advances in Geographic Information Systems, 2020.
Yusuke Morikawa, Yasuhiro Ishihara, Takanori Ide, Eiji Moriyama, Taku Akita, Yasuo Tabei, Takehito Utsuro, Hiroshi Nakagawa: Classification of Time Series Measurement Data for Shift Control of Automatic Transmission of Vehicles Using Machine Learning Techniques, Society of Automotive Engineers World Congress Experience (SAE-WCX), 2020.
Shunsuke Kanda and Yasuo Tabei: b-Bit Sketch Trie: Scalable Similarity Search on Integer Sketches, 2019 IEEE International Conference on BigData(IEEE BigData), 2019. (acceptance rate: (106/550=)19.2%)
Vo Nuguyen Le Duy, Takuto Sakuma, Taiju Ishiyama, Hiroki Toda, Kazuya Nishi, Masayuki Karasuyama, Yuta Okubo, Masayuki Sunaga, Yasuo Tabei, Ichiro Takeuchi: Statistically Discriminative Sub-trajectory Mining with Multiple Testing Correction, 27th ACM SIGSPATIAL International Conference on Advances in Geographic Information Systems, 2019.
Yasuo Tabei, Yoshihiro Yamanishi, Rasmus Pagh: Space-efficient feature maps for string alignment kernels, 19th IEEE International Conference on Data Mining (ICDM), 2019. (acceptance rate: (194/1046=)18.5%)
Takaaki Nishimoto and Yasuo Tabei: Conversion from RLBWT to LZ77, 30th International Symposium on Combinatorial Pattern Matching (CPM), 2019. Link to the arXiv
Michio Iwata, Longhao Yuan, Qibin Zhao, Yasuo Tabei, Francois Berenger, Ryusuke Sawada, Sayaka Akiyoshi, Momoko Hamano and Yoshihiro Yamanishi: Predicting drug-induced transcriptome responses of a wide range of human cell lines by a novel tensor-train decomposition algorithm, International Conference on Intelligence Systems for Molecular Biology (ISMB), 2019. (acceptance rate: (69/366=)18%)
Takaaki Nishimoto and Yasuo Tabei: LZRR: LZ77 Parsing with Right Reference, Data Compression Conference (DCC), 2019.
Yasuo Tabei, Masaaki Kotera, Ryusuke Sawada, Yoshihiro Yamanishi: Network-based characterization of drug-protein interaction signatures with a space-efficient approach, 17th Asia Pacific Bioinformatics Conference (APBC), 2019. Link to the paper
Yasuo Tabei: Scalable Machine Learning on Compressed Data Representations, In Proceedings of the 2018 International Symposium on Information Theory and Its Applications.
Mirai Takayanagi, Yasuo Tabei, Hiroto Saigo: Entire regularization path for sparse nonnegative interaction model, 2018 IEEE International Conference on Data Mining (ICDM). (acceptance rate: (189/984=)19%), 2018.
Takaaki Nishimoto, Yoshimasa Takabatake, Yasuo Tabei: A dynamic compressed self-index for highly repetitive text collections, Data Compression Conference (DCC), 2018.
Yasuo Tabei and Simon J. Puglisi: Scalable similarity search for molecular descriptors, 10th International Conference on Similarity Search and Applications (SISAP), 2017. Link to the paper
Naoya Takeishi, Yoshinobu Kawahara, Yasuo Tabei, Takehisa Yairi: Bayesian dynamic mode decomposition, 26th International Joint Conference on Artificial Intelligence (IJCAI), 2017. Link to the paper
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, Masaaki 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. Link to the paper slide(slideshare)
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. Link to the paper
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. Link to the paper
Shirou Maruyama, Yasuo Tabei, Hiroshi Sakamoto, Kunihiko Sadakane: Fully-Online Grammar Compression, 20th String Processing and Information Retrieval Symposium (SPIRE), 2013. paper(pdf) slide(slideshare)
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)
田部井靖生, 浅井潔, RNAを発見するためのローカルマルチプルアライメント手法, 第１１回RNAミーティング 2009, 27--29 July, 新潟, 2009.
Yasuo Tabei, Daisuke Okanohara, Koji Tsuda: Mining Frequent Patterns from Linear Graphs, The Fourth International Workshop on Data-mining Statistical Science(DMSS), 7--8 July, Kyoto, Japan, 2009.
本
マテリアルズインフォマティクスのためのデータ作成とその解析、応用事例, 技術情報協会, ISBN：978-4-86104-854-8
受賞
第19回情報論的学習理論ワークショップ(IBIS), ベストプレゼンテーション賞, 2016年11月17日(木) Link
研究助成
戦略的創造研究推進事業(科学技術振興機構)
官民研究開発投資拡大プログラム（PRISM) (平成29年度-令和3年度)
さきがけ「ビッグデータ統合利活用のための次世代基盤技術の創出・体系化」 (平成25年度第一期採択）
科学研究費補助金(日本学術振興会)
学術変革領域A「サイバー・フィジカル空間を融合した階層的生物ナビゲーション」(分担) (令和3年-7年度)
基盤研究 B (分担) (平成28-30年度)
基盤研究 B (分担) (平成26-28年度）
若手研究 B (代表) (平成24-26年度）
特別研究員奨励費 (代表) (平成20-22年度)
特許
中川裕志, 田部井靖生, 宇津呂武仁 (理研), 森川祐介, 井手貴範, 石原靖弘, 森山英二,秋田拓(アイシン), “変速機の開発支援システムおよび方法”, JP7245464, 2019年5月22日
田部井靖生, 末廣大貴 (理研), 葛西亮平 (東日本旅客鉄道株式会社), “変化点を含む軌道変位時系列データに対するノイズ除去方法”, 特許出願中
田部井靖生, 末廣大貴 (理研), 葛西亮平 (東日本旅客鉄道株式会社), “相関係数を尺度とした軌道変位動的位置合わせ手法”, 特許出願中