学位

• 博士（工学）(東京大学)
• Doctor of Engineering(The University of Tokyo)

経歴

学歴

受賞

• コンピュータサイエンス領域功績賞
• "40th Anniversary of Theoretical Computer Science – Top Cited Articles: 1975-2014"
• 情報処理学会数理モデル化と問題解決研究会「功績賞」
• 船井情報科学振興賞
• NGC (New Generation Computing) Distinguished Paper Award

その他

論文

• A Proposal of Real-Time DNA Queue Automaton
• Three step design of DNA sequences for temperature dependent devices
• A method to simulate the derivation process of context-free grammars by DNA strand displacements
• Renewable Time-Responsive DNA Circuits with Photo-Responsive Bases
• Monotone Control of R Systems [DOI] [Scopus] [Scopus]
• On Monotone Control of Right Linear Grammars with Unknown Behaviors
• DNA Sequence Search for Temperature Dependent DNA Devices
• Reducing Control Alphabet Size for the Control of Right Linear Grammars with Unknown Behaviors [DOI] [Scopus] [Scopus]
• Monotonically controlling right linear grammars with unknown behaviors to output a target string [DOI] [Web of Scientce]
• Leak-free Million-fold DNA Amplification with Locked Nucleic Acid and Targeted Hybridization in One Pot
• DNA Computing Boosted by a Cationic Copolymer [DOI]
• Photochemical Acceleration of DNA Strand Displacement by Using Ultrafast DNA Photo-crosslinking [DOI] [Web of Scientce]
• Engineering multistate DNA molecules: a tunable thermal band-pass filter [DOI] [Web of Scientce]
• Molecular computers for molecular robots as hybrid systems [DOI] [Web of Scientce]
• Analog DNA Computing Devices Toward the Control of Molecular Robots
• Molecular Robots with Sensors and Intelligence [DOI] [Web of Scientce]
• DNA Domino Toppling: Speeding Up DNA Logic Circuits by Localizing Reaction -- Simulation Study --
• Enumeration approach to computing chemical equilibria [DOI] [Web of Scientce]
• Molecular Robotics: A New Paradigm for Artifacts [DOI] [Web of Scientce]
• Enumeration Approach to the Analysis of Interacting Nucleic Acid Strands [DOI]
• On the properties of language classes defined by bounded reaction automata [DOI] [Web of Scientce]
• Reaction automata [DOI] [Web of Scientce]
• Molecular computing machineries-computing models and wet implementations [DOI]
• Enumeration Approach to the Analysis of Interacting Nucleic Acid Strands
• Enumeration Approach to the Computational Analysis of High-Dimensional Monomolecular Chemical Master Equation
• Efficient and Approximate Simulation Algorithm of Kinetic Folding of an RNA Molecule
• DNA Logic Circuits with a DNA Polymerase and a Nicking Enzyme
• Efficient State Minimization Algorithm of Linear Separation Automata
• Theory of Minimizing Linear Separation Automata [DOI] [CiNii Research (CiNii Articles)] [Othres link]
• Necessary and Sufficient Conditions for Learning with Correction Queries
• State and Threshold Sequence Minimization Algorithm of Linear Separation Automata [DOI] [CiNii Research (CiNii Articles)] [CiNii Books] [Othres link] [Othres link]
• Applying Symmetric Enumeration Method to One-Dimensional Assembly of Rotatable Tiles [DOI] [Web of Scientce]
• A Software Tool for Analyzing Combinatorial Hybridization Reaction Systems
• Symmetric Enumeration Method: A New Approach to Computing Equilibria
• Exact and Efficient Equilibrium State Analysis of Interacting RNA Molecules
• Stochastically Approximating Tree Grammars by Regular Grammars and Its Application to Faster ncRNA Family Annotation
• A Characterization of Language Classes Learnable with Correction Queries
• Stochastic Regular Approximation of Tree Grammars and Its Application to Faster ncRNA Family Annotation [CiNii Research (CiNii Articles)] [CiNii Books] [Othres link]
• Stochastically Approximating Tree Grammars by Regular Grammars and Its Application to Faster ncRNA Family Annotation
• A New Approach to Computing Equilibrium State of Combinatorial Hybridization Reaction Systems [Web of Scientce]
• A New Approach to Computing Equilibrium State of Combinatorial Chemical Reaction Systems
• Efficient algorithm for testing structure freeness of finite set of biomolecular sequences [DOI]
• Probabilistic Inference in Test Tube and Its Application to Gene Expression Profiles
• A grammatical approach to the alignment of structure-annotated strings [DOI] [Web of Scientce]
• Efficient Algorithms for Testing Structure Freeness of Finite Set of Biomolecular Sequences
• An algorithm for testing structure freeness of biomolecular sequences [Web of Scientce]
• Testing Structure Freeness of Regular Sets of Biomolecular Sequences [CiNii Research (CiNii Articles)]
• Evaluating Biomolecular Sequences Using Hydrogen Bond Network Graph
• Efficient learning of k-reversible context-free grammars from positive structural examples [Web of Scientce]
• On template method for DNA sequence design [Web of Scientce]
• DNA sequence design using templates [Web of Scientce]
• A Magic Pot : Self-assembly computation revisited
• Multiple splicing systems and the universal computability [Web of Scientce]
• Formal properties of PA-matching [Web of Scientce]
• Approximate Identification and Finite Elasticity
• Sticker Systems with Complex Structures
• Concentration Prediction of Ligation Reaction Systems
• Horn Clause Computation by Self Assembly of DNA Molecules
• Concentration Prediction of Pattern Reaction Systems
• Iterated transductions and efficient learning from positive data: A unifying view [Web of Scientce]
• On the universality of Post and splicing systems [Web of Scientce]
• Horn clause computation with DNA molecules [Web of Scientce]
• Tree adjoining grammars for RNA structure prediction [Web of Scientce]
• Learning local languages and their application to DNA sequence analysis [Web of Scientce]
• Locality, reversibility, and beyond: Learning languages from positive data [Web of Scientce]
• Learning approximately regular languages with reversible languages [Web of Scientce]
• DNA implementation of simple Horn clause computation [Web of Scientce]
• On the power of circular splicing systems and DNA computability [Web of Scientce]
• Identifiability of subspaces and homomorphic images of zero-reversible languages [Web of Scientce]
• Families of Noncounting Languages and their Learnability from Positive Data
• DNA Splicing Systems and Post Systems [CiNii Research (CiNii Articles)]
• IDENTIFYING STRATEGIES USING DECISION LISTS FROM TRACE INFORMATION [Web of Scientce]
• DNA Evolutionary Linguistics and RNA Structure Modeling [CiNii Research (CiNii Articles)]
• Approximately Learning Regular Languages with respect to Reversible Languages, A Rough Set Based Analysis [CiNii Research (CiNii Articles)]
• On Approximately Identifying Concept Classes in the Limit [CiNii Research (CiNii Articles)]
• Grammatically Modeling and Predicting RNA Secondary Structures [CiNii Research (CiNii Articles)]
• Learning Local Languages and Its Application to Protein alpha-chain Identification [CiNii Research (CiNii Articles)]
• Learning Concatenations of Locally Testable Languages from Positive Data
• An Extended Rough Set Theory Toward Approximate Learning of Formal Languages [CiNii Research (CiNii Articles)]
• Inductive Learning of Regular Sets from Examples: A Rough Set Approach
• Modeling RNA Secondary Structures Using Tree Grammars [CiNii Research (CiNii Articles)]
• ALGORITHMS FOR FINDING THE LARGEST SUBTREE WHOSE COPIES COVER ALL THE LEAVES [Web of Scientce]
• 木パターン上の決定リストの学習とその推論制御への応用
• LEARNING DECISION LISTS OVER TREE PATTERNS AND ITS APPLICATION [Web of Scientce]
• Learning Strategies Using Decision Lists [CiNii Research (CiNii Articles)]
• A Similarity Measure for DNA Sequence Analysis Based on Locality [DOI] [CiNii Research (CiNii Articles)] [Othres link]
• 情報保存的な問題領域におけるトレースからの問題分割戦略の獲得
• トレースを利用した戦略の獲得と知識の分類手法 [CiNii Research (CiNii Articles)] [CiNii Books] [Othres link]

その他業績

• 分子コンピュータ設計のための計算モデル
• 分子計算の理論モデル [CiNii Research (CiNii Articles)] [CiNii Books] [Othres link]
• 形式言語の帰納的学習 (<特集>計算学習理論の進展と応用可能性) [CiNii Research (CiNii Articles)] [CiNii Books] [Othres link] [Othres link]
• 分子コンピュータ --- その理論と実験 [CiNii Research (CiNii Articles)] [CiNii Books] [Othres link]
• 形式言語の帰納的学習
• ラフ集合理論とその応用
• 計算論的言語理論と DNA 計算
• ラフ集合--その理論と応用-3-ラフ集合と意志決定 [CiNii Research (CiNii Articles)] [CiNii Books] [Othres link]
• ラフ集合と意思決定 [CiNii Research (CiNii Articles)]

講演・口頭発表等

• DNA分子による FIFO データ構造の実装方法の提案
• 未知の振る舞いを持つ制御付き右正則文法の生成能力について
• 未知の振る舞いを持つ正則文法に対する制御システムの信号数の削減
• 反応システムの制御における信号数の削減
• Hill型の融解曲線をもつDNA塩基配列の設計
• 未知の振る舞いを持つ正則文法とその制御
• 反応システムの制御によるブール関数の計算
• Toward Design and Analysis of Analog Computing Chemical Reaction Circuits
• Toward Efficient Computation of Chemical Equilibria of Interacting Nucleic Acid Strands Including Pseudoknots
• On Time Responsive DNA Analog Computing Devices
• Reaction Graphs Controlled by External Signals
• 鎖置換反応ダイナミクスを利用したアナログコンピュータの構築に向けて
• 分子ロボットに知性は実現できるか -計算論的立場から-
• グラフによる分子種の数え上げと化学反応系の解析
• 分子ロボティクス --- 感覚と知能を備えた分子ロボットの創成 ---
• Progress in Enumeration Approach to Computing Chemical Equilibrium of Interacting Nucleic Acid Strands
• DNA を用いた組み合わせ回路の高速化について
• 知能を実現する化学反応回路の構築を目指して
• 仮想核酸配列インタラクション反応系の平衡状態解析
• Enumeration Approach to the Analysis of Complex Chemical Reaction Systems
• Enumeration of Structures and Efficient Analysis of Complicated Chemical Reaction Systems
• Minimization Algorithm of Linear Separation Automata
• RNAインタラクション反応の線形な2次構造レベルでの解析アルゴリズム
• Theory of Minimizing Linear Separation Automata
• 線形分離オートマトンを用いたパターン識別手法の理論的基礎について
• RNA フォールディングシミュレーションのための新しいアルゴリズム
• On State-Merging Strategies of RPNI Algorithm that Guarantee Identifiability in the Limit
• A General Framework for Efficient Equilibrium State Analysis of Hybridization Reaction Systems
• 組合せ爆発を内包する化学反応系の平衡状態計算
• 確率木文法近似理論の RNA 二次構造解析への応用
• Tree Grammars for RNA Secondary Structure Analysis
• Efficient Tree Grammatical Modeling of RNA Secondary Structures from Alignment Data
• A Grammatical Approach to the Alignment of SA-Strings
• Efficiently Evaluating Structure Freeness of Biomolecular Sequences
• Hierarchical Alignment of RNA Secondary Structures Including Pseudoknots
• Efficient Alignment Method for RNA Secondary Structures Including Pseudoknots
• Algorithms for Evaluating Sequence Sets for DNA Computing
• バルジ・内部ループを形成しない DNA 配列セットの設計
• Learning Locally Testable Languages and Its Application to Protein Identification
• Modeling RNA Secondary Structures using Tree Grammars and Its Application to RNA Secondary Structure Prediction
• Modeling RNA Secondary Structures using Tree Grammars and Its Application to RNA Secondary Structure Prediction
• DNA コンピューティング --- その概観と理論的研究
• 確率計算システムとしての分子反応系について
• 制御付き離散事象システムの学習について
• DNA分子を用いたホーン節の計算について (A Note on Horn Clause Computation with DNA Molecules)

書籍等出版物

• 自然計算へのいざない
• DNA Computing and Molecular Programming, 20th International Conference
• Grammatical Inference: Algorithms and Applications, 8th International Colloquium, ICGI 2006
• Recent Advances in Formal Languages and Applications
• 計算論的学習
• DNA コンピューティング --- 新しい計算パラダイム

作品等

共同研究・競争的資金等の研究課題

• 制御信号系列によって多機能性を実現する分子計算システムの理論とその設計基盤の構築
• 分子ロボティクスの支援と広報
• 新学術領域「分子ロボティクス」 「知能分子ロボット実現に向けた化学反応回路の設計と構築」（計画研究）
• ＤＮＡナノエンジニアリングによる分子ロボティクスの創成
• 分子ロボティクスのための反応系解析アルゴリズムの理論
• DNA分子複合体を形成するためのハイブリッド型高速配列設計システムの開発
• 効率的な組合せ最適化アルゴリズムの開発と応用
• 構造的分子計算理論-自律的計算系の解析と設計のための基礎理論
• 例からの学習を行う効率的アルゴリズムの開発
• 分子コンピュータのための確率的計算理論
• 演繹を基本演算とする超並列分子計算モデルに関する研究
• DNA配列の相補性を利用した並列計算の理論
• 文法学習アルゴリズムに基づく蛋白質高次構造予測システムの開発
• 文法の近似学習理論と遺伝子構造解析への応用
• 文法学習理論に基づく蛋白質の高次構造予測システムの開発

メディア報道

産業財産権

所属学協会

• 人工知能学会
• 情報処理学会

委員歴

担当経験のある科目

• コンピュータサイエンス実験第二
• 国際科目・アルゴリズム
• 応用アルゴリズム論
• 三大学連携学部・英語科目・アルゴリズム
• アルゴリズム論第二
• 情報・ネットワーク工学専攻基礎
• コンピュータサイエンス実験第二
• 応用アルゴリズム論
• 国際科目（Computer Algorithms）
• アルゴリズム論第二
• 情報・ネットワーク工学専攻基礎
• 国際科目（Computer Algorithms）
• Advanced Communication Engineering and Informatics IV
• Advanced Communication Engineering and Informatics IV
• Advanced Communication Engineering and Informatics IV

社会貢献活動

学術貢献活動

• PC member of International Conference on DNA Computers and Molecular Programming