Tatsuya Akutsu

341 papers A* 5A 1B 39C 11Misc 9Journal 241Unranked 32
YearRankTypeTitle / Venue / Authors
2026 J jnl
MTSCCleav: A Multivariate Time Series Classification (MTSC)-Based Method for Predicting Human Dicer Cleavage Sites.
IEEE Access
Coleman Yu, Raymond Chi-Wing Wong, Tatsuya Akutsu
2026 J jnl
Observability and approximate observability of Boolean control networks from finite offline data.
Sci. China Inf. Sci.
Xingyu Ge, Tatsuya Akutsu, Liangjie Sun, Jianquan Lu, Jie Zhong
2026 J jnl
On the Number of Control Nodes in Boolean Networks With Degree Constraints.
IEEE Trans. Cybern.
Liangjie Sun, Wai-Ki Ching, Tatsuya Akutsu
2026 J jnl
Scaling With Multiple Scaling Factors in Time Series Searching.
IEEE Access
Coleman Yu, Tatsuya Akutsu, Raymond Chi-Wing Wong
2025 J jnl
A Method for Computing the Minimum Common Feedback Set for a Multilayer Network and Its Application to Analysis of Biological Data.
J. Inf. Process.
Shogo Nakashima, Tomoya Mori, Ruiming Li, Tatsuya Akutsu
2025 J jnl
A unified approach to inferring chemical compounds with the desired aqueous solubility.
J. Cheminformatics
Muniba Batool, Naveed Ahmed Azam, Jianshen Zhu, Kazuya Haraguchi, Liang Zhao, Tatsuya Akutsu
2025 J jnl
Combining Graph Neural Networks and Mixed Integer Linear Programming for Molecular Inference under the Two-Layered Model.
CoRR
Jianshen Zhu, Naveed Ahmed Azam, Kazuya Haraguchi, Liang Zhao, Tatsuya Akutsu
2025 J jnl
Computing Hamming Distance and Levenshtein Distance Using ReLU Neural Networks.
IEEE Access
Masahiro Ohtomo, Atsuhiro Takasu, Tatsuya Akutsu
2025 J jnl
Cycle-configuration descriptors: a novel graph-theoretic approach to enhancing molecular inference.
J. Cheminformatics
Bowen Song, Jianshen Zhu, Naveed Ahmed Azam, Kazuya Haraguchi, Liang Zhao, Tatsuya Akutsu
2025 J jnl
Designing ReLU Generative Networks to Enumerate Trees with a Given Tree Edit Distance.
CoRR
Mamoona Ghafoor, Tatsuya Akutsu
2025 J jnl
On the Compressive Power of Autoencoders With Linear and ReLU Activation Functions.
Neural Comput.
Liangjie Sun, Chenyao Wu, Wai-Ki Ching, Tatsuya Akutsu
2025 J jnl
On the Number of Control Nodes in Boolean Networks with Degree Constraints.
CoRR
Liangjie Sun, Wai-Ki Ching, Tatsuya Akutsu
2025 J jnl
On the Number of Control Nodes of Threshold and XOR Boolean Networks.
CoRR
Christopher H. Fok, Liangjie Sun, Tatsuya Akutsu, Wai-Ki Ching
2025 J jnl
On the Size and Width of the Decoder of a Boolean Threshold Autoencoder.
IEEE Trans. Neural Networks Learn. Syst.
Tatsuya Akutsu, Avraham A. Melkman
2025 J jnl
SFM-Net: Selective Fusion of Multiway Protein Feature Network for Predicting Binding Affinity Changes upon Mutations.
J. Chem. Inf. Model.
Chunting Liu, Sudong Cai, Tong Pan, Hiroyuki Ogata, Jiangning Song, Tatsuya Akutsu
2025 J jnl
Towards Environment-Sensitive Molecular Inference via Mixed Integer Linear Programming.
CoRR
Jianshen Zhu, Mao Takekida, Naveed Ahmed Azam, Kazuya Haraguchi, Liang Zhao, Tatsuya Akutsu
2025 J jnl
Unsupervised Dual Deep Hashing With Semantic-Index and Content-Code for Cross-Modal Retrieval.
IEEE Trans. Pattern Anal. Mach. Intell.
Bin Zhang, Yue Zhang, Junyu Li, Jiazhou Chen, Tatsuya Akutsu, Yiu-ming Cheung, Hongmin Cai
2024 J jnl
A Method for Inferring Polymers Based on Linear Regression and Integer Programming.
IEEE ACM Trans. Comput. Biol. Bioinform.
Ryota Ido, Shengjuan Cao, Jianshen Zhu, Naveed Ahmed Azam, Kazuya Haraguchi, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu
2024 J jnl
A Unified Approach to Inferring Chemical Compounds with the Desired Aqueous Solubility.
CoRR
Muniba Batool, Naveed Ahmed Azam, Jianshen Zhu, Kazuya Haraguchi, Liang Zhao, Tatsuya Akutsu
2024 J jnl
Accurate multi-view clustering to seek the cross-viewed yet uniform sample assignment via tensor feature matching.
Inf. Sci.
Yue Zhang, Wuxiu Quan, Tatsuya Akutsu, Li Liu, Hongmin Cai, Bin Zhang
2024 — conf
Cycle-Configuration: A Novel Graph-theoretic Descriptor Set for Molecular Inference.
BIBM
Bowen Song, Jianshen Zhu, Naveed Ahmed Azam, Kazuya Haraguchi, Liang Zhao, Tatsuya Akutsu
2024 J jnl
Cycle-Configuration: A Novel Graph-theoretic Descriptor Set for Molecular Inference.
CoRR
Bowen Song, Jianshen Zhu, Naveed Ahmed Azam, Kazuya Haraguchi, Liang Zhao, Tatsuya Akutsu
2024 J jnl
DiCleave: a deep learning model for predicting human Dicer cleavage sites.
BMC Bioinform.
Lixuan Mu, Jiangning Song, Tatsuya Akutsu, Tomoya Mori
2024 J jnl
Distributed Pinning Control: Stabilizing Large Boolean Networks Subjected to Perturbations.
IEEE Trans. Cybern.
Qinyao Pan, Jie Zhong, Tatsuya Akutsu, Yang Liu, Rongjian Liu
2024 J jnl
Molecular Design Based on Integer Programming and Splitting Data Sets by Hyperplanes.
IEEE ACM Trans. Comput. Biol. Bioinform.
Jianshen Zhu, Naveed Ahmed Azam, Kazuya Haraguchi, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu
2024 J jnl
On the Generative Power of ReLU Network for Generating Similar Strings.
IEEE Access
Mamoona Ghafoor, Tatsuya Akutsu
2024 J jnl
On the Number of Observation Nodes in Boolean Networks.
CoRR
Liangjie Sun, Wai-Ki Ching, Tatsuya Akutsu
2023 J jnl
Common Attractors in Multiple Boolean Networks.
IEEE ACM Trans. Comput. Biol. Bioinform.
Yu Cao, Wenya Pi, Chun-Yu Lin, Ulrike Münzner, Masahiro Ohtomo, Tatsuya Akutsu
2023 J jnl
Identifying miRNA-Gene Common and Specific Regulatory Modules for Cancer Subtyping by a High-Order Graph Matching Model.
IEEE ACM Trans. Comput. Biol. Bioinform.
Jiazhou Chen, Guoqiang Han, Aodan Xu, Tatsuya Akutsu, Hongmin Cai
2023 J jnl
Molecular Design Based on Integer Programming and Splitting Data Sets by Hyperplanes.
CoRR
Jianshen Zhu, Naveed Ahmed Azam, Kazuya Haraguchi, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu
2023 J jnl
On the Compressive Power of Boolean Threshold Autoencoders.
IEEE Trans. Neural Networks Learn. Syst.
Avraham A. Melkman, Sini Guo, Wai-Ki Ching, Pengyu Liu, Tatsuya Akutsu
2023 J jnl
On the Trade-off between the Number of Nodes and the Number of Trees in a Random Forest.
CoRR
Tatsuya Akutsu, Avraham A. Melkman, Atsuhiro Takasu
2023 J jnl
PFresGO: an attention mechanism-based deep-learning approach for protein annotation by integrating gene ontology inter-relationships.
Bioinform.
Tong Pan, Chen Li, Yue Bi, Zhikang Wang, Robin B. Gasser, Anthony W. Purcell, Tatsuya Akutsu, Geoffrey I. Webb, Seiya Imoto, Jiangning Song
2023 J jnl
ResNetKhib: a novel cell type-specific tool for predicting lysine 2-hydroxyisobutylation sites via transfer learning.
Briefings Bioinform.
Xiaoti Jia, Pei Zhao, Fuyi Li, Zhaohui Qin, Haoran Ren, Junzhou Li, Chunbo Miao, Quanzhi Zhao, Tatsuya Akutsu, Gensheng Dou, Zhen Chen, Jiangning Song
2023 J jnl
SMG: self-supervised masked graph learning for cancer gene identification.
Briefings Bioinform.
Yan Cui, Zhikang Wang, Xiaoyu Wang, Yiwen Zhang, Ying Zhang, Tong Pan, Zhe Zhang, Shanshan Li, Yuming Guo, Tatsuya Akutsu, Jiangning Song
2023 J jnl
eSPRESSO: topological clustering of single-cell transcriptomics data to reveal informative genes for spatio-temporal architectures of cells.
BMC Bioinform.
Tomoya Mori, Toshiro Takase, Kuan-Chun Lan, Junko Yamane, Cantas Alev, Azuma Kimura, Kenji Osafune, Jun K. Yamashita, Tatsuya Akutsu, Hiroaki Kitano, Wataru Fujibuchi
2023 J jnl
iAMPCN: a deep-learning approach for identifying antimicrobial peptides and their functional activities.
Briefings Bioinform.
Jing Xu, Fuyi Li, Chen Li, Xudong Guo, Cornelia B. Landersdorfer, Hsin-Hui Shen, Anton Y. Peleg, Jian Li, Seiya Imoto, Jianhua Yao, Tatsuya Akutsu, Jiangning Song
2022 — conf
A Method for Molecular Design Based on Linear Regression and Integer Programming.
ICBBB
Jianshen Zhu, Naveed Ahmed Azam, Kazuya Haraguchi, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu
2022 J jnl
A Novel Method for Inferring Chemical Compounds With Prescribed Topological Substructures Based on Integer Programming.
IEEE ACM Trans. Comput. Biol. Bioinform.
Jianshen Zhu, Naveed Ahmed Azam, Fan Zhang, Aleksandar Shurbevski, Kazuya Haraguchi, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu
2022 J jnl
A new approach to the design of acyclic chemical compounds using skeleton trees and integer linear programming.
Appl. Intell.
Fan Zhang, Jianshen Zhu, Rachaya Chiewvanichakorn, Aleksandar Shurbevski, Hiroshi Nagamochi, Tatsuya Akutsu
2022 — conf
Adjustive Linear Regression and Its Application to the Inverse QSAR.
BIOINFORMATICS
Jianshen Zhu, Kazuya Haraguchi, Hiroshi Nagamochi, Tatsuya Akutsu
2022 J jnl
An FVS-Based Approach to Attractor Detection in Asynchronous Random Boolean Networks.
IEEE ACM Trans. Comput. Biol. Bioinform.
Trinh Van Giang, Tatsuya Akutsu, Kunihiko Hiraishi
2022 J jnl
Comparison of the Representational Power of Random Forests, Binary Decision Diagrams, and Neural Networks.
Neural Comput.
So Kumano, Tatsuya Akutsu
2022 J jnl
Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction.
Briefings Bioinform.
Meng Zhang, Cangzhi Jia, Fuyi Li, Chen Li, Yan Zhu, Tatsuya Akutsu, Geoffrey I. Webb, Quan Zou, Lachlan J. M. Coin, Jiangning Song
2022 J jnl
Densest subgraph-based methods for protein-protein interaction hot spot prediction.
BMC Bioinform.
Ruiming Li, Jung-Yu Lee, Jinn-Moon Yang, Tatsuya Akutsu
2022 J jnl
Guest Editorial for Special Section on the 16th International Conference on Intelligent Computing (ICIC).
IEEE ACM Trans. Comput. Biol. Bioinform.
De-Shuang Huang, Kyungsook Han, Tatsuya Akutsu
2022 J jnl
Identification of periodic attractors in Boolean networks using a priori information.
PLoS Comput. Biol.
Ulrike Münzner, Tomoya Mori, Marcus Krantz, Edda Klipp, Tatsuya Akutsu
2022 J jnl
MSNet-4mC: learning effective multi-scale representations for identifying DNA N4-methylcytosine sites.
Bioinform.
Chunting Liu, Jiangning Song, Hiroyuki Ogata, Tatsuya Akutsu
2022 J jnl
Molecular Design Based on Integer Programming and Quadratic Descriptors in a Two-layered Model.
CoRR
Jianshen Zhu, Naveed Ahmed Azam, Shengjuan Cao, Ryota Ido, Kazuya Haraguchi, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu
2022 B conf
On the Complexity of Tree Edit Distance with Variables.
ISAAC
Tatsuya Akutsu, Tomoya Mori, Naotoshi Nakamura, Satoshi Kozawa, Yuhei Ueno, Thomas N. Sato
2022 J jnl
On the Distribution of Successor States in Boolean Threshold Networks.
IEEE Trans. Neural Networks Learn. Syst.
Sini Guo, Pengyu Liu, Wai-Ki Ching, Tatsuya Akutsu
2022 J jnl
PROST: AlphaFold2-aware Sequence-Based Predictor to Estimate Protein Stability Changes upon Missense Mutations.
J. Chem. Inf. Model.
Shahid Iqbal, Fang Ge, Fuyi Li, Tatsuya Akutsu, Yuanting Zheng, Robin B. Gasser, Dong-Jun Yu, Geoffrey I. Webb, Jiangning Song
2021 J jnl
A Method for Inferring Polymers Based on Linear Regression and Integer Programming.
CoRR
Ryota Ido, Shengjuan Cao, Jianshen Zhu, Naveed Ahmed Azam, Kazuya Haraguchi, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu
2021 J jnl
A novel method for inference of acyclic chemical compounds with bounded branch-height based on artificial neural networks and integer programming.
Algorithms Mol. Biol.
Naveed Ahmed Azam, Jianshen Zhu, Yanming Sun, Yu Shi, Aleksandar Shurbevski, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu
2021 — conf
An Improved Integer Programming Formulation for Inferring Chemical Compounds with Prescribed Topological Structures.
IEA/AIE (1)
Jianshen Zhu, Naveed Ahmed Azam, Kazuya Haraguchi, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu
2021 — conf
An Inverse QSAR Method Based on Decision Tree and Integer Programming.
ICIC (2)
Kouki Tanaka, Jianshen Zhu, Naveed Ahmed Azam, Kazuya Haraguchi, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu
2021 J jnl
An Inverse QSAR Method Based on Linear Regression and Integer Programming.
CoRR
Jianshen Zhu, Naveed Ahmed Azam, Kazuya Haraguchi, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu
2021 J jnl
Anthem: a user customised tool for fast and accurate prediction of binding between peptides and HLA class I molecules.
Briefings Bioinform.
Shutao Mei, Fuyi Li, Dongxu Xiang, Rochelle Ayala, Pouya Faridi, Geoffrey I. Webb, Patricia T. Illing, Jamie Rossjohn, Tatsuya Akutsu, Nathan P. Croft, Anthony W. Purcell, Jiangning Song
2021 J jnl
Assessing the performance of computational predictors for estimating protein stability changes upon missense mutations.
Briefings Bioinform.
Shahid Iqbal, Fuyi Li, Tatsuya Akutsu, David B. Ascher, Geoffrey I. Webb, Jiangning Song
2021 J jnl
Computational identification of eukaryotic promoters based on cascaded deep capsule neural networks.
Briefings Bioinform.
Yan Zhu, Fuyi Li, Dongxu Xiang, Tatsuya Akutsu, Jiangning Song, Cangzhi Jia
2021 J jnl
DeepBL: a deep learning-based approach for
Briefings Bioinform.
Yanan Wang, Fuyi Li, Manasa Bharathwaj, Natalia C. Rosas, André Leier, Tatsuya Akutsu, Geoffrey I. Webb, Tatiana T. Marquez-Lago, Jian Li, Trevor Lithgow, Jiangning Song
2021 J jnl
DeepVF: a deep learning-based hybrid framework for identifying virulence factors using the stacking strategy.
Briefings Bioinform.
Ruopeng Xie, Jiahui Li, Jiawei Wang, Wei Dai, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Trevor Lithgow, Jiangning Song, Yanju Zhang
2021 J jnl
Discrimination of attractors with noisy nodes in Boolean networks.
Autom.
Xiaoqing Cheng, Wai-Ki Ching, Sini Guo, Tatsuya Akutsu
2021 J jnl
Editorial: Inference of Biological Networks.
Frontiers Bioinform.
Tatsuya Akutsu, Hongmin Cai
2021 J jnl
Inhibitory neurons exhibit high controlling ability in the cortical microconnectome.
PLoS Comput. Biol.
Motoki Kajiwara, Ritsuki Nomura, Felix Goetze, Masanori Kawabata, Yoshikazu Isomura, Tatsuya Akutsu, Masanori Shimono
2021 — conf
Molecular Design Based on Artificial Neural Networks, Integer Programming and Grid Neighbor Search.
BIBM
Naveed Ahmed Azam, Jianshen Zhu, Kazuya Haraguchi, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu
2021 J jnl
Molecular Design Based on Artificial Neural Networks, Integer Programming and Grid Neighbor Search.
CoRR
Naveed Ahmed Azam, Jianshen Zhu, Kazuya Haraguchi, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu
2021 J jnl
New and improved algorithms for unordered tree inclusion.
Theor. Comput. Sci.
Tatsuya Akutsu, Jesper Jansson, Ruiming Li, Atsuhiro Takasu, Takeyuki Tamura
2021 J jnl
On the Size and Width of the Decoder of a Boolean Threshold Autoencoder.
CoRR
Tatsuya Akutsu, Avraham A. Melkman
2021 J jnl
ReCGBM: a gradient boosting-based method for predicting human dicer cleavage sites.
BMC Bioinform.
Pengyu Liu, Jiangning Song, Chun-Yu Lin, Tatsuya Akutsu
2021 J jnl
Tree Edit Distance with Variables. Measuring the Similarity between Mathematical Formulas.
CoRR
Tatsuya Akutsu, Tomoya Mori, Naotoshi Nakamura, Satoshi Kozawa, Yuhei Ueno, Thomas N. Sato
2021 J jnl
Weighted minimum feedback vertex sets and implementation in human cancer genes detection.
BMC Bioinform.
Ruiming Li, Chun-Yu Lin, Weifeng Guo, Tatsuya Akutsu
2020 — conf
A Method for the Inverse QSAR/QSPR Based on Artificial Neural Networks and Mixed Integer Linear Programming.
ICBBB
Rachaya Chiewvanichakorn, Chenxi Wang, Zhe Zhang, Aleksandar Shurbevski, Hiroshi Nagamochi, Tatsuya Akutsu
2020 C conf
A New Integer Linear Programming Formulation to the Inverse QSAR/QSPR for Acyclic Chemical Compounds Using Skeleton Trees.
IEA/AIE
Fan Zhang, Jianshen Zhu, Rachaya Chiewvanichakorn, Aleksandar Shurbevski, Hiroshi Nagamochi, Tatsuya Akutsu
2020 J jnl
A Novel Method for Inference of Acyclic Chemical Compounds with Bounded Branch-height Based on Artificial Neural Networks and Integer Programming.
CoRR
Naveed Ahmed Azam, Jianshen Zhu, Yanming Sun, Yu Shi, Aleksandar Shurbevski, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu
2020 J jnl
A Novel Method for Inference of Chemical Compounds of Cycle Index Two with Desired Properties Based on Artificial Neural Networks and Integer Programming.
Algorithms
Jianshen Zhu, Chenxi Wang, Aleksandar Shurbevski, Hiroshi Nagamochi, Tatsuya Akutsu
2020 — conf
A Novel Method for the Inverse QSAR/QSPR based on Artificial Neural Networks and Mixed Integer Linear Programming with Guaranteed Admissibility.
BIOINFORMATICS
Naveed Ahmed Azam, Rachaya Chiewvanichakorn, Fan Zhang, Aleksandar Shurbevski, Hiroshi Nagamochi, Tatsuya Akutsu
2020 J jnl
A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction.
Briefings Bioinform.
Shutao Mei, Fuyi Li, André Leier, Tatiana T. Marquez-Lago, Kailin Giam, Nathan P. Croft, Tatsuya Akutsu, Alexander Ian Smith, Jian Li, Jamie Rossjohn, Anthony W. Purcell, Jiangning Song
2020 J jnl
A novel method for inference of chemical compounds with prescribed topological substructures based on integer programming.
CoRR
Tatsuya Akutsu, Hiroshi Nagamochi
2020 — conf
Breast Cancer Subtype by Imbalanced Omics Data through A Deep Learning Fusion Model.
ICBBB
Jingwen Zeng, Hongmin Cai, Tatsuya Akutsu
2020 J jnl
Comparison of Pseudoknotted RNA Secondary Structures by Topological Centroid Identification and Tree Edit Distance.
J. Comput. Biol.
Feiqi Wang, Tatsuya Akutsu, Tomoya Mori
2020 J jnl
Comprehensive review and assessment of computational methods for predicting RNA post-transcriptional modification sites from RNA sequences.
Briefings Bioinform.
Zhen Chen, Pei Zhao, Fuyi Li, Yanan Wang, Alexander Ian Smith, Geoffrey I. Webb, Tatsuya Akutsu, Abdelkader Baggag, Halima Bensmail, Jiangning Song
2020 J jnl
DeepCleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites.
Bioinform.
Fuyi Li, Jinxiang Chen, André Leier, Tatiana T. Marquez-Lago, Quanzhong Liu, Yanze Wang, Jerico Nico De Leon Revote, Alexander Ian Smith, Tatsuya Akutsu, Geoffrey I. Webb, Lukasz A. Kurgan, Jiangning Song
2020 J jnl
Discrimination of attractors with noisy nodes in Boolean networks.
CoRR
Xiaoqing Cheng, Wai-Ki Ching, Sini Guo, Tatsuya Akutsu
2020 J jnl
Enumerating Chemical Graphs with Mono-block 2-Augmented Tree Structure from Given Upper and Lower Bounds on Path Frequencies.
CoRR
Yuui Tamura, Yuhei Nishiyama, Chenxi Wang, Yanming Sun, Aleksandar Shurbevski, Hiroshi Nagamochi, Tatsuya Akutsu
2020 J jnl
Enumerating Chemical Graphs with Two Disjoint Cycles Satisfying Given Path Frequency Specifications.
CoRR
Kyousuke Yamashita, Ryuji Masui, Xiang Zhou, Chenxi Wang, Aleksandar Shurbevski, Hiroshi Nagamochi, Tatsuya Akutsu
2020 J jnl
Extracting boolean and probabilistic rules from trained neural networks.
Neural Networks
Pengyu Liu, Avraham A. Melkman, Tatsuya Akutsu
2020 J jnl
Improved Hardness of Maximum Common Subgraph Problems on Labeled Graphs of Bounded Treewidth and Bounded Degree.
Int. J. Found. Comput. Sci.
Tatsuya Akutsu, Avraham A. Melkman, Takeyuki Tamura
2020 J jnl
Network control principles for identifying personalized driver genes in cancer.
Briefings Bioinform.
Weifeng Guo, Shaowu Zhang, Tao Zeng, Tatsuya Akutsu, Luonan Chen
2020 J jnl
On the Compressive Power of Boolean Threshold Autoencoders.
CoRR
Avraham A. Melkman, Sini Guo, Wai-Ki Ching, Pengyu Liu, Tatsuya Akutsu
2020 J jnl
PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins.
Bioinform.
Yanju Zhang, Sha Yu, Ruopeng Xie, Jiahui Li, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Alexander Ian Smith, Zongyuan Ge, Jiawei Wang, Trevor Lithgow, Jiangning Song
2020 J jnl
Procleave: Predicting Protease-specific Substrate Cleavage Sites by Combining Sequence and Structural Information.
Genom. Proteom. Bioinform.
Fuyi Li, André Leier, Quanzhong Liu, Yanan Wang, Dongxu Xiang, Tatsuya Akutsu, Geoffrey I. Webb, Alexander Ian Smith, Tatiana T. Marquez-Lago, Jian Li, Jiangning Song
2020 J jnl
iLearn : an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data.
Briefings Bioinform.
Zhen Chen, Pei Zhao, Fuyi Li, Tatiana T. Marquez-Lago, André Leier, Jerico Nico De Leon Revote, Yan Zhu, David R. Powell, Tatsuya Akutsu, Geoffrey I. Webb, Kuo-Chen Chou, Alexander Ian Smith, Roger J. Daly, Jian Li, Jiangning Song
2019 J jnl
Bastion3: a two-layer ensemble predictor of type III secreted effectors.
Bioinform.
Jiawei Wang, Jiahui Li, Bingjiao Yang, Ruopeng Xie, Tatiana T. Marquez-Lago, André Leier, Morihiro Hayashida, Tatsuya Akutsu, Yanju Zhang, Kuo-Chen Chou, Joel Selkrig, Tieli Zhou, Jiangning Song, Trevor Lithgow
2019 J jnl
Computational analysis and prediction of lysine malonylation sites by exploiting informative features in an integrative machine-learning framework.
Briefings Bioinform.
Yanju Zhang, Ruopeng Xie, Jiawei Wang, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Geoffrey I. Webb, Kuo-Chen Chou, Jiangning Song
2019 J jnl
Convolutional neural network approach to lung cancer classification integrating protein interaction network and gene expression profiles.
J. Bioinform. Comput. Biol.
Teppei Matsubara, Tomoshiro Ochiai, Morihiro Hayashida, Tatsuya Akutsu, Jose C. Nacher
2019 J jnl
Deep learning with evolutionary and genomic profiles for identifying cancer subtypes.
J. Bioinform. Comput. Biol.
Chun-Yu Lin, Peiying Ruan, Ruiming Li, Jinn-Moon Yang, Simon See, Jiangning Song, Tatsuya Akutsu
2019 J jnl
Identification of the Structure of a Probabilistic Boolean Network From Samples Including Frequencies of Outcomes.
IEEE Trans. Neural Networks Learn. Syst.
Tatsuya Akutsu, Avraham A. Melkman
2019 J jnl
Large-scale comparative assessment of computational predictors for lysine post-translational modification sites.
Briefings Bioinform.
Zhen Chen, Xuhan Liu, Fuyi Li, Chen Li, Tatiana T. Marquez-Lago, André Leier, Tatsuya Akutsu, Geoffrey I. Webb, Dakang Xu, Alexander Ian Smith, Lei Li, Kuo-Chen Chou, Jiangning Song
2019 J jnl
Optimal string clustering based on a Laplace-like mixture and EM algorithm on a set of strings.
J. Comput. Syst. Sci.
Hitoshi Koyano, Morihiro Hayashida, Tatsuya Akutsu
2019 J jnl
Protease target prediction via matrix factorization.
Bioinform.
Simone Marini, Francesca Vitali, Sara Rampazzi, Andrea Demartini, Tatsuya Akutsu
2019 J jnl
Resource Cut, a New Bounding Procedure to Algorithms for Enumerating Tree-Like Chemical Graphs.
IEEE ACM Trans. Comput. Biol. Bioinform.
Yuhei Nishiyama, Aleksandar Shurbevski, Hiroshi Nagamochi, Tatsuya Akutsu
2019 J jnl
Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches.
Briefings Bioinform.
Jiawei Wang, Bingjiao Yang, Yi An, Tatiana T. Marquez-Lago, André Leier, Jonathan Wilksch, Qingyang Hong, Yang Zhang, Morihiro Hayashida, Tatsuya Akutsu, Geoffrey I. Webb, Richard A. Strugnell, Jiangning Song, Trevor Lithgow
2019 J jnl
Toward more accurate prediction of caspase cleavage sites: a comprehensive review of current methods, tools and features.
Briefings Bioinform.
Yu Bao, Simone Marini, Takeyuki Tamura, Mayumi Kamada, Shingo Maegawa, Hiroshi Hosokawa, Jiangning Song, Tatsuya Akutsu
2019 J jnl
Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods.
Briefings Bioinform.
Fuyi Li, Yanan Wang, Chen Li, Tatiana T. Marquez-Lago, André Leier, Neil D. Rawlings, Gholamreza Haffari, Jerico Nico De Leon Revote, Tatsuya Akutsu, Kuo-Chen Chou, Anthony W. Purcell, Robert N. Pike, Geoffrey I. Webb, Alexander Ian Smith, Trevor Lithgow, Roger J. Daly, James C. Whisstock, Jiangning Song
2019 J jnl
iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites.
Briefings Bioinform.
Jiangning Song, Yanan Wang, Fuyi Li, Tatsuya Akutsu, Neil D. Rawlings, Geoffrey I. Webb, Kuo-Chen Chou
2018 B conf
A Simple Linear-Time Algorithm for Computing the Centroid and Canonical Form of a Plane Graph and Its Applications.
CPM
Tatsuya Akutsu, Colin de la Higuera, Takeyuki Tamura
2018 — conf
Algorithms for Analysis and Control of Boolean Networks.
AlCoB
Tatsuya Akutsu
2018 — book
Algorithms for Analysis, Inference, and Control of Boolean Networks
Tatsuya Akutsu
2018 J jnl
Analysis of Critical and Redundant Vertices in Controlling Directed Complex Networks Using Feedback Vertex Sets.
J. Comput. Biol.
Yu Bao, Morihiro Hayashida, Pengyu Liu, Masayuki Ishitsuka, Jose C. Nacher, Tatsuya Akutsu
2018 J jnl
Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors.
Bioinform.
Jiawei Wang, Bingjiao Yang, André Leier, Tatiana T. Marquez-Lago, Morihiro Hayashida, Andrea Rocker, Yanju Zhang, Tatsuya Akutsu, Kuo-Chen Chou, Richard A. Strugnell, Jiangning Song, Trevor Lithgow
2018 J jnl
Computing Minimum Reaction Modifications in a Boolean Metabolic Network.
IEEE ACM Trans. Comput. Biol. Bioinform.
Takeyuki Tamura, Wei Lu, Jiangning Song, Tatsuya Akutsu
2018 C conf
Convolutional Neural Network Approach to Lung Cancer Classification Integrating Protein Interaction Network and Gene Expression Profiles.
BIBE
Teppei Matsubara, Tomoshiro Ochiai, Morihiro Hayashida, Tatsuya Akutsu, Jose C. Nacher
2018 C conf
Deep Learning with Evolutionary and Genomic Profiles for Identifying Cancer Subtypes.
BIBE
Chun-Yu Lin, Peiying Ruan, Ruiming Li, Jinn-Moon Yang, Simon See, Tatsuya Akutsu
2018 — conf
Enumerating Chemical Mono-Block 3-Augmented Trees with Two Junctions.
ICBBB
Yuui Tamura, Aleksandar Shurbevski, Hiroshi Nagamochi, Tatsuya Akutsu
2018 J jnl
Enumerating Substituted Benzene Isomers of Tree-Like Chemical Graphs.
IEEE ACM Trans. Comput. Biol. Bioinform.
Jinghui Li, Hiroshi Nagamochi, Tatsuya Akutsu
2018 — conf
Grammar-based Compression for Directed and Undirected Generalized Series-parallel Graphs using Integer Linear Programming.
BIOINFORMATICS
Morihiro Hayashida, Hitoshi Koyano, Tatsuya Akutsu
2018 J jnl
Identifying a Probabilistic Boolean Threshold Network From Samples.
IEEE Trans. Neural Networks Learn. Syst.
Avraham A. Melkman, Xiaoqing Cheng, Wai-Ki Ching, Tatsuya Akutsu
2018 J jnl
Improving prediction of heterodimeric protein complexes using combination with pairwise kernel.
BMC Bioinform.
Peiying Ruan, Morihiro Hayashida, Tatsuya Akutsu, Jean-Philippe Vert
2018 B conf
New and Improved Algorithms for Unordered Tree Inclusion.
ISAAC
Tatsuya Akutsu, Jesper Jansson, Ruiming Li, Atsuhiro Takasu, Takeyuki Tamura
2018 J jnl
PROSPERous: high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy.
Bioinform.
Jiangning Song, Fuyi Li, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Gholamreza Haffari, Kuo-Chen Chou, Geoffrey I. Webb, Robert N. Pike
2018 J jnl
Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome.
Bioinform.
Fuyi Li, Chen Li, Tatiana T. Marquez-Lago, André Leier, Tatsuya Akutsu, Anthony W. Purcell, Alexander Ian Smith, Trevor Lithgow, Roger J. Daly, Jiangning Song, Kuo-Chen Chou
2018 J jnl
ncRNA-disease association prediction based on sequence information and tripartite network.
BMC Syst. Biol.
Takuya Mori, Hayliang Ngouv, Morihiro Hayashida, Tatsuya Akutsu, Jose C. Nacher
2017 J jnl
An accessibility-incorporated method for accurate prediction of RNA-RNA interactions from sequence data.
Bioinform.
Yuki Kato, Tomoya Mori, Kengo Sato, Shingo Maegawa, Hiroshi Hosokawa, Tatsuya Akutsu
2017 J jnl
Discrimination of singleton and periodic attractors in Boolean networks.
Autom.
Xiaoqing Cheng, Takeyuki Tamura, Wai-Ki Ching, Tatsuya Akutsu
2017 J jnl
New Algorithms for Unordered Tree Inclusion.
CoRR
Tatsuya Akutsu, Jesper Jansson, Ruiming Li, Atsuhiro Takasu, Takeyuki Tamura
2017 J jnl
On the parameterized complexity of associative and commutative unification.
Theor. Comput. Sci.
Tatsuya Akutsu, Jesper Jansson, Atsuhiro Takasu, Takeyuki Tamura
2017 J jnl
Selected Papers from the 16th International Conference on Bioinformatics (InCoB 2017).
J. Bioinform. Comput. Biol.
Tatsuya Akutsu
2016 J jnl
A likelihood-free filtering method via approximate Bayesian computation in evaluating biological simulation models.
Comput. Stat. Data Anal.
Takanori Hasegawa, Atsushi Niida, Tomoya Mori, Teppei Shimamura, Rui Yamaguchi, Satoru Miyano, Tatsuya Akutsu, Seiya Imoto
2016 J jnl
Critical evaluation of
Briefings Bioinform.
Chen Li, Catherine Ching Han Chang, Jeremy Nagel, Benjamin T. Porebski, Morihiro Hayashida, Tatsuya Akutsu, Jiangning Song, Ashley M. Buckle
2016 — conf
Enumerating Naphthalene Isomers of Tree-like Chemical Graphs.
BIOINFORMATICS
Fei He, Akiyoshi Hanai, Hiroshi Nagamochi, Tatsuya Akutsu
2016 J jnl
Enumeration Method for Structural Isomers Containing User-Defined Structures Based on Breadth-First Search Approach.
J. Comput. Biol.
Jira Jindalertudomdee, Morihiro Hayashida, Tatsuya Akutsu
2016 J jnl
Enumeration method for tree-like chemical compounds with benzene rings and naphthalene rings by breadth-first search order.
BMC Bioinform.
Jira Jindalertudomdee, Morihiro Hayashida, Yang Zhao, Tatsuya Akutsu
2016 J jnl
Exact Identification of the Structure of a Probabilistic Boolean Network from Samples.
IEEE ACM Trans. Comput. Biol. Bioinform.
Xiaoqing Cheng, Tomoya Mori, Yushan Qiu, Wai-Ki Ching, Tatsuya Akutsu
2016 C conf
Finding Influential Genes Using Gene Expression Data and Boolean Models of Metabolic Networks.
BIBE
Takeyuki Tamura, Tatsuya Akutsu, Chun-Yu Lin, Jinn-Moon Yang
2016 J jnl
Finding and Analyzing the Minimum Set of Driver Nodes in control of Boolean Networks.
Adv. Complex Syst.
Wenpin Hou, Takeyuki Tamura, Wai-Ki Ching, Tatsuya Akutsu
2016 C conf
Host-Pathogen Protein Interaction Prediction Based on Local Topology Structures of a Protein Interaction Network.
BIBE
Jira Jindalertudomdee, Morihiro Hayashida, Jiangning Song, Tatsuya Akutsu
2016 J jnl
LBSizeCleav: improved support vector machine (SVM)-based prediction of Dicer cleavage sites using loop/bulge length.
BMC Bioinform.
Yu Bao, Morihiro Hayashida, Tatsuya Akutsu
2016 A* conf
Similar subtree search using extended tree inclusion.
ICDE
Tomoya Mori, Atsuhiro Takasu, Jesper Jansson, Jaewook Hwang, Takeyuki Tamura, Tatsuya Akutsu
2015 J jnl
A Fixed-Parameter Algorithm for Detecting a Singleton Attractor in an AND/OR Boolean Network with Bounded Treewidth.
IEICE Trans. Fundam. Electron. Commun. Comput. Sci.
Chia-Jung Chang, Takeyuki Tamura, Kun-Mao Chao, Tatsuya Akutsu
2015 J jnl
Computing Smallest Intervention Strategies for Multiple Metabolic Networks in a Boolean Model.
J. Comput. Biol.
Wei Lu, Takeyuki Tamura, Jiangning Song, Tatsuya Akutsu
2015 J jnl
Genomic data assimilation using a higher moment filtering technique for restoration of gene regulatory networks.
BMC Syst. Biol.
Takanori Hasegawa, Tomoya Mori, Rui Yamaguchi, Teppei Shimamura, Satoru Miyano, Seiya Imoto, Tatsuya Akutsu
2015 J jnl
Grammar-based compression approach to extraction of common rules among multiple trees of glycans and RNAs.
BMC Bioinform.
Yang Zhao, Morihiro Hayashida, Yue Cao, Jaewook Hwang, Tatsuya Akutsu
2015 J jnl
Matrix Network: A New Data Structure for Efficient Enumeration of Microstates of a Genetic Regulatory Network.
J. Inf. Process.
Xiao Cong, Tatsuya Akutsu
2015 — conf
On observability of attractors in Boolean Networks.
BIBM
Yushan Qiu, Xiaoqing Cheng, Wai-Ki Ching, Hao Jiang, Tatsuya Akutsu
2015 J jnl
On the complexity of finding a largest common subtree of bounded degree.
Theor. Comput. Sci.
Tatsuya Akutsu, Takeyuki Tamura, Avraham A. Melkman, Atsuhiro Takasu
2015 J jnl
Similar Subtree Search Using Extended Tree Inclusion.
IEEE Trans. Knowl. Data Eng.
Tomoya Mori, Atsuhiro Takasu, Jesper Jansson, Jaewook Hwang, Takeyuki Tamura, Tatsuya Akutsu
2015 J jnl
Stochastic simulation of Boolean rxncon models: towards quantitative analysis of large signaling networks.
BMC Syst. Biol.
Tomoya Mori, Max Flöttmann, Marcus Krantz, Tatsuya Akutsu, Edda Klipp
2014 J jnl
An Efficient Data Assimilation Schema for Restoration and Extension of Gene Regulatory Networks Using Time-Course Observation Data.
J. Comput. Biol.
Takanori Hasegawa, Tomoya Mori, Rui Yamaguchi, Seiya Imoto, Satoru Miyano, Tatsuya Akutsu
2014 J jnl
Analysis of critical and redundant nodes in controlling directed and undirected complex networks using dominating sets.
J. Complex Networks
Jose C. Nacher, Tatsuya Akutsu
2014 J jnl
Cascleave 2.0, a new approach for predicting caspase and granzyme cleavage targets.
Bioinform.
Mingjun Wang, Xing-Ming Zhao, Hao Tan, Tatsuya Akutsu, James C. Whisstock, Jiangning Song
2014 J jnl
Domain-Based Approaches to Prediction and Analysis of Protein-Protein Interactions.
Int. J. Knowl. Discov. Bioinform.
Morihiro Hayashida, Tatsuya Akutsu
2014 J jnl
Efficient enumeration of monocyclic chemical graphs with given path frequencies.
J. Cheminformatics
Masaki Suzuki, Hiroshi Nagamochi, Tatsuya Akutsu
2014 J jnl
Efficient exponential-time algorithms for edit distance between unordered trees.
J. Discrete Algorithms
Tatsuya Akutsu, Takeyuki Tamura, Daiji Fukagawa, Atsuhiro Takasu
2014 J jnl
Feature weight estimation for gene selection: a local hyperlinear learning approach.
BMC Bioinform.
Hongmin Cai, Peiying Ruan, Michael Kwok-Po Ng, Tatsuya Akutsu
2014 J jnl
Network Completion for Static Gene Expression Data.
Adv. Bioinformatics
Natsu Nakajima, Tatsuya Akutsu
2014 J jnl
On control of singleton attractors in multiple Boolean networks: integer programming-based method.
BMC Syst. Biol.
Yushan Qiu, Takeyuki Tamura, Wai-Ki Ching, Tatsuya Akutsu
2014 B conf
On the Parameterized Complexity of Associative and Commutative Unification.
IPEC
Tatsuya Akutsu, Jesper Jansson, Atsuhiro Takasu, Takeyuki Tamura
2014 J jnl
Prediction of heterotrimeric protein complexes by two-phase learning using neighboring kernels.
BMC Bioinform.
Peiying Ruan, Morihiro Hayashida, Osamu Maruyama, Tatsuya Akutsu
2013 J jnl
A Polynomial-Time Algorithm for Computing the Maximum Common Connected Edge Subgraph of Outerplanar Graphs of Bounded Degree.
Algorithms
Tatsuya Akutsu, Takeyuki Tamura
2013 J jnl
An Improved Satisfiability Algorithm for Nested Canalyzing Functions and its Application to Determining a Singleton Attractor of a Boolean Network.
J. Comput. Biol.
Avraham A. Melkman, Tatsuya Akutsu
2013 — conf
Analysis on critical nodes in controlling complex networks using dominating sets.
SITIS
Jose C. Nacher, Tatsuya Akutsu
2013 J jnl
Approximation and parameterized algorithms for common subtrees and edit distance between unordered trees.
Theor. Comput. Sci.
Tatsuya Akutsu, Daiji Fukagawa, Magnús M. Halldórsson, Atsuhiro Takasu, Keisuke Tanaka
2013 J jnl
Breadth-First Search Approach to Enumeration of Tree-like Chemical Compounds.
J. Bioinform. Comput. Biol.
Yang Zhao, Morihiro Hayashida, Jira Jindalertudomdee, Hiroshi Nagamochi, Tatsuya Akutsu
2013 J jnl
Finding optimal control policy in probabilistic Boolean Networks with hard constraints by using integer programming and dynamic programming.
Int. J. Data Min. Bioinform.
Xi Chen, Tatsuya Akutsu, Takeyuki Tamura, Wai-Ki Ching
2013 J jnl
Flux balance impact degree: a new definition of impact degree to properly treat reversible reactions in metabolic networks.
Bioinform.
Yang Zhao, Takeyuki Tamura, Tatsuya Akutsu, Jean-Philippe Vert
2013 Misc conf
Network Completion for Time Varying Genetic Networks.
CISIS
Natsu Nakajima, Tatsuya Akutsu
2013 B conf
On the Complexity of Finding a Largest Common Subtree of Bounded Degree.
FCT
Tatsuya Akutsu, Takeyuki Tamura, Avraham A. Melkman, Atsuhiro Takasu
2013 J jnl
On the Complexity of Inference and Completion of Boolean Networks from Given Singleton Attractors.
IEICE Trans. Fundam. Electron. Commun. Comput. Sci.
Hao Jiang, Takeyuki Tamura, Wai-Ki Ching, Tatsuya Akutsu
2013 J jnl
On the Parameterized Complexity of Associative and Commutative Unification.
CoRR
Tatsuya Akutsu, Takeyuki Tamura, Atsuhiro Takasu
2013 J jnl
Prediction of protein-RNA residue-base contacts using two-dimensional conditional random field with the lasso.
BMC Syst. Biol.
Morihiro Hayashida, Mayumi Kamada, Jiangning Song, Tatsuya Akutsu
2012 J jnl
A Clique-Based Method Using Dynamic Programming for Computing Edit Distance Between Unordered Trees.
J. Comput. Biol.
Tomoya Mori, Takeyuki Tamura, Daiji Fukagawa, Atsuhiro Takasu, Etsuji Tomita, Tatsuya Akutsu
2012 B conf
A Polynomial-Time Algorithm for Computing the Maximum Common Subgraph of Outerplanar Graphs of Bounded Degree.
MFCS
Tatsuya Akutsu, Takeyuki Tamura
2012 J jnl
A quadsection algorithm for grammar-based image compression.
Integr. Comput. Aided Eng.
Morihiro Hayashida, Peiying Ruan, Tatsuya Akutsu
2012 J jnl
DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition.
Bioinform.
Kengo Sato, Yuki Kato, Tatsuya Akutsu, Kiyoshi Asai, Yasubumi Sakakibara
2012 B conf
Efficient Exponential Time Algorithms for Edit Distance between Unordered Trees.
CPM
Tatsuya Akutsu, Takeyuki Tamura, Daiji Fukagawa, Atsuhiro Takasu
2012 — conf
Finding Conserved Regions in Protein Structures Using Support Vector Machines and Structure Alignment.
PRIB
Tatsuya Akutsu, Morihiro Hayashida, Takeyuki Tamura
2012 J jnl
Finding a Periodic Attractor of a Boolean Network.
IEEE ACM Trans. Comput. Biol. Bioinform.
Tatsuya Akutsu, Sven Kosub, Avraham A. Melkman, Takeyuki Tamura
2012 J jnl
Inferring a graph from path frequency.
Discret. Appl. Math.
Tatsuya Akutsu, Daiji Fukagawa, Jesper Jansson, Kunihiko Sadakane
2012 J jnl
Integer Programming-Based Approach to Attractor Detection and Control of Boolean Networks.
IEICE Trans. Inf. Syst.
Tatsuya Akutsu, Yang Zhao, Morihiro Hayashida, Takeyuki Tamura
2012 B conf
On the Complexity of the Maximum Common Subgraph Problem for Partial k-Trees of Bounded Degree.
ISAAC
Tatsuya Akutsu, Takeyuki Tamura
2012 — conf
Predicting protein-RNA residue-base contacts using two-dimensional conditional random field.
ISB
Morihiro Hayashida, Mayumi Kamada, Jiangning Song, Tatsuya Akutsu
2012 J jnl
Protein complex prediction via improved verification methods using constrained domain-domain matching.
Int. J. Bioinform. Res. Appl.
Yang Zhao, Morihiro Hayashida, Jose C. Nacher, Hiroshi Nagamochi, Tatsuya Akutsu
2012 J jnl
Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming.
Nucleic Acids Res.
Yuki Kato, Kengo Sato, Kiyoshi Asai, Tatsuya Akutsu
2012 J jnl
Singleton and 2-periodic attractors of sign-definite Boolean networks.
Inf. Process. Lett.
Tatsuya Akutsu, Avraham A. Melkman, Takeyuki Tamura
2011 J jnl
A clique-based method for the edit distance between unordered trees and its application to analysis of glycan structures.
BMC Bioinform.
Daiji Fukagawa, Takeyuki Tamura, Atsuhiro Takasu, Etsuji Tomita, Tatsuya Akutsu
2011 J jnl
An Efficient Method of Computing Impact Degrees for Multiple Reactions in Metabolic Networks with Cycles.
IEICE Trans. Inf. Syst.
Takeyuki Tamura, Yang Cong, Tatsuya Akutsu, Wai-Ki Ching
2011 Misc conf
An Improved Clique-Based Method for Computing Edit Distance between Unordered Trees and Its Application to Comparison of Glycan Structures.
CISIS
Tatsuya Akutsu, Tomoya Mori, Takeyuki Tamura, Daiji Fukagawa, Atsuhiro Takasu, Etsuji Tomita
2011 J jnl
Bioinformatic Approaches for Predicting substrates of Proteases.
J. Bioinform. Comput. Biol.
Jiangning Song, Hao Tan, Sarah E. Boyd, Hong-Bin Shen, Khalid Mahmood, Geoffrey I. Webb, Tatsuya Akutsu, James C. Whisstock, Robert N. Pike
2011 J jnl
Conditional random field approach to prediction of protein-protein interactions using domain information.
BMC Syst. Biol.
Morihiro Hayashida, Mayumi Kamada, Jiangning Song, Tatsuya Akutsu
2011 J jnl
Determining a Singleton Attractor of a Boolean Network with Nested Canalyzing Functions.
J. Comput. Biol.
Tatsuya Akutsu, Avraham A. Melkman, Takeyuki Tamura, Masaki Yamamoto
2011 J jnl
Efficient Enumeration of Stereoisomers of Outerplanar Chemical Graphs Using Dynamic Programming.
J. Chem. Inf. Model.
Tomoki Imada, Shunsuke Ota, Hiroshi Nagamochi, Tatsuya Akutsu
2011 J jnl
Enumerating tree-like chemical graphs with given upper and lower bounds on path frequencies.
BMC Bioinform.
Masaaki Shimizu, Hiroshi Nagamochi, Tatsuya Akutsu
2011 J jnl
Exact algorithms for computing the tree edit distance between unordered trees.
Theor. Comput. Sci.
Tatsuya Akutsu, Daiji Fukagawa, Atsuhiro Takasu, Takeyuki Tamura
2011 J jnl
IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming.
Bioinform.
Kengo Sato, Yuki Kato, Michiaki Hamada, Tatsuya Akutsu, Kiyoshi Asai
2011 J jnl
Kernel Methods for Chemical Compounds: From Classification to Design.
IEICE Trans. Inf. Syst.
Tatsuya Akutsu, Hiroshi Nagamochi
2011 J jnl
Measuring the Similarity of Protein Structures Using Image Compression Algorithms.
IEICE Trans. Inf. Syst.
Morihiro Hayashida, Tatsuya Akutsu
2011 J jnl
Prediction using step-wise L1, L2 regularization and feature selection for small data sets with large number of features.
BMC Bioinform.
Ozgur Demir-Kavuk, Mayumi Kamada, Tatsuya Akutsu, Ernst-Walter Knapp
2011 J jnl
Using binding Profiles to Predict binding sites of Target RNAs.
J. Bioinform. Comput. Biol.
Unyanee Poolsap, Yuki Kato, Kengo Sato, Tatsuya Akutsu
2010 — conf
A Quadsection Algorithm for Grammar-Based Image Compression.
FGIT
Morihiro Hayashida, Peiying Ruan, Tatsuya Akutsu
2010 B conf
A Variational Bayesian EM Algorithm for Tree Similarity.
ICPR
Atsuhiro Takasu, Daiji Fukagawa, Tatsuya Akutsu
2010 J jnl
A bisection algorithm for grammar-based compression of ordered trees.
Inf. Process. Lett.
Tatsuya Akutsu
2010 J jnl
Approximating Tree Edit Distance through String Edit Distance.
Algorithmica
Tatsuya Akutsu, Daiji Fukagawa, Atsuhiro Takasu
2010 J jnl
Branch-and-Bound Algorithms for Enumerating Treelike Chemical Graphs with Given Path Frequency Using Detachment-Cut.
J. Chem. Inf. Model.
Yusuke Ishida, Yuki Kato, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu
2010 J jnl
Cascleave: towards more accurate prediction of caspase substrate cleavage sites.
Bioinform.
Jiangning Song, Hao Tan, Hong-Bin Shen, Khalid Mahmood, Sarah E. Boyd, Geoffrey I. Webb, Tatsuya Akutsu, James C. Whisstock
2010 J jnl
Comparing biological networks via graph compression.
BMC Syst. Biol.
Morihiro Hayashida, Tatsuya Akutsu
2010 J jnl
Determining a singleton attractor of an AND/OR Boolean network in O(1.587
Inf. Process. Lett.
Avraham A. Melkman, Takeyuki Tamura, Tatsuya Akutsu
2010 Misc conf
Dynamic Programming Algorithms for RNA Structure Prediction with Binding Sites.
Pacific Symposium on Biocomputing
Unyanee Poolsap, Yuki Kato, Tatsuya Akutsu
2010 J jnl
Exact Algorithms for Finding a Minimum Reaction Cut under a Boolean Model of Metabolic Networks.
IEICE Trans. Fundam. Electron. Commun. Comput. Sci.
Takeyuki Tamura, Tatsuya Akutsu
2010 J jnl
Finding Minimum Reaction Cuts of Metabolic Networks Under a Boolean Model Using Integer Programming and Feedback Vertex Sets.
Int. J. Knowl. Discov. Bioinform.
Takeyuki Tamura, Kazuhiro Takemoto, Tatsuya Akutsu
2010 — conf
Finding optimal control policy in Probabilistic Boolean Networks with hard constraints by using integer programming and dynamic programming.
BIBM
Xi Chen, Tatsuya Akutsu, Takeyuki Tamura, Wai-Ki Ching
2010 J jnl
Integer programming-based method for grammar-based tree compression and its application to pattern extraction of glycan tree structures.
BMC Bioinform.
Yang Zhao, Morihiro Hayashida, Tatsuya Akutsu
2010 J jnl
Prediction of Protein Folding Rates from Structural Topology and Complex Network Properties.
Inf. Media Technol.
Jiangning Song, Kazuhiro Takemoto, Hongbin Shen, Hao Tan, M. Michael Gromiha, Tatsuya Akutsu
2010 J jnl
RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming.
Bioinform.
Yuki Kato, Kengo Sato, Michiaki Hamada, Yoshihide Watanabe, Kiyoshi Asai, Tatsuya Akutsu
2010 J jnl
The role of internal duplication in the evolution of multi-domain proteins.
Biosyst.
Jose C. Nacher, Morihiro Hayashida, Tatsuya Akutsu
2010 J jnl
Tree Edit Distance Problems: Algorithms and Applications to Bioinformatics.
IEICE Trans. Inf. Syst.
Tatsuya Akutsu
2009 — conf
A Bipartite Graph Based Model of Protein Domain Networks.
Complex (1)
Jose C. Nacher, Tomoshiro Ochiai, Morihiro Hayashida, Tatsuya Akutsu
2009 J jnl
A grammatical approach to RNA-RNA interaction prediction.
Pattern Recognit.
Yuki Kato, Tatsuya Akutsu, Hiroyuki Seki
2009 J jnl
Algorithms for Singleton Attractor Detection in Planar and Nonplanar AND/OR Boolean Networks.
Math. Comput. Sci.
Takeyuki Tamura, Tatsuya Akutsu
2009 J jnl
Analyses and Algorithms for Predecessor and Control Problems for Boolean Networks of Bounded Indegree.
Inf. Media Technol.
Tatsuya Akutsu, Morihiro Hayashida, Shuqin Zhang, Wai-Ki Ching, Michael K. Ng
2009 B conf
Completing Networks Using Observed Data.
ALT
Tatsuya Akutsu, Takeyuki Tamura, Katsuhisa Horimoto
2009 C conf
Constant Factor Approximation of Edit Distance of Bounded Height Unordered Trees.
SPIRE
Daiji Fukagawa, Tatsuya Akutsu, Atsuhiro Takasu
2009 J jnl
Detecting a Singleton Attractor in a Boolean Network Utilizing SAT Algorithms.
IEICE Trans. Fundam. Electron. Commun. Comput. Sci.
Takeyuki Tamura, Tatsuya Akutsu
2009 J jnl
Dynamic Programming Algorithms and Grammatical Modeling for Protein Beta-Sheet Prediction.
J. Comput. Biol.
Yuki Kato, Tatsuya Akutsu, Hiroyuki Seki
2009 — conf
Efficient computation of impact degrees for multiple reactions in metabolic networks with cycles.
DTMBIO
Yang Cong, Takeyuki Tamura, Tatsuya Akutsu, Wai-Ki Ching
2009 J jnl
Emergence of scale-free distribution in protein-protein interaction networks based on random selection of interacting domain pairs.
Biosyst.
Jose C. Nacher, Morihiro Hayashida, Tatsuya Akutsu
2009 B conf
Enumerating Stereoisomers of Tree Structured Molecules Using Dynamic Programming.
ISAAC
Tomoki Imada, Shunsuke Ota, Hiroshi Nagamochi, Tatsuya Akutsu
2009 J jnl
Identification of novel DNA repair proteins via primary sequence, secondary structure, and homology.
BMC Bioinform.
J. B. Brown, Tatsuya Akutsu
2009 — conf
Integer programming-based methods for attractor detection and control of boolean networks.
CDC
Tatsuya Akutsu, Morihiro Hayashida, Takeyuki Tamura
2009 B conf
Latent Topic Extraction from Relational Table for Record Matching.
Discovery Science
Atsuhiro Takasu, Daiji Fukagawa, Tatsuya Akutsu
2009 Misc conf
Measuring Structural Robustness of Metabolic Networks under a Boolean Model Using Integer Programming and Feedback Vertex Sets.
CISIS
Takeyuki Tamura, Kazuhiro Takemoto, Tatsuya Akutsu
2009 J jnl
On Finding a Fixed Point in a Boolean Network with Maximum Indegree 2.
IEICE Trans. Fundam. Electron. Commun. Comput. Sci.
Tatsuya Akutsu, Takeyuki Tamura
2009 J jnl
Prediction of RNA secondary structure with pseudoknots using integer programming.
BMC Bioinform.
Unyanee Poolsap, Yuki Kato, Tatsuya Akutsu
2008 J jnl
A Clustering Method for Analysis of Sequence Similarity Networks of Proteins Using Maximal Components of Graphs.
Inf. Media Technol.
Morihiro Hayashida, Tatsuya Akutsu, Hiroshi Nagamochi
2008 J jnl
Algorithms and Complexity Analyses for Control of Singleton Attractors in Boolean Networks.
EURASIP J. Bioinform. Syst. Biol.
Morihiro Hayashida, Takeyuki Tamura, Tatsuya Akutsu, Shuqin Zhang, Wai-Ki Ching
2008 — conf
Algorithms for Inference, Analysis and Control of Boolean Networks.
AB
Tatsuya Akutsu, Morihiro Hayashida, Takeyuki Tamura
2008 — conf
An Improved Algorithm for Detecting a Singleton Attractor in a Boolean Network Consisting of AND/OR Nodes.
AB
Takeyuki Tamura, Tatsuya Akutsu
2008 — ch.
Bioinformatics.
Wiley Encyclopedia of Computer Science and Engineering
Tatsuya Akutsu
2008 J jnl
Enumerating Treelike Chemical Graphs with Given Path Frequency.
J. Chem. Inf. Model.
Hiroki Fujiwara, Jiexun Wang, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu
2008 J jnl
HSEpred: predict half-sphere exposure from protein sequences.
Bioinform.
Jiangning Song, Hao Tan, Kazuhiro Takemoto, Tatsuya Akutsu
2008 B conf
Image Compression-based Approach to Measuring the Similarity of Protein Structures.
APBC
Morihiro Hayashida, Tatsuya Akutsu
2008 J jnl
Improved approximation of the largest common subtree of two unordered trees of bounded height.
Inf. Process. Lett.
Tatsuya Akutsu, Daiji Fukagawa, Atsuhiro Takasu
2008 J jnl
Integer programming-based approach to allocation of reporter genes for cell array analysis.
Int. J. Bioinform. Res. Appl.
Morihiro Hayashida, Fuyan Sun, Sachiyo Aburatani, Katsuhisa Horimoto, Tatsuya Akutsu
2008 J jnl
Origin of structural difference in metabolic networks with respect to temperature.
BMC Syst. Biol.
Kazuhiro Takemoto, Tatsuya Akutsu
2008 — conf
Prediction of Protein Beta-Sheets: Dynamic Programming versus Grammatical Approach.
PRIB
Yuki Kato, Tatsuya Akutsu, Hiroyuki Seki
2008 B conf
Preface.
APBC
Alvis Brazma, Satoru Miyano, Tatsuya Akutsu
2008 B ed.
Proceedings of the 6th Asia-Pacific Bioinformatics Conference, APBC 2008, 14-17 January 2008, Kyoto, Japan
APBC
Alvis Brazma, Satoru Miyano, Tatsuya Akutsu
2007 B conf
A Novel Clustering Method for Analysis of Biological Networks using Maximal Components of Graphs.
APBC
Morihiro Hayashida, Tatsuya Akutsu, Hiroshi Nagamochi
2007 J jnl
Algorithms for Finding Small Attractors in Boolean Networks.
EURASIP J. Bioinform. Syst. Biol.
Shuqin Zhang, Morihiro Hayashida, Tatsuya Akutsu, Wai-Ki Ching, Michael Kwok-Po Ng
2007 C conf
An Efficient Algorithm for Generating Colored Outerplanar Graphs.
TAMC
Jiexun Wang, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu
2007 B conf
An O(1.787
FCT
Takeyuki Tamura, Tatsuya Akutsu
2007 J jnl
An approximation method for solving the steady-state probability distribution of probabilistic Boolean networks.
Bioinform.
Wai-Ki Ching, Shuqin Zhang, Michael K. Ng, Tatsuya Akutsu
2007 J jnl
Approximation Algorithms for Optimal RNA Secondary Structures Common to Multiple Sequences.
IEICE Trans. Fundam. Electron. Commun. Comput. Sci.
Takeyuki Tamura, Tatsuya Akutsu
2007 J jnl
Correlation between structure and temperature in prokaryotic metabolic networks.
BMC Bioinform.
Kazuhiro Takemoto, Jose C. Nacher, Tatsuya Akutsu
2007 J jnl
Genetic Regulatory Networks.
EURASIP J. Bioinform. Syst. Biol.
Edward R. Dougherty, Tatsuya Akutsu, Paul Dan Cristea, Ahmed H. Tewfik
2007 J jnl
Hardness Results on Local Multiple Alignment of Biological Sequences.
Inf. Media Technol.
Tatsuya Akutsu, Hiroki Arimura, Shinichi Shimozono
2007 B conf
Inferring a Chemical Structure from a Feature Vector Based on Frequency of Labeled Paths and Small Fragments.
APBC
Tatsuya Akutsu, Daiji Fukagawa
2007 J jnl
On the complexity of deriving position specific score matrices from positive and negative sequences.
Discret. Appl. Math.
Tatsuya Akutsu, Hideo Bannai, Satoru Miyano, Sascha Ott
2007 J jnl
Simulation study in Probabilistic Boolean Network models for genetic regulatory networks.
Int. J. Data Min. Bioinform.
Shuqin Zhang, Wai-Ki Ching, Michael K. Ng, Tatsuya Akutsu
2007 A* conf
Statistical Learning Algorithm for Tree Similarity.
ICDM
Atsuhiro Takasu, Daiji Fukagawa, Tatsuya Akutsu
2007 J jnl
Subcellular location prediction of proteins using support vector machines with alignment of block sequences utilizing amino acid composition.
BMC Bioinform.
Takeyuki Tamura, Tatsuya Akutsu
2007 — ch.
Topological aspects of protein networks.
Emergent Intelligence of Networked Agents
Jose C. Nacher, Morihiro Hayashida, Tatsuya Akutsu
2006 J jnl
A Control Model for Markovian Genetic Regulatory Networks.
Trans. Comp. Sys. Biology
Michael K. Ng, Shuqin Zhang, Wai-Ki Ching, Tatsuya Akutsu
2006 J jnl
A relation between edit distance for ordered trees and edit distance for Euler strings.
Inf. Process. Lett.
Tatsuya Akutsu
2006 J jnl
Algorithms for Point Set Matching with K-differences.
Int. J. Found. Comput. Sci.
Tatsuya Akutsu
2006 B conf
Approximating Tree Edit Distance Through String Edit Distance.
ISAAC
Tatsuya Akutsu, Daiji Fukagawa, Atsuhiro Takasu
2006 J jnl
Dynamic Programming and Clique Based Approaches for Protein Threading with Profiles and Constraints.
IEICE Trans. Fundam. Electron. Commun. Comput. Sci.
Tatsuya Akutsu, Morihiro Hayashida, Dukka Bahadur, Etsuji Tomita, Jun'ichi Suzuki, Katsuhisa Horimoto
2006 J jnl
Fast Algorithms for Comparison of Similar Unordered Trees.
Int. J. Found. Comput. Sci.
Daiji Fukagawa, Tatsuya Akutsu
2006 — conf
Identification of metabolic units induced by environmental signals.
ISMB (Supplement of Bioinformatics)
Jose C. Nacher, Jean-Marc Schwartz, Minoru Kanehisa, Tatsuya Akutsu
2006 B conf
On the Complexity of Finding Control Strategies for Boolean Networks.
APBC
Tatsuya Akutsu, Morihiro Hayashida, Wai-Ki Ching, Michael K. Ng
2006 J jnl
Optimizing amino acid substitution matrices with a local alignment kernel.
BMC Bioinform.
Hiroto Saigo, Jean-Philippe Vert, Tatsuya Akutsu
2006 J jnl
Protein Threading with Profiles and Distance Constraints Using Clique Based Algorithms.
J. Bioinform. Comput. Biol.
K. C. Dukka Bahadur, Etsuji Tomita, Jun'ichi Suzuki, Katsuhisa Horimoto, Tatsuya Akutsu
2005 J jnl
A Probabilistic Model for Mining Labeled Ordered Trees: Capturing Patterns in Carbohydrate Sugar Chains.
IEEE Trans. Knowl. Data Eng.
Nobuhisa Ueda, Kiyoko F. Aoki-Kinoshita, Atsuko Yamaguchi, Tatsuya Akutsu, Hiroshi Mamitsuka
2005 Misc conf
A linear control model for gene intervention in a genetic regulatory network.
GrC
Shuqin Zhang, Michael K. Ng, Wai-Ki Ching, Tatsuya Akutsu
2005 J jnl
A score matrix to reveal the hidden links in glycans.
Bioinform.
Kiyoko F. Aoki, Hiroshi Mamitsuka, Tatsuya Akutsu, Minoru Kanehisa
2005 B conf
Clique-based algorithms for protein threading with profiles and constraints.
APBC
Dukka Bahadur, Etsuji Tomita, Jun'ichi Suzuki, Katsuhisa Horimoto, Tatsuya Akutsu
2005 J jnl
Fast and accurate database homology search using upper bounds of local alignment scores.
Bioinform.
Masumi Itoh, Susumu Goto, Tatsuya Akutsu, Minoru Kanehisa
2005 J jnl
Graph Kernels for Molecular Structure-Activity Relationship Analysis with Support Vector Machines.
J. Chem. Inf. Model.
Pierre Mahé, Nobuhisa Ueda, Tatsuya Akutsu, Jean-Luc Perret, Jean-Philippe Vert
2005 B conf
Inferring a Graph from Path Frequency.
CPM
Tatsuya Akutsu, Daiji Fukagawa
2005 J jnl
On construction of stochastic genetic networks based on gene expression sequences.
Int. J. Neural Syst.
Wai-Ki Ching, Michael K. Ng, Eric S. Fung, Tatsuya Akutsu
2005 J jnl
Performance analysis of a greedy algorithm for inferring Boolean functions.
Inf. Process. Lett.
Daiji Fukagawa, Tatsuya Akutsu
2005 J jnl
Protein Side-chain Packing Problem: a Maximum Edge-weight Clique Algorithmic Approach.
J. Bioinform. Comput. Biol.
K. C. Dukka Bahadur, Etsuji Tomita, Jun'ichi Suzuki, Tatsuya Akutsu
2004 Misc conf
Algorithms for Point Set Matching with k-Differences.
COCOON
Tatsuya Akutsu
2004 — conf
Application of a new probabilistic model for recognizing complex patterns in glycans.
ISMB/ECCB (Supplement of Bioinformatics)
Kiyoko F. Aoki, Nobuhisa Ueda, Atsuko Yamaguchi, Minoru Kanehisa, Tatsuya Akutsu, Hiroshi Mamitsuka
2004 J jnl
Clustering under the line graph transformation: application to reaction network.
BMC Bioinform.
Jose C. Nacher, Nobuhisa Ueda, Takuji Yamada, Minoru Kanehisa, Tatsuya Akutsu
2004 J jnl
Efficient Extraction of Mapping Rules of Atoms from Enzymatic Reaction Data.
J. Comput. Biol.
Tatsuya Akutsu
2004 A* conf
Extensions of marginalized graph kernels.
ICML
Pierre Mahé, Nobuhisa Ueda, Tatsuya Akutsu, Jean-Luc Perret, Jean-Philippe Vert
2004 B conf
Fast Algorithms for Comparison of Similar Unordered Trees.
ISAAC
Daiji Fukagawa, Tatsuya Akutsu
2004 J jnl
KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains.
Nucleic Acids Res.
Kiyoko F. Aoki, Atsuko Yamaguchi, Nobuhisa Ueda, Tatsuya Akutsu, Hiroshi Mamitsuka, Susumu Goto, Minoru Kanehisa
2004 J jnl
Managing and Analyzing Carbohydrate Data.
SIGMOD Rec.
Kiyoko F. Aoki, Nobuhisa Ueda, Atsuko Yamaguchi, Tatsuya Akutsu, Minoru Kanehisa, Hiroshi Mamitsuka
2004 J jnl
Optimizing substitution matrices by separating score distributions.
Bioinform.
Yuichiro Hourai, Tatsuya Akutsu, Yutaka Akiyama
2004 B conf
Protein Side-chain Packing Problem: A Maximum Edge-weight Clique Algorithmic Approach.
APBC
Dukka Bahadur, Tatsuya Akutsu, Etsuji Tomita, Tomokazu Seki
2004 C conf
Protein Threading with Profiles and Constraints.
BIBE
Tatsuya Akutsu, Morihiro Hayashida, Etsuji Tomita, Jun'ichi Suzuki, Katsuhisa Horimoto
2004 J jnl
Protein homology detection using string alignment kernels.
Bioinform.
Hiroto Saigo, Jean-Philippe Vert, Nobuhisa Ueda, Tatsuya Akutsu
2003 J jnl
A simple greedy algorithm for finding functional relations: efficient implementation and average case analysis.
Theor. Comput. Sci.
Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara
2003 — conf
Computational and Statistical Methods in Bioinformatics.
Active Mining
Tatsuya Akutsu
2003 B conf
Efficient extraction of mapping rules of atoms from enzymatic reaction data.
RECOMB
Tatsuya Akutsu
2003 C conf
Finding optimal degenerate patterns in DNA sequences.
ECCB
Daisuke Shinozaki, Tatsuya Akutsu, Osamu Maruyama
2003 J jnl
Identification of genetic networks by strategic gene disruptions and gene overexpressions under a boolean model.
Theor. Comput. Sci.
Tatsuya Akutsu, Satoru Kuhara, Osamu Maruyama, Satoru Miyano
2003 C conf
Inferring strengths of protein-protein interactions from experimental data using linear programming.
ECCB
Morihiro Hayashida, Nobuhisa Ueda, Tatsuya Akutsu
2003 B conf
Performance Analysis of a Greedy Algorithm for Inferring Boolean Functions.
Discovery Science
Daiji Fukagawa, Tatsuya Akutsu
2003 J jnl
Point matching under non-uniform distortions.
Discret. Appl. Math.
Tatsuya Akutsu, Kyotetsu Kanaya, Akira Ohyama, Asao Fujiyama
2002 Misc conf
Inferring a Union of Halfspaces from Examples.
COCOON
Tatsuya Akutsu, Sascha Ott
2002 B conf
On the Complexity of Deriving Position Specific Score Matrices from Examples.
CPM
Tatsuya Akutsu, Hideo Bannai, Satoru Miyano, Sascha Ott
2000 B conf
A Simple Greedy Algorithm for Finding Functional Relations: Efficient Implementation and Average Case Anaylsis.
Discovery Science
Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara
2000 J jnl
Algorithms for Identifying Boolean Networks and Related Biological Networks Based on Matrix Multiplication and Fingerprint Function.
J. Comput. Biol.
Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara
2000 B conf
Algorithms for identifying Boolean networks and related biological networks based on matrix multiplication and fingerprint function.
RECOMB
Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara
2000 J jnl
Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots.
Discret. Appl. Math.
Tatsuya Akutsu
2000 J jnl
Inferring qualitative relations in genetic networks and metabolic pathways.
Bioinform.
Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara
2000 B conf
On approximation algorithms for local multiple alignment.
RECOMB
Tatsuya Akutsu, Hiroki Arimura, Shinichi Shimozono
2000 J jnl
On the approximation of largest common subtrees and largest common point sets.
Theor. Comput. Sci.
Tatsuya Akutsu, Magnús M. Halldórsson
1999 J jnl
Approximation and Exact Algorithms for RNA Secondary Structure Prediction and Recognition of Stochastic Context-free Languages.
J. Comb. Optim.
Tatsuya Akutsu
1999 Misc conf
Identification of Genetic Networks from a Small Number of Gene Expression Patterns Under the Boolean Network Model.
Pacific Symposium on Biocomputing
Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara
1999 B conf
Matching of Spots in 2D Electrophoresis Images. Point Matching Under Non-uniform Distortions.
CPM
Tatsuya Akutsu, Kyotetsu Kanaya, Akira Ohyama, Asao Fujiyama
1999 J jnl
On the Approximation of Protein Threading.
Theor. Comput. Sci.
Tatsuya Akutsu, Satoru Miyano
1998 B conf
Approximation and Exact Algorithms for RNA Secondary Structure Prediction and Recognition of Stochastic Context-Free Languages.
ISAAC
Tatsuya Akutsu
1998 J jnl
Distribution of Distances and Triangles in a Point Set and Algorithms for Computing the Largest Common Point Sets.
Discret. Comput. Geom.
Tatsuya Akutsu, Hisao Tamaki, Takeshi Tokuyama
1998 A* conf
Identification of Gene Regulatory Networks by Strategic Gene Disruptions and Gene Overexpressions.
SODA
Tatsuya Akutsu, Satoru Kuhara, Osamu Maruyama, Satoru Miyano
1998 J jnl
On determining the congruence of point sets in d dimensions.
Comput. Geom.
Tatsuya Akutsu
1998 A* conf
On the Complexity of Deriving Score Functions from Examples for Problems in Molecular Biology.
ICALP
Tatsuya Akutsu, Mutsunori Yagiura
1997 — conf
Distribution of Distances and Triangles in a Point Set and Algorithms for Computing the Largest Common Point Sets.
SCG
Tatsuya Akutsu, Hisao Tamaki, Takeshi Tokuyama
1997 B conf
On the approximation of protein threading.
RECOMB
Tatsuya Akutsu, Satoru Miyano
1997 J jnl
Rapid protein fragment search using hash functions based on the Fourier transform.
Comput. Appl. Biosci.
Tatsuya Akutsu, Kentaro Onizuka, Masato Ishikawa
1996 Misc conf
Approximating Minimum Keys and Optimal Substructure Screens.
COCOON
Tatsuya Akutsu, Feng Bao
1996 C conf
Sampling Effectiveness in Discovering Functional Relationships in Databases.
IEA/AIE
Atsuhiro Takasu, Tatsuya Akutsu, Moonis Ali
1995 J jnl
A Parallel Algorithm for Determining the Congruence of Point Sets in Three-Dimensions.
IEICE Trans. Inf. Syst.
Tatsuya Akutsu
1995 J jnl
Approximate String Matching with don't Care Characters.
Inf. Process. Lett.
Tatsuya Akutsu
1995 — conf
New hashing techniques and their application to a protein structure database system.
HICSS (5)
Tatsuya Akutsu, Kentaro Onizuka, Masato Ishikawa
1994 B conf
Approximate String Matching with Don't Care Characters.
CPM
Tatsuya Akutsu
1994 — conf
Efficient and Robust Three-Dimensional Pattern Matching Algorithms Using Hashing and Dynamic Programming Techniques.
HICSS (5)
Tatsuya Akutsu
1994 B conf
On Determining the Congruity of Point Sets in Higher Dimensions.
ISAAC
Tatsuya Akutsu
1994 J jnl
On PAC Learnability of Functional Depencies.
New Gener. Comput.
Tatsuya Akutsu, Atsuhiro Takasu
1994 B conf
On the Approximation of Largest Common Subtrees and Largest Common Point Sets.
ISAAC
Tatsuya Akutsu, Magnús M. Halldórsson
1993 B conf
A Linear Time Pattern Matching Algorithm Between a String and a Tree.
CPM
Tatsuya Akutsu
1993 J jnl
Knowledge-based system for computer-aided drug design.
Knowl. Based Syst.
Einoshin Suzuki, Tatsuya Akutsu, Setsuo Ohsuga
1992 B conf
Algorithms for Determining the Geometrical Congruity in Two and Three Dimensions.
ISAAC
Tatsuya Akutsu
1992 B conf
On PAC Learnability of Functional Dependencies.
ALT
Tatsuya Akutsu, Atsuhiro Takasu
1991 J jnl
A new method of computer representation of stereochemistry. Transforming a stereochemical structure into a graph.
J. Chem. Inf. Comput. Sci.
Tatsuya Akutsu
1991 A conf
Development and comparison of search algorithms for robot motion planning in the configuration space.
IROS
Tatsuya Akutsu, Satoshi Yaoi, Kazunari Sato, Susumu Enomoto
1991 J jnl
Logic-based approach to expert systems in chemistry.
Knowl. Based Syst.
Tatsuya Akutsu, Einoshin Suzuki, Setsuo Ohsuga
1988 — conf
CHEMILOG - A Logic Programming Language/System for Chemical Information Processing.
FGCS
Tatsuya Akutsu, Setsuo Ohsuga