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1

Noise-Tolerant Occam Algorithms and Their Applications to Learning Decision Trees

Sakakibara, Yasubumi

Journal:

Machine Learning

Year:

1993

Language:

english

File:

PDF, 1.27 MB

english, 1993

2

Learning context-free grammars using tabular representations

Yasubumi Sakakibara

Journal:

Pattern Recognition

Year:

2005

Language:

english

File:

PDF, 301 KB

english, 2005

3

Guest editorial to the special issue on grammatical inference

Georgios Paliouras, Yasubumi Sakakibara

Journal:

Machine Learning

Year:

2007

Language:

english

File:

PDF, 139 KB

english, 2007

4

Directed acyclic graph kernels for structural RNA analysis

Kengo Sato, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 371 KB

english, 2008

5

[Lecture Notes in Computer Science] DNA Computing and Molecular Programming Volume 6518 || Synthesizing Minimal Tile Sets for Patterned DNA Self-assembly

Sakakibara, Yasubumi, Mi, Yongli

Year:

2011

Language:

english

File:

PDF, 513 KB

english, 2011

6

Convolutional neural network based on SMILES representation of compounds for detecting chemical motif

Hirohara, Maya, Saito, Yutaka, Koda, Yuki, Sato, Kengo, Sakakibara, Yasubumi

Journal:

BMC Bioinformatics

Year:

2018

Language:

english

File:

PDF, 2.89 MB

english, 2018

7

On learning from queries and counterexamples in the presence of noise

Yasubumi Sakakibara

Journal:

Information Processing Letters

Year:

1991

Language:

english

File:

PDF, 786 KB

english, 1991

8

Learning context-free grammars from structural data in polynomial time

Yasubumi Sakakibara

Journal:

Theoretical Computer Science

Year:

1990

Language:

english

File:

PDF, 2.08 MB

english, 1990

9

Multiple splicing systems and the universal computability

Satoshi Kobayashi, Yasubumi Sakakibara

Journal:

Theoretical Computer Science

Year:

2001

Language:

english

File:

PDF, 187 KB

english, 2001

10

Recent advances of grammatical inference

Yasubumi Sakakibara

Journal:

Theoretical Computer Science

Year:

1997

Language:

english

File:

PDF, 2.26 MB

english, 1997

11

Splicing on tree-like structures

Yasubumi Sakakibara, Claudio Ferretti

Journal:

Theoretical Computer Science

Year:

1999

Language:

english

File:

PDF, 1.04 MB

english, 1999

12

Fast and accurate clustering of noncoding RNAs using ensembles of sequence alignments and secondary structures

Yutaka Saito, Kengo Sato, Yasubumi Sakakibara

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 657 KB

english, 2011

13

On case-based learnability of languages

Christoph Globig, Klaus P. Jantke, Steffen Lange, Yasubumi Sakakibara

Journal:

New Generation Computing

Year:

1997

Language:

english

File:

PDF, 1.36 MB

english, 1997

14

PSSMTS: position specific scoring matrices on tree structures

Kengo Sato, Kensuke Morita, Yasubumi Sakakibara

Journal:

Journal of Mathematical Biology

Year:

2008

Language:

english

File:

PDF, 391 KB

english, 2008

15

Operon structure optimization by random self-assembly

Yusuke Nakagawa, Katsuyuki Yugi, Kenji Tsuge, Mitsuhiro Itaya, Hiroshi Yanagawa, Yasubumi Sakakibara

Journal:

Natural Computing

Year:

2010

Language:

english

File:

PDF, 443 KB

english, 2010

16

Inductive inference of logic programs based on algebraic semantics

Yasubumi Sakakibara

Journal:

New Generation Computing

Year:

1990

Language:

english

File:

PDF, 739 KB

english, 1990

17

Foreword

Yasubumi Sakakibara, Yongli Mi

Journal:

Natural Computing

Year:

2012

Language:

english

File:

PDF, 100 KB

english, 2012

18

Efficient learning of context-free grammars from positive structural examples

Yasubumi Sakakibara

Journal:

Information and Computation

Year:

1992

Language:

english

File:

PDF, 2.19 MB

english, 1992

19

Robust and accurate prediction of noncoding RNAs from aligned sequences

Yutaka Saito, Kengo Sato, Yasubumi Sakakibara

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1.34 MB

english, 2010

20

Whole genome assembly of a natto production strain Bacillus subtilis natto from very short read data

Yukari Nishito, Yasunori Osana, Tsuyoshi Hachiya, Kris Popendorf, Atsushi Toyoda, Asao Fujiyama, Mitsuhiro Itaya, Yasubumi Sakakibara

Journal:

Year:

2010

Language:

english

File:

PDF, 1.18 MB

english, 2010

21

Construction of a genetic AND gate under a new standard for assembly of genetic parts

Shotaro Ayukawa, Akio Kobayashi, Yusaku Nakashima, Hidemasa Takagi, Shogo Hamada, Masahiko Uchiyama, Katsuyuki Yugi, Satoshi Murata, Yasubumi Sakakibara, Masami Hagiya, Masayuki Yamamura, Daisuke Kiga

Journal:

Year:

2010

Language:

english

File:

PDF, 603 KB

english, 2010

22

Functional and bioinformatic screening for the genes involved in the expansion of cerebral cortex during the primate evolution

Hidenori Tabata, Tsuyoshi Hachiya, Yasubumi Sakakibara, Kazunori Nakajima

Journal:

Neuroscience Research

Year:

2011

Language:

english

File:

PDF, 127 KB

english, 2011

23

[Lecture Notes in Computer Science] Grammatical Inference: Algorithms and Applications Volume 4201 ||

Sakakibara, Yasubumi, Kobayashi, Satoshi, Sato, Kengo, Nishino, Tetsuro, Tomita, Etsuji

Year:

2006

Language:

english

File:

PDF, 3.31 MB

english, 2006

24

Development of a rifampicin-resistant Bacillus subtilis strain for natto-fermentation showing enhanced exoenzyme production

Kubo, Yuji, Inaoka, Takashi, Hachiya, Tsuyoshi, Miyake, Masayuki, Hase, Sumitaka, Nakagawa, Rikio, Hasegawa, Hiromasa, Funane, Kazumi, Sakakibara, Yasubumi, Kimura, Keitarou

Journal:

Journal of Bioscience and Bioengineering

Year:

2013

Language:

english

File:

PDF, 338 KB

english, 2013

25

[IEEE 2007 2nd Bio-Inspired Models of Network, Information and Computing Systems (BIONETICS) - Budapest, Hungary (2007.12.10-2007.12.12)] 2007 2nd Bio-Inspired Models of Network, Information and Computing Systems - Implementing in vivo cellular automata using toggle switch and inter-bacteria communication mechanism

Yasubumi Sakakibara,, Hirotaka Nakagawa,, Yusaku Nakashima,, Katsuyuki Yugi,

Year:

2007

Language:

english

File:

PDF, 2.44 MB

english, 2007

26

Stochastic context-free grammers for tRNA modeling

Sakakibara, Yasubumi, Brown, Michael, Hughey, Richard, Mian, I. Saira, Sjölander, Kimmen, Underwood, Rebecca C., Haussler, David

Journal:

Nucleic Acids Research

Year:

1994

Language:

english

File:

PDF, 959 KB

english, 1994

27

[IEEE 2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) - Las Vegas, NV, USA (2012.02.23-2012.02.25)] 2012 IEEE 2nd International Conference on Computational Advances in Bio and medical Sciences (ICCABS) - Poster: In silico microarray algorithm: Accurate and fast taxonomic profiling from short read sequences

Tagami, Tomoya, Hachiya, Tsuyoshi, Sakakibara, Yasubumi

Year:

2012

Language:

english

File:

PDF, 52 KB

english, 2012

28

STEM KERNELS FOR RNA SEQUENCE ANALYSES

SAKAKIBARA, YASUBUMI, POPENDORF, KRIS, OGAWA, NANA, ASAI, KIYOSHI, SATO, KENGO

Journal:

Journal of Bioinformatics and Computational Biology

Year:

2007

Language:

english

File:

PDF, 420 KB

english, 2007

29

A NON-PARAMETRIC BAYESIAN APPROACH FOR PREDICTING RNA SECONDARY STRUCTURES

SATO, KENGO, HAMADA, MICHIAKI, MITUYAMA, TOUTAI, ASAI, KIYOSHI, SAKAKIBARA, YASUBUMI

Journal:

Journal of Bioinformatics and Computational Biology

Year:

2010

Language:

english

File:

PDF, 328 KB

english, 2010

30

[Lecture Notes in Computer Science] Grammatical Inference: Algorithms and Applications Volume 4201 || A Discriminative Model of Stochastic Edit Distance in the Form of a Conditional Transducer

Sakakibara, Yasubumi, Kobayashi, Satoshi, Sato, Kengo, Nishino, Tetsuro, Tomita, Etsuji

Year:

2006

Language:

english

File:

PDF, 574 KB

english, 2006

31

[Lecture Notes in Computer Science] Grammatical Inference: Algorithms and Applications Volume 4201 || Variational Bayesian Grammar Induction for Natural Language

Sakakibara, Yasubumi, Kobayashi, Satoshi, Sato, Kengo, Nishino, Tetsuro, Tomita, Etsuji

Year:

2006

Language:

english

File:

PDF, 473 KB

english, 2006

32

A machine learning approach to knowledge acquisitions from text databases

Sakakibara, Yasubumi, Misue, Kazuo, Koshiba, Takeshi

Journal:

International Journal of Human-Computer Interaction

Year:

1996

Language:

english

File:

PDF, 815 KB

english, 1996

33

BIOINFORMATICS EDUCATION AT KEIO UNIVERSITY

Sakakibara, Yasubumi

Journal:

Asia-Pacific Biotech News

Year:

2007

Language:

english

File:

PDF, 111 KB

english, 2007

34

A machine learning based approach to de novo sequencing of glycans from tandem mass spectrometry spectrum

Kumozaki, Shotaro, Sato, Kengo, Sakakibara, Yasubumi

Journal:

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Year:

2015

Language:

english

File:

PDF, 457 KB

english, 2015

35

Integrating Statistical Predictions and Experimental Verifications for Enhancing Protein-Chemical Interaction Predictions in Virtual Screening

Nagamine, Nobuyoshi, Shirakawa, Takayuki, Minato, Yusuke, Torii, Kentaro, Kobayashi, Hiroki, Imoto, Masaya, Sakakibara, Yasubumi, Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 690 KB

english, 2009

36

[ACM Press the fifth annual workshop - Pittsburgh, Pennsylvania, United States (1992.07.27-1992.07.29)] Proceedings of the fifth annual workshop on Computational learning theory - COLT '92 - A noise model on learning sets of strings

Sakakibara, Yasubumi, Siromoney, Rani

Year:

1992

Language:

english

File:

PDF, 698 KB

english, 1992

37

[ACM Press the 2nd ACM Conference - Chicago, Illinois (2011.08.01-2011.08.03)] Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine - BCB '11 - MetaVelvet

Namiki, Toshiaki, Hachiya, Tsuyoshi, Tanaka, Hideaki, Sakakibara, Yasubumi

Year:

2011

Language:

english

File:

PDF, 504 KB

english, 2011

38

A Bicyclic 1-Deoxygalactonojirimycin Derivative as a Novel Pharmacological Chaperone for GM1 Gangliosidosis

Takai, Tomoko, Higaki, Katsumi, Aguilar-Moncayo, Matilde, Mena-Barragán, Teresa, Hirano, Yuki, Yura, Kei, Yu, Liang, Ninomiya, Haruaki, García-Moreno, M. Isabel, Sakakibara, Yasubumi, Ohno, Kousaku, N

Journal:

Molecular Therapy

Year:

2013

Language:

english

File:

PDF, 637 KB

english, 2013

39

[Advances in Human Factors/Ergonomics] Symbiosis of Human and Artifact - Future Computing and Design for Human-Computer Interaction, Proceedings of the Sixth International Conference on Human-Computer Interaction, (HCI International '95) Volume 20 || Knowledge acquisitions from large databases using machine learning techniques

Sakakibara, Yasubumi

Year:

1995

Language:

english

File:

PDF, 470 KB

english, 1995

40

[Lecture Notes in Computer Science] Grammatical Inference: Algorithms and Applications Volume 3264 || Learning Stochastic Finite Automata

Paliouras, Georgios, Sakakibara, Yasubumi

Year:

2004

Language:

english

File:

PDF, 197 KB

english, 2004

41

[Lecture Notes in Computer Science] Grammatical Inference: Algorithms and Applications Volume 3264 || Grammatical Inference Using Suffix Trees

Paliouras, Georgios, Sakakibara, Yasubumi

Year:

2004

Language:

english

File:

PDF, 170 KB

english, 2004

42

[Lecture Notes in Computer Science] Grammatical Inference: Algorithms and Applications Volume 3264 || Identifying Clusters from Positive Data

Paliouras, Georgios, Sakakibara, Yasubumi

Year:

2004

Language:

english

File:

PDF, 199 KB

english, 2004

43

Recent Advances of DNA Based Computers

SAKAKIBARA, Yasubumi

Journal:

Year:

2007

File:

PDF, 557 KB

2007

44

Prediction of Gene Structures from RNA-seq Data Using Dual Decomposition

Inatsuki, Tatsumu, Sato, Kengo, Sakakibara, Yasubumi

Journal:

IPSJ Transactions on Bioinformatics

Year:

2016

Language:

english

File:

PDF, 977 KB

english, 2016

45

Support Vector Machine Prediction of N- and O-glycosylation Sites Using Whole Sequence Information and Subcellular Localization

Sasaki, Kenta, Nagamine, Nobuyoshi, Sakakibara, Yasubumi

Journal:

IPSJ Transactions on Bioinformatics

Year:

2009

Language:

english

File:

PDF, 973 KB

english, 2009

46

DNA Computers: A New Computing Paradigm.

Sakakibara, Yasubumi

Journal:

Journal of Photopolymer Science and Technology

Year:

1998

Language:

english

File:

PDF, 347 KB

english, 1998

47

SHARAKU: an algorithm for aligning and clustering read mapping profiles of deep sequencing in non-coding RNA processing

Tsuchiya, Mariko, Amano, Kojiro, Abe, Masaya, Seki, Misato, Hase, Sumitaka, Sato, Kengo, Sakakibara, Yasubumi

Journal:

Year:

2016

Language:

english

File:

PDF, 479 KB

english, 2016

48

Resequencing of the common marmoset genome improves genome assemblies and gene-coding sequence analysis

Sato, Kengo, Kuroki, Yoko, Kumita, Wakako, Fujiyama, Asao, Toyoda, Atsushi, Kawai, Jun, Iriki, Atsushi, Sasaki, Erika, Okano, Hideyuki, Sakakibara, Yasubumi

Journal:

Scientific Reports

Year:

2015

Language:

english

File:

PDF, 490 KB

english, 2015

49

Chaperone Therapy for Neuronopathic Lysosomal Diseases: Competitive Inhibitors as Chemical Chaperones for Enhancement of Mutant Enzyme Activities

Suzuki, Yoshiyuki, Ogawa, Seiichiro, Sakakibara, Yasubumi

Journal:

Perspectives in Medicinal Chemistry

Year:

2009

Language:

english

File:

PDF, 1.25 MB

english, 2009

50

Comprehensive evaluation of non-hybrid genome assembly tools for third-generation PacBio long-read sequence data

Jayakumar, Vasanthan, Sakakibara, Yasubumi

Journal:

Briefings in Bioinformatics

Year:

2017

Language:

english

File:

PDF, 576 KB

english, 2017

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