Yasubumi Sakakibara

Orcid: 0000-0002-6932-3452

According to our database1, Yasubumi Sakakibara authored at least 85 papers between 1986 and 2024.

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Bibliography

2024
Deep learning of multimodal networks with topological regularization for drug repositioning.
J. Cheminformatics, December, 2024

2022
Graph Kernels Encoding Features of All Subgraphs by Quantum Superposition.
IEEE J. Emerg. Sel. Topics Circuits Syst., 2022

2021
Deep learning integration of molecular and interactome data for protein-compound interaction prediction.
J. Cheminformatics, 2021

MetaVelvet-DL: a MetaVelvet deep learning extension for de novo metagenome assembly.
BMC Bioinform., 2021

2019
Guest Editorial for the 16th Asia Pacific Bioinformatics Conference.
IEEE ACM Trans. Comput. Biol. Bioinform., 2019

Comprehensive evaluation of non-hybrid genome assembly tools for third-generation PacBio long-read sequence data.
Briefings Bioinform., 2019

2018
A max-margin training of RNA secondary structure prediction integrated with the thermodynamic model.
J. Bioinform. Comput. Biol., 2018

Convolutional neural network based on SMILES representation of compounds for detecting chemical motif.
BMC Bioinform., 2018

Convolutional neural networks for classification of alignments of non-coding RNA sequences.
Bioinform., 2018

2017
Probabilistic Context-Free Grammars.
Proceedings of the Encyclopedia of Machine Learning and Data Mining, 2017

2016
SHARAKU: an algorithm for aligning and clustering read mapping profiles of deep sequencing in non-coding RNA processing.
Bioinform., 2016

2015
A Machine Learning Based Approach to de novo Sequencing of Glycans from Tandem Mass Spectrometry Spectrum.
IEEE ACM Trans. Comput. Biol. Bioinform., 2015

2012
Bacterial Computing and Molecular Communication.
Proceedings of the Handbook of Natural Computing, 2012

Foreword.
Nat. Comput., 2012

An efficient algorithm for de novo predictions of biochemical pathways between chemical compounds.
BMC Bioinform., 2012

DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition.
Bioinform., 2012

COPICAT: a software system for predicting interactions between proteins and chemical compounds.
Bioinform., 2012

SAMSCOPE: an OpenGL-based real-time interactive scale-free SAM viewer.
Bioinform., 2012

Poster: In silico microarray algorithm: Accurate and fast taxonomic profiling from short read sequences.
Proceedings of the IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, 2012

2011
Fast and accurate clustering of noncoding RNAs using ensembles of sequence alignments and secondary structures.
BMC Bioinform., 2011

MetaVelvet: an extension of Velvet assembler to <i>de novo</i> metagenome assembly from short sequence reads.
Proceedings of the ACM International Conference on Bioinformatics, 2011

2010
Probabilistic Context-Free Grammars.
Proceedings of the Encyclopedia of Machine Learning, 2010

Operon structure optimization by random self-assembly.
Nat. Comput., 2010

A Non-Parametric Bayesian Approach for Predicting RNA Secondary Structures.
J. Bioinform. Comput. Biol., 2010

Robust and accurate prediction of noncoding RNAs from aligned sequences.
BMC Bioinform., 2010

Improvement of Structure Conservation Index with Centroid Estimators.
Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010

Development of a Bacteria Computer: From <i>in silico</i> Finite Automata to <i>in vitro</i> and <i>in vivo</i>.
Proceedings of the Programs, Proofs, Processes, 6th Conference on Computability in Europe, 2010

2009
Integrating Statistical Predictions and Experimental Verifications for Enhancing Protein-Chemical Interaction Predictions in Virtual Screening.
PLoS Comput. Biol., 2009

Support Vector Machine Prediction of N- and O-glycosylation Sites Using Whole Sequence Information and Subcellular Localization.
Inf. Media Technol., 2009

Accurate identification of orthologous segments among multiple genomes.
Bioinform., 2009

Sequence and Structural Analyses for Functional Non-coding RNAs.
Proceedings of the Algorithmic Bioprocesses, 2009

2008
Software.ncrna.org: web servers for analyses of RNA sequences.
Nucleic Acids Res., 2008

Directed acyclic graph kernels for structural RNA analysis.
BMC Bioinform., 2008

Bio-Molecular Computing of Finite-State Machine.
Proceedings of the 3rd International ICST Conference on Bio-Inspired Models of Network, 2008

2007
Guest editorial to the special issue on grammatical inference.
Mach. Learn., 2007

Stem Kernels for RNA Sequence Analyses.
J. Bioinform. Comput. Biol., 2007

Statistical prediction of protein-chemical interactions based on chemical structure and mass spectrometry data.
Bioinform., 2007

Probabilistic Inference in Test Tube and its Application to Gene Expression Profiles.
Proceedings of the Formal Models, 2007

Stem Kernels for RNA Sequence Analyses.
Proceedings of the Bioinformatics Research and Development, First International Conference, 2007

Implementing in vivo Cellular Automata using Toggle Switch and Inter-Bacteria Communication Mechanism.
Proceedings of the 2nd International ICST Conference on Bio-Inspired Models of Network, 2007

2006
Discriminative Detection of Cis-Acting Regulatory Variation From Location Data.
Proceedings of 4th Asia-Pacific Bioinformatics Conference. 13-16 February 2006, 2006

2005
Learning context-free grammars using tabular representations.
Pattern Recognit., 2005

Grammatical Inference in Bioinformatics.
IEEE Trans. Pattern Anal. Mach. Intell., 2005

Development of a Bacteria Computer: From in silico Finite Automata to in virto AND in vivo.
Bull. EATCS, 2005

Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures.
Bioinform., 2005

RNA secondary structural alignment with conditional random fields.
Proceedings of the ECCB/JBI'05 Proceedings, Fourth European Conference on Computational Biology/Sixth Meeting of the Spanish Bioinformatics Network (Jornadas de BioInformática), Palacio de Congresos, Madrid, Spain, September 28, 2005

Development of an <i>In Vivo</i> Computer Based on <i>Escherichia coli</i>.
Proceedings of the DNA Computing, 11th International Workshop on DNA Computing, 2005

Intensive <i>In Vitro</i> Experiments of Implementing and Executing Finite Automata in Test Tube.
Proceedings of the DNA Computing, 11th International Workshop on DNA Computing, 2005

Discriminative Discovery of Transcription Factor Binding Sites from Location Data.
Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference, 2005

2004
A DNA-Based Computational Model Using a Specific Type of Restriction Enzymes.
J. Autom. Lang. Comb., 2004

An Algorithm for Testing Structure Freeness of Biomolecular Sequences.
Proceedings of the Aspects of Molecular Computing, 2004

2003
DNA-based algorithms for learning Boolean formulae.
Nat. Comput., 2003

Pair hidden Markov models on tree structures.
Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology, June 29, 2003

In Vitro Translation-Based Computations.
Proceedings of the DNA Computing, 9th International Workshop on DNA Based Computers, 2003

2002
A DNA-based Computational Model Using a Specific Type of Restriction Enzyme.
Proceedings of the DNA Computing, 8th International Workshop on DNA Based Computers, 2002

A Magic Pot : Self-assembly Computation Revisited.
Proceedings of the Formal and Natural Computing, 2002

2001
Multiple splicing systems and the universal computability.
Theor. Comput. Sci., 2001

Sticker systems with complex structures.
Soft Comput., 2001

Population Computation and Majority Inference in Test Tube.
Proceedings of the DNA Computing, 7th International Workshop on DNA-Based Computers, 2001

Probabilistic logical inference using quantities of DNA strands.
Proceedings of the 2001 Congress on Evolutionary Computation, 2001

Approximate identification of finite elasticity.
Proceedings of the Where Mathematics, 2001

2000
Learning Context-Free Grammars from Partially Structured Examples.
Proceedings of the Grammatical Inference: Algorithms and Applications, 2000

Solving Computational Learning Problems of Boolean Formulae on DNA Computers.
Proceedings of the DNA Computing, 6th International Workshop on DNA-Based Computers, 2000

1999
Splicing on Tree-Like Structures.
Theor. Comput. Sci., 1999

GA-based Learning of Context-Free Grammars using Tabular Representations.
Proceedings of the Sixteenth International Conference on Machine Learning (ICML 1999), Bled, Slovenia, June 27, 1999

1997
Recent Advances of Grammatical Inference.
Theor. Comput. Sci., 1997

On Case Based Learnability of Language.
New Gener. Comput., 1997

1996
A machine learning approach to knowledge acquisitions from text databases.
Int. J. Hum. Comput. Interact., 1996

Stochastic simple recurrent neural networks.
Proceedings of the Grammatical Inference: Learning Syntax from Sentences, 1996

1995
Simple recurrent networks as generalized hidden Markov models with distributed representations.
Proceedings of International Conference on Neural Networks (ICNN'95), Perth, WA, Australia, November 27, 1995

Grammatical Inference: An Old and New Paradigm.
Proceedings of the Algorithmic Learning Theory, 6th International Conference, 1995

1994
Stochastic Context-Free Grammars for Modeling RN.
Proceedings of the 27th Annual Hawaii International Conference on System Sciences (HICSS-27), 1994

Recent Methods for RNA Modeling Using Stochastic Context-Free Grammars.
Proceedings of the Combinatorial Pattern Matching, 5th Annual Symposium, 1994

Learning Languages by Collecting Cases and Tuning Parameters.
Proceedings of the Algorithmic Learning Theory, 1994

1993
Noise-Tolerant Occam Algorithms and Their Applications to Learning Decision Trees.
Mach. Learn., 1993

1992
Efficient Learning of Context-Free Grammars from Positive Structural Examples
Inf. Comput., March, 1992

A Noise Model on Learning Sets of Strings.
Proceedings of the Fifth Annual ACM Conference on Computational Learning Theory, 1992

1991
On Learning from Queries and Counterexamples in the Presence of Noise.
Inf. Process. Lett., 1991

ACE: A syntax-directed editor customizable from examples and queries.
Proceedings of the Algorithmic Learning Theory, 2nd International Workshop, 1991

1990
Learning Context-Free Grammars from Structural Data in Polynomial Time.
Theor. Comput. Sci., 1990

Inductive inference of logic programs based on algebraic semantics.
New Gener. Comput., 1990

Exact Learning of Semilinear Sets.
Proceedings of the Algorithmic Learning Theory, First International Workshop, 1990

Occam Algorithms for Learning From Noisy Examples.
Proceedings of the Algorithmic Learning Theory, First International Workshop, 1990

1988
An Efficient Learning of Context-Free Grammars for Bottom-Up Parsers.
Proceedings of the International Conference on Fifth Generation Computer Systems, 1988

1986
Programming in Modal Logic: An Extension of PROLOG based on Modal Logic.
Proceedings of the Logic Programming '86, 1986


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