Koji Tsuda

Koji Tsuda

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Koji Tsuda

Koji Tsuda

Publications by authors named "Koji Tsuda"

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Enhancing Biomolecular Sampling with Reinforcement Learning: A Tree Search Molecular Dynamics Simulation Method.

ACS Omega 2019 Aug 19;4(9):13853-13862. Epub 2019 Aug 19.

Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwa-no-ha, Kashiwa, Chiba 277-8561, Japan.

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https://pubs.acs.org/doi/10.1021/acsomega.9b01480
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http://dx.doi.org/10.1021/acsomega.9b01480DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6714528PMC
August 2019

Multiple Testing Tool to Detect Combinatorial Effects in Biology.

Methods Mol Biol 2018 ;1807:83-94

Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.

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http://dx.doi.org/10.1007/978-1-4939-8561-6_7DOI Listing
March 2019

An interpretable machine learning model for diagnosis of Alzheimer's disease.

PeerJ 2019 1;7:e6543. Epub 2019 Mar 1.

Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.

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http://dx.doi.org/10.7717/peerj.6543DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6398390PMC
March 2019

Machine-Learning-Assisted Development and Theoretical Consideration for the AlFeSi Thermoelectric Material.

ACS Appl Mater Interfaces 2019 Mar 18;11(12):11545-11554. Epub 2019 Mar 18.

Graduate School of Frontier Sciences , The University of Tokyo , 5-1-5 Kashiwa-no-ha , Kashiwa 277-8561 , Japan.

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http://dx.doi.org/10.1021/acsami.9b02381DOI Listing
March 2019

Improving the Accuracy of Protein-Ligand Binding Mode Prediction Using a Molecular Dynamics-Based Pocket Generation Approach.

J Comput Chem 2018 12;39(32):2679-2689

Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto, 606-8507, Japan.

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http://doi.wiley.com/10.1002/jcc.25715
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http://dx.doi.org/10.1002/jcc.25715DOI Listing
December 2018

MP-LAMP: parallel detection of statistically significant multi-loci markers on cloud platforms.

Bioinformatics 2018 09;34(17):3047-3049

Center for Advanced Intelligence Project, RIKEN, Tokyo, Japan.

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http://dx.doi.org/10.1093/bioinformatics/bty219DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6129301PMC
September 2018

Machine-Learning-Guided Mutagenesis for Directed Evolution of Fluorescent Proteins.

ACS Synth Biol 2018 09 20;7(9):2014-2022. Epub 2018 Aug 20.

Department of Biomolecular Engineering, Graduate School of Engineering , Tohoku University , 6-6-11 Aoba, Aramaki, Aoba-ku , Sendai 980-8579 , Japan.

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http://dx.doi.org/10.1021/acssynbio.8b00155DOI Listing
September 2018

Data-driven approach for the prediction and interpretation of core-electron loss spectroscopy.

Sci Rep 2018 09 6;8(1):13548. Epub 2018 Sep 6.

Institute of Industrial Science, The University of Tokyo, 153-8505, Tokyo, Japan.

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http://www.nature.com/articles/s41598-018-30994-6
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http://dx.doi.org/10.1038/s41598-018-30994-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6127203PMC
September 2018

Hunting for Organic Molecules with Artificial Intelligence: Molecules Optimized for Desired Excitation Energies.

ACS Cent Sci 2018 Sep 20;4(9):1126-1133. Epub 2018 Aug 20.

Center for Advanced Intelligence Project, RIKEN, 1-4-1 Nihombashi, Chuo-ku, Tokyo 103-0027, Japan.

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http://dx.doi.org/10.1021/acscentsci.8b00213DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6161049PMC
September 2018

Functional Nanoparticles-Coated Nanomechanical Sensor Arrays for Machine Learning-Based Quantitative Odor Analysis.

ACS Sens 2018 08 15;3(8):1592-1600. Epub 2018 Aug 15.

Materials Science and Engineering, Graduate School of Pure and Applied Science , University of Tsukuba , 1-1-1 Tennodai , Tsukuba , Ibaraki 305-8571 , Japan.

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http://dx.doi.org/10.1021/acssensors.8b00450DOI Listing
August 2018

Structure prediction of boron-doped graphene by machine learning.

J Chem Phys 2018 Jun;148(24):241716

Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.

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http://dx.doi.org/10.1063/1.5018065DOI Listing
June 2018

Machine learning accelerates MD-based binding pose prediction between ligands and proteins.

Bioinformatics 2018 03;34(5):770-778

Department of Computational Biology and Medical Science, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8561, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btx638DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030886PMC
March 2018

RNA inverse folding using Monte Carlo tree search.

BMC Bioinformatics 2017 Nov 6;18(1):468. Epub 2017 Nov 6.

Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, 277-8561, Japan.

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http://dx.doi.org/10.1186/s12859-017-1882-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5674771PMC
November 2017

ChemTS: an efficient python library for molecular generation.

Sci Technol Adv Mater 2017 24;18(1):972-976. Epub 2017 Nov 24.

Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.

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http://dx.doi.org/10.1080/14686996.2017.1401424DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5801530PMC
November 2017

Machine learning reveals orbital interaction in materials.

Sci Technol Adv Mater 2017 26;18(1):756-765. Epub 2017 Oct 26.

Japan Advanced Institute of Science and Technology, Nomi, Japan.

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http://dx.doi.org/10.1080/14686996.2017.1378060DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5678453PMC
October 2017

MDTS: automatic complex materials design using Monte Carlo tree search.

Sci Technol Adv Mater 2017 20;18(1):498-503. Epub 2017 Jul 20.

National Institute for Materials Science, Tsukuba, Japan.

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http://dx.doi.org/10.1080/14686996.2017.1344083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5532970PMC
July 2017

LAMPLINK: detection of statistically significant SNP combinations from GWAS data.

Bioinformatics 2016 11 13;32(22):3513-3515. Epub 2016 Jul 13.

Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btw418DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5181558PMC
November 2016

Sparse modeling of EELS and EDX spectral imaging data by nonnegative matrix factorization.

Ultramicroscopy 2016 11 6;170:43-59. Epub 2016 Aug 6.

Division of Materials Research, Institute of Materials and Systems for Sustainability, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan.

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http://dx.doi.org/10.1016/j.ultramic.2016.08.006DOI Listing
November 2016

CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data.

BMC Bioinformatics 2016 Sep 13;17(1):363. Epub 2016 Sep 13.

Graduate School of Frontier Sciences at the University of Tokyo, 5-1-5 Kashiwa-no-ha, Kashiwa, Japan.

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http://dx.doi.org/10.1186/s12859-016-1175-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5020541PMC
September 2016

Prediction of Low-Thermal-Conductivity Compounds with First-Principles Anharmonic Lattice-Dynamics Calculations and Bayesian Optimization.

Phys Rev Lett 2015 Nov 10;115(20):205901. Epub 2015 Nov 10.

Department of Materials Science and Engineering, Kyoto University, Kyoto 606-8501, Japan.

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http://dx.doi.org/10.1103/PhysRevLett.115.205901DOI Listing
November 2015

On the performance of methods for finding a switching mechanism in gene expression.

Genome Inform 2010 ;24:69-83

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji 611-0011, Japan.

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January 2014

Discovering combinatorial interactions in survival data.

Bioinformatics 2013 Dec 13;29(23):3053-9. Epub 2013 Sep 13.

Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan, Department of Computer Science, Nagoya Institute of Technology, Nagoya, Japan, Division of Molecular Oncology, Aichi Cancer Center, Nagoya, Japan and Department of Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btt532DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3834797PMC
December 2013

An in silico model for interpreting polypharmacology in drug-target networks.

Methods Mol Biol 2013 ;993:67-80

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan.

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http://dx.doi.org/10.1007/978-1-62703-342-8_5DOI Listing
September 2013

Statistical significance of combinatorial regulations.

Proc Natl Acad Sci U S A 2013 Aug 23;110(32):12996-3001. Epub 2013 Jul 23.

Department of Computer Science, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan.

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http://www.pnas.org/content/110/32/12996.full.pdf
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http://www.pnas.org/cgi/doi/10.1073/pnas.1302233110
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http://dx.doi.org/10.1073/pnas.1302233110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3740841PMC
August 2013

Dense module enumeration in biological networks.

Methods Mol Biol 2013 ;939:1-8

AIST Computational Biology Research Center, Tokyo, Japan.

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http://dx.doi.org/10.1007/978-1-62703-107-3_1DOI Listing
June 2013

PDB-scale analysis of known and putative ligand-binding sites with structural sketches.

Proteins 2012 Mar 24;80(3):747-63. Epub 2011 Nov 24.

Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8568, Japan.

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http://dx.doi.org/10.1002/prot.23232DOI Listing
March 2012

PoSSuM: a database of similar protein-ligand binding and putative pockets.

Nucleic Acids Res 2012 Jan 1;40(Database issue):D541-8. Epub 2011 Dec 1.

Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8568, Japan.

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http://dx.doi.org/10.1093/nar/gkr1130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245044PMC
January 2012

SketchSort: Fast All Pairs Similarity Search for Large Databases of Molecular Fingerprints.

Mol Inform 2011 Sep 12;30(9):801-7. Epub 2011 Jul 12.

Minato Discrete Structure Manipulation System Project, ERATO, Japan Science and Technology Agency, Sapporo, 060-0814, Japan.

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http://dx.doi.org/10.1002/minf.201100050DOI Listing
September 2011

ROS-DET: robust detector of switching mechanisms in gene expression.

Nucleic Acids Res 2011 Jun 1;39(11):e74. Epub 2011 Apr 1.

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji 611-0011, Japan.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkr130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3113587PMC
June 2011

SlideSort: all pairs similarity search for short reads.

Bioinformatics 2011 Feb 9;27(4):464-70. Epub 2010 Dec 9.

Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btq677DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035798PMC
February 2011

Mining significant substructure pairs for interpreting polypharmacology in drug-target network.

PLoS One 2011 Feb 23;6(2):e16999. Epub 2011 Feb 23.

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0016999PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3044142PMC
February 2011

Reaction graph kernels predict EC numbers of unknown enzymatic reactions in plant secondary metabolism.

BMC Bioinformatics 2010 Jan 18;11 Suppl 1:S31. Epub 2010 Jan 18.

Max Planck Institute for Informatics, Campus E1 4, 66123 Saarbrucken, Germany.

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http://dx.doi.org/10.1186/1471-2105-11-S1-S31DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3009503PMC
January 2010

Simultaneous inference of biological networks of multiple species from genome-wide data and evolutionary information: a semi-supervised approach.

Bioinformatics 2009 Nov 17;25(22):2962-8. Epub 2009 Aug 17.

IBM Research, Tokyo Research Laboratory, 1623-14 Shimo-tsuruma, Yamato, Kanagawa 242-8502, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btp494DOI Listing
November 2009

Efficiently finding genome-wide three-way gene interactions from transcript- and genotype-data.

Bioinformatics 2009 Nov 7;25(21):2735-43. Epub 2009 Sep 7.

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji 611-0011, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btp531DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2781753PMC
November 2009

Enumeration of condition-dependent dense modules in protein interaction networks.

Bioinformatics 2009 Apr 11;25(7):933-40. Epub 2009 Feb 11.

Max Planck Institute for Biological Cybernetics, Tübingen, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btp080DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2660875PMC
April 2009

The DICS repository: module-assisted analysis of disease-related gene lists.

Bioinformatics 2009 Mar 28;25(6):830-1. Epub 2009 Jan 28.

Institute for Bioinformatics and Systems Biology, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, D-85764 Neuherberg, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btp055DOI Listing
March 2009

Experimental design for efficient identification of gene regulatory networks using sparse Bayesian models.

BMC Syst Biol 2007 Nov 16;1:51. Epub 2007 Nov 16.

Max Planck Institute for Biological Cybernetics, Spemannstr, 38, 72076 Tübingen, Germany.

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http://dx.doi.org/10.1186/1752-0509-1-51DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2233642PMC
November 2007

Mining complex genotypic features for predicting HIV-1 drug resistance.

Bioinformatics 2007 Sep 13;23(18):2455-62. Epub 2007 Aug 13.

Max Planck Institute for Biological Cybernetics, 72076 Tübingen, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btm353DOI Listing
September 2007

Mining frequent stem patterns from unaligned RNA sequences.

Bioinformatics 2006 Oct 14;22(20):2480-7. Epub 2006 Aug 14.

Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST) 2-43 Aomi, Koto-ku, Tokyo, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btl431DOI Listing
October 2006

SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments.

Bioinformatics 2006 Jul 11;22(14):1723-9. Epub 2006 May 11.

Department of Computational Biology, Graduate School of Frontier Science, University of Tokyo, CB04 Kiban-tou 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btl177DOI Listing
July 2006

Network-based de-noising improves prediction from microarray data.

BMC Bioinformatics 2006 Mar 20;7 Suppl 1:S4. Epub 2006 Mar 20.

Graduate School of Frontier Sciences, University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, 277 - 8562, Japan.

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http://dx.doi.org/10.1186/1471-2105-7-S1-S4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1810315PMC
March 2006

Modeling splicing sites with pairwise correlations.

Bioinformatics 2002 ;18 Suppl 2:S27-34

Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan.

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http://dx.doi.org/10.1093/bioinformatics/18.suppl_2.s27DOI Listing
September 2005

Fast protein classification with multiple networks.

Bioinformatics 2005 Sep;21 Suppl 2:ii59-65

Max Planck Institute for Biological Cybernetics, Tübingen, Germany.

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http://dx.doi.org/10.1093/bioinformatics/bti1110DOI Listing
September 2005

Image reconstruction by linear programming.

IEEE Trans Image Process 2005 Jun;14(6):737-44

Max Planck Institute for Biological Cybernetics, 72076 Tübingen, Germany.

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June 2005

Selective integration of multiple biological data for supervised network inference.

Bioinformatics 2005 May 22;21(10):2488-95. Epub 2005 Feb 22.

Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan.

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http://dx.doi.org/10.1093/bioinformatics/bti339DOI Listing
May 2005

Marginalized kernels for biological sequences.

Bioinformatics 2002 ;18 Suppl 1:S268-75

Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-41-6 Aomi Koto-ku, Tokyo 135-0064, Japan.

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http://dx.doi.org/10.1093/bioinformatics/18.suppl_1.s268DOI Listing
October 2004

Learning kernels from biological networks by maximizing entropy.

Bioinformatics 2004 Aug;20 Suppl 1:i326-33

Max Planck Institute for Biological Cybernetics, Tübingen, Germany.

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http://dx.doi.org/10.1093/bioinformatics/bth906DOI Listing
August 2004

Asymptotic properties of the Fisher kernel.

Neural Comput 2004 Jan;16(1):115-37

Max Planck Institute for Biological Cybernetics, Tübingen, Germany.

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January 2004

Marginalized kernels for RNA sequence data analysis.

Genome Inform 2002 ;13:112-22

Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, 2-41-6 Aomi, Koto-ku, Tokyo 135-0064, Japan.

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November 2003

A new discriminative kernel from probabilistic models.

Neural Comput 2002 Oct;14(10):2397-414

AIST Computational Biology Research Center, Koto-ku, Tokyo, 135-0064, Japan.

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http://dx.doi.org/10.1162/08997660260293274DOI Listing
October 2002