toby eating okonomiyaki TbDyHo, atomic elements 65, 66, 67 Toby Dylan Hocking
Sugiyama laboratory
Tokyo Institute of Technology
2-12-1-W8E-74 O-okayama, Meguro-ku
Tokyo, 152-8552, Japan.

I worked in Masashi Sugiyama's machine learning laboratory from Jan 2013 to Nov 2013, but now this page will no longer be updated

My 3 main research projects this year were

My short CV/résumé is a 1-page PDF and my list of publications is in BibTeX.

My principal research interests are

Publications, talks, posters [RSS feed]

papers/2013-10-10-Support-vector-comparison-machines/description.html Support vector comparison machines, Oct 2013. [4 pages source] [7 pages with some black and white figures source] [poster source] [code] [2d viz varying sample size source] [2d viz varying proportion of equality pairs source] [3d viz]
papers/2013-08-06-Learning-to-rank-and-compare-graph-layouts/description.html Learning to rank and compare graph layouts. [source] Talk for MLAB Sapporo 6 Aug 2013.
papers/2013-04-12-SegAnnDB-interactive-genomic-segmentation/description.html SegAnnDB: interactive genomic data segmentation on the web. Talk for Sugiyama lab 12 April 2013, McGill 2 July 2013, IRCM 3 July 2013, BRI 5 July 2013, CBRC 18 Sept 2013. [slides] [handout] [source] [screencasts] [installation]
papers/2012-12-03-Code-for-calculating-error-with-respect-to-latent-breakpoints/description.html An R package for calculating the breakpointError model selection function, which compares latent and guessed breakpoints. Work related to chapter 4 of my PHD, Dec 2012. [R-Forge]
papers/2012-11-30-SegAnnot-for-segmentation-of-annotated-piecewise-constant-signals/description.html SegAnnot: an R package for fast segmentation of annotated piecewise constant signals. [HAL tech report Nov 2012] [local copy] [source] [R-Forge project]
papers/2012-11-20-PhD-thesis/description.html Learning algorithms and statistical software, with applications to bioinformatics. PhD defense 20 November 2012. [order a copy printed in color and bound like a book for US$50] [slides] [224MB source]
papers/2012-10-12-Learning-penalties-for-change-point-detection/description.html Learning penalties for change-point detection using max-margin interval regression. Accepted for ICML 2013 and Invited talk in Rennes 12 Oct 2012, Angers 15 Oct 2012, Lille 25 Oct 2012, Google New York Dec 2012, Uganda 28 Mar 2013, Kyushu Tech 12 Apr 2013, Nagoya Tech 9 May 2013, Kyoto 11 June 2013. [70MB demo source] [2-page handout source] [Digiteo poster source 64MB built] [ICML poster]
papers/2012-06-20-Advances-in-Neuroblastoma-Research-poster/description.html A map of genomic copy number alterations in neuroblastoma based on annotation-guided breakpoint detection. [source] Poster for Advances in Neuroblastoma Research, Toronto, Canada, 20 June 2012.
papers/2012-03-28-Recent-advances-in-direct-labeled-graphics/description.html Recent advances in direct labeled graphics. [source] Invited talk for semin-r, the Paris R user group (2012).
papers/2012-01-27-Breakpoint-annotation-model-smoothing/description.html Hocking TD, Schleiermacher G, Janoueix-Lerosey I, Boeva V, Cappo J, Delattre O, Bach F, Vert J-P. Learning smoothing models of copy number profiles using breakpoint annotations. BMC Bioinformatics 2013, 14:164. [14-page HAL preprint] [Python annotation GUI] [Model training R code] [Annotated neuroblastoma copy number data] [Invited talks in 2012: Evry, May 10 Mines, June 14 McGill, June 26 source]
papers/2011-08-16-directlabels-and-regular-expressions-for-useR-2011/description.html Adding direct labels to plots, which was awarded Best Student Poster, [source] and Fast, named capture regular expressions in R 2.14, a 5-minute lightning talk, [source] at useR 2011.
papers/2011-06-09-R-package-development-presentations-for-IBL/description.html Collaborative R package development using R-Forge and updated Sustainable R package development using documentation generation. [source] Invited talks for a seminar on bioinformatics at the Institut de Biologie de Lille, 9 June 2011.
papers/2011-05-01-clusterpath/description.html Hocking TD, Joulin A, Bach F and Vert J-P. Clusterpath: An Algorithm for Clustering using Convex Fusion Penalties. In proceedings of the 28th International Conference on Machine Learning (2011). [8 page conference paper] [HAL preprint] [ICML poster] [Digiteo poster] [slides] [video] [L1/L2 solvers in R local copy] [L∞ solver in MATLAB] [source]
papers/2010-10-21-inlinedocs-presentation-for-Paris-seminR/description.html Sustainable package development using documentation generation. Invited talk for semin-r, the Paris R user group (2010).
papers/2010-08-10-Bayesian-graphical-models-for-studying-evolution-plos-paper/description.html Gautier M, Hocking TD, Foulley J-L. A Bayesian Outlier Criterion to Detect SNPs under Selection in Large Data Sets, PLoS ONE 5(8). Work related to my masters thesis (2010).
papers/2009-10-15-lattice-direct-labels/description.html Visualizing multivariate data using lattice and direct labels. Invited talk for semin-r, the Paris R user group (2009).
papers/2009-09-30-Masters-thesis-on-Bayesian-graphical-models-for-studying-evolution/description.html Identifying genetic loci under selective pressure using a hierarchical Bayesian model with a posterior predictive p-value classifier. Masters thesis for Pierre and Marie Curie University, with advisors Mathieu Gautier and Jean-Louis Foulley of INRA Jouy-en-Josas (2009).
papers/2009-07-15-sublogo-dendrograms/description.html Sublogo dendrograms: visualizing correlation in biological sequence motifs. Poster for useR! 2009.
papers/2008-06-29-Targeted-genome-editing-using-zinc-finger-nucleases-for-HIV-resistance/description.html Perez et al. Establishment of HIV-1 resistance in CD4+ T cells by genome editing using zinc-finger nucleases. Nature Biotechnology 26, 808 - 816 (2008). I did the analysis of the evolution of the HIV V3 loop after the cells were treated with ZFNs, resulting in Supplementary Figures 4c and 4d.
papers/2008-06-29-Heritable-targeted-gene-disruption-in-zebrafish-using-zinc-finger-nucleases/description.html Doyon Y, McCammon JM, Miller JC, Faraji F, Ngo C, Katibah GE, Amora R, Hocking TD, Zhang L, Rebar EJ, Gregory PD, Urnov FD, Amacher SL. Heritable targeted gene disruption in zebrafish using designed zinc-finger nucleases, Nature Biotechnology, 26, 702-708 (2008). I did the experiments that characterized the DNA-binding specificity of the ZFNs used for the knock-outs, described in Supplementary Figure 11.
papers/2006-06-01-Undergrad-thesis-on-chromosomal-copy-number-analysis-using-SNP-arrays/description.html Chromosomal copy number analysis using SNP microarrays: an extension of RLMM with a binomial test statistic. Undergraduate thesis at UC Berkeley with advisor Terry Speed (2006).



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