My lab is recruiting masters and PhD students who are interested in working on new machine learning algorithms based on convex and discrete optimization – if you are interested in joining my lab please email me your CV and a cover letter.
- 2018-present: Assistant Professor, Northern Arizona University, School of Informatics, Computing, and Cyber Systems.
- 2014-2018: Postdoc, McGill University, Human Genetics Department, with Guillaume Bourque.
- 2013: Postdoc, Tokyo Institute of Technology, Computer Science Department, with Masashi Sugiyama.
- 2009-2012: PhD student, Ecole Normale Superieure de Cachan, Computer Science Department, with Francis Bach and Jean-Philippe Vert.
- 2008-2009: Masters student, Université Paris 6, Statistics Department, with Mathieu Gautier and Jean-Louis Foulley.
- 2006-2008: research assistant at Sangamo BioSciences.
- 2002-2006: undergraduate, UC Berkeley, Double major in Molecular & Cell Biology and Statistics, with Terry Speed.
- Full CV
Research interests: fast and accurate algorithms for convex optimization (clustering, regression, ranking, classification) and discrete optimization (changepoint detection, dynamic programming). The main application domain for the algorithms I develop are in genomic data analysis (DNA copy number, ChIP-seq, etc); other applications include neuroscience, audio, internet, sensors, recommendation and ranking systems.
I think reproducible research is important, so in addition to every paper I write, I also provide
- A reference implementation of the algorithm(s) described in the paper, typically as an R package.
- Source code for doing the analyses and creating the figures, typically in a GitHub repo.
If you want to send me encrypted/signed messages, you can use my GPG key (fingerprint 1D46 6295 2738 32E6 F70B 9F64 45B0 8611 CDB1 FA96).
My ORCID is 0000-0002-3146-0865.
|Nov 12, 2019||Our paper about Machine Learning Algorithms for Simultaneous Supervised Detection of Peaks in Multiple Samples and Cell Types is accepted for publication in the proceedings of the 2020 Pacific Symposium on Biocomputing.|
|Jul 19, 2019||At useR 2019, I gave a talk about the fast algorithm for optimal peak detection implemented in the PeakSegDisk R package, slides, video.|
|Feb 27, 2019||Our paper about Fast nonconvex deconvolution of calcium imaging data has been published in Biostatistics.|
|Oct 30, 2018||Our paper about Meta-mining of copy number profiles of high-risk neuroblastoma tumors has been published in Scientific Data.|
|Sep 16, 2018||Our paper about a supervised machine learning method for predicting pathogenicity of genetic variants has been accepted in the American Journal of Human Genetics.|