Alexandre Bouchard-Côté

STAT 548 (qualifying exam)


This academic year, I will supervise papers during second term only. I will probably add a few more papers on new MCMC/SMC methodological developments around December.
Please come talk to me if you are interested in one of these papers. I will give you a more precise description of what I expect in the report. I will supervise two in the first semester, and possibly one for the second semester.

Suggested papers


Variational inference

Reparameterizing the Birkhoff Polytope for Variational Permutation Inference
Scott Linderman, Gonzalo Mena, Hal Cooper, Liam Paninski, John Cunningham (2018)
AISTATS
Variational Rejection Sampling
Aditya Grover, Ramki Gummadi, Miguel Lazaro-Gredilla, Dale Schuurmans, Stefano Ermon (2018)
AISTATS

Phylogenetics

Phylogenetic Factor Analysis
Tolkoff MR, Alfaro ME, Baele G, Lemey P, Suchard MA (2018)
Syst Biol.
Integrative inference of subclonal tumour evolution from single-cell and bulk sequencing data
Salem Malikic, Katharina Jahn, Jack Kuipers, Cenk Sahinalp, Niko Beerenwinkel (2017)
Infectious Disease Dynamics Inferred from Genetic Data via Sequential Monte Carlo
R.A. Smith, E.L. Ionides, A.A. King (2017)
A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera
Fredrik Ronquist, Seraina Klopfstein, Lars Vilhelmsen, Susanne Schulmeister, Debra L. Murray, Alexandr P. Rasnitsyn (2012)
Syst Biol.

Monte Carlo methods

Schrodinger Bridge Samplers
Espen Bernton, Jeremy Heng, Arnaud Doucet, Pierre E Jacob (2020)
Variational Rejection Sampling
Aditya Grover, Ramki Gummadi, Miguel Lazaro-Gredilla, Dale Schuurmans, Stefano Ermon (2018)
AISTATS
Scalable Importance Tempering and Bayesian Variable Selection
Giacomo Zanella, Gareth O. Roberts (2018)
Tree-based Particle Smoothing Algorithms in a Hidden Markov Model
Dong Ding, Axel Gandy (2018)
The sample size required in importance sampling
Sourav Chatterjee and Persi Diaconis (2018)
Ann. Appl. Probab.
Unbiased Hamiltonian Monte Carlo with couplings
Jeremy Heng, Pierre E. Jacob (2017)
Infectious Disease Dynamics Inferred from Genetic Data via Sequential Monte Carlo
R.A. Smith, E.L. Ionides, A.A. King (2017)
Control functionals for Monte Carlo integration
Chris J. Oates, Mark Girolami, Nicolas Chopin (2016)

Evolutionary dynamics and phylogeny of cancer

Integrative inference of subclonal tumour evolution from single-cell and bulk sequencing data
Salem Malikic, Katharina Jahn, Jack Kuipers, Cenk Sahinalp, Niko Beerenwinkel (2017)

Bayesian statistics

Better together? Statistical learning in models made of modules
Pierre E. Jacob, Lawrence M. Murray, Chris C. Holmes, Christian P. Robert (2017)
Infectious Disease Dynamics Inferred from Genetic Data via Sequential Monte Carlo
R.A. Smith, E.L. Ionides, A.A. King (2017)
Nonparametric Bayesian sparse factor models with application to gene expression modeling
David Knowles, Zoubin Ghahramani (2011)