- Email: bouchard AT stat.ubc.ca
- Assistant Professor in the Department of Statistics at UBC
- Path: McGill -> UCB -> UBC.
- AKA: Alex, Bouchard, or 卜利森. See also: how to typeset my last name.
- Office: ESB, Room 3124

My main field of research is in statistical machine learning. I am interested in the mathematical side of the subject as well as in applications in linguistics and biology.

On the methodology side, I am interested in Monte Carlo methods such as SMC and MCMC, graphical models, non-parametric Bayesian statistics, randomized algorithms, and variational inference.

My favoriate applications, both in linguistics and biology, are related to phylogenetics in one way or another. Some examples of things I have currently/recently been working on: automated reconstruction of proto-languages; cancer phylogenetics; population genetics; pedigrees, tree and alignment inference.

In the past, I also did some work on machine translation, on logical characterization and approximation of labeled Markov processes, and on reinforcement learning.

- Seong-Hwan Jun and Alexandre Bouchard-Côté. (2014)
Implicit Particle Sequential Monte Carlo.
*International Conference on Machine Learning (ICML).*(In Press)

[bib] - Alexandre Bouchard-Côté. (2014)
Sequential Monte Carlo (SMC) for Bayesian phylogenetics.
*Bayesian phylogenetics: methods, algorithms, and applications.*Chen, M.-H., Kuo, L., and Lewis, P. O. (eds.)

[link][bib] - A. Roth, J. Khattra, D. Yap, A. Wan, E. Laks, J. Biele, G. Ha, S. Aparicio, A. Bouchard-Côté, S. Shah. (2014)
PyClone: Statistical inference of clonal population structure in cancer.
*Nature Methods.*10.1038/nmeth.2883

[paper][supplementary material][bib] - Monir Hajiaghayi, Bonnie Kirkpatrick, Liangliang Wang and Alexandre Bouchard-Côté. (2014)
Efficient Continuous-Time Markov Chain Estimation.
*International Conference on Machine Learning (ICML).*(In Press)

[paper][supplementary material][bib] - Alexandre Bouchard-Côté. (2013)
A Note on Probabilistic Models over Strings: The Linear Algebra Approach.
*Bulletin of Mathematical Biology.*75:2529-2550

[paper][bib] - Alexandre Bouchard-Côté, David Hall, Thomas L. Griffiths and Dan Klein. (2013)
Automated reconstruction of ancient languages using probabilistic models of sound change.
*Proceedings of the National Academy of Sciences.*10.1073/pnas.1204678110

[paper][supplementary material][bib] - Alexandre Bouchard-Côté and Michael I. Jordan. (2013)
Evolutionary inference via the Poisson indel process.
*Proceedings of the National Academy of Sciences.*10.1073/pnas.1220450110

[paper][supplementary material][errata][bib] - Seong-Hwan Jun, Liangliang Wang and Alexandre Bouchard-Côté. (2012)
Entangled Monte Carlo.
*Advances in Neural Information Processing Systems 25 (NIPS).*25:2735-2743

[paper][supplementary material][bib] - Alexandre Bouchard-Côté and Bonnie Kirkpatrick. (2012)
Bayesian Pedigree Analysis using Measure Factorization.
*Advances in Neural Information Processing Systems 25 (NIPS).*25:2906-2914

[paper][supplementary material][bib] - Alexandre Bouchard-Côté, Sriram Sankararaman and Michael I. Jordan. (2012)
Phylogenetic Inference via Sequential Monte Carlo.
*Systematic Biology.*61:579-593

[paper][code][bib] - Ardavan Saeedi and Alexandre Bouchard-Côté. (2011)
Priors over Recurrent Continuous Time Processes.
*Advances in Neural Information Processing Systems 24 (NIPS).*24:2052-2060

[paper][supplementary material][code][bib]*Best paper award* - Alexandre Bouchard-Côté and Michael I. Jordan. (2010)
Variational Inference over Combinatorial Spaces.
*Advances in Neural Information Processing Systems 23 (NIPS).*23:280-288

[paper][slides][supplementary material][bib] - Taylor Berg-Kirkpatrick, Alexandre Bouchard-Côté, John DeNero and Dan Klein. (2010)
Painless Unsupervised Learning with Features.
*Proceedings of the North American Chapter of the Association for Computational Linguistics (NAACL10).*8:582-590

[paper][supplementary material][bib] - Alexandre Bouchard-Côté, Slav Petrov and Dan Klein. (2009)
Randomized Pruning: Efficiently Calculating Expectations in Large Dynamic Programs.
*Advances in Neural Information Processing Systems 22 (NIPS).*22:144-152

[paper][slides][bib] - Alexandre Bouchard-Côté and Michael I. Jordan. (2009)
Optimization of Structured Mean Field Objectives.
*Proceedings of the 25th Conference on Uncertainty in Artificial Intelligence (UAI09).*25:67-74

[paper][slides][poster][bib] - Alexandre Bouchard-Côté, Thomas L. Griffiths and Dan Klein. (2009)
Improved Reconstruction of Protolanguage Word Forms.
*Proceedings of the North American Chapter of the Association for Computational Linguistics (NAACL09).*7:65-73

[paper][slides][bib] - Alexandre Bouchard-Côté, Michael I. Jordan and Dan Klein. (2009)
Efficient Inference in Phylogenetic InDel Trees.
*Advances in Neural Information Processing Systems 21 (NIPS).*21:177-184

[paper][slides][poster][bib] - John DeNero, Alexandre Bouchard-Côté and Dan Klein. (2008)
Sampling Alignment Structure under a Bayesian Translation Model.
*Proceedings of the 2008 Conference on Empirical Methods on Natural Language Processing (EMNLP08).*13:314-323

[paper][bib] - Alexandre Bouchard-Côté, Percy Liang, Thomas Griffiths and Dan Klein. (2008)
A Probabilistic Approach to Language Change.
*Advances in Neural Information Processing Systems 20 (NIPS).*

[paper][poster][bib] - Alexandre Bouchard-Côté, Percy Liang, Thomas Griffiths, and Dan Klein. (2007)
A Probabilistic Approach to Diachronic Phonology.
*Proceedings of the 2007 Conference on Empirical Methods on Natural Language Processing (EMNLP07).*12:887-896

[paper][slides][data][bib] - Percy Liang, Alexandre Bouchard-Côté, Dan Klein, and Ben Taskar. (2006)
An End-to-End Discriminative Approach to Machine Translation.
*Proceedings of the 44th Annual Meeting of the Association for Computational Linguistics (ACL06).*21:761-768

[paper][bib] - Alexandre Bouchard-Côté, Norm Ferns, Prakash Panangaden, and Doina Precup. (2005)
An Approximation Algorithm for Labelled Markov Processes: towards Realistic Approximation.
*Proceedings of the International Conference on Quantitative Evaluation of Systems.*2:54-62

[paper][slides][code][bib]

- Fredrik Lindsten, Adam M. Johansen, Christian A. Naesseth, Bonnie Kirkpatrick, Thomas B. Schön, John Aston, and Alexandre Bouchard-Côté. (2014)
Divide-and-Conquer with Sequential Monte Carlo.
*arXiv.*

[paper][bib] - Bobak Shahriari, Ziyu Wang, Matthew W. Hoffman, Alexandre Bouchard-Côté, and Nando de Freitas. (2014)
An Entropy Search Portfolio for Bayesian Optimization.
*arXiv.*

[paper][bib] - Seong-Hwan Jun and Alexandre Bouchard-Côté. (2013)
Using a Stochastic Map View of Sequential Monte Carlo for Memory and Network Efficiency.
*Randomized Algorithm Workshop at Advances in Neural Information Processing Systems 26 (NIPS).*

[bib] - Monir Hajiaghayi, Bonnie Kirkpatrick, Liangliang Wang and Alexandre Bouchard-Côté. (2013)
Efficient Continuous-Time Markov Chain Estimation.
*arXiv.*

[paper][bib] - Alexandre Bouchard-Côté. (2013)
A Note on Probabilistic Models over Strings: Inference and Representation with Indexed Matrices.
*arXiv.*

[paper][bib] - Alexandre Bouchard-Côté and Michael I. Jordan. (2012)
The Poisson Indel Process.
*arXiv.*

[paper][bib] - Liangliang Wang and Alexandre Bouchard-Côté. (2012)
Harnessing Non-Local Evolutionary Events for Tree Inference.
*Society for Molecular Biology and Evolution.*

[bib] - Alexandre Bouchard-Côté and James V. Zidek. (2011)
Discussion: Bayesian priors for loss matching.
*International Statistical Review.*80:83-86

[paper][bib] - Alexandre Bouchard-Côté, Sriram Sankararaman and Michael I. Jordan. (2010)
Bayesian Phylogenetic Inference using Sequential Monte Carlo Algorithms.
*Society for Molecular Biology and Evolution.*

[slides][bib] - Sriram Sankararaman, Alexandre Bouchard-Côté and Michael I. Jordan. (2010)
Joint Probabilistic Modeling of Languages and Genes.
*Society for Molecular Biology and Evolution.*

[bib] - John DeNero and Alexandre Bouchard-Côté. (2009)
A Hierarchical Dirichlet Process Prior for a Conditional Model of Phrase Alignment.
*Workshop on statistical NLP at Advances in Neural Information Processing Systems 21 (NIPS).*

[bib] - Alexandre Bouchard-Côté (2005). Domaines et languages. CUMC 2005. Kingston, Canada.
- Alexandre Bouchard-Côté (2004). Sparse distributed memories: some theoretical and empirical results. Report and presentation for the Courtemanche
Scholarship (first prize).

[slides][report][code] - Alexandre Bouchard-Côté (2004). Reinforcement learning and function approximation. CUMC 2004. Halifax, Canada.

[slides]

- Stat 302, "Intro to probability"
- Stat 547C, "Topics in probability"
- Stat 547Q, "Statistical Modeling with Stochastic Processes, version 2"
- Stat 302, "Introduction to Probability"
- Stat 302, "Intro to probability"
- Stat 547C, "Topics in probability"
- Stat 302, "Introduction to Probability"
- Stat 460/560, "Statistical Theory I"
- Stat 547C, "Topics in probability"
- Stat 302, "Introduction to Probability"
- Stat 547C, "Topics in probability"
- Stat 100, "Statistical Thinking," co-taught with P. Gustafson, C. Riddell, M. Salibian-Barrera, and W. Welch
- Stat 547Q, "Statistical Modeling with Stochastic Processes"

- Notes prepared about LMP approximation,
- A java program that computes the minimal bisimilar system of a given finite LMP,
- Notes on a specialized data structure used by the SDM architecture,
- C++ code (mostly written by Bohdana Ratitch) implementing SDM,
- An AI for the game knockabout.

There are only two accents in my last name, but it's amazing how many mistakes I have seen in these two letters. Here is a guide on how to do it correctly:

- In WYSIWYGs, you can usually just copy and paste: Alexandre Bouchard-Côté
- In Latex: Alexandre Bouchard-C\^ot\'e
- In HTML: Alexandre Bouchard-Côté
- If that does not work, I prefer you just write "Alexandre Bouchard" rather than "Alexandre Bouchard-Cote", or a combination of missing/wrong accents