Alexandre Bouchard-Côté

2017

Particle Gibbs split-merge sampling for Bayesian inference in mixture models
Alexandre Bouchard-Côté, Arnaud Doucet, Andrew Roth (2017)
Journal of Machine Learning Research 18:1–39
Divide-and-conquer with sequential Monte Carlo
Fredrik Lindsten,  Adam M. Johansen,  Christian A. Naesseth,  Bonnie Kirkpatrick,  Thomas B. Schon,  John Aston, Alexandre Bouchard-Côté (2017)
Journal of Computational Statistics and Graphics 26:445–458
A Poissonian model of indel rate variation for phylogenetic tree inference
Yongliang Zhai, Alexandre Bouchard-Côté (2017)
Systematic Biology 66:698–714
The Bouncy Particle Sampler: A non-reversible rejection-free Markov chain Monte Carlo method
Alexandre Bouchard-Côté, Sebastian J. Vollmer, Arnaud Doucet (2017)
Journal of the American Statistical Association (Accepted)
ddClone: joint statistical inference of clonal populations from single-cell and bulk tumor sequencing data
Sohrab Salehi, Adi Steif, Andrew Roth, Samuel Aparicio, Alexandre Bouchard-Côté, Sohrab P. Shah (2017)
Genome Biology 18
Sequential Graph Matching with Sequential Monte Carlo
Seong-Hwan Jun, Samuel W.K. Wong, James V. Zidek, Alexandre Bouchard-Côté (2017)
AISTATS 20:1075–1084
ReMixT: clone-specific genomic structure estimation in cancer
A. McPherson, A. Roth, G. Ha, C. Chauve, A. Steif, C. P. E. de Souza, P. Eirew, A. Bouchard-Côté, S. Aparicio, S. Sahinalp, S. Shah. (2017)
Genome Biology 18

2016

Unbounded Bayesian optimization via regularization
Bobak Shahriari, Alexandre Bouchard-Côté, Nando de Freitas (2016)
AISTATS 19:1168–1176
Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer
Andrew McPherson, et al. (2016)
Nature Genetics 48:758–767
Clonal genotype and population structure inference from single-cell tumor sequencing
A Roth, Andrew McPherson, Emma Laks, Justina Biele, Damian Yap, Adrian Wan, Maia Smith, Cydney Nielsen, Jessica N. McAlpine, Samuel Aparicio, Alexandre Bouchard-Côté, Sohrab P. Shah (2016)
Nature Methods 13:575–576
Inferring history of human populations using single-nucleotide polymorphism
Yongliang Zhai, Alexandre Bouchard-Côté (2016)
Annals of Applied Stat 10:2047–2074

2015

Atomic spatial processes
Sean Jewell, Neil Spencer, Alexandre Bouchard-Côté (2015)
International Conference on Machine Learning (ICML) 32:248–256
Bayesian analysis of continuous time Markov chains with application to phylogenetic modelling
Tingting Zhao, Alex Cumberworth, Ziyu Wang, Joerg Gsponer, Nando de Freitas, Alexandre Bouchard-Côté (2015)
Bayesian Analysis 11:1203–1237
Bayesian phylogenetic inference using the combinatorial sequential Monte Carlo method
Liangliang Wang, Alexandre Bouchard-Côté, Arnaud Doucet (2015)
Journal of the American Statistical Association 110:1362–1374

2014

Efficient continuous-time Markov chain estimation
Monir Hajiaghayi, Bonnie Kirkpatrick, Liangliang Wang, Alexandre Bouchard-Côté (2014)
International Conference on Machine Learning (ICML) 31:638–646
PyClone: statistical inference of clonal population structure in cancer
A Roth, J. Khattra, D. Yap, A. Wan, E. Laks, J. Biele, G. Ha, S. Aparicio, A. Bouchard-Côté, S. Shah (2014)
Nature Methods 11:396–398
Sequential Monte Carlo (SMC) for Bayesian phylogenetics
Alexandre Bouchard-Côté (2014)
Bayesian phylogenetics: methods, algorithms, and applications 163–186
Memory (and time) efficient sequential Monte Carlo
Seong-Hwan Jun, Alexandre Bouchard-Côté (2014)
International Conference on Machine Learning (ICML) 31:514–522

2013

Evolutionary inference via the Poisson indel process
Alexandre Bouchard-Côté, Michael I. Jordan (2013)
Proceedings of the National Academy of Sciences 110:1160–1166
Automated reconstruction of ancient languages using probabilistic models of sound change
Alexandre Bouchard-Côté, David Hall, Thomas L. Griffiths, Dan Klein (2013)
Proceedings of the National Academy of Sciences 110:4224–4229
A note on probabilistic models over strings: the linear algebra approach
Alexandre Bouchard-Côté (2013)
Bulletin of Mathematical Biology 75:2529–2550

2012

Phylogenetic inference via sequential Monte Carlo
Alexandre Bouchard-Côté, Sriram Sankararaman, Michael I. Jordan (2012)
Systematic Biology 61:579–593
Bayesian pedigree analysis using measure factorization
Alexandre Bouchard-Côté, Bonnie Kirkpatrick (2012)
Advances in Neural Information Processing Systems 25 (NIPS) 25:2906–2914
Entangled Monte Carlo
Seong-Hwan Jun, Liangliang Wang, Alexandre Bouchard-Côté (2012)
Advances in Neural Information Processing Systems 25 (NIPS) 25:2735–2743

2011

Priors over recurrent continuous time processes
Ardavan Saeedi, Alexandre Bouchard-Côté (2011)
Advances in Neural Information Processing Systems 24 (NIPS) 24:2052–2060

2010

Painless unsupervised learning with features
Taylor Berg-Kirkpatrick, Alexandre Bouchard-Côté, John DeNero, Dan Klein (2010)
Proceedings of the North American Chapter of the Association for Computational Linguistics (NAACL10) 8:582–590
Variational inference over combinatorial spaces
Alexandre Bouchard-Côté, Michael I. Jordan (2010)
Advances in Neural Information Processing Systems 23 (NIPS) 23:280–288

2009

Improved reconstruction of protolanguage word forms
Alexandre Bouchard-Côté, Thomas L. Griffiths, Dan Klein (2009)
Proceedings of the North American Chapter of the Association for Computational Linguistics (NAACL09) 7:65–73
Optimization of structured mean field objectives
Alexandre Bouchard-Côté, Michael I. Jordan (2009)
Proceedings of the 25th Conference on Uncertainty in Artificial Intelligence (UAI09) 25:67–74
Randomized pruning: efficiently calculating expectations in large dynamic programs
Alexandre Bouchard-Côté, Slav Petrov, Dan Klein (2009)
Advances in Neural Information Processing Systems 22 (NIPS) 22:144–152

2008

Sampling alignment structure under a Bayesian translation model
John DeNero, Alexandre Bouchard-Côté, Dan Klein (2008)
Proceedings of the 2008 Conference on Empirical Methods on Natural Language Processing (EMNLP08) 13:314–323
Efficient inference in phylogenetic InDel trees
Alexandre Bouchard-Côté, Michael I. Jordan, Dan Klein (2008)
Advances in Neural Information Processing Systems 21 (NIPS) 21:177–184

2007

A probabilistic approach to diachronic phonology
Alexandre Bouchard-Côté, Percy Liang, Thomas Griffiths, Dan Klein (2007)
Proceedings of the 2007 Conference on Empirical Methods on Natural Language Processing (EMNLP07) 12:887–896
A probabilistic approach to language change
Alexandre Bouchard-Côté, Percy Liang, Thomas Griffiths, Dan Klein (2007)
Advances in Neural Information Processing Systems 20 (NIPS) 20

2006

An end-to-end discriminative approach to machine translation
Percy Liang, Alexandre Bouchard-Côté, Dan Klein, Ben Taskar (2006)
Proceedings of the 44th Annual Meeting of the Association for Computational Linguistics (ACL06) 21:761–768

2005

An approximation algorithm for labelled Markov processes: towards realistic approximation
Alexandre Bouchard-Côté, Norm Ferns, Prakash Panangaden, Doina Precup (2005)
Proceedings of the International Conference on Quantitative Evaluation of Systems 2:54–62

Variational inference

ReMixT: clone-specific genomic structure estimation in cancer
A. McPherson, A. Roth, G. Ha, C. Chauve, A. Steif, C. P. E. de Souza, P. Eirew, A. Bouchard-Côté, S. Aparicio, S. Sahinalp, S. Shah. (2017)
Genome Biology 18
Clonal genotype and population structure inference from single-cell tumor sequencing
A Roth, Andrew McPherson, Emma Laks, Justina Biele, Damian Yap, Adrian Wan, Maia Smith, Cydney Nielsen, Jessica N. McAlpine, Samuel Aparicio, Alexandre Bouchard-Côté, Sohrab P. Shah (2016)
Nature Methods 13:575–576
Bayesian pedigree analysis using measure factorization
Alexandre Bouchard-Côté, Bonnie Kirkpatrick (2012)
Advances in Neural Information Processing Systems 25 (NIPS) 25:2906–2914
Variational inference over combinatorial spaces
Alexandre Bouchard-Côté, Michael I. Jordan (2010)
Advances in Neural Information Processing Systems 23 (NIPS) 23:280–288
Optimization of structured mean field objectives
Alexandre Bouchard-Côté, Michael I. Jordan (2009)
Proceedings of the 25th Conference on Uncertainty in Artificial Intelligence (UAI09) 25:67–74

Phylogenetics

A Poissonian model of indel rate variation for phylogenetic tree inference
Yongliang Zhai, Alexandre Bouchard-Côté (2017)
Systematic Biology 66:698–714
Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer
Andrew McPherson, et al. (2016)
Nature Genetics 48:758–767
Inferring history of human populations using single-nucleotide polymorphism
Yongliang Zhai, Alexandre Bouchard-Côté (2016)
Annals of Applied Stat 10:2047–2074
Bayesian analysis of continuous time Markov chains with application to phylogenetic modelling
Tingting Zhao, Alex Cumberworth, Ziyu Wang, Joerg Gsponer, Nando de Freitas, Alexandre Bouchard-Côté (2015)
Bayesian Analysis 11:1203–1237
Bayesian phylogenetic inference using the combinatorial sequential Monte Carlo method
Liangliang Wang, Alexandre Bouchard-Côté, Arnaud Doucet (2015)
Journal of the American Statistical Association 110:1362–1374
Efficient continuous-time Markov chain estimation
Monir Hajiaghayi, Bonnie Kirkpatrick, Liangliang Wang, Alexandre Bouchard-Côté (2014)
International Conference on Machine Learning (ICML) 31:638–646
Sequential Monte Carlo (SMC) for Bayesian phylogenetics
Alexandre Bouchard-Côté (2014)
Bayesian phylogenetics: methods, algorithms, and applications 163–186
Evolutionary inference via the Poisson indel process
Alexandre Bouchard-Côté, Michael I. Jordan (2013)
Proceedings of the National Academy of Sciences 110:1160–1166
A note on probabilistic models over strings: the linear algebra approach
Alexandre Bouchard-Côté (2013)
Bulletin of Mathematical Biology 75:2529–2550
Phylogenetic inference via sequential Monte Carlo
Alexandre Bouchard-Côté, Sriram Sankararaman, Michael I. Jordan (2012)
Systematic Biology 61:579–593
Efficient inference in phylogenetic InDel trees
Alexandre Bouchard-Côté, Michael I. Jordan, Dan Klein (2008)
Advances in Neural Information Processing Systems 21 (NIPS) 21:177–184

Natural language processing

Painless unsupervised learning with features
Taylor Berg-Kirkpatrick, Alexandre Bouchard-Côté, John DeNero, Dan Klein (2010)
Proceedings of the North American Chapter of the Association for Computational Linguistics (NAACL10) 8:582–590
Improved reconstruction of protolanguage word forms
Alexandre Bouchard-Côté, Thomas L. Griffiths, Dan Klein (2009)
Proceedings of the North American Chapter of the Association for Computational Linguistics (NAACL09) 7:65–73
Randomized pruning: efficiently calculating expectations in large dynamic programs
Alexandre Bouchard-Côté, Slav Petrov, Dan Klein (2009)
Advances in Neural Information Processing Systems 22 (NIPS) 22:144–152
Sampling alignment structure under a Bayesian translation model
John DeNero, Alexandre Bouchard-Côté, Dan Klein (2008)
Proceedings of the 2008 Conference on Empirical Methods on Natural Language Processing (EMNLP08) 13:314–323
A probabilistic approach to diachronic phonology
Alexandre Bouchard-Côté, Percy Liang, Thomas Griffiths, Dan Klein (2007)
Proceedings of the 2007 Conference on Empirical Methods on Natural Language Processing (EMNLP07) 12:887–896
A probabilistic approach to language change
Alexandre Bouchard-Côté, Percy Liang, Thomas Griffiths, Dan Klein (2007)
Advances in Neural Information Processing Systems 20 (NIPS) 20
An end-to-end discriminative approach to machine translation
Percy Liang, Alexandre Bouchard-Côté, Dan Klein, Ben Taskar (2006)
Proceedings of the 44th Annual Meeting of the Association for Computational Linguistics (ACL06) 21:761–768

Monte Carlo methods

Particle Gibbs split-merge sampling for Bayesian inference in mixture models
Alexandre Bouchard-Côté, Arnaud Doucet, Andrew Roth (2017)
Journal of Machine Learning Research 18:1–39
Divide-and-conquer with sequential Monte Carlo
Fredrik Lindsten,  Adam M. Johansen,  Christian A. Naesseth,  Bonnie Kirkpatrick,  Thomas B. Schon,  John Aston, Alexandre Bouchard-Côté (2017)
Journal of Computational Statistics and Graphics 26:445–458
The Bouncy Particle Sampler: A non-reversible rejection-free Markov chain Monte Carlo method
Alexandre Bouchard-Côté, Sebastian J. Vollmer, Arnaud Doucet (2017)
Journal of the American Statistical Association (Accepted)
Sequential Graph Matching with Sequential Monte Carlo
Seong-Hwan Jun, Samuel W.K. Wong, James V. Zidek, Alexandre Bouchard-Côté (2017)
AISTATS 20:1075–1084
Bayesian analysis of continuous time Markov chains with application to phylogenetic modelling
Tingting Zhao, Alex Cumberworth, Ziyu Wang, Joerg Gsponer, Nando de Freitas, Alexandre Bouchard-Côté (2015)
Bayesian Analysis 11:1203–1237
Bayesian phylogenetic inference using the combinatorial sequential Monte Carlo method
Liangliang Wang, Alexandre Bouchard-Côté, Arnaud Doucet (2015)
Journal of the American Statistical Association 110:1362–1374
Efficient continuous-time Markov chain estimation
Monir Hajiaghayi, Bonnie Kirkpatrick, Liangliang Wang, Alexandre Bouchard-Côté (2014)
International Conference on Machine Learning (ICML) 31:638–646
Sequential Monte Carlo (SMC) for Bayesian phylogenetics
Alexandre Bouchard-Côté (2014)
Bayesian phylogenetics: methods, algorithms, and applications 163–186
Memory (and time) efficient sequential Monte Carlo
Seong-Hwan Jun, Alexandre Bouchard-Côté (2014)
International Conference on Machine Learning (ICML) 31:514–522
Phylogenetic inference via sequential Monte Carlo
Alexandre Bouchard-Côté, Sriram Sankararaman, Michael I. Jordan (2012)
Systematic Biology 61:579–593
Entangled Monte Carlo
Seong-Hwan Jun, Liangliang Wang, Alexandre Bouchard-Côté (2012)
Advances in Neural Information Processing Systems 25 (NIPS) 25:2735–2743
Randomized pruning: efficiently calculating expectations in large dynamic programs
Alexandre Bouchard-Côté, Slav Petrov, Dan Klein (2009)
Advances in Neural Information Processing Systems 22 (NIPS) 22:144–152
Sampling alignment structure under a Bayesian translation model
John DeNero, Alexandre Bouchard-Côté, Dan Klein (2008)
Proceedings of the 2008 Conference on Empirical Methods on Natural Language Processing (EMNLP08) 13:314–323
Efficient inference in phylogenetic InDel trees
Alexandre Bouchard-Côté, Michael I. Jordan, Dan Klein (2008)
Advances in Neural Information Processing Systems 21 (NIPS) 21:177–184

Evolutionary dynamics and phylogeny of cancer

ddClone: joint statistical inference of clonal populations from single-cell and bulk tumor sequencing data
Sohrab Salehi, Adi Steif, Andrew Roth, Samuel Aparicio, Alexandre Bouchard-Côté, Sohrab P. Shah (2017)
Genome Biology 18
ReMixT: clone-specific genomic structure estimation in cancer
A. McPherson, A. Roth, G. Ha, C. Chauve, A. Steif, C. P. E. de Souza, P. Eirew, A. Bouchard-Côté, S. Aparicio, S. Sahinalp, S. Shah. (2017)
Genome Biology 18
Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer
Andrew McPherson, et al. (2016)
Nature Genetics 48:758–767
Clonal genotype and population structure inference from single-cell tumor sequencing
A Roth, Andrew McPherson, Emma Laks, Justina Biele, Damian Yap, Adrian Wan, Maia Smith, Cydney Nielsen, Jessica N. McAlpine, Samuel Aparicio, Alexandre Bouchard-Côté, Sohrab P. Shah (2016)
Nature Methods 13:575–576
PyClone: statistical inference of clonal population structure in cancer
A Roth, J. Khattra, D. Yap, A. Wan, E. Laks, J. Biele, G. Ha, S. Aparicio, A. Bouchard-Côté, S. Shah (2014)
Nature Methods 11:396–398

Computational historical linguistics

Automated reconstruction of ancient languages using probabilistic models of sound change
Alexandre Bouchard-Côté, David Hall, Thomas L. Griffiths, Dan Klein (2013)
Proceedings of the National Academy of Sciences 110:4224–4229
Improved reconstruction of protolanguage word forms
Alexandre Bouchard-Côté, Thomas L. Griffiths, Dan Klein (2009)
Proceedings of the North American Chapter of the Association for Computational Linguistics (NAACL09) 7:65–73
A probabilistic approach to diachronic phonology
Alexandre Bouchard-Côté, Percy Liang, Thomas Griffiths, Dan Klein (2007)
Proceedings of the 2007 Conference on Empirical Methods on Natural Language Processing (EMNLP07) 12:887–896
A probabilistic approach to language change
Alexandre Bouchard-Côté, Percy Liang, Thomas Griffiths, Dan Klein (2007)
Advances in Neural Information Processing Systems 20 (NIPS) 20

Bayesian non-parametric statistics

Particle Gibbs split-merge sampling for Bayesian inference in mixture models
Alexandre Bouchard-Côté, Arnaud Doucet, Andrew Roth (2017)
Journal of Machine Learning Research 18:1–39
Atomic spatial processes
Sean Jewell, Neil Spencer, Alexandre Bouchard-Côté (2015)
International Conference on Machine Learning (ICML) 32:248–256
PyClone: statistical inference of clonal population structure in cancer
A Roth, J. Khattra, D. Yap, A. Wan, E. Laks, J. Biele, G. Ha, S. Aparicio, A. Bouchard-Côté, S. Shah (2014)
Nature Methods 11:396–398
Priors over recurrent continuous time processes
Ardavan Saeedi, Alexandre Bouchard-Côté (2011)
Advances in Neural Information Processing Systems 24 (NIPS) 24:2052–2060
Sampling alignment structure under a Bayesian translation model
John DeNero, Alexandre Bouchard-Côté, Dan Klein (2008)
Proceedings of the 2008 Conference on Empirical Methods on Natural Language Processing (EMNLP08) 13:314–323