Alexandre Bouchard-Côté

See also: my arXiv pre-prints

2021

Blang: Probabilitistic Programming for Combinatorial Spaces
Alexandre Bouchard-Côté, Kevin Chern, Davor Cubranic, Sahand Hosseini, Justin Hume, Matteo Lepur, Zihui Ouyang, Giorgio Sgarbi (2021)
Journal of Statistical Software (Accepted)
Parallel Tempering on Optimized Paths
Saifuddin Syed,  Vittorio Romaniello,  Trevor Campbell,  Alexandre Bouchard-Côté (2021)
International Conference on Machine Learning (ICML) (Accepted)
Analysis of high-dimensional Continuous Time Markov Chains using the Local Bouncy Particle Sampler
Tingting Zhao, Alexandre Bouchard-Côté (2021)
Journal of Machine Learning Research 22:1–41
Non-Reversible Parallel Tempering: a Scalable Highly Parallel MCMC Scheme
Saifuddin Syed,  Alexandre Bouchard-Côté,  George Deligiannidis,  Arnaud Doucet (2021)
Journal of Royal Statistical Society, Series B (Accepted)
Clonal fitness inferred from time-series modelling of single-cell cancer genomes
Sohrab Salehi, Farhia Kabeer, Nicholas Ceglia, Mirela Andronescu, Marc J. Williams, Kieran R. Campbell, Tehmina Masud, Beixi Wang, Justina Biele, Jazmine Brimhall, David Gee, Hakwoo Lee, Jerome Ting, Allen W. Zhang, Hoa Tran, Ciara O’Flanagan, Fatemeh Dorri, Nicole Rusk, Teresa Ruiz de Algara, So Ra Lee, Brian Yu Chieh Cheng, Peter Eirew, Takako Kono, Jenifer Pham, Diljot Grewal, Daniel Lai, Richard Moore, Andrew J. Mungall, Marco A. Marra, IMAXT Consortium, Andrew McPherson, Alexandre Bouchard-Côté, Samuel Aparicio, Sohrab P. Shah (2021)
Nature 595:585–590
Particle-Gibbs Sampling For Bayesian Feature Allocation Models
Andrew Roth, Alexandre Bouchard-Côté (2021)
Journal of Machine Learning Research 22:1–105

2020

Slice Sampling for General Completely Random Measures
Peiyuan Zhu, Alexandre Bouchard-Côté, Trevor Campbell (2020)
Proceedings of the 36th Conference on Uncertainty in Artificial Intelligence (UAI) 36:699–708
Randomized Hamiltonian Monte Carlo as Scaling Limit of the Bouncy Particle Sampler and Dimension-Free Convergence Rates
George Deligiannidis, Daniel Paulin, Alexandre Bouchard-Côté, Arnaud Doucet (2020)
Annals of Applied Probability (Accepted)

2019

Exponential Ergodicity of the Bouncy Particle Sampler
George Deligiannidis, Alexandre Bouchard-Côté, Arnaud Doucet (2019)
Annals of Statistics 47:1268–1287
A new perspective on the benefits of the gene-environment independence in case-control studies
Hao Luo, Gabriela V. Cohen Freue, Xin Zhao, Alexandre Bouchard-Côté, Igor Burstyn, Paul Gustafson (2019)
The Canadian Journal of Statistics 47:473–486
An Annealed Sequential Monte Carlo Method for Bayesian Phylogenetics
Liangliang Wang,  Shijia Wang,  Alexandre Bouchard-Côté (2019)
Systematic Biology 69:155–183
clonealign: statistical integration of independent single-cell RNA and DNA-seq from human cancers
Kieran Campbell,  et al (2019)
Genome Biology 20:1–12
Sequential decision model for inference and prediction on non-uniform hypergraphs with application to knot matching from computational forestry
Seong-Hwan Jun, Samuel W.K. Wong, James V. Zidek, Alexandre Bouchard-Côté (2019)
Annals of Applied Statistics 13:1678–1707
Scalable Metropolis-Hastings for Exact Bayesian Inference with Large Datasets
Robert Cornish, Paul Vanetti, Alexandre Bouchard-Côté, George Deligiannidis, Arnaud Doucet (2019)
International Conference on Machine Learning (ICML) 97:1351–1360
Efficient Parameter Estimation for DNA Kinetics Modeled as Continuous-Time Markov Chains
Sedigheh Zolaktaf, Frits Dannenberg, Erik Winfree, Alexandre Bouchard-Côté, Mark Schmidt, Anne Condon (2019)
The 25th International Conference on DNA Computing and Molecular Programming 25:80–99

2018

The Bouncy Particle Sampler: A non-reversible rejection-free Markov chain Monte Carlo method
Alexandre Bouchard-Côté, Sebastian J. Vollmer, Arnaud Doucet (2018)
Journal of the American Statistical Association 113:855–867
Piecewise Deterministic Markov Processes for Scalable Monte Carlo on Restricted Domains
Joris Bierkens, Alexandre Bouchard-Côté, Arnaud Doucet, Andrew B Duncan, Paul Fearnhead, Thibaut Lienart, Gareth Roberts, Sebastian J Vollmer (2018)
Statistics and Probability Letters 136:148–154
Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer
Allen Zhang, et al. (2018)
Cell 173:1755–1769
MuClone: somatic mutation detection and classification through probabilistic integration of clonal population information
Fatemeh Dorri, Sean Jewell, Alexandre Bouchard-Côté, Sohrab Shah (2018)
Communications Biology  2:1–10

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
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 Statistics 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 (NeurIPS) 25:2906–2914
Entangled Monte Carlo
Seong-Hwan Jun, Liangliang Wang, Alexandre Bouchard-Côté (2012)
Advances in Neural Information Processing Systems 25 (NeurIPS) 25:2735–2743

2011

Priors over recurrent continuous time processes
Ardavan Saeedi, Alexandre Bouchard-Côté (2011)
Advances in Neural Information Processing Systems 24 (NeurIPS) 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 (NeurIPS) 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 (NeurIPS) 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 (NeurIPS) 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 (NeurIPS) 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

Parallel Tempering on Optimized Paths
Saifuddin Syed,  Vittorio Romaniello,  Trevor Campbell,  Alexandre Bouchard-Côté (2021)
International Conference on Machine Learning (ICML) (Accepted)
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 (NeurIPS) 25:2906–2914
Variational inference over combinatorial spaces
Alexandre Bouchard-Côté, Michael I. Jordan (2010)
Advances in Neural Information Processing Systems 23 (NeurIPS) 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

Blang: Probabilitistic Programming for Combinatorial Spaces
Alexandre Bouchard-Côté, Kevin Chern, Davor Cubranic, Sahand Hosseini, Justin Hume, Matteo Lepur, Zihui Ouyang, Giorgio Sgarbi (2021)
Journal of Statistical Software (Accepted)
Analysis of high-dimensional Continuous Time Markov Chains using the Local Bouncy Particle Sampler
Tingting Zhao, Alexandre Bouchard-Côté (2021)
Journal of Machine Learning Research 22:1–41
An Annealed Sequential Monte Carlo Method for Bayesian Phylogenetics
Liangliang Wang,  Shijia Wang,  Alexandre Bouchard-Côté (2019)
Systematic Biology 69:155–183
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 Statistics 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 (NeurIPS) 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 (NeurIPS) 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 (NeurIPS) 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

Blang: Probabilitistic Programming for Combinatorial Spaces
Alexandre Bouchard-Côté, Kevin Chern, Davor Cubranic, Sahand Hosseini, Justin Hume, Matteo Lepur, Zihui Ouyang, Giorgio Sgarbi (2021)
Journal of Statistical Software (Accepted)
Parallel Tempering on Optimized Paths
Saifuddin Syed,  Vittorio Romaniello,  Trevor Campbell,  Alexandre Bouchard-Côté (2021)
International Conference on Machine Learning (ICML) (Accepted)
Analysis of high-dimensional Continuous Time Markov Chains using the Local Bouncy Particle Sampler
Tingting Zhao, Alexandre Bouchard-Côté (2021)
Journal of Machine Learning Research 22:1–41
Non-Reversible Parallel Tempering: a Scalable Highly Parallel MCMC Scheme
Saifuddin Syed,  Alexandre Bouchard-Côté,  George Deligiannidis,  Arnaud Doucet (2021)
Journal of Royal Statistical Society, Series B (Accepted)
Clonal fitness inferred from time-series modelling of single-cell cancer genomes
Sohrab Salehi, Farhia Kabeer, Nicholas Ceglia, Mirela Andronescu, Marc J. Williams, Kieran R. Campbell, Tehmina Masud, Beixi Wang, Justina Biele, Jazmine Brimhall, David Gee, Hakwoo Lee, Jerome Ting, Allen W. Zhang, Hoa Tran, Ciara O’Flanagan, Fatemeh Dorri, Nicole Rusk, Teresa Ruiz de Algara, So Ra Lee, Brian Yu Chieh Cheng, Peter Eirew, Takako Kono, Jenifer Pham, Diljot Grewal, Daniel Lai, Richard Moore, Andrew J. Mungall, Marco A. Marra, IMAXT Consortium, Andrew McPherson, Alexandre Bouchard-Côté, Samuel Aparicio, Sohrab P. Shah (2021)
Nature 595:585–590
Particle-Gibbs Sampling For Bayesian Feature Allocation Models
Andrew Roth, Alexandre Bouchard-Côté (2021)
Journal of Machine Learning Research 22:1–105
Slice Sampling for General Completely Random Measures
Peiyuan Zhu, Alexandre Bouchard-Côté, Trevor Campbell (2020)
Proceedings of the 36th Conference on Uncertainty in Artificial Intelligence (UAI) 36:699–708
Randomized Hamiltonian Monte Carlo as Scaling Limit of the Bouncy Particle Sampler and Dimension-Free Convergence Rates
George Deligiannidis, Daniel Paulin, Alexandre Bouchard-Côté, Arnaud Doucet (2020)
Annals of Applied Probability (Accepted)
Exponential Ergodicity of the Bouncy Particle Sampler
George Deligiannidis, Alexandre Bouchard-Côté, Arnaud Doucet (2019)
Annals of Statistics 47:1268–1287
An Annealed Sequential Monte Carlo Method for Bayesian Phylogenetics
Liangliang Wang,  Shijia Wang,  Alexandre Bouchard-Côté (2019)
Systematic Biology 69:155–183
Scalable Metropolis-Hastings for Exact Bayesian Inference with Large Datasets
Robert Cornish, Paul Vanetti, Alexandre Bouchard-Côté, George Deligiannidis, Arnaud Doucet (2019)
International Conference on Machine Learning (ICML) 97:1351–1360
Efficient Parameter Estimation for DNA Kinetics Modeled as Continuous-Time Markov Chains
Sedigheh Zolaktaf, Frits Dannenberg, Erik Winfree, Alexandre Bouchard-Côté, Mark Schmidt, Anne Condon (2019)
The 25th International Conference on DNA Computing and Molecular Programming 25:80–99
The Bouncy Particle Sampler: A non-reversible rejection-free Markov chain Monte Carlo method
Alexandre Bouchard-Côté, Sebastian J. Vollmer, Arnaud Doucet (2018)
Journal of the American Statistical Association 113:855–867
Piecewise Deterministic Markov Processes for Scalable Monte Carlo on Restricted Domains
Joris Bierkens, Alexandre Bouchard-Côté, Arnaud Doucet, Andrew B Duncan, Paul Fearnhead, Thibaut Lienart, Gareth Roberts, Sebastian J Vollmer (2018)
Statistics and Probability Letters 136:148–154
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
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 (NeurIPS) 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 (NeurIPS) 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 (NeurIPS) 21:177–184

Evolutionary dynamics and phylogeny of cancer

Clonal fitness inferred from time-series modelling of single-cell cancer genomes
Sohrab Salehi, Farhia Kabeer, Nicholas Ceglia, Mirela Andronescu, Marc J. Williams, Kieran R. Campbell, Tehmina Masud, Beixi Wang, Justina Biele, Jazmine Brimhall, David Gee, Hakwoo Lee, Jerome Ting, Allen W. Zhang, Hoa Tran, Ciara O’Flanagan, Fatemeh Dorri, Nicole Rusk, Teresa Ruiz de Algara, So Ra Lee, Brian Yu Chieh Cheng, Peter Eirew, Takako Kono, Jenifer Pham, Diljot Grewal, Daniel Lai, Richard Moore, Andrew J. Mungall, Marco A. Marra, IMAXT Consortium, Andrew McPherson, Alexandre Bouchard-Côté, Samuel Aparicio, Sohrab P. Shah (2021)
Nature 595:585–590
clonealign: statistical integration of independent single-cell RNA and DNA-seq from human cancers
Kieran Campbell,  et al (2019)
Genome Biology 20:1–12
Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer
Allen Zhang, et al. (2018)
Cell 173:1755–1769
MuClone: somatic mutation detection and classification through probabilistic integration of clonal population information
Fatemeh Dorri, Sean Jewell, Alexandre Bouchard-Côté, Sohrab Shah (2018)
Communications Biology  2:1–10
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 (NeurIPS) 20

Bayesian non-parametric statistics

Particle-Gibbs Sampling For Bayesian Feature Allocation Models
Andrew Roth, Alexandre Bouchard-Côté (2021)
Journal of Machine Learning Research 22:1–105
Slice Sampling for General Completely Random Measures
Peiyuan Zhu, Alexandre Bouchard-Côté, Trevor Campbell (2020)
Proceedings of the 36th Conference on Uncertainty in Artificial Intelligence (UAI) 36:699–708
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 (NeurIPS) 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