Alexandre Bouchard-Côté

See also: my arXiv pre-prints

2024

autoMALA: Locally adaptive Metropolis-adjusted Langevin algorithm
Miguel Biron-Lattes, Nikola Surjanovic, Saifuddin Syed, Trevor Campbell, Alexandre Bouchard-Côté (2024)
AISTATS (Accepted)
Code ArXiv Bib
Automatic Regenerative Simulation via Non-Reversible Simulated Tempering
Miguel Biron-Lattes, Trevor Campbell, Alexandre Bouchard-Côté (2024)
Journal of the American Statistical Association (Accepted)
Publisher link Code ArXiv Bib
Variance-reduced stochastic optimization for efficient inference of hidden Markov models
Evan Sidrow, Nancy Heckman, Alexandre Bouchard-Côté, Sarah M. E. Fortune, Andrew W. Trites, Marie Auger-Méthé (2024)
Journal of Machine Learning Research (Accepted)
Bib
MCMC-driven learning
Alexandre Bouchard-Côté, Trevor Campbell, Geoff Pleiss, Nikola Surjanovic (2024)
Handbook of Markov Chain Monte Carlo (Accepted)
ArXiv Bib

2023

Cancer phylogenetic tree inference at scale from 1000s of single cell genomes
Sohrab Salehi, Fatemeh Dorri, Kevin Chern, Farhia Kabeer, Nicole Rusk, Tyler Funnell, Marc J Williams, Daniel Lai, Mirela Andronescu, Kieran R. Campbell, Andrew McPherson, Samuel Aparicio, Andrew Roth, Sohrab Shah, Alexandre Bouchard-Côté (2023)
PCI Math Comp Biol 3:1–38
Publisher link Back-up PDF Code Bib
Past, Present, and Future of Software for Bayesian Inference
Erik Štrumbelj, Alexandre Bouchard-Côté, Jukka Corander, Andrew Gelman, Håvard Rue, Lawrence Murray, Henri Pesonen, Martyn Plummer, Aki Vehtari (2023)
Statistical Science 39:46–61
Publisher link Bib
SpatialSort: a Bayesian model for clustering and cell population annotation of spatial proteomics data
Eric Lee,  Kevin Chern,  Michael Nissen,  Xuehai Wang,  IMAXT Consortium,  Chris Huang,  Anita K Gandhi,  Alexandre Bouchard-Côté,  Andrew P Weng,  Andrew Roth (2023)
Bioinformatics 39:i131–i139
Publisher link Back-up PDF Code Data Bib

2022

Blang: Probabilitistic Programming for Combinatorial Spaces
Alexandre Bouchard-Côté, Kevin Chern, Davor Cubranic, Sahand Hosseini, Justin Hume, Matteo Lepur, Zihui Ouyang, Giorgio Sgarbi (2022)
Journal of Statistical Software 103:1–98
Publisher link Slides Code ArXiv Bib
Pseudo-marginal Inference for CTMCs on Infinite Spaces via Monotonic Likelihood Approximations
Miguel Biron-Lattes, Alexandre Bouchard-Côté, Trevor Campbell (2022)
Journal of Computational and Graphical Statistics 32:513–527
Publisher link Supplement Code ArXiv Bib
Accurate determination of CRISPR-mediated gene fitness in transplantable tumours
Peter Eirew, Ciara O'Flanagan, Jerome Ting, Sohrab Salehi, Jazmine Brimhall, Beixi Wang, Justina Biele, Teresa Algara, So Ra Lee, Corey Hoang, Damian Yap, Steven McKinney, Cherie Bates, Esther Kong, Daniel Lai, Sean Beatty, Mirela Andronescu, Elena Zaikova, Tyler Funnell, Nicholas Ceglia, Stephen Chia, Karen Gelmon, Colin Mar, Sohrab Shah, Andrew Roth, Alexandre Bouchard-Côté, Samuel Aparicio (2022)
Nature Communications 13:1–19
Publisher link Supplement Code Data Bib
Parallel Tempering With a Variational Reference
Nikola Surjanovic, Saifuddin Syed, Alexandre Bouchard-Côté, Trevor Campbell (2022)
Advances in Neural Information Processing Systems 36 (NeurIPS) 36:565–577
Publisher link Supplement Code ArXiv Bib

2021

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 (2021)
Annals of Applied Probability 31:2612–2662
Publisher link ArXiv Bib
Parallel Tempering on Optimized Paths
Saifuddin Syed,  Vittorio Romaniello,  Trevor Campbell,  Alexandre Bouchard-Côté (2021)
International Conference on Machine Learning (ICML) 139:10033–10042
Publisher link Slides Supplement Code Errata ArXiv Bib
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
Publisher link Code ArXiv Bib
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 84:321–350
Publisher link Slides Supplement Code Errata ArXiv Bib
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
Publisher link Slides Supplement Code Data Bib
Particle-Gibbs Sampling For Bayesian Feature Allocation Models
Andrew Roth, Alexandre Bouchard-Côté (2021)
Journal of Machine Learning Research 22:1–105
Publisher link Code ArXiv Bib

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
Publisher link Supplement ArXiv Bib

2019

Exponential Ergodicity of the Bouncy Particle Sampler
George Deligiannidis, Alexandre Bouchard-Côté, Arnaud Doucet (2019)
Annals of Statistics 47:1268–1287
Publisher link Back-up PDF Supplement ArXiv Bib
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
Publisher link Bib
An Annealed Sequential Monte Carlo Method for Bayesian Phylogenetics
Liangliang Wang,  Shijia Wang,  Alexandre Bouchard-Côté (2019)
Systematic Biology 69:155–183
Publisher link Back-up PDF Code ArXiv Bib
clonealign: statistical integration of independent single-cell RNA and DNA-seq from human cancers
Kieran Campbell,  et al (2019)
Genome Biology 20:1–12
Publisher link Back-up PDF Code Bib
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
Publisher link Code ArXiv Bib
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
Publisher link Supplement Code ArXiv Bib
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
Publisher link Bib

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
Publisher link Back-up PDF Supplement Code ArXiv Bib
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
Publisher link ArXiv Bib
Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer
Allen Zhang, et al. (2018)
Cell 173:1755–1769
Publisher link Bib
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
Publisher link Bib

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
Publisher link Back-up PDF PDF with browsable notation Code Data Errata ArXiv Bib
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 and Graphical Statistics 26:445–458
Publisher link Back-up PDF Supplement Code ArXiv Bib
A Poissonian model of indel rate variation for phylogenetic tree inference
Yongliang Zhai, Alexandre Bouchard-Côté (2017)
Systematic Biology 66:698–714
Publisher link Back-up PDF Code Bib
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
Publisher link Back-up PDF Supplement Code Bib
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
Publisher link Back-up PDF Supplement Code Bib
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
Publisher link Supplement Code Bib

2016

Unbounded Bayesian optimization via regularization
Bobak Shahriari, Alexandre Bouchard-Côté, Nando de Freitas (2016)
AISTATS 19:1168–1176
Publisher link Back-up PDF ArXiv Bib
Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer
Andrew McPherson, et al. (2016)
Nature Genetics 48:758–767
Publisher link Supplement Bib
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
Publisher link Supplement Code Bib
Inferring history of human populations using single-nucleotide polymorphism
Yongliang Zhai, Alexandre Bouchard-Côté (2016)
Annals of Applied Statistics 10:2047–2074
Publisher link Bib

2015

Atomic spatial processes
Sean Jewell, Neil Spencer, Alexandre Bouchard-Côté (2015)
International Conference on Machine Learning (ICML) 32:248–256
Publisher link Back-up PDF Supplement Bib
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
Publisher link Back-up PDF PDF with browsable notation Supplement Bib
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
Publisher link Back-up PDF Supplement Bib

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
Publisher link Back-up PDF Supplement Code ArXiv Bib
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
Publisher link Supplement Code Bib
Sequential Monte Carlo (SMC) for Bayesian phylogenetics
Alexandre Bouchard-Côté (2014)
Bayesian phylogenetics: methods, algorithms, and applications 163–186
Publisher link Back-up PDF Bib
Memory (and time) efficient sequential Monte Carlo
Seong-Hwan Jun, Alexandre Bouchard-Côté (2014)
International Conference on Machine Learning (ICML) 31:514–522
Publisher link Back-up PDF Supplement Bib

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
Publisher link Back-up PDF Slides Supplement Errata ArXiv Bib
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
Publisher link Back-up PDF Supplement Bib
A note on probabilistic models over strings: the linear algebra approach
Alexandre Bouchard-Côté (2013)
Bulletin of Mathematical Biology 75:2529–2550
Publisher link Back-up PDF ArXiv Bib

2012

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

2011

Priors over recurrent continuous time processes
Ardavan Saeedi, Alexandre Bouchard-Côté (2011)
Advances in Neural Information Processing Systems 24 (NeurIPS) 24:2052–2060
Publisher link Back-up PDF Supplement Code Bib
 Best student paper award

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
Publisher link Back-up PDF Supplement Bib
Variational inference over combinatorial spaces
Alexandre Bouchard-Côté, Michael I. Jordan (2010)
Advances in Neural Information Processing Systems 23 (NeurIPS) 23:280–288
Publisher link Back-up PDF Slides Supplement Bib

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
Publisher link Back-up PDF Slides Bib
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
Publisher link Back-up PDF Slides Poster ArXiv Bib
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
Publisher link Back-up PDF Slides Bib

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
Publisher link Back-up PDF Bib
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
Publisher link Back-up PDF Slides Poster Bib

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
Publisher link Back-up PDF Slides Data Bib
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
Publisher link Back-up PDF Poster Bib

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
Publisher link Back-up PDF Bib

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
Publisher link Back-up PDF Slides Code Bib

Variational inference

Variance-reduced stochastic optimization for efficient inference of hidden Markov models
Evan Sidrow, Nancy Heckman, Alexandre Bouchard-Côté, Sarah M. E. Fortune, Andrew W. Trites, Marie Auger-Méthé (2024)
Journal of Machine Learning Research (Accepted)
Bib
MCMC-driven learning
Alexandre Bouchard-Côté, Trevor Campbell, Geoff Pleiss, Nikola Surjanovic (2024)
Handbook of Markov Chain Monte Carlo (Accepted)
ArXiv Bib
Parallel Tempering With a Variational Reference
Nikola Surjanovic, Saifuddin Syed, Alexandre Bouchard-Côté, Trevor Campbell (2022)
Advances in Neural Information Processing Systems 36 (NeurIPS) 36:565–577
Publisher link Supplement Code ArXiv Bib
Parallel Tempering on Optimized Paths
Saifuddin Syed,  Vittorio Romaniello,  Trevor Campbell,  Alexandre Bouchard-Côté (2021)
International Conference on Machine Learning (ICML) 139:10033–10042
Publisher link Slides Supplement Code Errata ArXiv Bib
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
Publisher link Supplement Code Bib
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
Publisher link Supplement Code Bib
Bayesian pedigree analysis using measure factorization
Alexandre Bouchard-Côté, Bonnie Kirkpatrick (2012)
Advances in Neural Information Processing Systems 25 (NeurIPS) 25:2906–2914
Publisher link Back-up PDF Supplement Bib
Variational inference over combinatorial spaces
Alexandre Bouchard-Côté, Michael I. Jordan (2010)
Advances in Neural Information Processing Systems 23 (NeurIPS) 23:280–288
Publisher link Back-up PDF Slides Supplement Bib
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
Publisher link Back-up PDF Slides Poster ArXiv Bib

Phylogenetics

Cancer phylogenetic tree inference at scale from 1000s of single cell genomes
Sohrab Salehi, Fatemeh Dorri, Kevin Chern, Farhia Kabeer, Nicole Rusk, Tyler Funnell, Marc J Williams, Daniel Lai, Mirela Andronescu, Kieran R. Campbell, Andrew McPherson, Samuel Aparicio, Andrew Roth, Sohrab Shah, Alexandre Bouchard-Côté (2023)
PCI Math Comp Biol 3:1–38
Publisher link Back-up PDF Code Bib
Blang: Probabilitistic Programming for Combinatorial Spaces
Alexandre Bouchard-Côté, Kevin Chern, Davor Cubranic, Sahand Hosseini, Justin Hume, Matteo Lepur, Zihui Ouyang, Giorgio Sgarbi (2022)
Journal of Statistical Software 103:1–98
Publisher link Slides Code ArXiv Bib
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
Publisher link Code ArXiv Bib
An Annealed Sequential Monte Carlo Method for Bayesian Phylogenetics
Liangliang Wang,  Shijia Wang,  Alexandre Bouchard-Côté (2019)
Systematic Biology 69:155–183
Publisher link Back-up PDF Code ArXiv Bib
A Poissonian model of indel rate variation for phylogenetic tree inference
Yongliang Zhai, Alexandre Bouchard-Côté (2017)
Systematic Biology 66:698–714
Publisher link Back-up PDF Code Bib
Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer
Andrew McPherson, et al. (2016)
Nature Genetics 48:758–767
Publisher link Supplement Bib
Inferring history of human populations using single-nucleotide polymorphism
Yongliang Zhai, Alexandre Bouchard-Côté (2016)
Annals of Applied Statistics 10:2047–2074
Publisher link Bib
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
Publisher link Back-up PDF PDF with browsable notation Supplement Bib
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
Publisher link Back-up PDF Supplement Bib
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
Publisher link Back-up PDF Supplement Code ArXiv Bib
Sequential Monte Carlo (SMC) for Bayesian phylogenetics
Alexandre Bouchard-Côté (2014)
Bayesian phylogenetics: methods, algorithms, and applications 163–186
Publisher link Back-up PDF Bib
Evolutionary inference via the Poisson indel process
Alexandre Bouchard-Côté, Michael I. Jordan (2013)
Proceedings of the National Academy of Sciences 110:1160–1166
Publisher link Back-up PDF Slides Supplement Errata ArXiv Bib
A note on probabilistic models over strings: the linear algebra approach
Alexandre Bouchard-Côté (2013)
Bulletin of Mathematical Biology 75:2529–2550
Publisher link Back-up PDF ArXiv Bib
Phylogenetic inference via sequential Monte Carlo
Alexandre Bouchard-Côté, Sriram Sankararaman, Michael I. Jordan (2012)
Systematic Biology 61:579–593
Publisher link Back-up PDF Code Errata Bib
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
Publisher link Back-up PDF Slides Poster Bib

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
Publisher link Back-up PDF Supplement Bib
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
Publisher link Back-up PDF Slides Bib
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
Publisher link Back-up PDF Slides Bib
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
Publisher link Back-up PDF Bib
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
Publisher link Back-up PDF Slides Data Bib
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
Publisher link Back-up PDF Poster Bib
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
Publisher link Back-up PDF Bib

Monte Carlo methods

autoMALA: Locally adaptive Metropolis-adjusted Langevin algorithm
Miguel Biron-Lattes, Nikola Surjanovic, Saifuddin Syed, Trevor Campbell, Alexandre Bouchard-Côté (2024)
AISTATS (Accepted)
Code ArXiv Bib
Automatic Regenerative Simulation via Non-Reversible Simulated Tempering
Miguel Biron-Lattes, Trevor Campbell, Alexandre Bouchard-Côté (2024)
Journal of the American Statistical Association (Accepted)
Publisher link Code ArXiv Bib
MCMC-driven learning
Alexandre Bouchard-Côté, Trevor Campbell, Geoff Pleiss, Nikola Surjanovic (2024)
Handbook of Markov Chain Monte Carlo (Accepted)
ArXiv Bib
Cancer phylogenetic tree inference at scale from 1000s of single cell genomes
Sohrab Salehi, Fatemeh Dorri, Kevin Chern, Farhia Kabeer, Nicole Rusk, Tyler Funnell, Marc J Williams, Daniel Lai, Mirela Andronescu, Kieran R. Campbell, Andrew McPherson, Samuel Aparicio, Andrew Roth, Sohrab Shah, Alexandre Bouchard-Côté (2023)
PCI Math Comp Biol 3:1–38
Publisher link Back-up PDF Code Bib
Past, Present, and Future of Software for Bayesian Inference
Erik Štrumbelj, Alexandre Bouchard-Côté, Jukka Corander, Andrew Gelman, Håvard Rue, Lawrence Murray, Henri Pesonen, Martyn Plummer, Aki Vehtari (2023)
Statistical Science 39:46–61
Publisher link Bib
SpatialSort: a Bayesian model for clustering and cell population annotation of spatial proteomics data
Eric Lee,  Kevin Chern,  Michael Nissen,  Xuehai Wang,  IMAXT Consortium,  Chris Huang,  Anita K Gandhi,  Alexandre Bouchard-Côté,  Andrew P Weng,  Andrew Roth (2023)
Bioinformatics 39:i131–i139
Publisher link Back-up PDF Code Data Bib
Blang: Probabilitistic Programming for Combinatorial Spaces
Alexandre Bouchard-Côté, Kevin Chern, Davor Cubranic, Sahand Hosseini, Justin Hume, Matteo Lepur, Zihui Ouyang, Giorgio Sgarbi (2022)
Journal of Statistical Software 103:1–98
Publisher link Slides Code ArXiv Bib
Pseudo-marginal Inference for CTMCs on Infinite Spaces via Monotonic Likelihood Approximations
Miguel Biron-Lattes, Alexandre Bouchard-Côté, Trevor Campbell (2022)
Journal of Computational and Graphical Statistics 32:513–527
Publisher link Supplement Code ArXiv Bib
Parallel Tempering With a Variational Reference
Nikola Surjanovic, Saifuddin Syed, Alexandre Bouchard-Côté, Trevor Campbell (2022)
Advances in Neural Information Processing Systems 36 (NeurIPS) 36:565–577
Publisher link Supplement Code ArXiv Bib
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 (2021)
Annals of Applied Probability 31:2612–2662
Publisher link ArXiv Bib
Parallel Tempering on Optimized Paths
Saifuddin Syed,  Vittorio Romaniello,  Trevor Campbell,  Alexandre Bouchard-Côté (2021)
International Conference on Machine Learning (ICML) 139:10033–10042
Publisher link Slides Supplement Code Errata ArXiv Bib
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
Publisher link Code ArXiv Bib
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 84:321–350
Publisher link Slides Supplement Code Errata ArXiv Bib
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
Publisher link Slides Supplement Code Data Bib
Particle-Gibbs Sampling For Bayesian Feature Allocation Models
Andrew Roth, Alexandre Bouchard-Côté (2021)
Journal of Machine Learning Research 22:1–105
Publisher link Code ArXiv Bib
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
Publisher link Supplement ArXiv Bib
Exponential Ergodicity of the Bouncy Particle Sampler
George Deligiannidis, Alexandre Bouchard-Côté, Arnaud Doucet (2019)
Annals of Statistics 47:1268–1287
Publisher link Back-up PDF Supplement ArXiv Bib
An Annealed Sequential Monte Carlo Method for Bayesian Phylogenetics
Liangliang Wang,  Shijia Wang,  Alexandre Bouchard-Côté (2019)
Systematic Biology 69:155–183
Publisher link Back-up PDF Code ArXiv Bib
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
Publisher link Supplement Code ArXiv Bib
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
Publisher link Bib
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
Publisher link Back-up PDF Supplement Code ArXiv Bib
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
Publisher link ArXiv Bib
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
Publisher link Back-up PDF PDF with browsable notation Code Data Errata ArXiv Bib
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 and Graphical Statistics 26:445–458
Publisher link Back-up PDF Supplement Code ArXiv Bib
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
Publisher link Back-up PDF Supplement Code Bib
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
Publisher link Back-up PDF PDF with browsable notation Supplement Bib
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
Publisher link Back-up PDF Supplement Bib
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
Publisher link Back-up PDF Supplement Code ArXiv Bib
Sequential Monte Carlo (SMC) for Bayesian phylogenetics
Alexandre Bouchard-Côté (2014)
Bayesian phylogenetics: methods, algorithms, and applications 163–186
Publisher link Back-up PDF Bib
Memory (and time) efficient sequential Monte Carlo
Seong-Hwan Jun, Alexandre Bouchard-Côté (2014)
International Conference on Machine Learning (ICML) 31:514–522
Publisher link Back-up PDF Supplement Bib
Phylogenetic inference via sequential Monte Carlo
Alexandre Bouchard-Côté, Sriram Sankararaman, Michael I. Jordan (2012)
Systematic Biology 61:579–593
Publisher link Back-up PDF Code Errata Bib
Entangled Monte Carlo
Seong-Hwan Jun, Liangliang Wang, Alexandre Bouchard-Côté (2012)
Advances in Neural Information Processing Systems 25 (NeurIPS) 25:2735–2743
Publisher link Back-up PDF Supplement Bib
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
Publisher link Back-up PDF Slides Bib
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
Publisher link Back-up PDF Bib
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
Publisher link Back-up PDF Slides Poster Bib

Evolutionary dynamics and phylogeny of cancer

Cancer phylogenetic tree inference at scale from 1000s of single cell genomes
Sohrab Salehi, Fatemeh Dorri, Kevin Chern, Farhia Kabeer, Nicole Rusk, Tyler Funnell, Marc J Williams, Daniel Lai, Mirela Andronescu, Kieran R. Campbell, Andrew McPherson, Samuel Aparicio, Andrew Roth, Sohrab Shah, Alexandre Bouchard-Côté (2023)
PCI Math Comp Biol 3:1–38
Publisher link Back-up PDF Code Bib
SpatialSort: a Bayesian model for clustering and cell population annotation of spatial proteomics data
Eric Lee,  Kevin Chern,  Michael Nissen,  Xuehai Wang,  IMAXT Consortium,  Chris Huang,  Anita K Gandhi,  Alexandre Bouchard-Côté,  Andrew P Weng,  Andrew Roth (2023)
Bioinformatics 39:i131–i139
Publisher link Back-up PDF Code Data Bib
Accurate determination of CRISPR-mediated gene fitness in transplantable tumours
Peter Eirew, Ciara O'Flanagan, Jerome Ting, Sohrab Salehi, Jazmine Brimhall, Beixi Wang, Justina Biele, Teresa Algara, So Ra Lee, Corey Hoang, Damian Yap, Steven McKinney, Cherie Bates, Esther Kong, Daniel Lai, Sean Beatty, Mirela Andronescu, Elena Zaikova, Tyler Funnell, Nicholas Ceglia, Stephen Chia, Karen Gelmon, Colin Mar, Sohrab Shah, Andrew Roth, Alexandre Bouchard-Côté, Samuel Aparicio (2022)
Nature Communications 13:1–19
Publisher link Supplement Code Data Bib
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
Publisher link Slides Supplement Code Data Bib
clonealign: statistical integration of independent single-cell RNA and DNA-seq from human cancers
Kieran Campbell,  et al (2019)
Genome Biology 20:1–12
Publisher link Back-up PDF Code Bib
Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer
Allen Zhang, et al. (2018)
Cell 173:1755–1769
Publisher link Bib
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
Publisher link Bib
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
Publisher link Back-up PDF Supplement Code Bib
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
Publisher link Supplement Code Bib
Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer
Andrew McPherson, et al. (2016)
Nature Genetics 48:758–767
Publisher link Supplement Bib
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
Publisher link Supplement Code Bib
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
Publisher link Supplement Code Bib

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
Publisher link Back-up PDF Supplement Bib
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
Publisher link Back-up PDF Slides Bib
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
Publisher link Back-up PDF Slides Data Bib
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
Publisher link Back-up PDF Poster Bib

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
Publisher link Code ArXiv Bib
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
Publisher link Supplement ArXiv Bib
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
Publisher link Back-up PDF PDF with browsable notation Code Data Errata ArXiv Bib
Atomic spatial processes
Sean Jewell, Neil Spencer, Alexandre Bouchard-Côté (2015)
International Conference on Machine Learning (ICML) 32:248–256
Publisher link Back-up PDF Supplement Bib
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
Publisher link Supplement Code Bib
Priors over recurrent continuous time processes
Ardavan Saeedi, Alexandre Bouchard-Côté (2011)
Advances in Neural Information Processing Systems 24 (NeurIPS) 24:2052–2060
Publisher link Back-up PDF Supplement Code Bib
 Best student paper award
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
Publisher link Back-up PDF Bib