Publications by Alexandre Bouchard-Côté
2014
. Efficient continuous-time Markov chain estimation. In International Conference on Machine Learning (ICML). 2014. pp. 638–646.
. Divide-and-Conquer with Sequential Monte Carlo. arXiv. 2014; 1406.4993.
. PyClone: statistical inference of clonal population structure in cancer. Nature Methods. 2014; 11: 396–398.
. An Entropy Search Portfolio for Bayesian Optimization. arXiv. 2014; 1406.4625.
. Sequential Monte Carlo (SMC) for Bayesian phylogenetics. In: . Bayesian phylogenetics: methods, algorithms, and applications. 2014. pp. 163–186.
. Memory (and time) efficient sequential Monte Carlo. In International Conference on Machine Learning (ICML). 2014. pp. 514–522.
2013
. Efficient Continuous-Time Markov Chain Estimation. arXiv. 2013; 1309.325.
. A Stochastic Map View of Sequential Monte Carlo with Applications to Memory and Network Efficiency. In Randomized Algorithm Workshop at Advances in Neural Information Processing Systems 26 (NIPS). 2013.
. Evolutionary inference via the Poisson indel process. Proceedings of the National Academy of Sciences. 2013; 110: 1160–1166.
. Automated reconstruction of ancient languages using probabilistic models of sound change. Proceedings of the National Academy of Sciences. 2013; 110: 4224–4229.
. A Note on Probabilistic Models over Strings: Inference and Representation with Indexed Matrices. arXiv. 2013; 1301.5054.
. A note on probabilistic models over strings: the linear algebra approach. Bulletin of Mathematical Biology. 2013; 75: 2529–2550.
. A Note on Probabilistic Models over Strings: Inference and Representation with Indexed Matrices. arXiv. 2013; 1301.5054.
2012
. Phylogenetic inference via sequential Monte Carlo. Systematic Biology. 2012; 61: 579–593.
. Bayesian pedigree analysis using measure factorization. In Advances in Neural Information Processing Systems 25 (NIPS). 2012. pp. 2906–2914.
. Entangled Monte Carlo. In Advances in Neural Information Processing Systems 25 (NIPS). 2012. pp. 2735–2743.
. The Poisson Indel Process. arXiv. 2012; 1207.6327.
. Harnessing Non-Local Evolutionary Events for Tree Inference. In Society for Molecular Biology and Evolution. 2012.
2011
. Priors over recurrent continuous time processes. In Advances in Neural Information Processing Systems 24 (NIPS). 2011. pp. 2052–2060.
. Discussion: Bayesian priors for loss matching. International Statistical Review. 2011; 80: 83–86.
2010
. Painless unsupervised learning with features. In Proceedings of the North American Chapter of the Association for Computational Linguistics (NAACL10). 2010. pp. 582–590.
. Variational inference over combinatorial spaces. In Advances in Neural Information Processing Systems 23 (NIPS). 2010. pp. 280–288.
. Bayesian Phylogenetic Inference using Sequential Monte Carlo Algorithms. In Society for Molecular Biology and Evolution. 2010.
. Probabilistic Models of Evolution and Language Change. UC Berkeley; 2010.
. Joint Probabilistic Modeling of Languages and Genes. In Society for Molecular Biology and Evolution. 2010.
2009
. Improved reconstruction of protolanguage word forms. In Proceedings of the North American Chapter of the Association for Computational Linguistics (NAACL09). 2009. pp. 65–73.
. Optimization of structured mean field objectives. In Proceedings of the 25th Conference on Uncertainty in Artificial Intelligence (UAI09). 2009. pp. 67–74.
. Randomized pruning: efficiently calculating expectations in large dynamic programs. In Advances in Neural Information Processing Systems 22 (NIPS). 2009. pp. 144–152.
. A Hierarchical Dirichlet Process Prior for a Conditional Model of Phrase Alignment. In Workshop on statistical NLP at Advances in Neural Information Processing Systems 21 (NIPS). 2009.
2008
. Sampling alignment structure under a Bayesian translation model. In Proceedings of the 2008 Conference on Empirical Methods on Natural Language Processing (EMNLP08). 2008. pp. 314–323.
. Efficient inference in phylogenetic InDel trees. In Advances in Neural Information Processing Systems 21 (NIPS). 2008. pp. 177–184.
2007
. A probabilistic approach to diachronic phonology. In Proceedings of the 2007 Conference on Empirical Methods on Natural Language Processing (EMNLP07). 2007. pp. 887–896.
. A probabilistic approach to language change. In Advances in Neural Information Processing Systems 20 (NIPS). 2007.
2006
. An end-to-end discriminative approach to machine translation. In Proceedings of the 44th Annual Meeting of the Association for Computational Linguistics (ACL06). 2006. pp. 761–768.
2005
. An approximation algorithm for labelled Markov processes: towards realistic approximation. In Proceedings of the International Conference on Quantitative Evaluation of Systems. 2005. pp. 54–62.