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We present a perceptron-style discriminative approach to machine translation in which large feature sets can be exploited. Unlike discriminative rerank-ing approaches, our system can take advantage of learned features in all stages of decoding. We first discuss several challenges to error-driven discrim-inative approaches. In particular, we explore(More)
We show how features can easily be added to standard generative models for unsuper-vised learning, without requiring complex new training methods. In particular, each component multinomial of a generative model can be turned into a miniature logistic regression model if feature locality permits. The intuitive EM algorithm still applies, but with a(More)
We describe the first tractable Gibbs sampling procedure for estimating phrase pair frequencies under a probabilistic model of phrase alignment. We propose and evaluate two nonparametric priors that successfully avoid the degenerate behavior noted in previous work, where overly large phrases memorize the training data. Phrase table weights learned under our(More)
We introduce PyClone, a statistical model for inference of clonal population structures in cancers. PyClone is a Bayesian clustering method for grouping sets of deeply sequenced somatic mutations into putative clonal clusters while estimating their cellular prevalences and accounting for allelic imbalances introduced by segmental copy-number changes and(More)
Bayesian inference provides an appealing general framework for phylogenetic analysis, able to incorporate a wide variety of modeling assumptions and to provide a coherent treatment of uncertainty. Existing computational approaches to bayesian inference based on Markov chain Monte Carlo (MCMC) have not, however, kept pace with the scale of the data analysis(More)
We present a probabilistic model of di-achronic phonology in which individual word forms undergo stochastic edits along the branches of a phylogenetic tree. Our approach allows us to achieve three goals with a single unified model: (1) reconstruction of both ancient and modern word forms, (2) discovery of general phonological changes, and (3) selection(More)
In intractable, undirected graphical models, an intuitive way of creating structured mean field approximations is to select an acyclic tractable subgraph. We show that the hardness of computing the objective function and gradient of the mean field objective qualitatively depends on a simple graph property. If the tractable subgraph has this property— we(More)
We present an unsupervised approach to reconstructing ancient word forms. The present work addresses three limitations of previous work. First, previous work focused on faith-fulness features, which model changes between successive languages. We add marked-ness features, which model well-formedness within each language. Second, we introduce universal(More)
We address the problem of the joint statistical inference of phylogenetic trees and multiple sequence alignments from unaligned molecular sequences. This problem is generally formulated in terms of string-valued evolutionary processes along the branches of a phylogenetic tree. The classic evolutionary process, the TKF91 model [Thorne JL, Kishino H,(More)
One of the oldest problems in linguistics is reconstructing the words that appeared in the protolanguages from which modern languages evolved. Identifying the forms of these ancient languages makes it possible to evaluate proposals about the nature of language change and to draw inferences about human history. Protolanguages are typically reconstructed(More)