Model-based analyses of natural selection often categorize sites into a relatively small number of site classes. Forcing each site to belong to one of these classes places unrealistic constraints on the distribution of selection parameters, which can result in misleading inference due to model misspecification. We present an approximate hierarchical Bayesian method using a Markov chain Monte Carlo (MCMC) routine that ensures robustness against model misspecification by averaging over a large number of predefined site classes. This leaves the distribution of selection parameters essentially unconstrained, and also allows sites experiencing positive and purifying selection to be identified orders of magnitude faster than by existing methods. We demonstrate that popular random effects likelihood methods can produce misleading results when sites assigned to the same site class experience different levels of positive or purifying selection--an unavoidable scenario when using a small number of site classes. Our Fast Unconstrained Bayesian AppRoximation (FUBAR) is unaffected by this problem, while achieving higher power than existing unconstrained (fixed effects likelihood) methods. The speed advantage of FUBAR allows us to analyze larger data sets than other methods: We illustrate this on a large influenza hemagglutinin data set (3,142 sequences). FUBAR is available as a batch file within the latest HyPhy distribution (http://www.hyphy.org), as well as on the Datamonkey web server (http://www.datamonkey.org/).

Rhetorical structure trees have been shown to be useful for several document-level tasks including summarization and document classification. Previous approaches to RST parsing have used discriminative models; however, these are less sample efficient than generative models, and RST parsing datasets are typically small. In this paper, we present the first generative model for RST parsing. Our model is a document-level RNN grammar (RNNG) with a bottom-up traversal order. We show that, for our parser's traversal order, previous beam search algorithms for RNNGs have a left-branching bias which is ill-suited for RST parsing. We develop a novel beam search algorithm that keeps track of both structureand word-generating actions without exhibiting this branching bias and results in absolute improvements of 6.8 and 2.9 on unlabelled and labelled F1 over previous algorithms. Overall, our generative model outperforms a discriminative model with the same features by 2.6 F1 points and achieves performance comparable to the state-of-the-art, outperforming all published parsers from a recent replication study that do not use additional training data. ✠ JUSTIFY Acme Inc. has closed several widget factories. | ATTRIBUTION The CEO told investors they were no longer profitable.

We learn a mapping that negates adjectives by predicting an adjective's antonym in an arbitrary word embedding model. We show that both linear models and neural networks improve on this task when they have access to a vector representing the semantic domain of the input word, e.g. a centroid of temperature words when predicting the antonym of 'cold'. We introduce a continuous class-conditional bilinear neural network which is able to negate adjectives with high precision.

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