Pairwise alignment incorporating dipeptide covariation

Motivation: Standard algorithms for pairwise protein sequence alignment make the simplifying assumption that amino acid substitutions at neighboring sites are uncorrelated. This assumption allows implementation of fast algorithms for pairwise sequence alignment, but it ignores information that could conceivably increase the power of remote homolog detection. We examine the validity of this assumption by constructing extended substitution matrixes that encapsulate the observed correlations between neighboring sites, by developing an efficient and rigorous algorithm for pairwise protein sequence alignment that incorporates these local substitution correlations, and by assessing the ability of this algorithm to detect remote homologies. Results: Our analysis indicates that local correlations between substitutions are not strong on the average. Furthermore, incorporating local substitution correlations into pairwise alignment did not lead to a statistically significant improvement in remote homology detection. Therefore, the standard assumption that individual residues within protein sequences evolve independently of neighboring positions appears to be an efficient and appropriate approximation

Conditional Random Field Autoencoders for Unsupervised Structured Prediction

We introduce a framework for unsupervised learning of structured predictors with overlapping, global features. Each input's latent representation is predicted conditional on the observable data using a feature-rich conditional random field. Then a reconstruction of the input is (re)generated, conditional on the latent structure, using models for which maximum likelihood estimation has a closed-form. Our autoencoder formulation enables efficient learning without making unrealistic independence assumptions or restricting the kinds of features that can be used. We illustrate insightful connections to traditional autoencoders, posterior regularization and multi-view learning. We show competitive results with instantiations of the model for two canonical NLP tasks: part-of-speech induction and bitext word alignment, and show that training our model can be substantially more efficient than comparable feature-rich baselines

Accelerated Parallel Non-conjugate Sampling for Bayesian Non-parametric Models

Inference of latent feature models in the Bayesian nonparametric setting is generally difficult, especially in high dimensional settings, because it usually requires proposing features from some prior distribution. In special cases, where the integration is tractable, we could sample new feature assignments according to a predictive likelihood. However, this still may not be efficient in high dimensions. We present a novel method to accelerate the mixing of latent variable model inference by proposing feature locations from the data, as opposed to the prior. First, we introduce our accelerated feature proposal mechanism that we will show is a valid Bayesian inference algorithm and next we propose an approximate inference strategy to perform accelerated inference in parallel. This sampling method is efficient for proper mixing of the Markov chain Monte Carlo sampler, computationally attractive, and is theoretically guaranteed to converge to the posterior distribution as its limiting distribution.Comment: Previously known as "Accelerated Inference for Latent Variable Models

Hybrid modeling, HMM/NN architectures, and protein applications

We describe a hybrid modeling approach where the parameters of a model are calculated and modulated by another model, typically a neural network (NN), to avoid both overfitting and underfitting. We develop the approach for the case of Hidden Markov Models (HMMs), by deriving a class of hybrid HMM/NN architectures. These architectures can be trained with unified algorithms that blend HMM dynamic programming with NN backpropagation. In the case of complex data, mixtures of HMMs or modulated HMMs must be used. NNs can then be applied both to the parameters of each single HMM, and to the switching or modulation of the models, as a function of input or context. Hybrid HMM/NN architectures provide a flexible NN parameterization for the control of model structure and complexity. At the same time, they can capture distributions that, in practice, are inaccessible to single HMMs. The HMM/NN hybrid approach is tested, in its simplest form, by constructing a model of the immunoglobulin protein family. A hybrid model is trained, and a multiple alignment derived, with less than a fourth of the number of parameters used with previous single HMMs

Topic modeling-based domain adaptation for system combination

This paper gives the system description of the domain adaptation team of Dublin City University for our participation in the system combination task in the Second Workshop on Applying Machine Learning Techniques to Optimise the Division of Labour in Hybrid MT (ML4HMT-12). We used the results of unsupervised document classification as meta information to the system combination module. For the Spanish-English data, our strategy achieved 26.33 BLEU points, 0.33 BLEU points absolute improvement over the standard confusion-network-based system combination. This was the best score in terms of BLEU among six participants in ML4HMT-12