Developing and applying heterogeneous phylogenetic models with XRate

Modeling sequence evolution on phylogenetic trees is a useful technique in computational biology. Especially powerful are models which take account of the heterogeneous nature of sequence evolution according to the "grammar" of the encoded gene features. However, beyond a modest level of model complexity, manual coding of models becomes prohibitively labor-intensive. We demonstrate, via a set of case studies, the new built-in model-prototyping capabilities of XRate (macros and Scheme extensions). These features allow rapid implementation of phylogenetic models which would have previously been far more labor-intensive. XRate's new capabilities for lineage-specific models, ancestral sequence reconstruction, and improved annotation output are also discussed. XRate's flexible model-specification capabilities and computational efficiency make it well-suited to developing and prototyping phylogenetic grammar models. XRate is available as part of the DART software package: http://biowiki.org/DART .Comment: 34 pages, 3 figures, glossary of XRate model terminolog

Modeling Dependencies in Natural Languages with Latent Variables

In this thesis, we investigate the use of latent variables to model complex dependencies in natural languages. Traditional models, which have a fixed parameterization, often make strong independence assumptions that lead to poor performance. This problem is often addressed by incorporating additional dependencies into the model (e.g., using higher order N-grams for language modeling). These added dependencies can increase data sparsity and/or require expert knowledge, together with trial and error, in order to identify and incorporate the most important dependencies (as in lexicalized parsing models). Traditional models, when developed for a particular genre, domain, or language, are also often difficult to adapt to another. In contrast, previous work has shown that latent variable models, which automatically learn dependencies in a data-driven way, are able to flexibly adjust the number of parameters based on the type and the amount of training data available. We have created several different types of latent variable models for a diverse set of natural language processing applications, including novel models for part-of-speech tagging, language modeling, and machine translation, and an improved model for parsing. These models perform significantly better than traditional models. We have also created and evaluated three different methods for improving the performance of latent variable models. While these methods can be applied to any of our applications, we focus our experiments on parsing. The first method involves self-training, i.e., we train models using a combination of gold standard training data and a large amount of automatically labeled training data. We conclude from a series of experiments that the latent variable models benefit much more from self-training than conventional models, apparently due to their flexibility to adjust their model parameterization to learn more accurate models from the additional automatically labeled training data. The second method takes advantage of the variability among latent variable models to combine multiple models for enhanced performance. We investigate several different training protocols to combine self-training with model combination. We conclude that these two techniques are complementary to each other and can be effectively combined to train very high quality parsing models. The third method replaces the generative multinomial lexical model of latent variable grammars with a feature-rich log-linear lexical model to provide a principled solution to address data sparsity, handle out-of-vocabulary words, and exploit overlapping features during model induction. We conclude from experiments that the resulting grammars are able to effectively parse three different languages. This work contributes to natural language processing by creating flexible and effective latent variable models for several different languages. Our investigation of self-training, model combination, and log-linear models also provides insights into the effective application of these machine learning techniques to other disciplines

A tree does not make a well-formed sentence: Improving syntactic string-to-tree statistical machine translation with more linguistic knowledge

AbstractSynchronous context-free grammars (SCFGs) can be learned from parallel texts that are annotated with target-side syntax, and can produce translations by building target-side syntactic trees from source strings. Ideally, producing syntactic trees would entail that the translation is grammatically well-formed, but in reality, this is often not the case. Focusing on translation into German, we discuss various ways in which string-to-tree translation models over- or undergeneralise. We show how these problems can be addressed by choosing a suitable parser and modifying its output, by introducing linguistic constraints that enforce morphological agreement and constrain subcategorisation, and by modelling the productive generation of German compounds

A Formal Model of Ambiguity and its Applications in Machine Translation

Systems that process natural language must cope with and resolve ambiguity. In this dissertation, a model of language processing is advocated in which multiple inputs and multiple analyses of inputs are considered concurrently and a single analysis is only a last resort. Compared to conventional models, this approach can be understood as replacing single-element inputs and outputs with weighted sets of inputs and outputs. Although processing components must deal with sets (rather than individual elements), constraints are imposed on the elements of these sets, and the representations from existing models may be reused. However, to deal efficiently with large (or infinite) sets, compact representations of sets that share structure between elements, such as weighted finite-state transducers and synchronous context-free grammars, are necessary. These representations and algorithms for manipulating them are discussed in depth in depth. To establish the effectiveness and tractability of the proposed processing model, it is applied to several problems in machine translation. Starting with spoken language translation, it is shown that translating a set of transcription hypotheses yields better translations compared to a baseline in which a single (1-best) transcription hypothesis is selected and then translated, independent of the translation model formalism used. More subtle forms of ambiguity that arise even in text-only translation (such as decisions conventionally made during system development about how to preprocess text) are then discussed, and it is shown that the ambiguity-preserving paradigm can be employed in these cases as well, again leading to improved translation quality. A model for supervised learning that learns from training data where sets (rather than single elements) of correct labels are provided for each training instance and use it to learn a model of compound word segmentation is also introduced, which is used as a preprocessing step in machine translation

Getting Past the Language Gap: Innovations in Machine Translation

In this chapter, we will be reviewing state of the art machine translation systems, and will discuss innovative methods for machine translation, highlighting the most promising techniques and applications. Machine translation (MT) has benefited from a revitalization in the last 10 years or so, after a period of relatively slow activity. In 2005 the field received a jumpstart when a powerful complete experimental package for building MT systems from scratch became freely available as a result of the unified efforts of the MOSES international consortium. Around the same time, hierarchical methods had been introduced by Chinese researchers, which allowed the introduction and use of syntactic information in translation modeling. Furthermore, the advances in the related field of computational linguistics, making off-the-shelf taggers and parsers readily available, helped give MT an additional boost. Yet there is still more progress to be made. For example, MT will be enhanced greatly when both syntax and semantics are on board: this still presents a major challenge though many advanced research groups are currently pursuing ways to meet this challenge head-on. The next generation of MT will consist of a collection of hybrid systems. It also augurs well for the mobile environment, as we look forward to more advanced and improved technologies that enable the working of Speech-To-Speech machine translation on hand-held devices, i.e. speech recognition and speech synthesis. We review all of these developments and point out in the final section some of the most promising research avenues for the future of MT

Improving Compositional Generalization with Latent Structure and Data Augmentation

Generic unstructured neural networks have been shown to struggle on out-of-distribution compositional generalization. Compositional data augmentation via example recombination has transferred some prior knowledge about compositionality to such black-box neural models for several semantic parsing tasks, but this often required task-specific engineering or provided limited gains. We present a more powerful data recombination method using a model called Compositional Structure Learner (CSL). CSL is a generative model with a quasi-synchronous context-free grammar backbone, which we induce from the training data. We sample recombined examples from CSL and add them to the fine-tuning data of a pre-trained sequence-to-sequence model (T5). This procedure effectively transfers most of CSL's compositional bias to T5 for diagnostic tasks, and results in a model even stronger than a T5-CSL ensemble on two real world compositional generalization tasks. This results in new state-of-the-art performance for these challenging semantic parsing tasks requiring generalization to both natural language variation and novel compositions of elements.Comment: NAACL 202

Latent-Variable Synchronous CFGs for Hierarchical Translation

Data-driven refinement of non-terminal categories has been demonstrated to be a reliable technique for improving mono-lingual parsing with PCFGs. In this pa-per, we extend these techniques to learn latent refinements of single-category syn-chronous grammars, so as to improve translation performance. We compare two estimators for this latent-variable model: one based on EM and the other is a spec-tral algorithm based on the method of mo-ments. We evaluate their performance on a Chinese–English translation task. The re-sults indicate that we can achieve signifi-cant gains over the baseline with both ap-proaches, but in particular the moments-based estimator is both faster and performs better than EM.