Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

Background: Phylogenetic reconstruction is a necessary first step in many analyses which use whole genome sequence data from bacterial populations. There are many available methods to infer phylogenies, and these have various advantages and disadvantages, but few unbiased comparisons of the range of approaches have been made. Methods: We simulated data from a defined "true tree" using a realistic evolutionary model. We built phylogenies from this data using a range of methods, and compared reconstructed trees to the true tree using two measures, noting the computational time needed for different phylogenetic reconstructions. We also used real data from Streptococcus pneumoniae alignments to compare individual core gene trees to a core genome tree. Results: We found that, as expected, maximum likelihood trees from good quality alignments were the most accurate, but also the most computationally intensive. Using less accurate phylogenetic reconstruction methods, we were able to obtain results of comparable accuracy; we found that approximate results can rapidly be obtained using genetic distance based methods. In real data we found that highly conserved core genes, such as those involved in translation, gave an inaccurate tree topology, whereas genes involved in recombination events gave inaccurate branch lengths. We also show a tree-of-trees, relating the results of different phylogenetic reconstructions to each other. Conclusions: We recommend three approaches, depending on requirements for accuracy and computational time. Quicker approaches that do not perform full maximum likelihood optimisation may be useful for many analyses requiring a phylogeny, as generating a high quality input alignment is likely to be the major limiting factor of accurate tree topology. We have publicly released our simulated data and code to enable further comparisons

Joint morphological-lexical language modeling for processing morphologically rich languages with application to dialectal Arabic

Language modeling for an inflected language such as Arabic poses new challenges for speech recognition and machine translation due to its rich morphology. Rich morphology results in large increases in out-of-vocabulary (OOV) rate and poor language model parameter estimation in the absence of large quantities of data. In this study, we present a joint morphological-lexical language model (JMLLM) that takes advantage of Arabic morphology. JMLLM combines morphological segments with the underlying lexical items and additional available information sources with regards to morphological segments and lexical items in a single joint model. Joint representation and modeling of morphological and lexical items reduces the OOV rate and provides smooth probability estimates while keeping the predictive power of whole words. Speech recognition and machine translation experiments in dialectal-Arabic show improvements over word and morpheme based trigram language models. We also show that as the tightness of integration between different information sources increases, both speech recognition and machine translation performances improve

A Survey of Word Reordering in Statistical Machine Translation: Computational Models and Language Phenomena

Word reordering is one of the most difficult aspects of statistical machine translation (SMT), and an important factor of its quality and efficiency. Despite the vast amount of research published to date, the interest of the community in this problem has not decreased, and no single method appears to be strongly dominant across language pairs. Instead, the choice of the optimal approach for a new translation task still seems to be mostly driven by empirical trials. To orientate the reader in this vast and complex research area, we present a comprehensive survey of word reordering viewed as a statistical modeling challenge and as a natural language phenomenon. The survey describes in detail how word reordering is modeled within different string-based and tree-based SMT frameworks and as a stand-alone task, including systematic overviews of the literature in advanced reordering modeling. We then question why some approaches are more successful than others in different language pairs. We argue that, besides measuring the amount of reordering, it is important to understand which kinds of reordering occur in a given language pair. To this end, we conduct a qualitative analysis of word reordering phenomena in a diverse sample of language pairs, based on a large collection of linguistic knowledge. Empirical results in the SMT literature are shown to support the hypothesis that a few linguistic facts can be very useful to anticipate the reordering characteristics of a language pair and to select the SMT framework that best suits them.Comment: 44 pages, to appear in Computational Linguistic

A discriminative latent variable-based "DE" classifier for Chinese–English SMT

Syntactic reordering on the source-side is an effective way of handling word order differences. The (DE) construction is a flexible and ubiquitous syntactic structure in Chinese which is a major source of error in translation quality. In this paper, we propose a new classifier model — discriminative latent variable model (DPLVM) — to classify the DE construction to improve the accuracy of the classification and hence the translation quality. We also propose a new feature which can automatically learn the reordering rules to a certain extent. The experimental results show that the MT systems using the data reordered by our proposed model outperform the baseline systems by 6.42% and 3.08% relative points in terms of the BLEU score on PB-SMT and hierarchical phrase-based MT respectively. In addition, we analyse the impact of DE annotation on word alignment and on the SMT phrase table

Robust language pair-independent sub-tree alignment

Data-driven approaches to machine translation (MT) achieve state-of-the-art results. Many syntax-aware approaches, such as Example-Based MT and Data-Oriented Translation, make use of tree pairs aligned at sub-sentential level. Obtaining sub-sentential alignments manually is time-consuming and error-prone, and requires expert knowledge of both source and target languages. We propose a novel, language pair-independent algorithm which automatically induces alignments between phrase-structure trees. We evaluate the alignments themselves against a manually aligned gold standard, and perform an extrinsic evaluation by using the aligned data to train and test a DOT system. Our results show that translation accuracy is comparable to that of the same translation system trained on manually aligned data, and coverage improves

The Mathematics of Phylogenomics

The grand challenges in biology today are being shaped by powerful high-throughput technologies that have revealed the genomes of many organisms, global expression patterns of genes and detailed information about variation within populations. We are therefore able to ask, for the first time, fundamental questions about the evolution of genomes, the structure of genes and their regulation, and the connections between genotypes and phenotypes of individuals. The answers to these questions are all predicated on progress in a variety of computational, statistical, and mathematical fields. The rapid growth in the characterization of genomes has led to the advancement of a new discipline called Phylogenomics. This discipline results from the combination of two major fields in the life sciences: Genomics, i.e., the study of the function and structure of genes and genomes; and Molecular Phylogenetics, i.e., the study of the hierarchical evolutionary relationships among organisms and their genomes. The objective of this article is to offer mathematicians a first introduction to this emerging field, and to discuss specific mathematical problems and developments arising from phylogenomics.Comment: 41 pages, 4 figure