Expectation Maximization and Posterior Constraints

The expectation maximization (EM) algorithm is a widely used maximum likelihood estimation procedure for statistical models when the values of some of the variables in the model are not observed. Very often, however, our aim is primarily to find a model that assigns values to the latent variables that have intended meaning for our data and maximizing expected likelihood only sometimes accomplishes this. Unfortunately, it is typically difficult to add even simple a-priori information about latent variables in graphical models without making the models overly complex or intractable. In this paper, we present an efficient, principled way to inject rich constraints on the posteriors of latent variables into the EM algorithm. Our method can be used to learn tractable graphical models that satisfy additional, otherwise intractable constraints. Focusing on clustering and the alignment problem for statistical machine translation, we show that simple, intuitive posterior constraints can greatly improve the performance over standard baselines and be competitive with more complex, intractable models

Learning Tractable Word Alignment Models with Complex Constraints

Word-level alignment of bilingual text is a critical resource for a growing variety of tasks. Probabilistic models for word alignment present a fundamental trade-off between richness of captured constraints and correlations versus efficiency and tractability of inference. In this article, we use the Posterior Regularization framework (Graça, Ganchev, and Taskar 2007) to incorporate complex constraints into probabilistic models during learning without changing the efficiency of the underlying model. We focus on the simple and tractable hidden Markov model, and present an efficient learning algorithm for incorporating approximate bijectivity and symmetry constraints. Models estimated with these constraints produce a significant boost in performance as measured by both precision and recall of manually annotated alignments for six language pairs. We also report experiments on two different tasks where word alignments are required: phrase-based machine translation and syntax transfer, and show promising improvements over standard methods

Mathematical Modelling Method Application for Optimisation of Catalytic Reforming process

The application of mathematical modelling method monitoring of catalytic reforming unit of Komsomolsk oil-refinery is proposed. The mathematical model-based system “Catalyst's Control” which takes into account both the physical and chemical mechanisms of hydrocarbon mixture conversion reaction as well as the catalyst deactivation was used for catalytic reforming installation monitoring. The models created can be used for optimization and prediction of operating parameters (octane number, reactors outlet temperature and yield) of the reforming process. It is shown, that the work on the optimal activity allows increasing product output with a constant level of production costs, and get the information about Pt-Re catalyst work efficiency

Helium-oxygen reduces the production of carbon dioxide during weaning from mechanical ventilation

<p>Abstract</p> <p>Background</p> <p>Prolonged weaning from mechanical ventilation has a major impact on ICU bed occupancy and patient outcome, and has significant cost implications.</p> <p>There is evidence in patients around the period of extubation that helium-oxygen leads to a reduction in the work of breathing. Therefore breathing helium-oxygen during weaning may be a useful adjunct to facilitate weaning. We hypothesised that breathing helium-oxygen would reduce carbon dioxide production during the weaning phase of mechanical ventilation.</p> <p>Materials/patients and methods</p> <p>We performed a prospective randomised controlled single blinded cross-over trial on 19 adult intensive care patients without significant airways disease who fulfilled criteria for weaning with CPAP. Patients were randomised to helium-oxygen and air-oxygen delivered during a 2 hour period of CPAP ventilation. Carbon dioxide production (VCO₂) was measured using a near patient main stream infrared carbon dioxide sensor and fixed orifice pneumotachograph.</p> <p>Results</p> <p>Compared to air-oxygen, helium-oxygen significantly decreased VCO₂production at the end of the 2 hour period of CPAP ventilation; there was a mean difference in CO₂production of 48.9 ml/min (95% CI 18.7-79.2 p = 0.003) between the groups. There were no significant differences in other respiratory and haemodynamic parameters.</p> <p>Conclusion</p> <p>This study shows that breathing a helium-oxygen mixture during weaning reduces carbon dioxide production. This physiological study supports the need for a clinical trial of helium-oxygen mixture during the weaning phase of mechanical ventilation with duration of weaning as the primary outcome.</p> <p>Trial registration</p> <p>ISRCTN56470948</p

Global Methylation Patterns in Idiopathic Pulmonary Fibrosis

BACKGROUND: Idiopathic Pulmonary Fibrosis (IPF) is characterized by profound changes in the lung phenotype including excessive extracellular matrix deposition, myofibroblast foci, alveolar epithelial cell hyperplasia and extensive remodeling. The role of epigenetic changes in determining the lung phenotype in IPF is unknown. In this study we determine whether IPF lungs exhibit an altered global methylation profile.\ud \ud METHODOLOGY/PRINCIPAL FINDINGS: Immunoprecipitated methylated DNA from 12 IPF lungs, 10 lung adenocarcinomas and 10 normal histology lungs was hybridized to Agilent human CpG Islands Microarrays and data analysis was performed using BRB-Array Tools and DAVID Bioinformatics Resources software packages. Array results were validated using the EpiTYPER MassARRAY platform for 3 CpG islands. 625 CpG islands were differentially methylated between IPF and control lungs with an estimated False Discovery Rate less than 5%. The genes associated with the differentially methylated CpG islands are involved in regulation of apoptosis, morphogenesis and cellular biosynthetic processes. The expression of three genes (STK17B, STK3 and HIST1H2AH) with hypomethylated promoters was increased in IPF lungs. Comparison of IPF methylation patterns to lung cancer or control samples, revealed that IPF lungs display an intermediate methylation profile, partly similar to lung cancer and partly similar to control with 402 differentially methylated CpG islands overlapping between IPF and cancer. Despite their similarity to cancer, IPF lungs did not exhibit hypomethylation of long interspersed nuclear element 1 (LINE-1) retrotransposon while lung cancer samples did, suggesting that the global hypomethylation observed in cancer was not typical of IPF.\ud \ud CONCLUSIONS/SIGNIFICANCE: Our results provide evidence that epigenetic changes in IPF are widespread and potentially important. The partial similarity to cancer may signify similar pathogenetic mechanisms while the differences constitute IPF or cancer specific changes. Elucidating the role of these specific changes will potentially allow better understanding of the pathogenesis of IPF.\ud \u

A cross-sectional observational study of the nutritional intake of UK primary school children from deprived and non-deprived backgrounds: implications for school breakfast schemes

BACKGROUND: This study examined the nutritional intake of 9-11 year old children in Wales, UK, to assess the rationale for, and potential of, school breakfast initiatives. It also examined the possible unintended consequence of over consumption. METHODS: The study employed a cross-sectional observational design within a randomized controlled trial of a free school breakfast programme. A total of 111 primary schools were randomly assigned to an intervention condition (in which a free school breakfast programme was implemented) or a control condition (in which implementation of the scheme was delayed). Sub-samples of children completed multiple-pass 24-hr dietary recall interviews at baseline (n = 581), and 12 months later (n = 582). Deprivation was assessed for each child in terms of whether or not they were entitled to free school meals. RESULTS: Prior to the introduction of the programme, rates of breakfast skipping were low and there was little evidence of widespread nutritional deficiency. However, there was a subset of children who consumed inadequate levels of a range of vitamins and minerals and 29 % of children ate very little for breakfast (less than 100 kcal). Children that ate larger breakfasts, had higher daily intakes of all nutrients that were examined. Children from deprived backgrounds consumed significantly lower levels of several vitamins and minerals at breakfast. Following the introduction of the breakfast scheme in intervention schools, there was little difference in the nutritional quality of school versus home breakfasts (n = 35 and 211 respectively). Where children ate breakfast at both school and home (n = 33), their overall energy intake was higher, but not significantly so. CONCLUSIONS: Although the overall diet of this group of children was generally good prior to the breakfast scheme, the results suggest that such schemes could be beneficial for a subset of children who are poorly nourished and for those children who consume very little for breakfast. TRIAL REGISTRATION: Current Controlled Trials ISRCTN18336527

Non-specific interstitial pneumonia in cigarette smokers: a CT study

The goal of this study was to seek indirect evidence that smoking is an aetiological factor in some patients with non-specific interstitial pneumonia (NSIP). Ten current and eight ex-smokers with NSIP were compared to controls including 137 current smokers with no known interstitial lung disease and 11 non-smokers with NSIP. Prevalence and extent of emphysema in 18 smokers with NSIP were compared with subjects meeting GOLD criteria for chronic obstructive pulmonary disease (COPD; group A; n = 34) and healthy smokers (normal FEV1; group B; n = 103), respectively. Emphysema was present in 14/18 (77.8%) smokers with NSIP. Emphysema did not differ in prevalence between NSIP patients and group A controls (25/34, 73.5%), but was strikingly more prevalent in NSIP patients than in group B controls (18/103, 17.5%, P < 0.0005). On multiple logistic regression, the likelihood of emphysema increased when NSIP was present (OR = 18.8; 95% CI = 5.3–66.3; P < 0.0005) and with increasing age (OR = 1.04; 95% CI = 0.99–1.11; P = 0.08). Emphysema is as prevalent in smokers with NSIP as in smokers with COPD, and is strikingly more prevalent in these two groups than in healthy smoking controls. The association between NSIP and emphysema provides indirect support for a smoking pathogenesis hypothesis in some NSIP patients