Exponentiated gradient algorithms for conditional random fields and max-margin Markov Networks

Log-linear and maximum-margin models are two commonly-used methods in supervised machine learning, and are frequently used in structured prediction problems. Efficient learning of parameters in these models is therefore an important problem, and becomes a key factor when learning from very large data sets. This paper describes exponentiated gradient (EG) algorithms for training such models, where EG updates are applied to the convex dual of either the log-linear or max-margin objective function; the dual in both the log-linear and max-margin cases corresponds to minimizing a convex function with simplex constraints. We study both batch and online variants of the algorithm, and provide rates of convergence for both cases. In the max-margin case, O(1/ε) EG updates are required to reach a given accuracy ε in the dual; in contrast, for log-linear models only O(log(1/ε)) updates are required. For both the max-margin and log-linear cases, our bounds suggest that the online EG algorithm requires a factor of n less computation to reach a desired accuracy than the batch EG algorithm, where n is the number of training examples. Our experiments confirm that the online algorithms are much faster than the batch algorithms in practice. We describe how the EG updates factor in a convenient way for structured prediction problems, allowing the algorithms to be efficiently applied to problems such as sequence learning or natural language parsing. We perform extensive evaluation of the algorithms, comparing them to L-BFGS and stochastic gradient descent for log-linear models, and to SVM-Struct for max-margin models. The algorithms are applied to a multi-class problem as well as to a more complex large-scale parsing task. In all these settings, the EG algorithms presented here outperform the other methods.

Sequential Monte Carlo for Bayesian sequentially designed experiments for discrete data

In this paper we present a sequential Monte Carlo algorithm for Bayesian sequential experimental design applied to generalised non-linear models for discrete data. The approach is computationally convenient in that the information of newly observed data can be incorporated through a simple re-weighting step. We also consider a flexible parametric model for the stimulus-response relationship together with a newly developed hybrid design utility that can produce more robust estimates of the target stimulus in the presence of substantial model and parameter uncertainty. The algorithm is applied to hypothetical clinical trial or bioassay scenarios. In the discussion, potential generalisations of the algorithm are suggested to possibly extend its applicability to a wide variety of scenarios

Patterns of correlation between vehicle occupant seat pressure and anthropometry

Seat pressure is known as a major factor of seat comfort in vehicles. In passenger vehicles, there is lacking research into the seat comfort of rear seat occupants. As accurate seat pressure measurement requires significant effort, simulation of seat pressure is evolving as a preferred method. However, analytic methods are based on complex finite element modeling and therefore are time consuming and involve high investment. Based on accurate anthropometric measurements of 64 male subjects and outboard rear seat pressure measurements in three different passenger vehicles, this study investigates if a set of parameters derived from seat pressure mapping are sensitive enough to differentiate between different seats and whether they correlate with anthropometry in linear models. In addition to the pressure map analysis, H-Points were measured with a coordinate measurement system based on palpated body landmarks and the range of H-Point locations in the three seats is provided. It was found that for the cushion, cushion contact area and cushion front area/force could be modeled by subject anthropometry,while only seatback contact area could be modeled based on anthropometry for all three vehicles. Major differences were found between the vehicles for other parameters.

Is diurnal temperature range a risk factor for childhood diarrhea?

Background Previous studies have found that high and cold temperatures increase the risk of childhood diarrhea. However, little is known about whether the within-day variation of temperature has any effect on childhood diarrhea. Methods A Poisson generalized linear regression model combined with a distributed lag non-linear model was used to examine the relationship between diurnal temperature range and emergency department admissions for diarrhea among children under five years in Brisbane, from 1st January 2003 to 31st December 2009. Results There was a statistically significant relationship between diurnal temperature range and childhood diarrhea. The effect of diurnal temperature range on childhood diarrhea was the greatest at one day lag, with a 3% (95% confidence interval: 2%–5%) increase of emergency department admissions per 1°C increment of diurnal temperature range. Conclusion Within-day variation of temperature appeared to be a risk factor for childhood diarrhea. The incidence of childhood diarrhea may increase if climate variability increases as predicted.

Real, complex, and binary semantic vectors

This paper presents a combined structure for using real, complex, and binary valued vectors for semantic representation. The theory, implementation, and application of this structure are all significant. For the theory underlying quantum interaction, it is important to develop a core set of mathematical operators that describe systems of information, just as core mathematical operators in quantum mechanics are used to describe the behavior of physical systems. The system described in this paper enables us to compare more traditional quantum mechanical models (which use complex state vectors), alongside more generalized quantum models that use real and binary vectors. The implementation of such a system presents fundamental computational challenges. For large and sometimes sparse datasets, the demands on time and space are different for real, complex, and binary vectors. To accommodate these demands, the Semantic Vectors package has been carefully adapted and can now switch between different number types comparatively seamlessly. This paper describes the key abstract operations in our semantic vector models, and describes the implementations for real, complex, and binary vectors. We also discuss some of the key questions that arise in the field of quantum interaction and informatics, explaining how the wide availability of modelling options for different number fields will help to investigate some of these questions.

The effect of exercise on sleep quality in heart failure

Purpose The primary objective of this study was to examine the effect of exercise on subjective sleep quality in heart failure patients. Methods This study used a randomised, controlled trial design with blinded end-point analysis. Participants were randomly assigned to a 12-week programme of education and self-management support (control) or to the same programme with the addition of a tailored physical activity programme designed and supervised by an exercise specialist (intervention). The intervention consisted of 1 hour of aerobic and resistance exercise twice a week. Participants included 108 patients referred to three hospital heart failure services in Queensland, Australia. Results Patients who participated in supervised exercise classes showed significant improvement in subjective sleep quality, sleep latency, sleep disturbance and global sleep quality scores after 12 weeks of supervised hospital based exercise. Secondary analysis showed that improvements in sleep quality were correlated with improvements in geriatric depression score (p=0.00) and exercise performance (p=0.03). General linear models were used to examine whether the changes in sleep quality following intervention occurred independently of changes in depression, exercise performance and weight. Separate models adjusting for each covariate were performed. Results suggest that exercise significantly improved sleep quality independent of changes in depression, exercise performance and weight. Conclusion This study supports the hypothesis that a 12 week program of aerobic and resistance exercise improves subjective sleep quality in patients with heart failure. This is the first randomised controlled trial to examine the role of exercise in the improvement of sleep quality for patients with this disease. While this study establishes exercise as a therapy for poor sleep quality, further research is needed to investigate exercise as a treatment for other parameters of sleep in this population. Study investigators plan to undertake a more in-depth examination within the next 12 months

Diurnal temperature range and childhood asthma : a time-series study

BACKGROUND: Hot and cold temperatures have been associated with childhood asthma. However, the relationship between daily temperature variation and childhood asthma is not well understood. This study aimed to examine the relationship between diurnal temperature range (DTR) and childhood asthma. METHODS: A Poisson generalized linear model combined with a distributed lag non-linear model was used to examine the relationship between DTR and emergency department admissions for childhood asthma in Brisbane, from January 1st 2003 to December 31st 2009. RESULTS: There was a statistically significant relationship between DTR and childhood asthma. The DTR effect on childhood asthma increased above a DTR of 10[degree sign]C. The effect of DTR on childhood asthma was the greatest for lag 0--9 days, with a 31% (95% confidence interval: 11% -- 58%) increase of emergency department admissions per 5[degree sign]C increment of DTR. Male children and children aged 5--9 years appeared to be more vulnerable to the DTR effect than others. CONCLUSIONS: Large DTR may trigger childhood asthma. Future measures to control and prevent childhood asthma should include taking temperature variability into account. More protective measures should be taken after a day of DTR above10[degree sign]C.

A web application to perform linkage disequilibrium and linkage analyses on a computational grid

Motivation: Unravelling the genetic architecture of complex traits requires large amounts of data, sophisticated models and large computational resources. The lack of user-friendly software incorporating all these requisites is delaying progress in the analysis of complex traits. Methods: Linkage disequilibrium and linkage analysis (LDLA) is a high-resolution gene mapping approach based on sophisticated mixed linear models, applicable to any population structure. LDLA can use population history information in addition to pedigree and molecular markers to decompose traits into genetic components. Analyses are distributed in parallel over a large public grid of computers in the UK. Results: We have proven the performance of LDLA with analyses of simulated data. There are real gains in statistical power to detect quantitative trait loci when using historical information compared with traditional linkage analysis. Moreover, the use of a grid of computers significantly increases computational speed, hence allowing analyses that would have been prohibitive on a single computer. © The Author 2009. Published by Oxford University Press. All rights reserved.

Candidate gene analysis for quantitative traits using the transmission disequilibrium test : the example of the melanocortin 4-receptor in pigs

Population-wide associations between loci due to linkage disequilibrium can be used to map quantitative trait loci (QTL) with high resolution. However, spurious associations between markers and QTL can also arise as a consequence of population stratification. Statistical methods that cannot differentiate between loci associations due to linkage disequilibria from those caused in other ways can render false-positive results. The transmission-disequilibrium test (TDT) is a robust test for detecting QTL. The TDT exploits within-family associations that are not affected by population stratification. However, some TDTs are formulated in a rigid-form, with reduced potential applications. In this study we generalize TDT using mixed linear models to allow greater statistical flexibility. Allelic effects are estimated with two independent parameters: one exploiting the robust within-family information and the other the potentially biased between-family information. A significant difference between these two parameters can be used as evidence for spurious association. This methodology was then used to test the effects of the fourth melanocortin receptor (MC4R) on production traits in the pig. The new analyses supported the previously reported results; i.e., the studied polymorphism is either causal of in very strong linkage disequilibrium with the causal mutation, and provided no evidence for spurious association.

Estimating the effects of ambient temperature on mortality : methodological challenges and proposed solutions

The health impacts of exposure to ambient temperature have been drawing increasing attention from the environmental health research community, government, society, industries, and the public. Case-crossover and time series models are most commonly used to examine the effects of ambient temperature on mortality. However, some key methodological issues remain to be addressed. For example, few studies have used spatiotemporal models to assess the effects of spatial temperatures on mortality. Few studies have used a case-crossover design to examine the delayed (distributed lag) and non-linear relationship between temperature and mortality. Also, little evidence is available on the effects of temperature changes on mortality, and on differences in heat-related mortality over time. This thesis aimed to address the following research questions: 1. How to combine case-crossover design and distributed lag non-linear models? 2. Is there any significant difference in effect estimates between time series and spatiotemporal models? 3. How to assess the effects of temperature changes between neighbouring days on mortality? 4. Is there any change in temperature effects on mortality over time? To combine the case-crossover design and distributed lag non-linear model, datasets including deaths, and weather conditions (minimum temperature, mean temperature, maximum temperature, and relative humidity), and air pollution were acquired from Tianjin China, for the years 2005 to 2007. I demonstrated how to combine the case-crossover design with a distributed lag non-linear model. This allows the case-crossover design to estimate the non-linear and delayed effects of temperature whilst controlling for seasonality. There was consistent U-shaped relationship between temperature and mortality. Cold effects were delayed by 3 days, and persisted for 10 days. Hot effects were acute and lasted for three days, and were followed by mortality displacement for non-accidental, cardiopulmonary, and cardiovascular deaths. Mean temperature was a better predictor of mortality (based on model fit) than maximum or minimum temperature. It is still unclear whether spatiotemporal models using spatial temperature exposure produce better estimates of mortality risk compared with time series models that use a single site’s temperature or averaged temperature from a network of sites. Daily mortality data were obtained from 163 locations across Brisbane city, Australia from 2000 to 2004. Ordinary kriging was used to interpolate spatial temperatures across the city based on 19 monitoring sites. A spatiotemporal model was used to examine the impact of spatial temperature on mortality. A time series model was used to assess the effects of single site’s temperature, and averaged temperature from 3 monitoring sites on mortality. Squared Pearson scaled residuals were used to check the model fit. The results of this study show that even though spatiotemporal models gave a better model fit than time series models, spatiotemporal and time series models gave similar effect estimates. Time series analyses using temperature recorded from a single monitoring site or average temperature of multiple sites were equally good at estimating the association between temperature and mortality as compared with a spatiotemporal model. A time series Poisson regression model was used to estimate the association between temperature change and mortality in summer in Brisbane, Australia during 1996–2004 and Los Angeles, United States during 1987–2000. Temperature change was calculated by the current day's mean temperature minus the previous day's mean. In Brisbane, a drop of more than 3 �C in temperature between days was associated with relative risks (RRs) of 1.16 (95% confidence interval (CI): 1.02, 1.31) for non-external mortality (NEM), 1.19 (95% CI: 1.00, 1.41) for NEM in females, and 1.44 (95% CI: 1.10, 1.89) for NEM aged 65.74 years. An increase of more than 3 �C was associated with RRs of 1.35 (95% CI: 1.03, 1.77) for cardiovascular mortality and 1.67 (95% CI: 1.15, 2.43) for people aged < 65 years. In Los Angeles, only a drop of more than 3 �C was significantly associated with RRs of 1.13 (95% CI: 1.05, 1.22) for total NEM, 1.25 (95% CI: 1.13, 1.39) for cardiovascular mortality, and 1.25 (95% CI: 1.14, 1.39) for people aged . 75 years. In both cities, there were joint effects of temperature change and mean temperature on NEM. A change in temperature of more than 3 �C, whether positive or negative, has an adverse impact on mortality even after controlling for mean temperature. I examined the variation in the effects of high temperatures on elderly mortality (age . 75 years) by year, city and region for 83 large US cities between 1987 and 2000. High temperature days were defined as two or more consecutive days with temperatures above the 90th percentile for each city during each warm season (May 1 to September 30). The mortality risk for high temperatures was decomposed into: a "main effect" due to high temperatures using a distributed lag non-linear function, and an "added effect" due to consecutive high temperature days. I pooled yearly effects across regions and overall effects at both regional and national levels. The effects of high temperature (both main and added effects) on elderly mortality varied greatly by year, city and region. The years with higher heat-related mortality were often followed by those with relatively lower mortality. Understanding this variability in the effects of high temperatures is important for the development of heat-warning systems. In conclusion, this thesis makes contribution in several aspects. Case-crossover design was combined with distribute lag non-linear model to assess the effects of temperature on mortality in Tianjin. This makes the case-crossover design flexibly estimate the non-linear and delayed effects of temperature. Both extreme cold and high temperatures increased the risk of mortality in Tianjin. Time series model using single site’s temperature or averaged temperature from some sites can be used to examine the effects of temperature on mortality. Temperature change (no matter significant temperature drop or great temperature increase) increases the risk of mortality. The high temperature effect on mortality is highly variable from year to year.

Travel time prediction on signalised urban arterials by applying SARIMA modelling on Bluetooth data

Travel time prediction has long been the topic of transportation research. But most relevant prediction models in the literature are limited to motorways. Travel time prediction on arterial networks is challenging due to involving traffic signals and significant variability of individual vehicle travel time. The limited availability of traffic data from arterial networks makes travel time prediction even more challenging. Recently, there has been significant interest of exploiting Bluetooth data for travel time estimation. This research analysed the real travel time data collected by the Brisbane City Council using the Bluetooth technology on arterials. Databases, including experienced average daily travel time are created and classified for approximately 8 months. Thereafter, based on data characteristics, Seasonal Auto Regressive Integrated Moving Average (SARIMA) modelling is applied on the database for short-term travel time prediction. The SARMIA model not only takes the previous continuous lags into account, but also uses the values from the same time of previous days for travel time prediction. This is carried out by defining a seasonality coefficient which improves the accuracy of travel time prediction in linear models. The accuracy, robustness and transferability of the model are evaluated through comparing the real and predicted values on three sites within Brisbane network. The results contain the detailed validation for different prediction horizons (5 min to 90 minutes). The model performance is evaluated mainly on congested periods and compared to the naive technique of considering the historical average.

The effects of hot and cold temperatures on emergency hospital admissions in Brisbane, Australia

As Earth's climate is rapidly changing, the impact of ambient temperature on health outcomes has attracted increasing attention in the recent time. Considerable number of excess deaths has been reported because of exposure to ambient hot and cold temperatures. However, relatively little research has been conducted on the relation between temperature and morbidity. The aim of this study was to characterize the relationship between both hot and cold temperatures and emergency hospital admissions in Brisbane, Australia, and to examine whether the relation varied by age and socioeconomic factors. It aimed to explore lag structures of temperature–morbidity association for respiratory causes, and to estimate the magnitude of emergency hospital admissions for cardiovascular diseases attributable to hot and cold temperatures for the large contribution of both diseases to the total emergency hospital admissions. A time series study design was applied using routinely collected data of daily emergency hospital admissions, weather and air pollution variables in Brisbane during 1996–2005. Poisson regression model with a distributed lag non-linear structure was adopted to assess the impact of temperature on emergency hospital admissions after adjustment for confounding factors. Both hot and cold effects were found, with higher risk of hot temperatures than that of cold temperatures. Increases in mean temperature above 24.2oC were associated with increased morbidity, especially for the elderly ≥ 75 years old with the largest effect. The magnitude of the risk estimates of hot temperature varied by age and socioeconomic factors. High population density, low household income, and unemployment appeared to modify the temperature–morbidity relation. There were different lag structures for hot and cold temperatures, with the acute hot effect within 3 days after hot exposure and about 2-week lagged cold effect on respiratory diseases. A strong harvesting effect after 3 days was evident for respiratory diseases. People suffering from cardiovascular diseases were found to be more vulnerable to hot temperatures than cold temperatures. However, more patients admitted for cardiovascular diseases were attributable to cold temperatures in Brisbane compared with hot temperatures. This study contributes to the knowledge base about the association between temperature and morbidity. It is vitally important in the context of ongoing climate change. The findings of this study may provide useful information for the development and implementation of public health policy and strategic initiatives designed to reduce and prevent the burden of disease due to the impact of climate change.

Reliability of spatiotemporal and kinetic gait parameters determined by a new instrumented treadmill system

Background Despite the emerging use of treadmills integrated with pressure platforms as outcome tools in both clinical and research settings, published evidence regarding the measurement properties of these new systems is limited. This study evaluated the within– and between–day repeatability of spatial, temporal and vertical ground reaction forces measured by a treadmill system instrumented with a capacitance–based pressure platform. Methods Thirty three healthy adults (mean age, 21.5 ± 2.8 years; height, 168.4 ± 9.9 cm; and mass, 67.8 ± 18.6 kg), walked barefoot on a treadmill system (FDM–THM–S, Zebris Medical GmbH) on three separate occasions. For each testing session, participants set their preferred pace but were blinded to treadmill speed. Spatial (foot rotation, step width, stride and step length), temporal (stride and step times, duration of stance, swing and single and double support) and peak vertical ground reaction force variables were collected over a 30–second capture period, equating to an average of 52 ± 5 steps of steady–state walking. Testing was repeated one week following the initial trial and again, for a third time, 20 minutes later. Repeated measures ANOVAs within a generalized linear modelling framework were used to assess between–session differences in gait parameters. Agreement between gait parameters measured within the same day (session 2 and 3) and between days (session 1 and 2; 1 and 3) were evaluated using the 95% repeatability coefficient. Results There were statistically significant differences in the majority (14/16) of temporal, spatial and kinetic gait parameters over the three test sessions (P < .01). The minimum change that could be detected with 95% confidence ranged between 3% and 17% for temporal parameters, 14% and 33% for spatial parameters, and 4% and 20% for kinetic parameters between days. Within–day repeatability was similar to that observed between days. Temporal and kinetic gait parameters were typically more consistent than spatial parameters. The 95% repeatability coefficient for vertical force peaks ranged between ± 53 and ± 63 N. Conclusions The limits of agreement in spatial parameters and ground reaction forces for the treadmill system encompass previously reported changes with neuromuscular pathology and footwear interventions. These findings provide clinicians and researchers with an indication of the repeatability and sensitivity of the Zebris treadmill system to detect changes in common spatiotemporal gait parameters and vertical ground reaction forces.

Plasmodium vivax malaria incidence over time and its association with temperature and rainfall in four counties of Yunnan Province, China

Background Transmission of Plasmodium vivax malaria is dependent on vector availability, biting rates and parasite development. In turn, each of these is influenced by climatic conditions. Correlations have previously been detected between seasonal rainfall, temperature and malaria incidence patterns in various settings. An understanding of seasonal patterns of malaria, and their weather drivers, can provide vital information for control and elimination activities. This research aimed to describe temporal patterns in malaria, rainfall and temperature, and to examine the relationships between these variables within four counties of Yunnan Province, China. Methods Plasmodium vivax malaria surveillance data (1991–2006), and average monthly temperature and rainfall were acquired. Seasonal trend decomposition was used to examine secular trends and seasonal patterns in malaria. Distributed lag non-linear models were used to estimate the weather drivers of malaria seasonality, including the lag periods between weather conditions and malaria incidence. Results There was a declining trend in malaria incidence in all four counties. Increasing temperature resulted in increased malaria risk in all four areas and increasing rainfall resulted in increased malaria risk in one area and decreased malaria risk in one area. The lag times for these associations varied between areas. Conclusions The differences detected between the four counties highlight the need for local understanding of seasonal patterns of malaria and its climatic drivers.

Silver absorption on burns after the application of Acticoat : data from pediatric patients and a porcine burn model

Silver dressings have been widely used to successfully prevent burn wound infection and sepsis. However, a few case studies have reported the functional abnormality and failure of vital organs, possibly caused by silver deposits. The aim of this study was to investigate the serum silver level in the pediatric burn population and also in several internal organs in a porcine burn model after the application of Acticoat. A total of 125 blood samples were collected from 46 pediatric burn patients. Thirty-six patients with a mean of 13.4% TBSA burns had a mean peak serum silver level of 114 microg/L, whereas 10 patients with a mean of 1.85% TBSA burns had an undetectable level of silver (<5.4 microg/L). Overall, serum silver levels were closely related to burn sizes. However, the highest serum silver was 735 microg/L in a 15-month-old toddler with 10% TBSA burns and the second highest was 367 microg/L in a 3-year old with 28% TBSA burns. In a porcine model with 2% TBSA burns, the mean peak silver level was 38 microg/L at 2 to 3 weeks after application of Acticoat and was then significantly reduced to an almost undetectable level at 6 weeks. Of a total of four pigs, silver was detected in all four livers (1.413 microg/g) and all four hearts (0.342 microg/g), three of four kidneys (1.113 microg/g), and two of four brains (0.402 microg/g). This result demonstrated that although variable, the level of serum silver was positively associated with the size of burns, and significant amounts of silver were deposited in internal organs in pigs with only 2% TBSA burns, after application of Acticoat.