Flexible And Robust Iterative Methods For The Partial Singular Value Decomposition

The Singular Value Decomposition (SVD) is one of the most fundamental matrix factorizations in linear algebra. As a generalization of the eigenvalue decomposition, the SVD is essential for a wide variety of fields including statistics, signal and image processing, chemistry, quantum physics and even weather prediction. The methods for numerically computing the SVD mostly fall under three main categories: direct, iterative, and streaming. Direct methods focus on solving the SVD in its entirety, making them suitable for smaller dense matrices where the computation cost is tractable. On the other end of the spectrum, streaming methods were created to provide an on-line algorithm that computes an approximate SVD as data is created or read-in over time. Consequently, they can also work on extremely large datasets that cannot fit within memory. To do this, they attempt to obtain only a few singular values and rely on probabilistic guarantees which limit their overall accuracy. Iterative SVD solvers fill in the large gap between these two extremes by providing accurate solutions for a subset of singular values on large (often sparse) matrices. In this dissertation, we focus on the development of flexible and robust iterative SVD solvers that provide fast convergence to high precision. We first introduce a novel iterative solver based on the Golub-Kahan and Davidson methods named GKD. GKD efficiently provides high-precision SVD solutions for large sparse matrices as demonstrated through comparisons with the PRIMME software package. Then, we investigate the use of flexible stopping criteria for GKD and other SVD solvers that are tailored to specific applications. Finally, we analyze the effect of SVD stopping criteria on matrix completion algorithms

Clinical BERTScore: An Improved Measure of Automatic Speech Recognition Performance in Clinical Settings

Automatic Speech Recognition (ASR) in medical contexts has the potential to save time, cut costs, increase report accuracy, and reduce physician burnout. However, the healthcare industry has been slower to adopt this technology, in part due to the importance of avoiding medically-relevant transcription mistakes. In this work, we present the Clinical BERTScore (CBERTScore), an ASR metric that penalizes clinically-relevant mistakes more than others. We demonstrate that this metric more closely aligns with clinician preferences on medical sentences as compared to other metrics (WER, BLUE, METEOR, etc), sometimes by wide margins. We collect a benchmark of 13 clinician preferences on 149 realistic medical sentences called the Clinician Transcript Preference benchmark (CTP), demonstrate that CBERTScore more closely matches what clinicians prefer, and release the benchmark for the community to further develop clinically-aware ASR metrics

Multi-module based CVAE to predict HVCM faults in the SNS accelerator

We present a multi-module framework based on Conditional Variational Autoencoder (CVAE) to detect anomalies in the power signals coming from multiple High Voltage Converter Modulators (HVCMs). We condition the model with the specific modulator type to capture different representations of the normal waveforms and to improve the sensitivity of the model to identify a specific type of fault when we have limited samples for a given module type. We studied several neural network (NN) architectures for our CVAE model and evaluated the model performance by looking at their loss landscape for stability and generalization. Our results for the Spallation Neutron Source (SNS) experimental data show that the trained model generalizes well to detecting multiple fault types for several HVCM module types. The results of this study can be used to improve the HVCM reliability and overall SNS uptim

The HAT TRICK programme for improving physical activity, healthy eating and connectedness among overweight, inactive men: Study protocol of a pragmatic feasibility trial

Introduction  Physical activity, healthy eating and maintaining a healthy weight are associated with reduced risk of cardiovascular disease, type 2 diabetes and cancer and with improved mental health. Despite these benefits, many men do not meet recommended physical activity guidelines and have poor eating behaviours. Many health promotion programmes hold little appeal to men and consequently fail to influence men's health practices. HAT TRICK was designed as a 12-week face-to-face, gender-sensitised intervention for overweight and inactive men focusing on physical activity, healthy eating and social connectedness and was delivered in collaboration with a major junior Canadian ice hockey team (age range 16-20 years). The programme was implemented and evaluated to assess its feasibility. This article describes the intervention design and study protocol of HAT TRICK.  Methods and analysis  HAT TRICK participants (n=60) were men age 35 years, residing in the Okanagan Region of British Columbia, who accumulate 150 min of moderate to vigorous physical activity a week, with a body mass index of >25 kg/m 2 and a pant waist size of >38'. Each 90 min weekly session included targeted health education and theory-guided behavioural change techniques, as well as a progressive (ie, an increase in duration and intensity) group physical activity component. Outcome measures were collected at baseline, 12 weeks and 9 months and included the following: objectively measured anthropometrics, blood pressure, heart rate, physical activity and sedentary behaviour, as well as self-reported physical activity, sedentary behaviour, diet, smoking, alcohol consumption, sleep habits, risk of depression, health-related quality of life and social connectedness. Programme feasibility data (eg, recruitment, satisfaction, adherence, content delivery) were assessed at 12 weeks via interviews and self-report.  Ethics and dissemination  Ethical approval was obtained from the University of British Columbia Okanagan Behavioural Research Ethics Board (reference no H1600736). Study findings will be disseminated through academic meetings, peer-reviewed publication, web-based podcasts, social media, plain language summaries and co-delivered community presentations.  Trial registration number  ISRCTN43361357,Pre results

The Association of Parasitic Infections in Pregnancy and Maternal and Fetal Anemia: A Cohort Study in Coastal Kenya

Background: Relative contribution of these infections on anemia in pregnancy is not certain. While measures to protect pregnant women against malaria have been scaling up, interventions against helminthes have received much less attention. In this study, we determine the relative impact of helminthes and malaria on maternal anemia. Methods: A prospective observational study was conducted in coastal Kenya among a cohort of pregnant women who were recruited at their first antenatal care (ANC) visit and tested for malaria, hookworm, and other parasitic infections and anemia at enrollment. All women enrolled in the study received presumptive treatment with sulfadoxine-pyrimethamine, iron and multi-vitamins and women diagnosed with helminthic infections were treated with albendazole. Women delivering a live, term birth, were also tested for maternal anemia, fetal anemia and presence of infection at delivery. Principal Findings: Of the 706 women studied, at the first ANC visit, 27% had moderate/severe anemia and 71% of women were anemic overall. The infections with highest prevalence were hookworm (24%), urogenital schistosomiasis (17%), trichuria (10%), and malaria (9%). In adjusted and unadjusted analyses, moderate/severe anemia at first ANC visit was associated with the higher intensities of hookworm and P. falciparum microscopy-malaria infections. At delivery, 34% of women had moderate/severe anemia and 18% of infants' cord hemoglobin was consistent with fetal anemia. While none of the maternal infections were significantly associated with fetal anemia, moderate/severe maternal anemia was associated with fetal anemia. Conclusions: More than one quarter of women receiving standard ANC with IPTp for malaria had moderate/severe anemia in pregnancy and high rates of parasitic infection. Thus, addressing the role of co-infections, such as hookworm, as well as under-nutrition, and their contribution to anemia is needed

Place Based Learning Community Planning Guide

The introduction of Place Based Learning Communities (PBLCs) at HSU in 2015 has become an increasingly discussed topic throughout the university. We use the term “Learning Community” in its strictest sense - a curricular approach to education that intentionally links a cluster of courses around an interdisciplinary theme and enrolls a common cohort of students. The production of higher GPAs and retention and significant achievement gap closure among the HSU PBLC cohorts is undeniable. All components are comprehensive in the fact that they build a sense of community, belonging, and accountability within the students which serve as factors for higher retention and academic success. Each class, event, study session, field trip, and staff and faculty member are all parts of what make PBLC such a success. There are many components that need to be established and collaborations that need to be formed in order to make student achievement possible. In this manual, you will read what these components and collaborations look like and upon conclusion you will understand what goes into creating a successful Place Based Learning Community

Economics of local food systems: a toolkit to guide community discussions, assessments and choices, The

As consumers across the Nation express a growing interest in a closer connection to their food producers—whether through access to more localized markets and/or shorter supply chains— cities and regions have begun to regard the expansion of local food marketing activities as a critical component of their economic development strategies. Rising demand for locally produced, source-identified, and differentiated food products has generated a plethora of new and spinoff businesses in many communities, which aim to increase the range of and accessibility to local food items for both retail and wholesale customers. In turn, this emergence of local food businesses has sparked a groundswell of financial support and interest from private foundations and public agencies on the assumption that the development of local food systems contributes to positive economic outcomes, especially with respect to local economic development and improved farm viability. Unfortunately, given the nascent nature of local food demand growth and the scarcity of available data, relatively few of these efforts have been guided by rigorous assessments. In response, the United States Department of Agriculture (USDA) has formed new initiatives and programs to develop new markets and support existing markets so that producers and their communities may leverage these new opportunities. Specifically, the USDA, Agricultural Marketing Service (AMS) has managed the Farmers Market Promotion Program (now expanded to the Local Foods Promotion Program), with great expectations of positive outcomes, but no standardized approach on how to evaluate market and economic outcomes. As a result, a team of regional economists and food system specialists were assembled through a project hosted by Colorado State University (CSU) to develop a Toolkit comprised of food system assessment principles and economic indicators a community may expect to share. Given the real-world projects, experiences, and applied research of the CSU-led team, the Toolkit is grounded in practices that are credible and useable within the economic development discussions guiding communities. The goal of this Toolkit is to guide and enhance the capacity of local organizations to make more deliberate and credible measurements of local and regional economic activity and other ancillary benefits

Trial protocol OPPTIMUM : does progesterone prophylaxis for the prevention of preterm labour improve outcome?

Background Preterm birth is a global problem, with a prevalence of 8 to 12% depending on location. Several large trials and systematic reviews have shown progestogens to be effective in preventing or delaying preterm birth in selected high risk women with a singleton pregnancy (including those with a short cervix or previous preterm birth). Although an improvement in short term neonatal outcomes has been shown in some trials these have not consistently been confirmed in meta-analyses. Additionally data on longer term outcomes is limited to a single trial where no difference in outcomes was demonstrated at four years of age of the child, despite those in the “progesterone” group having a lower incidence of preterm birth. Methods/Design The OPPTIMUM study is a double blind randomized placebo controlled trial to determine whether progesterone prophylaxis to prevent preterm birth has long term neonatal or infant benefit. Specifically it will study whether, in women with singleton pregnancy and at high risk of preterm labour, prophylactic vaginal natural progesterone, 200 mg daily from 22 – 34 weeks gestation, compared to placebo, improves obstetric outcome by lengthening pregnancy thus reducing the incidence of preterm delivery (before 34 weeks), improves neonatal outcome by reducing a composite of death and major morbidity, and leads to improved childhood cognitive and neurosensory outcomes at two years of age. Recruitment began in 2009 and is scheduled to close in Spring 2013. As of May 2012, over 800 women had been randomized in 60 sites. Discussion OPPTIMUM will provide further evidence on the effectiveness of vaginal progesterone for prevention of preterm birth and improvement of neonatal outcomes in selected groups of women with singleton pregnancy at high risk of preterm birth. Additionally it will determine whether any reduction in the incidence of preterm birth is accompanied by improved childhood outcome

A cohort study of Plasmodium falciparum malaria in pregnancy and associations with uteroplacental blood flow and fetal anthropometrics in Kenya

To use ultrasound to explore the impact of malaria in pregnancy on fetal growth and newborn outcomes among a cohort of women enrolled in an intermittent presumptive treatment in pregnancy (IPTp) with sulfadoxine/pyrimethamine (SP) program in coastal Kenya