Classification with class noises through probabilistic sampling

© 2017 Accurately labeling training data plays a critical role in various supervised learning tasks. Now a wide range of algorithms have been developed to identify and remove mislabeled data as labeling in practical applications might be erroneous due to various reasons. In essence, these algorithms adopt the strategy of one-zero sampling (OSAM), wherein a sample will be selected and retained only if it is recognized as clean. There are two types of errors in OSAM: identifying a clean sample as mislabeled and discarding it, or identifying a mislabeled sample as clean and retaining it. These errors could lead to poor classification performance. To improve classification accuracy, this paper proposes a novel probabilistic sampling (PSAM) scheme. In PSAM, a cleaner sample has more chance to be selected. The degree of cleanliness is measured by the confidence on the label. To accurately estimate the confidence value, a probabilistic multiple voting idea is proposed which is able to assign a high confidence value to a clean sample and a low confidence value to a mislabeled sample. Finally, we demonstrate that PSAM could effectively improve the classification accuracy over existing OSAM methods

Cost-sensitive elimination of mislabeled training data

© 2017 Elsevier Inc. Accurately labeling training data plays a critical role in various supervised learning tasks. Since labeling in practical applications might be erroneous due to various reasons, a wide range of algorithms have been developed to eliminate mislabeled data. These algorithms may make the following two types of errors: identifying a noise-free data as mislabeled, or identifying a mislabeled data as noise free. The effects of these errors may generate different costs, depending on the training datasets and applications. However, the cost variations are usually ignored thus existing works are not optimal regarding costs. In this work, the novel problem of cost-sensitive mislabeled data filtering is studied. By wrapping a cost-minimizing procedure, we propose the prototype cost-sensitive ensemble learning based mislabeled data filtering algorithm, named CSENF. Based on CSENF, we further propose two novel algorithms: the cost-sensitive repeated majority filtering algorithm CSRMF and cost-sensitive repeated consensus filtering algorithm CSRCF. Compared to CSENF, these two algorithms could estimate the mislabeling probability of each training data more confidently. Therefore, they produce less cost compared to CSENF and cost-blind mislabeling filters. Empirical and theoretical evaluations on a set of benchmark datasets illustrate the superior performance of the proposed methods

VeSV- Value at the end of the Sanitation Value Chain: Final Report

Bangladesh is no stranger to composting projects using both green waste and faecal sludge (FS). There have been many initiatives over the years with varying degrees of success. Similarly there have been hundreds, if not thousands of projects to improve access to latrines, latrine use and latrine management. Again there has been a great deal of success, especially in increasing the number of latrines being built. However, a key gap regarding the safe collection and processing of the waste from the pit still remains. In cases where projects have attempted addressing this, the solution has rarely been viable on a large scale. That is where this project—VeSV—is different. The aim of this project is to provide scientific evidence to support the commercial viability of collecting and composting faecal sludge for use in agriculture and horticulture. The gap between a good idea and commercial success is bridged on this project by producing primary scientific data based on qualitative and quantitative research methods and by engaging a number of stakeholders across sectors. A rigorous research was conducted to characterize raw faecal sludge material from single pit latrines in rural Bangladesh, as the starting point to develop value across the sanitation chain from processing FS material, through adding value by recovering nutrient and finally by assessing the potential commercialization of the final product in the fertilizer market. Crucially academics, NGOs, business groups and existing fertilizer, composting and latrine management companies were involved as part of our Reference Group, which helped to develop practical engineering solutions in harmony with the right and relevant context in rural Bangladesh. Our research outcomes include the development of safe methodologies for pit emptying; the assessment of people's intentions to change current operation and maintenance practices of pit latrines at household level and their willingness to participate in commercially viable and sustainable methods for FS management; the assessment of optimised engineering process for FS stabilisation and the production of a safe, high quality fertilizer that is desirable to farmers; and the identification of potential hurdles that may obstruct the widespread adoption of business models for FS fertiliser

Qualitative Assessment of the Pharmacist’s Role in Punjab, Pakistan: Medical Practitioners’ Views

Purpose: To assess the perception of Pakistani doctors regarding pharmacist’s role in Punjab Pakistan.Methods: A qualitative approach was used to assess the perception of doctors regarding pharmacist’s role in the study setting. A total of 12 doctors were interviewed using a semi- structured interview guide. The study was conducted for a period of 3 months in the Pakistani cities of Islamabad and Lahore, from July to September 2011. Doctors were informed regarding the aim, objective and nature of the study.Results: All the interviews were transcribed verbatim and thematically analyzed for their content. Thematic content analysis yielded four major themes: 1) Availability of pharmacist in Pakistan’s healthcare setting. 2) Willingness to collaborate with pharmacist. 3) Separation of prescribing from dispensing. 4) Difference in academic levels of doctors and pharmacist.Conclusion: Doctors are receptive to an expanded role for pharmacists, also regard them as drug information experts, but their expectations fall short of the quality of clinically-focused pharmacy services that pharmacists are actually rendering.Keywords: Doctors’ expectation, Pharmacist, Clinical pharmacy services, Qualitative study, Prescribin

Towards sustainable sanitation management: Establishing the costs and willingness to pay for emptying and transporting sludge in rural districts with high rates of access to latrines

MOTIVATION: Proper management of fecal sludge has significant positive health and environmental externalities. Most research on managing onsite sanitation so far either simulates the costs of, or the welfare effects from, managing sludge in situ in pit latrines. Thus, designing management strategies for onsite rural sanitation is challenging, because the actual costs of transporting sludge for treatment, and sources for financing these transport costs, are not well understood. METHODS: In this paper we calculate the actual cost of sludge management from onsite latrines, and identify the contributions that latrine owners are willing to make to finance the costs. A spreadsheet-based model is used to identify a cost-effective transport option, and to calculate the cost per household. Then a double-bound contingent valuation method is used to elicit from pit-latrine owners their willingness-to-pay to have sludge transported away. This methodology is employed for the case of a rural subdistrict in Bangladesh called Bhaluka, a unit of administration at which sludge management services are being piloted by the Government of Bangladesh. RESULTS: The typical sludge accumulation rate in Bhaluka is calculated at 0.11 liters/person/day and a typical latrine will need to be emptied approximately once every 3 to 4 years. The costs of emptying and transport are high; approximately USD 13 per emptying event (circa 14% of average monthly income); household contributions could cover around 47% of this cost. However, if costs were spread over time, the service would cost USD 4 per year per household, or USD 0.31 per month per household-comparable to current expenditures of rural households on telecommunications. CONCLUSION: This is one of few research papers that brings the costs of waste management together with financing of that cost, to provide evidence for an implementable solution. This framework can be used to identify cost effective sludge management options and private contributions towards that cost in other (context-specific) administrative areas where onsite sanitation is widespread

Machine learning model demonstrates stunting at birth and systemic inflammatory biomarkers as predictors of subsequent infant growth - A four-year prospective study

Background: Stunting affects up to one-third of the children in low-to-middle income countries (LMICs) and has been correlated with decline in cognitive capacity and vaccine immunogenicity. Early identification of infants at risk is critical for early intervention and prevention of morbidity. The aim of this study was to investigate patterns of growth in infants up through 48 months of age to assess whether the growth of infants with stunting eventually improved as well as the potential predictors of growth.Methods: Height-for-age z-scores (HAZ) of children from Matiari (rural site, Pakistan) at birth, 18 months, and 48 months were obtained. Results of serum-based biomarkers collected at 6 and 9 months were recorded. A descriptive analysis of the population was followed by assessment of growth predictors via traditional machine learning random forest models.Results: Of the 107 children who were followed up till 48 months of age, 51% were stunted (HAZ \u3c - 2) at birth which increased to 54% by 48 months of age. Stunting status for the majority of children at 48 months was found to be the same as at 18 months. Most children with large gains started off stunted or severely stunted, while all of those with notably large losses were not stunted at birth. Random forest models identified HAZ at birth as the most important feature in predicting HAZ at 18 months. Of the biomarkers, AGP (Alpha- 1-acid Glycoprotein), CRP (C-Reactive Protein), and IL1 (interleukin-1) were identified as strong subsequent growth predictors across both the classification and regressor models.Conclusion: We demonstrated that children most children with stunting at birth remained stunted at 48 months of age. Value was added for predicting growth outcomes with the use of traditional machine learning random forest models. HAZ at birth was found to be a strong predictor of subsequent growth in infants up through 48 months of age. Biomarkers of systemic inflammation, AGP, CRP, IL1, were also strong predictors of growth outcomes. These findings provide support for continued focus on interventions prenatally, at birth, and early infancy in children at risk for stunting who live in resource-constrained regions of the world

Promising biomarkers of environmental enteric dysfunction: a prospective cohort study in Pakistani children.

Environmental Enteric Dysfunction (EED), a syndrome characterized by chronic gut inflammation, contributes towards stunting and poor response to enteric vaccines in children in developing countries. In this study, we evaluated major putative biomarkers of EED using growth faltering as its clinical proxy. Newborns (n = 380) were enrolled and followed till 18 months with monthly anthropometry. Biomarkersassociated with gut and systemic inflammation were assessed at 6 and 9 months. Linear mixed effects model was used to determine the associations of these biomarkers with growth faltering between birth and 18 months. Fecal myeloperoxidase (neutrophil activation marker) at 6 months [β = -0.207, p = 0.005], and serum GLP 2 (enterocyte proliferation marker) at 6 and 9 months [6M: β = -0.271, p = 0.035; 9M: β = -0.267, p = 0.045] were associated with decreasing LAZ score. Ferritin at 6 and 9 months was associated with decreasing LAZ score [6M: β = -0.882, p \u3c 0.0001; 9M: β = -0.714, p \u3c 0.0001] and so was CRP [β = -0.451, p = 0.039] and AGP [β = -0.443, p = 0.012] at 9 months. Both gut specific and systemic biomarkers correlated negatively with IGF-1, but only weakly correlated, if at all with each other. We therefore conclude that EED may be contributing directly towards growth faltering, and this pathway is not entirely through the pathway of systemic inflammation

Study of environmental enteropathy and malnutrition (SEEM) in Pakistan: protocols for biopsy based biomarker discovery and validation

Background: Environmental Enteropathy (EE), characterized by alterations in intestinal structure, function, and immune activation, is believed to be an important contributor to childhood undernutrition and its associated morbidities, including stunting. Half of all global deaths in children \u3c 5 years are attributable to under-nutrition, making the study of EE an area of critical priority. Methods: Community based intervention study, divided into two sub-studies, 1) Longitudinal analyses and 2) Biopsy studies for identification of EE features via omics analyses. Birth cohorts in Matiari, Pakistan established: moderately or severely malnourished (weight for height Z score (WHZ) \u3c − 2) children, and well-nourished (WHZ \u3e 0) children. Blood, urine, and fecal samples, for evaluation of potential biomarkers, will be collected at various time points from all participants (longitudinal analyses). Participants will receive appropriate educational and nutritional interventions; non-responders will undergo further evaluation to determine eligibility for further workup, including upper gastrointestinal endoscopy. Histopathological changes in duodenal biopsies will be compared with duodenal biopsies obtained from USA controls who have celiac disease, Crohn’s disease, or who were found to have normal histopathology. RNA-Seq will be employed to characterize mucosal gene expression across groups. Duodenal biopsies, luminal aspirates from the duodenum, and fecal samples will be analyzed to define microbial community composition (omic analyses). The relationship between histopathology, mucosal gene expression, and community configuration will be assessed using a variety of bioinformatic tools to gain better understanding of disease pathogenesis and to identify mechanism-based biomarkers. Ethical review committees at all collaborating institutions have approved this study. All results will be made available to the scientific community. Discussion: Operational and ethical constraints for safely obtaining intestinal biopsies from children in resource-poor settings have led to a paucity of human tissue-based investigations to understand and reverse EE in vulnerable populations. Furthermore, EE biomarkers have rarely been correlated with gold standard histopathological confirmation. The Study of Environmental Enteropathy and Malnutrition (SEEM) is designed to better understand the pathophysiology, predictors, biomarkers, and potential management strategies of EE to inform strategies to eradicate this debilitating pathology and accelerate progress towards the 2030 Sustainable Development Goals. Trial registration: Retrospectively registered; clinicaltrials.gov ID NCT03588013

Pathobiome driven gut inflammation in Pakistani children with environmental enteric dysfunction

Environmental Enteric Dysfunction (EED) is an acquired small intestinal inflammatory condition underlying high rates of stunting in children \u3c5 years of age in low- and middle-income countries. Children with EED are known to have repeated exposures to enteropathogens and environmental toxins that leads to malabsorptive syndrome. We aimed to characterize association of linear growth faltering with enteropathogen burden and subsequent changes in EED biomarkers. In a longitudinal birth cohort (n = 272), monthly anthropometric measurements (Length for Age Z score- LAZ) of asymptomatic children were obtained up to 18 months. Biological samples were collected at 6 and 9 months for the assessment of biomarkers. A customized TaqMan array card was used to target 40 enteropathogens in fecal samples. Linear regression was applied to study the effect of specific enteropathogen infection on change in linear growth (ΔLAZ). Presence of any pathogen in fecal sample correlated with serum flagellin IgA (6 mo, r = 0.19, p = 0.002), fecal Reg 1b (6 mo, r = 0.16, p = 0.01; 9mo, r = 0.16, p = 0.008) and serum Reg 1b (6 mo, r = 0.26, p\u3c0.0001; 9 mo, r = 0.15, p = 0.008). At 6 months, presence of Campylobacter [β (SE) 7751.2 (2608.5), p = 0.003] and ETEC LT [β (SE) 7089.2 (3015.04), p = 0.019] was associated with increase in MPO. Giardia was associated with increase in Reg1b [β (SE) 72.189 (26.394), p = 0.006] and antiflic IgA[β (SE) 0.054 (0.021), p = 0.0091]. Multiple enteropathogen infections in early life negatively correlated with ΔLAZ, and simultaneous changes in gut inflammatory and permeability markers. A combination vaccine targeting enteropathogens in early life could help in the prevention of future stuntin

Gut integrity and duodenal enteropathogen burden in undernourished children with environmental enteric dysfunction

Environmental enteric dysfunction (EED) is a subclinical condition of intestinal inflammation, barrier dysfunction and malabsorption associated with growth faltering in children living in poverty. This study explores association of altered duodenal permeability (lactulose, rhamnose and their ratio) with higher burden of enteropathogen in the duodenal aspirate, altered histopathological findings and higher morbidity (diarrhea) that is collectively associated with linear growth faltering in children living in EED endemic setting. In a longitudinal birth cohort, 51 controls (WHZ \u3e 0, HAZ \u3e -1.0) and 63 cases (WHZ\u3c -2.0, refractory to nutritional intervention) were recruited. Anthropometry and morbidity were recorded on monthly bases up to 24 months of age. Dual sugar assay of urine collected after oral administration of lactulose and rhamnose was assessed in 96 children from both the groups. Duodenal histopathology (n = 63) and enteropathogen analysis of aspirate via Taqman array card (n = 60) was assessed in only cases. Giardia was the most frequent pathogen and was associated with raised L:R ratio (p = 0.068). Gastric microscopy was more sensitive than duodenal aspirate in H. pylori detection. Microscopically confirmed H. pylori negatively correlated with HAZ at 24 months (r = -0.313, p = 0.013). Regarding histopathological parameters, goblet cell reduction significantly correlated with decline in dual sugar excretion (p\u3c 0.05). Between cases and controls, there were no significant differences in the median (25th, 75th percentile) of urinary concentrations (μg/ml) of lactulose [27.0 (11.50, 59.50) for cases vs. 38.0 (12.0, 61.0) for controls], rhamnose [66.0 (28.0, 178.0) vs. 86.5 (29.5, 190.5)] and L:R ratio [0.47 (0.24, 0.90) vs. 0.51 (0.31, 0.71)] respectively. In multivariable regression model, 31% of variability in HAZ at 24 months of age among cases and controls was explained by final model including dual sugars. In conclusion, enteropathogen burden is associated with altered histopathological features and intestinal permeability. In cases and controls living in settings of endemic enteropathy, intestinal permeability test may predict linear growth. However, for adoption as a screening tool for EED, further validation is required due to its complex intestinal pathophysiology