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Register a new userMalaria Risk Mapping Using Routine Health System Incidence Data in Zambia
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Benjamin Taylor
Publication date
2021
fields
Mathematical Statistics
and research's language is
English
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Improvements to Zambias malaria surveillance system allow better monitoring of incidence and targetting of responses at refined spatial scales. As transmission decreases, understanding heterogeneity in risk at fine spatial scales becomes increasingly important. However, there are challenges in using health system data for high-resolution risk mapping: health facilities have undefined and overlapping catchment areas, and report on an inconsistent basis. We propose a novel inferential framework for risk mapping of malaria incidence data based on formal down-scaling of confirmed case data reported through the health system in Zambia. We combine data from large community intervention trials in 2011-2016 and model health facility catchments based upon treatment-seeking behaviours; our model for monthly incidence is an aggregated log-Gaussian Cox process, which allows us to predict incidence at fine scale. We predicted monthly malaria incidence at 5km$^2$ resolution nationally: whereas 4.8 million malaria cases were reported through the health system in 2016, we estimated that the number of cases occurring at the community level was closer to 10 million. As Zambia continues to scale up community-based reporting of malaria incidence, these outputs provide realistic estimates of community-level malaria burden as well as high resolution risk maps for targeting interventions at the sub-catchment level.
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Leveraging health administrative data (HAD) datasets for predicting the risk of chronic diseases including diabetes has gained a lot of attention in the machine learning community recently. In this paper, we use the largest health records datasets of patients in Ontario,Canada. Provided by the Institute of Clinical Evaluative Sciences (ICES), this database is age, gender and ethnicity-diverse. The datasets include demographics, lab measurements,drug benefits, healthcare system interactions, ambulatory and hospitalizations records. We perform one of the first large-scale machine learning studies with this data to study the task of predicting diabetes in a range of 1-10 years ahead, which requires no additional screening of individuals.In the best setup, we reach a test AUC of 80.3 with a single-model trained on an observation window of 5 years with a one-year buffer using all datasets. A subset of top 15 features alone (out of a total of 963) could provide a test AUC of 79.1. In this paper, we provide extensive machine learning model performance and feature contribution analysis, which enables us to narrow down to the most important features useful for diabetes forecasting. Examples include chronic conditions such as asthma and hypertension, lab results, diagnostic codes in insurance claims, age and geographical information.
Obtaining the ability to make informed decisions regarding the operation and maintenance of structures, provides a major incentive for the implementation of structural health monitoring (SHM) systems. Probabilistic risk assessment (PRA) is an established methodology that allows engineers to make risk-informed decisions regarding the design and operation of safety-critical and high-value assets in industries such as nuclear and aerospace. The current paper aims to formulate a risk-based decision framework for structural health monitoring that combines elements of PRA with the existing SHM paradigm. As an apt tool for reasoning and decision-making under uncertainty, probabilistic graphical models serve as the foundation of the framework. The framework involves modelling failure modes of structures as Bayesian network representations of fault trees and then assigning costs or utilities to the failure events. The fault trees allow for information to pass from probabilistic classifiers to influence diagram representations of decision processes whilst also providing nodes within the graphical model that may be queried to obtain marginal probability distributions over local damage states within a structure. Optimal courses of action for structures are selected by determining the strategies that maximise expected utility. The risk-based framework is demonstrated on a realistic truss-like structure and supported by experimental data. Finally, a discussion of the risk-based approach is made and further challenges pertaining to decision-making processes in the context of SHM are identified.
Predicting pregnancy has been a fundamental problem in womens health for more than 50 years. Previous datasets have been collected via carefully curated medical studies, but the recent growth of womens health tracking mobile apps offers potential for reaching a much broader population. However, the feasibility of predicting pregnancy from mobile health tracking data is unclear. Here we develop four models -- a logistic regression model, and 3 LSTM models -- to predict a womans probability of becoming pregnant using data from a womens health tracking app, Clue by BioWink GmbH. Evaluating our models on a dataset of 79 million logs from 65,276 women with ground truth pregnancy test data, we show that our predicted pregnancy probabilities meaningfully stratify women: women in the top 10% of predicted probabilities have a 89% chance of becoming pregnant over 6 menstrual cycles, as compared to a 27% chance for women in the bottom 10%. We develop a technique for extracting interpretable time trends from our deep learning models, and show these trends are consistent with previous fertility research. Our findings illustrate the potential that womens health tracking data offers for predicting pregnancy on a broader population; we conclude by discussing the steps needed to fulfill this potential.
Throughout the COVID-19 pandemic, government policy and healthcare implementation responses have been guided by reported positivity rates and counts of positive cases in the community. The selection bias of these data calls into question their validity as measures of the actual viral incidence in the community and as predictors of clinical burden. In the absence of any successful public or academic campaign for comprehensive or random testing, we have developed a proxy method for synthetic random sampling, based on viral RNA testing of patients who present for elective procedures within a hospital system. We present here an approach under multilevel regression and poststratification (MRP) to collecting and analyzing data on viral exposure among patients in a hospital system and performing statistical adjustment that has been made publicly available to estimate true viral incidence and trends in the community. We apply our MRP method to track viral behavior in a mixed urban-suburban-rural setting in Indiana. This method can be easily implemented in a wide variety of hospital settings. Finally, we provide evidence that this model predicts the clinical burden of SARS-CoV-2 earlier and more accurately than currently accepted metrics.
Electronic Health Records (EHRs) are typically stored as time-stamped encounter records. Observing temporal relationship between medical records is an integral part of interpreting the information. Hence, statistical analysis of EHRs requires that clinically informed time-interdependent analysis variables (TIAV) be created. Often, formulation and creation of these variables are iterative and requiring custom codes. We describe a technique of using sequences of time-referenced entities as the building blocks for TIAVs. These sequences represent different aspects of patients medical history in a contiguous fashion. To illustrate the principles and applications of the method, we provide examples using Veterans Health Administrations research databases. In the first example, sequences representing medication exposure were used to assess patient selection criteria for a treatment comparative effectiveness study. In the second example, sequences of Charlson Comorbidity conditions and clinical settings of inpatient or outpatient were used to create variables with which data anomalies and trends were revealed. The third example demonstrated the creation of an analysis variable derived from the temporal dependency of medication exposure and comorbidity. Complex time-interdependent analysis variables can be created from the sequences with simple, reusable codes, hence enable unscripted or automation of TIAV creation.
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