Longitudinal Suicide Risk Prediction and Interpretation with Deep Neural Networks and Shapely Additive Explanations
Abstract not provided.
Publications
Analysis of mobility data to build contact networks for COVID-19
PLoS ONE
As social distancing policies and recommendations went into effect in response to COVID-19, people made rapid changes to the places they visit. These changes are clearly seen in mobility data, which records foot traffic using location trackers in cell phones. While mobility data is often used to extract the number of customers that visit a particular business or business type, it is the frequency and duration of concurrent occupancy at those sites that governs transmission. Understanding the way people interact at different locations can help target policies and inform contact tracing and prevention strategies. This paper outlines methods to extract interactions from mobility data and build networks that can be used in epidemiological models. Several measures of interaction are extracted: interactions between people, the cumulative interactions for a single person, and cumulative interactions that occur at particular businesses. Network metrics are computed to identify structural trends which show clear changes based on the timing of stay-at-home orders. Measures of interaction and structural trends in the resulting networks can be used to better understand potential spreading events, the percent of interactions that can be classified as close contacts, and the impact of policy choices to control transmission.
COVID-19 Modeling
Abstract not provided.
COVID-19 Pandemic Modeling Phase 2 Project Final Report
Abstract not provided.
COVID-19 Medical Resource Demands
Abstract not provided.
Epidemiological and Economic Modeling of a Pandemic
Abstract not provided.
Data Science for Detection of Genome Editi
Abstract not provided.
Movement and spatial specificity support scaling in ant colonies and immune systems: Application to national biosurveillance
Springer Proceedings in Complexity
Data obtained from biosurveillance can be used by public health systems to detect and respond to disease outbreaks and save lives. However, existing data is distributed across large geographic areas, and both the quality and type of data vary in space and time. We discuss a framework for analyzing biosurveillance information to minimize detection time and maximize detection accuracy while scaling the analysis over large regions. We propose that strategies used by canonical biological complex systems, which are adapted to diverse environments, provide good models for the design of a robust, adaptive, and scalable biosurveillance system. Drawing from knowledge of the adaptive immune system, and ant colonies, we examine strategies that support the scaling of detection in order to search and respond in large areas with dynamic distributions of data. Based on this research, we discuss a bioinspired approach for a distributed, adaptive, and scalable biosurveillance system.
Machine Learning Techniques to Improve National Biosurveillance
Abstract not provided.
Biologically inspired approaches for biosurveillance anomaly detection and data fusion
This study developed and tested biologically inspired computational methods to detect anomalous signals in data streams that could indicate a pending outbreak or bio-weapon attack. Current large- scale biosurveillance systems are plagued by two principal deficiencies: (1) timely detection of disease-indicating signals in noisy data and (2) anomaly detection across multiple channels. Anomaly detectors and data fusion components modeled after human immune system processes were tested against a variety of natural and synthetic surveillance datasets. A pilot scale immune-system-based biosurveillance system performed at least as well as traditional statistical anomaly detection data fusion approaches. Machine learning approaches leveraging Deep Learning recurrent neural networks were developed and applied to challenging unstructured and multimodal health surveillance data. Within the limits imposed of data availability, both immune systems and deep learning methods were found to improve anomaly detection and data fusion performance for particularly challenging data subsets. ACKNOWLEDGEMENTS The authors acknowledge the close collaboration of Scott Lee, Jason Thomas, and Chad Heilig from the US Centers for Disease Control (CDC) in this effort. De-identified biosurveillance data provided by Ken Jeter of the New Mexico Department of Health proved to be an important contribution to our work. Discussions with members of the International Society of Disease Surveillance helped the researchers focus on questions relevant to practicing public health professionals. Funding for this work was provided by Sandia National Laboratories' Laboratory Directed Research and Development program.
Synthetic data generators for the evaluation of biosurveillance outbreak detection algorithms
The research and development of new algorithmic and statistical methods of outbreak detection is an ongoing research priority in the field of biosurveillance. The early detection of emergent disease outbreaks is crucial for effective treatment and mitigation. New detection methods must be compared to established approaches for proper evaluation. This comparison requires biosurveillance test data that accurately reflects the complexity of the real-world data it will be applied to. While the test and evaluation of new detection methods is best performed on real data, it is often impractical to obtain such data as it is either proprietary or limited in scope. Thus, scientists must turn to synthetic data generation to provide enough data to properly eval- uate new detection methodologies. This paper evaluates three such synthetic data sources: The WSARE dataset, the Noufilay equation-based approach, and the Project Mimic data generator.
Transportation Modeling and Global Health
Abstract not provided.
Laboratory Infrastructure Network Analysis (LINA) - Architecture and Schema
Abstract not provided.
Time Aware RNNs for Medical Risk Prediction
Abstract not provided.
Negative selection based anomaly detector for multimodal health data
2017 IEEE Symposium Series on Computational Intelligence, SSCI 2017 - Proceedings
Early detection of emerging disease outbreaks is crucial to effective containment and response, yet initial outbreak signatures can be difficult to detect with automated methods. Outbreaks may be masked by noisy data, and signs of an outbreak may be hidden across multiple data feeds. Current biosurveillance methods often perform unimodal statistical analyses that are unable to intelligently leverage multiple correlated data of different types while still retaining quantitative sensitivity. In this paper, we propose and implement an anomaly detection system for health data based upon the human immune system. The adaptive immune system operates over a high-dimensional antigen space in a distributed manner, allowing it to efficiently scale without relying on a centralized controller. Our negative selection algorithm based on the immune system provides effective and scalable distributed anomaly detection for biosurveillance. It detects anomalies in the large, complex data from modern health monitoring data feeds with low false positive rates. Our bootstrap aggregation method improves performance on high-dimensional data sets, and we implement a parallelized version of the algorithm to demonstrate the potential to implement it on a scalable distributed architecture. Our negative selection algorithm is able to detect 90% of all outbreaks with a false positive rate of 11.8% in a publicly available multimodal synthetic health record data set. The scalability and performance of the negative selection algorithm demonstrate that immune computation can provide effective approaches for national and global scale biosurveillence.
Resilience in Disease Outbreak Response: Modeling Medical Laboratory Networks in Developing Countries
Abstract not provided.
Evaluating Text Embedding Schemes for Medical Chief Complaint Classification
Abstract not provided.
Global Health Security: Insights from Sandia?s Recent Experience in West Africa
Abstract not provided.
A practitioner-driven research agenda for syndromic surveillance
Online Journal of Public Health Informatics
The objective here is to obtain feedback and seek future directions for an ISDS initiative to establish and update research questions in Informatics, Analytics,Communications, and Systems Research with the greatest perceived impact for improving surveillance practice.Introduction Over the past fifteen years, syndromic surveillance (SyS) has evolved from a set of ad hoc methods used mostly in post-disaster settings, then expanded with broad support and development because of bioterrorism concerns, and subsequently evolved to a mature technology that runs continuously to detect and monitor a wide range of health issues. Continued enhancements needed to meet the challenges of novel health threats with increasingly complex information sources will require technical advances focused on day-to-day public health needs.Since its formation in 2005, the International Society for Disease Surveillance (ISDS) has sought to clarify and coordinate global priorities in surveillance research. As part of a practitioner-driven initiative to identify current research priorities in SyS, ISDS polled its members about capabilities needed by SyS practitioners that could be improved as a result of research efforts. A taskforce of the ISDS Research Committee, consisting of national and global subject matter experts (SMEs) in SyS and ISDS professional staff, carried out the project. This panel will discuss the results and the preferred means to determine and communicate priorities in the future.
Recommended Research Directions for Improving the Validation of Complex Systems Models
Improved validation for models of complex systems has been a primary focus over the past year for the Resilience in Complex Systems Research Challenge. This document describes a set of research directions that are the result of distilling those ideas into three categories of research -- epistemic uncertainty, strong tests, and value of information. The content of this document can be used to transmit valuable information to future research activities, update the Resilience in Complex Systems Research Challenge's roadmap, inform the upcoming FY18 Laboratory Directed Research and Development (LDRD) call and research proposals, and facilitate collaborations between Sandia and external organizations. The recommended research directions can provide topics for collaborative research, development of proposals, workshops, and other opportunities.
Improving veterans' access to influenza vaccination: Modeling effectiveness of public-private partnerships
Abstract not provided.
Biosecurity through Public Health System Design
We applied modeling and simulation to examine the real-world tradeoffs between developingcountry public-health improvement and the need to improve the identification, tracking, and security of agents with bio-weapons potential. Traditionally, the international community has applied facility-focused strategies for improving biosecurity and biosafety. This work examines how system-level assessments and improvements can foster biosecurity and biosafety. We modeled medical laboratory resources and capabilities to identify scenarios where biosurveillance goals are transparently aligned with public health needs, and resource are distributed in a way that maximizes their ability to serve patients while minimizing security a nd safety risks. Our modeling platform simulates key processes involved in healthcare system operation, such as sample collection, transport, and analysis at medical laboratories. The research reported here extends the prior art by provided two key compone nts for comparative performance assessment: a model of patient interaction dynamics, and the capability to perform uncertainty quantification. In addition, we have outlined a process for incorporating quantitative biosecurity and biosafety risk measures. Two test problems were used to exercise these research products examine (a) Systemic effects of technological innovation and (b) Right -sizing of laboratory networks.
Online mapping and forecasting of epidemics using open-source indicators
Open-source indicators have been proposed as a way of tracking and forecasting disease outbreaks. Some, such are meteorological data, are readily available as reanalysis products. Others, such as those derived from our online behavior (web searches, media article etc.) are gathered easily and are more timely than public health reporting. In this study we investigate how these datastreams may be combined to provide useful epidemiological information. The investigation is performed by building data assimilation systems to track influenza in California and dengue in India. The first does not suffer from incomplete data and was chosen to explore disease modeling needs. The second explores the case when observational data is sparse and disease modeling complexities are beside the point. The two test cases are for opposite ends of the disease tracking spectrum. We find that data assimilation systems that produce disease activity maps can be constructed. Further, being able to combine multiple open-source datastreams is a necessity as any one individually is not very infor- mative. The data assimilation systems have very little in common except that they contain disease models, calibration algorithms and some ability to impute missing data. Thus while the data assimilation systems share the goal for accurate forecasting, they are practically designed to compensate for the shortcomings of the datastreams. Thus we expect them to be disease and location-specific.
Dynamic Social Network Analysis of Tobacco Behavior
Sample Transport Tool
Abstract not provided.
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