International Society for Disease Surveillance Conference 2011: Building the Future of Public Health Surveillance: Building the Future of Public Health Surveillance

Daniel Reidpath - ORCID: 0000-0002-8796-0420 https://orcid.org/0000-0002-8796-04204pubpub1117

Real-time classifiers from free-text for continuous surveillance of small animal disease

A wealth of information of epidemiological importance is held within unstructured narrative clinical records. Text mining provides computational techniques for extracting usable information from the language used to communicate between humans, including the spoken and written word. The aim of this work was to develop text-mining methodologies capable of rendering the large volume of information within veterinary clinical narratives accessible for research and surveillance purposes. The free-text records collated within the dataset of the Small Animal Veterinary Surveillance Network formed the development material and target of this work. The efficacy of pre-existent clinician-assigned coding applied to the dataset was evaluated and the nature of notation and vocabulary used in documenting consultations was explored and described. Consultation records were pre-processed to improve human and software readability, and software was developed to redact incidental identifiers present within the free-text. An automated system able to classify for the presence of clinical signs, utilising only information present within the free-text record, was developed with the aim that it would facilitate timely detection of spatio-temporal trends in clinical signs. Clinician-assigned main reason for visit coding provided a poor summary of the large quantity of information exchanged during a veterinary consultation and the nature of the coding and questionnaire triggering further obfuscated information. Delineation of the previously undocumented veterinary clinical sublanguage identified common themes and their manner of documentation, this was key to the development of programmatic methods. A rule-based classifier using logically-chosen dictionaries, sequential processing and data-masking redacted identifiers while maintaining research usability of records. Highly sensitive and specific free-text classification was achieved by applying classifiers for individual clinical signs within a context-sensitive scaffold, this permitted or prohibited matching dependent on the clinical context in which a clinical sign was documented. The mean sensitivity achieved within an unseen test dataset was 98.17 (74.47, 99.9)% and mean specificity 99.94 (77.1, 100.0)%. When used in combination to identify animals with any of a combination of gastrointestinal clinical signs, the sensitivity achieved was 99.44% (95% CI: 98.57, 99.78)% and specificity 99.74 (95% CI: 99.62, 99.83). This work illustrates the importance, utility and promise of free-text classification of clinical records and provides a framework within which this is possible whilst respecting the confidentiality of client and clinician

Biomedical Information Extraction Pipelines for Public Health in the Age of Deep Learning

abstract: Unstructured texts containing biomedical information from sources such as electronic health records, scientific literature, discussion forums, and social media offer an opportunity to extract information for a wide range of applications in biomedical informatics. Building scalable and efficient pipelines for natural language processing and extraction of biomedical information plays an important role in the implementation and adoption of applications in areas such as public health. Advancements in machine learning and deep learning techniques have enabled rapid development of such pipelines. This dissertation presents entity extraction pipelines for two public health applications: virus phylogeography and pharmacovigilance. For virus phylogeography, geographical locations are extracted from biomedical scientific texts for metadata enrichment in the GenBank database containing 2.9 million virus nucleotide sequences. For pharmacovigilance, tools are developed to extract adverse drug reactions from social media posts to open avenues for post-market drug surveillance from non-traditional sources. Across these pipelines, high variance is observed in extraction performance among the entities of interest while using state-of-the-art neural network architectures. To explain the variation, linguistic measures are proposed to serve as indicators for entity extraction performance and to provide deeper insight into the domain complexity and the challenges associated with entity extraction. For both the phylogeography and pharmacovigilance pipelines presented in this work the annotated datasets and applications are open source and freely available to the public to foster further research in public health.Dissertation/ThesisDoctoral Dissertation Biomedical Informatics 201

Social media mining under the COVID-19 context: Progress, challenges, and opportunities

Social media platforms allow users worldwide to create and share information, forging vast sensing networks that allow information on certain topics to be collected, stored, mined, and analyzed in a rapid manner. During the COVID-19 pandemic, extensive social media mining efforts have been undertaken to tackle COVID-19 challenges from various perspectives. This review summarizes the progress of social media data mining studies in the COVID-19 contexts and categorizes them into six major domains, including early warning and detection, human mobility monitoring, communication and information conveying, public attitudes and emotions, infodemic and misinformation, and hatred and violence. We further document essential features of publicly available COVID-19 related social media data archives that will benefit research communities in conducting replicable and repro�ducible studies. In addition, we discuss seven challenges in social media analytics associated with their potential impacts on derived COVID-19 findings, followed by our visions for the possible paths forward in regard to social media-based COVID-19 investigations. This review serves as a valuable reference that recaps social media mining efforts in COVID-19 related studies and provides future directions along which the information harnessed from social media can be used to address public health emergencies

Public health emergency preparedness and response capabilities : national standards for state, local, tribal, and territorial public health

In 2011, the Centers for Disease Control and Prevention (CDC) established the Public Health Preparedness Capabilities: National Standards for State and Local Planning, a set of 15 distinct, yet interrelated, capability standards designed to advance the emergency preparedness and response capacity of state and local public health systems. These standards pioneered a national capability-based framework that helped jurisdictional public health agencies structure emergency preparedness planning and further formalize their public health agency Emergency Support Function (ESF) #8 role(s) in partnership with emergency management agencies.CDC\u2019s 2018 Public Health Emergency Preparedness and Response Capabilities: National Standards for State, Local, Tribal, and Territorial Public Health include operational considerations that support the public health and medical components of the 32 core capabilities specified in the National Preparedness Goal. Jurisdictions should use these operational considerations to develop their public health agency response strategies in greater alignment with the jurisdictional public health agency ESF #8 role.Suggested Citation: Centers for Disease Control and Prevention (CDC). (2018). Public health emergency preparedness and response capabilities. Atlanta, GA: U.S. Department of Health and Human Services.CS290888-ACDC_PreparednesResponseCapabilities_October2018_Final_508.pdfIntroduction -- Using the Capability Standards for Strategic Planning -- At-A-Glance: Capability Definitions, Functions, and Summary of Changes -- Capability 1: Community Preparedness -- Capability 2: Community Recovery -- Capability 3: Emergency Operations Coordination -- Capability 4: Emergency Public Information and Warning -- Capability 5: Fatality Management -- Capability 6: Information Sharing -- Capability 7: Mass Care -- Capability 8: Medical Countermeasure Dispensing and Administration -- Capability 9: Medical Materiel Management and Distribution -- Capability 10: Medical Surge -- Capability 11: Nonpharmaceutical Interventions -- Capability 12: Public Health Laboratory Testing -- Capability 13: Public Health Surveillance and Epidemiological Investigation -- Capability 14: Responder Safety and Health -- Capability 15: Volunteer Management -- Glossary of Terms \u2013- Acknowledgements.201