BIOINFORMATICS SEMINAR SERIES
March 6, 2023
Ammon-Pinizzotto Biopharmaceutical Innovation (BPI) Building
Conference Room 140
Using NLP to Explore Long-term Functional Outcomes in Children following COVID-19
Drs. Cara Reedy and H. Timothy Bunnell
Research Data Scientist (Reedy)
Director, Center for Pediatric Auditory and Speech Sciences (Bunnell)
Neumors Children’s Hospital, Wilmington Delaware
Real-world evidence derived from Electronic Health Record (EHR) data is crucial in advancing our understanding of human disease and its effective treatment. Although most research involving EHR data deals primarily with discrete facts related to patient care such as diagnosis and procedure codes, laboratory test results, and drug prescriptions, unstructured clinical notes written by healthcare providers while administering care are a potentially rich source of complementary information that can supplement analyses of discrete EHR data. This is especially true for research that depends on discovering patient-related facts for which medical terminology does not provide specific diagnostic codes. A case in point is our effort to quantify how Post-Acute Sequalae of Covid-19 (PASC or “Long Covid”) impacts functioning in daily life activities of pediatric patients. Patients have reported cognitive effects, such as “brain fog”, confusion, and unusual difficulty with schoolwork, as well as physical difficulties, such as fatigue, poor sports performance, and breathlessness. These and other symptoms may not be well-represented by diagnostic codes. We will describe our work analyzing clinical notes with natural-language processing and the challenges presented by these data.
Dr. Bunnell received his Ph.D. in Experimental Psychology from The Pennsylvania State University in 1983, concentrating in human speech perception and the acoustic properties of speech (acoustic phonetics). From 1983 to 1989, he worked as a Research Scientist in the Sensory Communication Research Laboratory (later Center for Auditory and Speech Sciences) at Gallaudet University conducting research on the application of digital speech processing techniques to hearing enhancement, primarily for acoustic hearing aid users. In 1989 he became the director of the Speech Processing Laboratory at the Alfred I. duPont Hospital for Children where his research interests expanded to include text to speech synthesis and speech recognition. Dr. Bunnell is now the director of the Nemours Center for Pediatric Auditory and Speech Sciences (CPASS) and head of the Speech Research Laboratory within the CPASS. Since 2000, he has also served as director of the Biomedical Research Informatics Center (BRIC). BRIC maintains computing resources for Nemours Biomedical Research, and provides expertise in applications development, biostatistics, data mining, and numerical analysis. Dr Bunnell is presently the Nemours Institutional Co-PI (with Dr. Anne Kazak) for PEDSnet, and Institutional PI for the NIH-funded CTR Consortium N3C project as well as the NIH-funded RECOVER EHR project.
Dr. Reedy received a Ph.D in Cognitive Science from Rensselaer Polytechnic Institute in 2020 with a thesis combining genetic and social simulation. They joined the Biomedical Research Informatics Center at Nemours Children’s Hospital in 2022 as a research data scientist. At Nemours, they use machine learning, natural language processing, and data analysis to extract information from health records.