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NLM Training Meeting 2020 E-Book National Library of Medicine Annual Training Meeting June 22-24, 2020 Oregon Health & Science University Portland, OR TABLE OF CONTENTS Acknowledgements Page 3 Agenda – Monday, June 22, 2020 Welcome/Opening Session – 7:00 AM (PDT) Page 4 Plenary Session – 8:00 AM (PDT) Clinical and Population Informatics Page 4 Parallel Focus Session – 10:30 (PDT) Text Extraction - Summarization Page 5 HIE – Interoperability Page 5 Bioinformatics - Genomics Page 6 Poster Pitch – Noon (PDT) Page 6 Funding your Research: NLM R01 and SBIR/STTR Grants – 1:00 PM (PDT) Page 6 Dr. Alan VanBierlviet, National Library of Medicine/NIH Agenda – Tuesday, June 23, 2020 Plenary Session – 7:00 AM (PDT) Translational Bioinformatics Page 7 Poster Session 1 – 9:00 AM (PDT) Machine Learning in Clinical Environments Page 7 Literature Mining, Computational Phenotyping and Exploratory Analyses Page 8 Poster Session 2 – 9:45 AM (PDT) Genomics and Bioinformatics Page 9 Clinical Informatics Page 10 Director’s Meeting – Open to Program Director’s and Admin Staff registered for meeting – Page 10 10:00 AM (PDT) Career Panel – Preparing for Professions in Informatics – 10:30 AM (PDT) Page 10 Agenda – Wednesday, June 24, 2020 Parallel Focus Session – 7:00 AM (PDT) Machine/Deep Learning Page 11 Data Science/Population Health Page 12 Pharmacoinformatics Page 12 Open Mic Sessions – 8:30 AM (PDT) Data Science and Bioinformatics Page 13 Clinical and Public Health Informatics Page 14 Machine Learning Page 15 Ada Lovelace Computational Health Lecture – 10:00 AM (PDT) Page 16 Conference Closing and Award Ceremony – 11:00 AM (PDT) Page 16 Abstracts – by Session Pages 17-120 pg. 2 EBook Acknowledgements When OHSU volunteered to host the 2020 NLM Informatics Trainees Conference, we never envisioned the Covid-19 pandemic and the subsequent need to convert the conference to a virtual event. This first- ever Virtual NLM Informatics Trainees Conference would not have happened without the work of many people. We first wish to thank the staff of OHSU who planned initially for an in-person event but then transitioned to planning a virtual meeting. They include: Andrea Ilg Diane Doctor Monica Garlough Kate Fultz-Hollis Virginia Lankes Brent Solheim Lynne Schwabe Lauren Ludwig Dave Heron We also want to thank the Student Program Committee, who developed the conference program: Lily Cook, OHSU Rocky Aikens, Stanford Meena Mishra, OHSU Nicole Lopez. UCSD Sarah Mullin, Buffalo Aaron Bohlmann, North Carolina Tony Sun, Columbia YiFan Wu, Washington Peter Hong, Harvard Janette Vazquez, Utah Garret Eickelberg, Northwestern Marily Barron, Vanderbilt Brandan Dunham, Pittsubrgh Chris Magnano, Wisconsin Rebecca Rivera, Regenstrief David Chartash, Yale Varuna Chander. Baylor Finally, we want to thank the NLM leadership and staff for their support and assistance: Patricia Flatley Brennan Christine Ireland Valerie Florance Alan VanBiervliet William Hersh, MD, FACP, FACMI, FAMIA Program Director, OHSU NLM T15 Biomedical Informatics Training Grant Professor and Chair, Department of Medical Informatics & Clinical Epidemiology School of Medicine, Oregon Health & Science University pg. 3 2020 National Library of Medicine Training Meeting Oregon Health & Science University AGENDA Monday, June 22, 2020 7:00 – 8:00 Conference Opening and Welcome Dr. Sharon Anderson, Oregon Health & Science University Dr. Bill Hersh, Oregon Health & Science University Dr. Patricia Brennan, National Library of Medicine Dr. Valerie Florance, National Library of Medicine 8:00 – 10:30 Plenary Session Clinical and Population Health Informatics Moderator, Dr. Larry Hunter, University of Colorado Quantifying the Scope and Work of Secure Messaging Among Breast Cancer Care Team Members Bryan D. Steitz, Vanderbilt University Provider Adherence to Syphilis Testing Guidelines Among Stillbirth Cases Yenling A. Ho, Indiana University Utility of EHR to Replicate Cochrane Systematic Reviews Jason A. Thomas, University of Washington Predictive Modeling of Bacterial Infections and Antibiotic Therapy Needs in Critically Ill Adults Garrett Eickelberg, Northwestern University Designs: Extending Experimental Principles to Observational Studies Rachael C. Aikens, Stanford University PheKnowLator: An Optimized Library for Automated Construction of Large Scale Heterogeneous Biomedical Knowledge Graphs pg. 4 Tiffany J. Callahan, University of Colorado mHealth for Mental Health: Acceptance and Design of an App to Help African American Women Manage Anxiety and Depression Terika McCall, University of North Carolina at Chapel Hill Predicting Preventable Hospital Readmissions with Causal Machine Learning: From Data to Decisions Ben J. Marafino, Stanford University Family History and Phenotype Heritability in Type I Diabetes Erin M. Tallon, University of Missouri Automated Conversational Health Coaching Elliot G. Mitchell, Columbia University 10:30 – Noon Parallel Focus Sessions Focus Session 1 Text Extraction – Summarization Moderator, Dr. Harry Hochheiser, University of Pittsburgh Improving Physical Activity Among Prostate Cancer Survivors and Their Loved Ones Through a Peerbased Digital Walking Program Regina Casanova-Perez, University of Washington Extracting Housing Stability Concepts from Clinical Text Notes Andrew K. Teng, University of Washington Developing an Efficient Model for Identifying and Extracting Social Determinants of Health from Clinical Notes Rachel Stemerman, University of North Carolina at Chapel Hill Literature-Based Discovery of Drug Repurposing for Rare Diseases Daniel N. Sosa, Stanford University Learning to Identify Synonymous Terms Across Biomedical Terminologies Vinh Nguyen, National Library of Medicine Focus Session 2 HIE – Interoperability Moderator, Dr. Peter Elkin, University at Buffalo Identifying Acute Respiratory Distress Syndrome in De-Identified EHR Data V. Eric Kerchberger, Vanderbilt University pg. 5 Representation of Medical Knowledge Towards Generalizable Prediction Sarah Mullin, University at Buffalo Informatics of Early Intervention Referrals for Children with Disabilities Ben Sanders, Oregon Health & Science University Health Information Exchange Use During Dental Visits Heather L. Taylor, Indiana University A SMART on FHIR and CDS-Hooks Enabled Approach to the Exchange and Review of Genomic Test Results Michael Watkins, The University of Utah Focus Session 3 Bioinformatics – Genomics Moderator, Dr. Sylvia Katina Plevritis, Stanford University Vitessce: Visual Integration Tool for Exploration of Spatial Single-Cell Experiments Trevor Manz, Harvard University Integration of Large-Effect Expression Variants Enhances Polygenic Risk Prediction Craig Smail, Stanford University Identifying Protein-Metabolite Networks Associated with COPD Phenotypes Emily Mastej, University of Colorado Alternative Splicing Event Signatures of Drug Response in AML Julian Egger, Oregon Health & Science University Heritable Components Explain Variation in Acute Kidney Injury Recovery Rate Kathleen LaRow Brown, Columbia University Investigating Somatic Mosaicism in Blood for Cardiovascular Disease Risk Varuna Chander, Baylor College of Medicine Noon – 12:45 Poster Pitch Moderator, Dr. Karen Eden, Oregon Health & Science University 1:00 – 2:00 Funding your Research: NLM R01 and SBIR/STTR Grants Dr. Alan VanBiervliet, National Library of Medicine/NIH pg. 6 AGENDA Tuesday, June 23, 2020 7:00 – 9:00 Plenary Session Translational Bioinformatics Moderator, Dr. Mark Craven, University of Wisconsin-Madison Identifying MHC Class I Binding Peptides Using an Ultradense Peptide Array Amelia K. Haj, University of Wisconsin - Madison Elucidating Bio-Molecular Mechanisms of Disease for Novel Pathogenic Variants Using Structural Bioinformatics Approaches Rolando Hernandez, The University of Utah Prognostic Value of Imaging-Based Estimates of Glioma Pathology Pre-and Post-Surgery Evan D. H. Gates, University of Texas, MD Anderson Cancer Center An Empirical Bayes Approach to Image Normalization in Highly Multiplexed Cellular Imaging Data Coleman R. Harris, Vanderbilt University Benchmark and Best Practices for Biomedical Knowledge Graph Embeddings David Chang, Yale University Prediction of Drug Co-Prescription Induced Adverse Events Using CANDO Zachary Falls, University at Buffalo A Reward System Polygenic Risk Score for Predicting Obesity and Substance Use Disorders Kristen M. Stevens, Oregon Health & Science University Multi-region Expression Profiling of Archived Breast Ductal Carcinoma In Situ Adam Officer, University of California, San Diego Genome-Wide Detection of Epistasis in Antibiotic Resistance M. Tuberculosis Anna G. Green, Harvard Medical School 9:00 – 9:45 Poster Sessions Poster Session 1 Machine Learning in Clinical Environments pg. 7 Ethnicity-Associated Microbiome and Metabolome Differences Persist During a Short, Plant- based Diet Robert H. Markowitz, Vanderbilt University Clostridioides Difficile Infection Among Privately Insured Patients in the United States Jessica El Halabi, Harvard University Exploring How Temporal Representation Affects Deep Longitudinal Models Matthew C. Lenert, Vanderbilt University Fully Automatic Detection of REM Sleep Without Atonia Daniel Yaeger, Oregon Health & Science University Identifying Modifiable Predictors of Patient Outcomes after Intracerebral Hemorrhage with Machine Learning Andrew N. Hall, Northwestern University Improving Prediction of Survival for Extremely Premature Infants Born at 23 to 29 Weeks Gestational Age in the Neonatal Intensive Care Unit Angie Li, University at Buffalo Nonparametric
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