2020 National Library of Medicine Training Meeting

small ohsu logo

Here was the schedule for the virtual meeting.

All Times Pacific Daylight Time                           NLM Training Meeting 2020 E-Book     (as of June 22, 2020)  
NLM Virtual Conference Links   Passwords are in email to participants.
NLM Virtual Conference POSTER Links

Day 1 June 22         Day 2  June 23      Day 3 June 24

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  Opening Session Slides
  • Dr. Valerie Florance, National Library of Medicine

8:00 – 10:00 Plenary Session
Clinical and Population Health Informatics
Moderator, Dr. Larry Hunter, University of Colorado, Anshutz Medical School

  • 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
  • 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
  • Predictive Modeling of Bacterial Infections and Antibiotic Therapy Needs in Critically Ill Adults
    Garrett Eickelberg, Northwestern University
  • Utility of EHR to Replicate Cochrane Systematic Reviews
    Jason A. Thomas, University of Washington
  • Predicting Preventable Hospital Readmissions with Causal Machine Learning:  From Data to Decisions
    Ben J. Marafino, Stanford University
  • Pilot 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
    Tiffany J. Callahan, University of Colorado
  • 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
  • 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    Funding Your Research Slides

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

  • 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 Deep Survival Analysis:  Regularization & Missingness
    Shreyas Bhave, Columbia University
  • Optimizing Machine Learning Models for Clinical Application
    Collin Engstrom, University of Wisconsin-Madison
  • Predict Late Patients in Pediatric Ophthalmology Clinic Using Machine Learning
    Wei-Chun Lin, Oregon Health & Science University
  • Spatio-Temporal Analysis of the Effects of Air Pollution on COPD
    Janette Vazquez, The University of Utah
  • Using High-Dimensional Pharmacogenomics Data to Predict Effective Antidepressant Treatment in Major Depressive Disorder Patients
    Lauren M. Rost, University of Pittsburgh

Poster Session 1
Literature Mining, Computational Phenotyping and Exploratory Analyses

  • A Biomedical Use-Case Library and Voice Enabled Exploratory Search for Developing Intelligent User Interfaces
    Michael Segundo Ortiz, University of North Carolina at Chapel Hill
  • Geostatistical Visualization of Ecological Interactions in Tumors
    Hunter B. Boyce, Stanford University
  • Identifying Candidate Antibiotic Pairs for Alternating Treatment Strategies
    Andrew Beckley, University of Pittsburgh
  • Incorporating Electronic Health Record and Genetic Data to Improve Coronary Artery Disease Risk Prediction
    Harsh Patel, University of Washington
  • Data-driven Refinement of Gene Sets for Analysis of Disease Gene Expression
    Alexander Wenzel, University of California, San Diego
  • Leveraging the Electronic Health Record to Evaluate the Effect of Anti-Hypertensive Medications on Mortality in COVID-19 Patients
    Zachary Strasser, Harvard University
  • Unsupervised Literature Tagging of Computational Neuroscience Literature, Towards Question Answering
    Evan Cudone, Yale University

9:45 – 10:30 Poster Session
Poster Session 2
Genomics and Bioinformatics

  • An Ensemble Approach to Study Tumor Evolution Using Multiple Samples
    Carlos C. Vera Recio, University of Texas MD Anderson Cancer Center
  • Assessing the Influence of Regulatory Landscape Complexity on Gene Expression
    Mary Lauren Benton, Vanderbilt University
  • Correlated Mutation Analysis Related to HIV-1 Drug Resistance
    Skyler T. Kramer, University of Missouri
  • Inferring Signaling Pathways with Probabilistic Programming
    David Merrell, University of Wisconsin - Madison
  • Enhanced Biological Interpretability of Single-Nucleus RNA-Seq Via Computational Correction of Systematic Biases
    John Chamberlin, The University of Utah
  • Generalized Analysis of Environmental, Host, and Geographic Specificity in Microbiome Data
    John L. Darcy, Colorado University
  • Inference of Novel Disease-Gene Associations Through Network Communities
    Jennifer Asmussen, Baylor College of Medicine
  • Known Variant Aggregation to Aid Exome Variant Interpretation
    David W. Sant, The University of Utah
  • MRP: Rare-Variant Analysis Via Bayesian Model Comparison Prioritizes Strong Risk and Protective Effects Across Biomarkers and Diseases
    Guhan Ram Venkataraman, Stanford University
  • Sequencing Families Reveals Common Deletions that Contribute to Autism Risk
    Kelly Paskov, Stanford University
  • Integrated Omics Modeling of Transcriptional Regulation in Medulloblastoma
    Owen S. Chapman, University of California, San Diego
  • Zero-Inflated Random Forests for Genetic Regulatory Network Estimation in Single Cell RNA-Seq Data
    Daniel Conn, University of Wisconsin - Madison
  • Review of Herbal Natural Products for Pain Management in Biomedical Classification Systems
    Termeh Feinberg, Department of Veterans Affairs

Poster Session 2
Clinical Informatics

  • Computational Drug Repurposing Validation Strategies: A Review
    Malvika Pillai, University of North Carolina at Chapel Hill
  • Early Evaluation of Cancer Prevention and Survivorship Care TeleECHO (Extension for Community Health Care Outcomes) Program
    Zheng Milgrom, Regenstrief
  • EHR Utilization and Fragmentation: Sequence Analysis of Clinical Workflows
    Amanda J. Moy, Columbia University
  • New Clinical Decision Support System for Veterans
    Melissa Resnick, University at Buffalo
  • Syphilis Testing Adherence Among Women with Livebirth Deliveries: 2014-2016
    Opeyemi C. Ojo, Regenstrief
  • The Spectrum of Recognition and Engagement of Chronic Kidney Disease Care of a Single Healthcare System
    YiFan Wu, University of Washington
  • Ventilated Patients, Thromboprophylaxis and Major ICU Stay Related Outcomes:  An Analysis of MIMIC-III Clinical Database
    Mrigendra M. Bastola, National Institutes of Health

10:00 – 11:30 Director’s Meeting

10:30 – Noon Career Panel – Preparing for Professions in Informatics
Virginia Lankes, OHSU DMICE Career Development Specialist

  • Dr. Dana Womack - Academia
    A Learning Health Systems Science K Scholar in the OHSU-Kaiser Permanente Northwest Center of Excellence and K12 Training Program. Assistant Professor in the Department of Medical Informatics & Clinical Epidemiology and School of Nursing at Oregon Health & Science University in Portland, Oregon.
  • Dr. Mitzi Boardman – Government/Consulting
    Dentist and fellowship-trained informaticist supporting federal, enterprise electronic health record (EHR) implementations as well as contributing to the development of a research-based COVID-19 website and application.
  • Dr. Steven Kassakian – Operational Clinical Informatics
    Associate Chief Health Information Officer at OHSU.  His interest is in general internal medicine and particularly how health information technology can improve outcomes, provider efficiency and patient engagement.
  • Dr. Nathan Lazar - Industry
    Senior data scientist, leading a small team of researchers at Recursion Pharmaceuticals. Our work involves processing huge amounts of cellular imaging data from high-throughput drug screens and computationally searching for potential treatments for rare genetic diseases.

1:00pm Pacific 4pm Eastern  Social Session

Usually the Trainee Social takes place the evening before the conference begins, but by popular demand we have decided to hold the session this afternoon.  Check out Trainee Social Session and win prizes worth around $200!

Wednesday, June 24, 2020

7:00 – 8:30 Parallel Focus Session

Focus Session 4
Machine Deep Learning – Graphical Models

Moderator, Dr. Tsung-Ting Kuo, University of California, San Diego

  • Mechanism Generalization Using Mechanism Centrality
    Harrison Piekle-Lombardo, University of Colorado
  • A Bayesian Approach to Local Causal Discovery in the Presence of Latent Confounding
    Bryan Andrews, University of Pittsburgh
  • Lopsided Bootstrap Loss Enables Segmentation Networks to Learn from Annotations with Multiple False Negatives
    Darvin Yi, Stanford University
  • Decoding Cancer Evolution via Clinical Phylogenetics and Machine Learning
    J. Nick Fisk, Yale University
  • Identifying Novel, Precancer-Associated Stem Cell Subtypes Through Regulatory Network Inference and Machine Learning
    Bob Chen, Vanderbilt University
  • Predictive Modeling of Post-Operative Discharge to Skilled Nursing Facilities (SNF)
    Nicole E. Lopez, University of California, San Diego
  • Applying Open-Set Learning Methods to Cancer Treatment Predictions
    Alexander Cao, Northwestern University

Focus Session 5
Data Science – Population Health

Moderator, Dr. Chi-Ren Shyu, University of Missouri

  • Automatic Discovery of Complex Interactions Between Multiple Risk Factors
    William Baskett, University of Missouri
  • Interactive Visualization for Medical Images in Jupyter Notebooks
    Brian Pollack, University of Pittsburgh
  • Exploring Administrative Time-of-Day Efficacy for Seasonal Influenza Vaccinations
    Darwin Y. Fu, Vanderbilt University
  • Evaluating Electronic Health Record Use Among Academic Ophthalmologists
    Sally L. Baxter, University of California, San Diego
  • Investigating the Link Between Obstructive Sleep Apnea and Air Quality: What Can We Learn from CPAP Device Data?
    Jay P. Kitt, The University of Utah
  • Patient Perspectives on Using Conversational Agents for Hypertension Medication Self-Management
    Ashley C. Griffin, University of North Carolina at Chapel Hill
  • Characterizing Patterns of Disease Diagnosis Across Men and Women
    Tony Y. Sun, Columbia University

Focus Session 6
Moderator, Dr. Lydia Kavraki, Rice University

  • Toward in vivo Molecule Effect Prediction with Deep Learning and Fast Proteomics
    Jesse G. Meyer, University of Wisconsin - Madison
  • Leveraging Partitioning Statistics for Scalable Microbial Identification
    Pavan K. Kota, Rice University
  • Software for Drug Candidate Prediction with Application to SARS-CoV-2
    William Mangione, University at Buffalo
  • Identifying Neoantigens From Noncanonical Transcription and Translation Events at Complex Structural Variants in Human Cancers
    Vinayak Viswanadham, Harvard University
  • Investigating the Antibiotic Biosynthetic Potential of the ADT Microbiome
    Reed M. Stubbendieck, University of Wisconsin - Madison
  • The Unreasonable Effectiveness of Naïve Bayes for Predicting Combinatorial Drug Effects
    Hannah A. Burkhardt, University of Washington

8:30 – 10:00 Parallel Open Mic Session

Open Mic Session 1
Data Science and Bioinformatics
Moderator, Dr. Karen Eilbeck, The University of Utah

  • Dissecting the Tumor Ecosystem Mediating Metastatic Breast Cancer
    Emily K. Stroup, Northwestern University
  • Deep Generative Graph Neural Networks for de Novo Drug Design and Optimization
    Benjamin Kaufman, University of Wisconsin - Madison
  • Imputation of Sparse Metabolomic Data
    Elin Shaddox, University of Colorado
  • Modeling Histone Modifications at a Single-Cell Level Using EpiTOF
    Laurynas Kalesinskas, Stanford University
  • Diversity in Pharmacogenomics: A Review Article
    Roderick Gladney, University of North Carolina at Chapel Hill
  • Multidrug Resistant Organism Carriage in Wisconsin Children
    Ashley Kates, University of Wisconsin
  • Synteny Maps Lead to High Quality Ortholog Predictions
    Nicholas P. Cooley, University of Pittsburgh
  • A Grammar of Patient-Centered Communication Documentation
    David Chartash, Yale University
  • MREC: A Fast Framework for Aligning Single Cell Molecular Data
    Mathieu Carrière, Columbia University
  • Determining Optimal Patient Selection for Adjuvant Chemotherapy after Surgical Resection in Patients with Stage II and III Colorectal Cancer Using Computational Modeling
    Justin J. Hummel, University of Missouri
  • Automated Node-Positive Classification and Feature Extraction Using Tumor Micro-Environment Imaging
    Gautam Machiraju, Stanford University

Open Mic Session 2
Clinical and Public Health Informatics

Moderator, Dr. Robert McDougal, Yale University

  • Improved Physician Follow-Up Using Post-Handoff Report Outcomes (PHaROs)
    Cindy C. Reynolds, University of California, San Diego
  • A Convex Framework for Optimal Resource Allocation and Influence Maximization
    Michael Liou, University of Wisconsin - Madison
  • EHR-Based CDS Implemented to Deliver Public Health Information to Prevent and Manage Disease Outbreak Following the Inception of Meaningful Use – A Scoping Review
    Jean Frédo Louis, The University of Utah
  • Learning Tasks of Pediatric Providers from Electronic Health Record Audit Logs
    Barrett Jones, Vanderbilt University
  • Examining Organizational Characteristics and Perceptions of Clinical Event Notification Services in Health Care Settings
    Kevin Wiley, Jr., Indiana University
  • Delays in Care and Differential Presentation of Acute Myocardial Infarction
    Harry Reyes Nieva, Columbia University
  • Thinking Fast and Slow: Visualization of Financial Conflict of Interest Disclosure in Clinical Trial Publications
    Alex Rich, University of North Carolina at Chapel Hill
  • Private Insurance Market Participation by Psychiatrists in Massachusetts
    Nicole M. Benson, Harvard University
  • Impact of a Clinical Decision Support Tool in the Evaluation of Acute Pulmonary Embolism
    Keaton Morgan, The University of Utah
  • Health Information Exchange in Primary Care:  Use Among Teams
    Nate C. Apathy, Regenstrief
  • Yes, We Closed the Tap!  Now What?
    Meenakshi Mishra, Oregon Health & Science University
  • A Proposal for the Relationship Between Physical Therapy and Opioid Use for US Veterans
    Lindsey Brown-Taylor, Department of Veterans Affairs
  • Diagnostic Test Follow-Up Support:  Incomplete Test Notifications, Purge of Non-Essential Notifications, and Flexible Secondary Pool Assignment
    Peter Hong, Harvard University

Open Mic Session 3
Machine Learning

Moderator, Dr. Noemie Elhadad, Columbia University

  • Stabilized Image Segmentation in the Presence of Noise
    Jonas A. Actor, Rice University
  • Decomposition of Clinical Disparities with Machine Learning
    Noah Hammarlund, University of Washington
  • Electronic Health Record Phenotyping of Patients with Drug-Induced Renal Injury
    Zaid K. Yousif, University of California, San Diego
  • Developing and Testing Clinical Decision Support for Neonatal Ventilator Management
    Lindsey A. Knake, Vanderbilt University
  • Acceleration Signals in Determining Gait-Related Difficulties and the Motor Skill of Walking in Older Adults
    Pritika Dasgupta, University of Pittsburgh
  • Predicting Total Daily Dose of Insulin for Optimal Blood Glucose Control in Hospitalized Patients
    Minh Nguyen, Stanford University
  • Predicting Suicidal Ideation and Attempt in Children Aged 9-10
    Gareth Harman, Oregon Health & Science University
  • Clinical Decision Support for Predicting Postpartum Depression Using Machine Learning
    Houda Benlhabib, University of Washington
  • Developing a Predictive Model for Endometriosis Diagnosis
    Amber Kiser, The University of Utah
  • A Bayesian Hidden Markov Model for Assessing Seizure Risk
    Emily T. Wang, Rice University
  • How to Capture, Characterize, and Classify What We Don’t Know
    Mayla R. Boguslav, Colorado University
  • An Interpretable Electronic Health Record (EHR) Phenotype for Treatment Resistance in Depression (TRD)
    James T. Brown, Vanderbilt University

10:00 – 11:00 Ada Lovelace Computational Health Lecture

This lecture will be live-streamed globally at – currently in ‘Future Events’ section. The talk will be archived and available on the NIH Video Casting and will be in “Past Events’ section the day after the talk.

11:00 – 12:00pm Award Ceremony and Closing Session