• March 12 - 15, San Francisco

    AMIA 2018 Informatics Summit

    Translational | Clinical Research | Implementation | Data Science

AMIA 2018 Informatics Summit Oral Presentations

as of January 2, 2018

3:30 p.m. – 5:00 p.m.

S02: TBI Student Paper Competition

Pharmacogenomic Approaches for Automated Medication Risk Assessment in People with Polypharmacy
J. Liu, Steven Institute of Technology; C. Friedman, J. Finkelstein, Columbia University

Utility of Genetic Testing in Addition to Mammography for Determining Risk of Breast Cancer Depends on Patient Age
S. Feld, University of Wisconsin; J. Fan, Hong Kong Baptist University; M. Yuan, Columbia University; Y. Wu, K. Woo, R. Alexandridis, E. Burnside, University of Wisconsin

Comparing Existing Resources to Represent Dietary Supplements
R. Rizvi, T. Adam, E. Lindemann, J. Vasilakes, S. Pakhomov, J. Bishop, G. Melton, R. Zhang, University of Minnesota

Exploring the Potential of Direct-to-Consumer Genetic Test Data for Predicting Adverse Drug Events
P. Zhang, I. Sarkar, Brown University

Low Rank Methods for Phenotype Imputation and Clustering in Autism Spectrum Disorder
K. Paskov, D. Wall, Stanford University

S03: Oral Presentations – Data Science Innovations

Determining the Fundamental Building Blocks of the Apoptosis Pathway Across Multiple Cancers
Z. Abrams, H. Bai, M. Wang, K. Coombes, The Ohio State University

Computational Identification of Colorectal Adenoma-related Genes Using Machine Learning and Network Analysis
J. Ping, Vanderbilt University Medical Center; X. Pan, Shanghai Jiao Tong University; X. Dong, Albert Einstein College of Medicine; J. Wang, Shanghai Jiao Tong University

Molecular Modeling and Simulations to Discern the Consequences of Rare and Polymorphic STING Variants
M. Zimmermann, E. Voigt, I. Haralambieva, I. Ovsyannikova, S. Daniel, G. Poland, R. Kennedy, Mayo Clinic

Open Science Integration for Mechanistic Disease Discovery in Fanconi Anemia
M. Haendel, Oregon Health & Science University; C. Mungall, Lawrence Berkeley National Laboratory; J. McMurry, Oregon Health & Science University; C. Chute, Johns Hopkins University; M. Hoatlin, Oregon Health & Science University

Heart Rate Variability Response to Vasopressor Intervention in Critically Ill Patients
V. Tolls, E. Morin, K. Rudie, Queen's University; A. Seely, The Ottawa Hospital; D. Maslove, Queen's University

S04: Oral Presentations – A.I. and Clinical NLP

Word Repetition in Separate Conversations for Detecting Dementia: A Preliminary Evaluation on Regular Monitoring Service
K. Shinkawa, Y. Yamada, IBM Reseach – Tokyo

Adapting Word Embeddings from Multiple Domains to Symptom Recognition from Psychiatric Notes
Y. Zhang, H. Lee, J. Wang, T. Cohen, K. Roberts, H. Xu, The University of Texas Health Science Center at Houston

A Deep Learning Approach to Examine Ischemic ST Changes in Ambulatory ECG Recordings
R. Xiao, Y. Xu, M. Pelter, D. Mortara, X. Hu, University of California San Francisco

Identifying Supplement Use Within Clinical Notes Using Natural Language Processing
V. Sharma, I. Sarkar, Brown University

Influence of Bias Introduced by Filtering Patients with “Complete” Electronic Health Records (EHRs) on Predicting Diabetic Kidney Disease
X. Song, R. Waitman, University of Kansas Medical Center; Y. Hu, Jinan University; A. Yu, D. Robins, M. Liu, University of Kansas Medical Center

10:30 a.m. – 12:00 p.m.

S07: Oral Presentations – Open Data and Big Science

Deep Learning Data Integration for Better Risk Stratification Models of Bladder Cancer

O. Poirion, K. Chaudhary, University of Hawaii Cancer Center; L. Garmire, University of Hawaii Cancer Center/University of Hawaii at Manoa

GNOMICS: A One-stop Shop for Biomedical and Fenomic Data

C. Kronk, University of Cincinnati College of Medicine; A. Jegga, University of Cincinnati College of Medicine/Cincinnati Children's Hospital and Medical Center

Real-time Protection of Genomic Data Sharing in Beacon Services

D. Bu, X. Wang, H. Tang, Indiana University Bloomington

Open Access Economics in the Big Genomics Era

N. Stockham, Stanford University

Speeding Genetic Discovery in Autism through the iHART Information Commons

J. Jung, N. Stockham, K. Paskov, A. Gupta, M. Sun, D. Wall, Stanford University

10:30 a.m. – 12:00 p.m.

S09: Oral Presentation – Predicting Health Status

Memory-augmented Active Deep Learning for Identifying Relations Between Medical Concepts in Electroencephalography Reports

R. Maldonado, T. Goodwin, S. Harabagiu, The University of Texas at Dallas

Exacting Tobacco Exposure with the Smoking History and Pack-year Extraction System (SHAPES)

T. Osterman, J. Wu, D. Mize, W. Wei, J. Denny, Vanderbilt University

Web-based Dashboard for the Interactive Visualization and Analysis of National Risk Standardized Mortality Rates of Sepsis in the U.S.

F. Lin, National Taiwan University; M. Lee, National Taiwan University Hospital; F. Lai, National Taiwan University; C. Lee, National Taiwan University Hospital

Personalized Vital Sign Modeling to Predict Health Status

J. Dunn, L. Kidzinski, Stanford University; R. Runge, University of California Berkeley; S. Delp, M. Snyder, T. Hastie, Stanford University

Characterizing Functional Health Status of Surgical Patients in Clinical Notes

S. Skube, E. Lindemann, E. Arsoniadis, University of Minnesota; M. Akre, University of Minnesota Physicians; E. Wick, University of California San Francisco; G. Melton, University of Minnesota

S10: Oral Presentations

Beyond Cohorts: Multi-institution Datasets in the Cloud

J. Klann, Harvard University School of Medicine/Massachusetts General Hospital/Partners Healthcare; S. Boykin, Boston Children's Hospital; M. Vella, Harvard University School of Medicine; S. Schneeweiss, Harvard University School of Medicine/Brigham and Women's Hospital; D. Macfadden, Harvard University School of Medicine; M. Natter, Boston Children's Hospital/Harvard University School of Medicine; S. Weiler, Harvard University School of Medicine; K. Mandl, Harvard University School of Medicine/Boston Children's Hospital; S. Murphy, Partners Healthcare/Massachusetts General Hospital/Harvard University School of Medicine

Administration of Patient Reported Outcomes (PRO) Questionnaires in Clinical Settings Using Provider Workstations

M. Habrat, L. Moriera, J. Oates, J. Obeid, L. Lenert, Medical University of South Carolina

Design and Development of a Machine Learning Pipeline and Protected Computing Environment

S. Rusincovitch, E. Huang, Duke Health; C. Kneifel, Duke University; B. Willis, J. Fayson, S. Blackwelder, Duke Health; L. Carin, R. Henao, Duke University

Architecture of a Visual Interactive Analysis Tool for Filtering and Summarizing Large Data Sets Coded with Hierarchical Terminologies (VIADS)

X. Jing, M. Emerson, D. Gunderson, Ohio University; J. Cimino, University of Alabama at Birmingham; C. Liu, Ohio University; J. Shubrook, Touro University; B. Phillips, Ohio University

1:30 p.m. – 3:00 p.m.

S12: Oral Presentations – Precision and Data-driven Pharmacology

A Network-biology Informed Computational Drug Repositioning Strategy to Target Disease Risk Trajectories and Comorbidities of Peripheral Artery Disease

S. Khader, Northwell Health; G. Dow, Mayo Clinic; B. Glicksberg, K. Johnson, Icahn School of Medicine at Mount Sinai; Y. Ze, Mayo Clinic; M. Tomlinson, B. Readhead, J. Dudley, Icahn School of Medicine at Mount Sinai; I. Kullo, Mayo Clinic

Exploring Landscape of Drug-Target-Pathway-Side Effect Associations

H. Lim, The City University of New York; A. Poleksic, University of Northern Iowa; L. Xie, Hunter College of CUNY/The City University of New York

Vanderbilt University Medical Center’s Drug Repurposing Program: Using Human Genetic Information to Find Effective and Affordable Therapies

H. Naylor, J. Shirey-Rice, N. Zaleski, R. Jerome, R. Lavieri, A. Pruijssers, S. Chettiar, J. Pulley, N. Giuse, Vanderbilt University Medical Center

Multiscale Profiling and Predictive Modeling of Responders and Non-responders to Periodontal Therapies

R. Nagarajan, C. Miller, University of Kentucky; J. Ebersole, University of Nevada Las Vegas

Big Data Deep Neural Network to Analyze Adverse Vaccine Reactions

A.P. Tafti, Marshfield Clinic Research Institute; M. Assefi, University of Georgia; E. LaRose, J. Badger, Z. Ye N. Shimpi, Marshfield Clinic Research Institute; F. Bashiri, Marshfield Clinic Research Institute/University of Wisconsin-Milwaukee; E. Sagheb, H. McLean, P. Peissig, Marshfield Clinic Research Institute; D. Page, University of Wisconsin-Madison

S13: Oral Presentations – Clinical and Research Data Integration

Crowdsourcing for Research EEG Annotation and Accuracy Estimation

W. Bosl, University of San Francisco

Has Meaningful Use Improved Collection of Smoking Status Information?

F. Polubriaginof, Columbia University; A. Tariq, NewYork-Presbyterian Hospital; N. Tatonetti, Columbia University; D. Vawdrey, NewYork-Presbyterian Hospital/Columbia University

Vivli: A Global Secure Data Sharing Platform for Participant-level Clinical Trial Data

I. Sim, University of California San Francisco/Vivli Center for Global Clinical Research Data; R. Li, Vivli Center for Global Clinical Research Data/Brigham and Women's Hospital/Harvard Multi-Regional Clinical Trials Center; S. Carini, University of California San Francisco/Vivli Center for Global Clinical Research Data; P. Gazmuri, Blue Metal, Inc; C. Mavergames, Cochrane; B. Bierer, Brigham and Women's Hospital/Harvard Multi-Regional Clinical Trials Center, Vivli Center for Global Clinical Research Data

Blockchain Applications in Clinical Research

B. Adagarla, A. Tasneem, T. Reece, Duke Clinical Research Institute; S. Balu, Duke Institute for Health Innovation; A. Krishnamurthy, University of North Carolina at Chapel Hill; B. McCourt, Duke Clinical Research Institute

EHR-integrated, Machine Learning-driven SMART on FHIR Pharmacotherapy Decision Support System for Type 2 Diabetes Mellitus

W. Takeuchi, S. Tarumi, Hitachi Ltd.; S. Rodriguez, D. Shields, P. Warner, M. Flynn, K. Turner, F. Sakaguchi, University of Utah; H. Ban, Hitachi Ltd.; K. Kawamoto, University of Utah

S14: Oral Presentations – Patient Aspects in Clinical Research

From Sour Grapes to Low-hanging Fruit: A Case Study Demonstrating a Practical Strategy for Natural Language Processing Portability

S. Johnson, P. Adekkanattu, T. Campion, J. Flory, J. Pathak, Weill Cornell Medicine; O. Patterson, S. DuVall, VA Salt Lake City Health Care System/University of Utah; V. Major, Y. Aphinyanaphongs, New York University Langone Health

Using a Bedside Interactive Technology to Solicit and Record Pediatric Pain Reassessments: Parent and Nursing Perspectives on a Novel Workflow

R. Aldekhyyel, University of Minnesota/King Saud University; G. Melton, G. Hultman, M. Pitt, University of Minnesota

Effects of Site and Method of Administration on Patients’ Preferences for Participation in Research

A. Shoaibi, M. Habrat, J. Obeid, J. Oates, L. Lenert, Medical University of South Carolina

Research Permissions via a Patient Portal: Demographic Profile

J. Obeid, A. Shoaibi, J. Oates, M. Habrat, L. Lenert, Medical University of South Carolina

Patient Opinions About Digital Messaging for Clinical Research Recruitment

M. Cantor, M. Mishik, New York University Langone Medical Center

3:30 p.m. – 5:00 p.m.

S17: Oral Presentation – Clinical Data Mining and Machine Learning (Part 1)

Identifying Diagnostic Paths for Undifferentiated Abdominal Pain from Electronic Health Record Data

Y. Zhang, Weill Cornell Medical College/Cornell University; R. Padman, Carnegie Mellon University; P. Epner, Society to Improve Diagnosis in Medicine; V. Bauer, A. Solomonides, NorthShore University Health System; G. Rao, Case Western Reserve University School of Medicine

Executable Data Science Notebook for Phenotype Discovery Pipeline Using Observational Data

R. Chen, J. Duke, J. Sun, Georgia Institute of Technology

Using Misspellings in Word Vectors to Boost Information Retrieval Recall

R. McEwan, G. Melton, S. Pakhomov, University of Minnesota

Expanding the Practice of Reproducible Research in Biomedical Informatics with StatTag and Microsoft Word

L. Rasmussen, A. Baldridge, E. Whitley, L. Welty, Northwestern University

Adding Data Visualizations of Healthcare System Dynamics to i2b2

N. Benik, Harvard Medical School; D. Bolin, K. Borner, Indiana University; N. Brown, Harvard Medical School; S. Hutcheson, Indiana University; G. Weber, Harvard Medical School

S18: Oral Presentations – 'Omics Innovations in Methods and Applications

Discovering Biomarkers Associated with Type 2 Diabetes Mellitus using NHANES Database

Y. Li, IBM T.J. Watson Research Center; H. Yan, Columbia University ; X. Song, Icahn School of Medicine

Incorporating Protein Dynamics Through Ensemble Docking in Machine Learning Models to Predict Drug Binding

F. Alghamedy, J. Bopaiah, D. Jones, X. Zhang, University of Kentucky; H. Weiss, Markey Cancer Center; S. Ellingson, University of Kentucky

Generative Adversarial Networks: Evaluating Drug Effect in Synthetic Time Series Generated from EHR Data

A. Yahi, N. Tatonetti, Columbia University

Tandem Rank-goodness of Fit is a Feasible Measure to Guide Agnostic Metabolic Profile Selection in Automated Machine Learning Applications

A. Orlenko, J. Moore, D. Rader, S. Tuteja, M. Breitenstein, University of Pennsylvania, Perelman School of Medicine

Learning Opportunities for Drug Repositioning via GWAS and PheWAS Findings

W. Yin, Duke University; C. Gao, Y. Xu, B. Li, D. Ruderfer, Y. Chen, Vanderbilt University Medical Center

S19: Oral Presentations – Disease Models

Biopsy Records Do Not Reduce Diagnosis Variability in Cancer Patient EHRs: Are We More Uncertain After Knowing?

J. Diaz-Garelli, B. Wells, C. Yelton, R. Strowd, U. Topaloglu, WakeHealth

A Multi-scale Modeling Approach to Identify Optical Pathway Gliomas and Autism Spectrum Disorder in Individuals with Neurofibromatosis Type 1 (NF1)

M. Lui, A. Gupta, S. Morris, D. Gutmann, P. Payne, Washington University in St. Louis

Meta-analysis of Vaginal Microbiome Data Provides New Insights into Preterm Birth

I. Kosti, S. Lyalina, K. Pollard, A. Butte, M. Sirota, University of California San Francisco

Incorporating Observation Error in the Geospatial Assignment of Taxa for Virus Phylogeography

M. Scotch, T. Tahsin, D. Weissenbacher, K. O'Connor, University of Pennsylvania; A. Magge, Arizona State University; M. Suchard, University of California, Los Angeles; G. Gonzalez, University of Pennsylvania

Creating a Multi-organism Disease Model Resource at RGD

M. Shimoyama, S. Laulederkind, J. De Pons, E. Bolton, O. Ghiasvand, G. Hayman, H. Matthew, J. Smith, J. Thota, M. Tutaj, Y. Zhao, Marquette University/Medical College of Wisconsin; M. Dwinell, Medical College of Wisconsin

8:30 a.m. – 10:00 a.m.

S22: CRI Student Paper Competition

Emergency Department Clinician Perspectives on the Data Availability to Implement Clinical Decision Support Tools for Five Clinical Practice Guidelines
B. Douthit, R. Richesson, Duke University

Prototype of a Standards-based EHR and Genetic Test Reporting Tool Coupled with HL7-compliant Infobuttons
J. Crump, G. Del Fiol, University of Utah; M. Williams, Genomic Medicine Institute/Geisinger; R. Freimuth, Mayo Clinic

Trend Analysis of Aggregate Outcomes in Complex Health Survey Data
W. Durand, P. Stey, E. Chen, I. Sarkar, Brown University

Predicting Neonatal Encephalopathy from Maternal Data in Electronic Medical Records
T. Li, Duke University; C. Gao, C. Yan, Vanderbilt University; S. Osmundson, Vanderbilt University Medical Center; B. Malin, Y. Chen, Vanderbilt University

A Novel Representation of Vaccine Efficacy Trial Datasets for Use in Computer Simulation of Vaccination Policy
M. Tajgardoon, M. Wagner, S. Visweswaran, R. Zimmerman, University of Pittsburgh

S23: Oral Presentations – Transcriptomics

Genetic Variation Affecting Exon Skipping Contributes to Brain Structural Atrophy in Alzheimer’s Disease
Y. Lee, S. Han, D. Kim, University of Utah School of Medicine; D. Kim, Geisinger Health System; E. Horgousluoglu, S. Risacher, A. Saykin, K. Nho, Indiana University School of Medicine

Integrative Analysis of Immune Repertoire & Differential Gene Expression from RNA-seq in Kidney Organ Transplants
A. Ravoor, University of California, San Francisco/The Harker High School; S. Pineda, T. Sigdel, D. Rychkov, University of California, San Francisco; O. Bestard, Bellvitge Biomedical Research Institute; M. Sarwal, M. Sirota, University of California, San Francisco

Evaluating Generalizability of a Biospecimen Informatics Approach: Support for Local Requirements and Best Practices
C. Chen, E. Sholle, D. Kraemer, T. Campion, Weill Cornell Medicine

Understanding Immune System Sex Differences Through the Transcriptome
E. Bongen, P. Utz, P. Khatri, Stanford University

VenomSeq–A Platform for Drug Discovery from Animal Venoms Using Differential Gene Expression
J. Romano, H. Li, R. Realubit, C. Karan, N. Tatonetti, Columbia University

S24: Oral Presentations – Supplementing EHR data for research

Evaluation of Flowsheet Documentation in the Electronic Health Record for Residence, Living Situation, and Living Conditions
T. Winden, University of Kansas Medical Center/University of Minnesota; E. Chen, Brown University; Y. Wang, K. Monsen, G. Melton, University of Minnesota

ICD-10 Procedure Codes Produce Transition Challenges
A. Boyd, University of Illinois at Chicago; J. Li, C. Kenost, S. Rachid Zaim, University of Arizona; J. Krive, M. Mittal, University of Illinois at Chicago; R. Satava, University of Washington Medical Center; M. Burton, University of Illinois at Chicago; J. Smith, Y. Lussier, University of Arizona

Integrating Structured and Unstructured EHR Data Using an FHIR-based Type System: A Case Study with Medication Data
N. Hong, A. Wen, F. Shen, S. Sohn, S. Liu, H. Liu, G. Jiang, Mayo Clinic

A Model for Supplementing EHR Data with Location-based Information within an i2b2 System
B. Gardner, J. Pedersen, J. Campbell, University of Nebraska Medical Center; M. Campbell, Texas A&M University; W. Campbell, J. McClay, University of Nebraska Medical Center

A Cross-institutional Data Discovery Collaboration: Indexing Institutional Research Data
K. Read, N. Contaxis, I. Lamb, C. Larson, A. Surkis, New York University Langone Health

S25: Oral Presentations

Pediatric Emergency Assistance for Newborns Using Telehealth (PEANUT): Design and Implementation of a Neonatal Telemedicine Program
M. Dharmar, University of California Health

Research Informatics Infrastructure: Landscape and Sustainability
J. Obeid, Medical University of South Carolina; F. Wehbe, Northwestern University; P. Harris, Vanderbilt University; W. Barnett, Regenstrief Institute; N. Anderson, University of California Davis; P. Embi, Regenstrief Institute; W. Hogan, University of Florida; D. Bell, University of California Los Angeles; L. McIntosh, Research Data Alliance-US; U. Tachinardi, University of Wisconsin, Madison; J. Cimino, University of Alabama at Birmingham; P. Tarczy-Hornoch, University of Washington

Evaluation and Testing of Containerized i2b2 Deployment Using Docker
P. Dessai, University of California Los Angeles; K. Wagholikar, Massachusetts General Hospital; F. Sanz-Vidorreta, University of California Los Angeles

Improving Interoperability between Registries and EHRs
S. Blumenthal, PCPI

10:30 a.m. – 12:00 p.m.

S28: Oral Presentations – EHR

A Computational Approach for Prioritizing Selection of Therapies Targeting Drug Resistant Variation in Anaplastic Lymphoma Kinase
M. McCoy, S. Madhavan, Georgetown University

Somatic T-cell Receptor Diversity in a Chronic Kidney Disease Patient Population Linked to Electronic Health Records
D. Crawford, J. Cooke Bailey, P. Miron, Case Western Reserve University; J. McCauley, University of Miami; J. Sedor, J. O'Toole, W. Bush, Case Western Reserve University

Towards Patient-driven Phenotyping and Similarity for Precision Medicine
T. Callahan, University of Colorado Denver; O. Bodenreider, National Library of Medicine/National Institutes of Health; M. Kahn, University of Colorado Denver

An Automated Guidelines-based Approach for Variants Pathogenicity Assessment
G. Nicora, University of Pavia; I. Limongelli, engenome.srl; P. Gambelli, M. Memmi, C. Napolitano, Molecular Cardiology/IRCCS Istituti Clinici Maugeri; A. Malovini, University of Pavia; A. MazzantiS. Priori, Molecular Cardiology/IRCCS Istituti Clinici Maugeri; R. Bellazzi, University of Pavia/Istituti Clinici Maugeri

Rapid Mobilized Video Phenotyping for Autism Diagnosis
D. Wall, Q. Tariq, Stanford University

S29: Oral Presentations – Patient Outcomes Research Using Clinical Data

Inpatient Clinical Order Patterns Machine-learned From Teaching Versus Attending-only Medical Services
J. Wang, A. Schuler, N. Shah, M. Baiocchi, J. Chen, Stanford University

Evaluating the Utility of Personal Health Assessment (PHA) Data in Predictive and Outcomes Research
Z. Abrams, H. Bai, K. Coombes, T. Motiwala, The Ohio State University

Identifying Biologically Implausible Anthropometric Values in a Multisite Extraction of EHR Data for Secondary Use
D. Wieland, New York City Health+Hospitals/Jacobi, Albert Einstein College of Medicine; C. Jiang, Rockefeller University; A. Cheng, Clinical Director's Network; P. Holt, J. Breslow, Rockefeller University; D. Moftah, Clinical Director's Network; J. Tobin, Clinical Director's Network/Rockefeller University

Discrepancies in the Prevalence of Medical Conditions Based on VA vs. CMS Electronic Health Data
C. Meyer, N. Zhang, M. Whooley, San Francisco VA Medical Center

Translating Clinical Trial Results to a Target EHR Population Using Machine Learning and Causal Inference
B. Goldstein, Duke University/Duke Clinical Research Institute; M. Phelan, Duke Clinical Research Institute; N. Pagidipati, Duke University/Duke Clinical Research Institute

1:30 p.m. – 3:00 p.m.

S32: Oral Presentations – EHR as a Catalyst for Reverse Translation in Population Science

Binding Structured Molecular Pathology Test Data with i2b2 Datasets – A Preliminary Evaluation of Targeted Treatment Pathways in Cancer Patients
W. Campbell, University of Nebraska Medical Center; A. Bossler, University of Iowa Hospital; J. Campbell, University of Nebraska Medical Center

CATCH-KB: Establishing a Pharmacogenomics Variant Repository for Chemotherapy-induced Cardiotoxicity
M. Morash, H. Mitchell, Weill Cornell Medicine; A. Yu, Memorial Sloan Kettering Cancer Center; T. Campion, H. Beltran, O. Elemento, J. Pathak, Weill Cornell Medicine

Standardizing and Democratizing Access to Cancer Molecular Diagnostic Test Data from Patients to Drive Translational Research
S. Madhavan, Georgetown University; D. Ritter, Baylor College of Medicine; C. Micheel, Vanderbilt University; S. Rao, Georgetown University; A. Roy, Baylor College of Medicine; D. Sonkin, National Cancer Institute; M. McCoy, Georgetown University; M. Griffith, O. Griffith, Washington University; P. McGarvey, Georgetown University; S. Kulkarni, Baylor College of Medicine

REDESIGN: RDF-based Differential Signaling Framework for Precision Medicine Analytics
Z. Al-Taie, N. Thanintorn, I. Ersoy, O. Kholod, K. Taylor, R. Hammer, D. Shin, University of Missouri

Patient-led Deep Phenotyping Using a Lay-friendly Version of the Human Phenotype Ontology
M. Haendel, N. Vasilevsky, Oregon Health & Science University; C. Brownstein, I. Holm, Boston Children's Hospital; K. Rageth, Sanford Health; P. Robinson, Jackson Laboratory for Genomic Medicine; S. Köhler, Charite Hospital

S33: Partnerships in Innovation

A Patient Centric Approach to Research Preferences in the EHR
L. Lenert, J. Obeid, M. Habrat, Medical University of South Carolina; T. Johnson, A. Hsiao, Yale School of Medicine, Yale New Haven Health System; N. Smider, Epic

A Next-generation Approach to Drug Diversion Monitoring
N. Culbertson, Protenus; J. Smith, Johns Hopkins Health System

S34: Ignite-style Talks

Walking the Tightrope of Data Access and Data Security
T. Imler, Indiana University and Regenstrief Institute; F. Smith, Regenstrief Institute

Clinical Research Informatics Track in the University of Arkansas for Medical Sciences Graduate Program in Biomedical Informatics
M. Zozus, T. Williams, F. Prior, University of Arkansas for Medical Sciences

Identification, Replication, Visualization, and Interpretation of Patient Subgroups: Implications for Precision Medicine, and Predictive Modeling
S. Bhavnani, Y. Lin, L. Chennuri, Y. Kuo, University of Texas Medical Branch

Understanding Sociotechnical Factors for a Health Policy Informatics Project in South Africa
l. Snyder, A. Turner, J. Lane, A. Katz, University of Washington

Data Management for the Child Health and Mortality Prevention Surveillance (CHAMPS) Project
J. Lipsky, J Michael Consulting

A Common Clinical Registry Framework to Promote Interoperability across Healthcare, Research, Population Health and Registries
A. Walden, University of Arkansas for Medical Sciences; S. Blumenthal, PCPI; A. Shakir, Hi3 Solutions

8:30 a.m. – 10:00 a.m.

S37: Oral Presentations

Polypharmacology within the Full Kinome: A Machine Learning Approach
D. Jones, J. Bopaiah, F. Alghamedy, N. Jacobs, University of Kentucky; H. Weiss, Markey Cancer Center; W. de Jong, Lawrence Berkeley National Laboratory; S. Ellingson, University of Kentucky

Multi-omics Data Integration Strategy Improves Survival Prognostication in Renal Cell Carcinoma
H. Itakura, O. Gevaert, Stanford University

Characterizing Drug-related Adverse Events by Joint Analysis of Biomedical and Genomic Data: A Case Study of Drug-induced Pulmonary Fibrosis
A. Jiang, Cornell University/Cincinnati Children's Hospital Medical Center; A. Jegga, Cincinnati Children's Hospital Medical Center/University of Cincinnati College of Medicine/University of Cincinnati College of Engineering

Co-occurring Medical Complications Caused by Cocaine Usage in African American Diabetic Kidney Patients: Using Apriori Method
Y. Kim, P. Kathuria, University of Oklahoma; D. Delen, Oklahoma State University

Automated Extraction and Classification of Cancer Stage Mentions from Unstructured Text Fields in a Central Cancer Registry
A. AAlAbdulsalam, J. Garvin, A. Redd, M. Carter, C. Sweeny, University of Utah; S. Meystre, Medical University of South Carolina

S38: Predictive Modeling for Clinical Outcomes and Beyond (Part 1)

Predicting Causes of Data Quality Issues in a Clinical Data Research Network
R. Khare, B. Ruth, M. Miller, J. Tucker, L. Utidjian, H. Razzaghi, Children’s Hospital of Philadelphia; N. Patibandla, Children's Hospital Boston; E. Burrows, C. Bailey, Children’s Hospital of Philadelphia

Predicting the Outcome of Patient-provider Communication Sequences Using Recurrent Neural Networks and Probabilistic Models
M. Hasan, A. Kotov, Wayne State University; A. Carcone, Wayne State University School of Medicine; M. Dong, Wayne State University; S. Naar, Wayne State University School of Medicine

Improving Patient and Caregiver Engagement Through the Application of Data Science Methods to Audio Recorded Clinic Visits Stored in Personal Health Libraries Using ORALS
P. Barr, S. Hassanpour, W. Haslett, M. Dannenberg, C. Ganoe, R. Fail, A. Das, R. Arend, S. Piper, Dartmouth College; J. Ryan, Ryan Family Practice; M. Bruce, Geisel School of Medicine; G. Elwyn, Dartmouth College

Probabilistic Prognostic Estimates of Survival in Metastatic Cancer Patients (PPES-Met) Utilizing Free-text Clinical Narratives
I. Banerjee, M. Gensheimer, D. Wood, A. Henry, D. Chang, D. Rubin, Stanford University

S39: Oral Presentation – Clinical Data Interoperability

Usability Evaluation of an Unstructured Clinical Document Query Tool for Researchers
G. Hultman, R. McEwan,. Pakhomov, E. Lindemann, S. Skube, G. Melton, University of Minnesota

Provider Adoption of Speech Recognition and its Impact on Satisfaction, Documentation Quality, Efficiency, and Cost in an Inpatient EHR
K. Saxena, R. Diamond, Health-Quest; R. F. Conant, T. Mitchell, K. Yakimow, G. Gallopyn, (authors should be switched) Nuance Communications, Inc.

A Crowdsourcing Framework for Medical Data Sets
C. Ye, J. Coco, B. Malin, T. Lasko, L. Novak, J. Denny, Y. Vorobeychik, C. Hajaj, A. Epishova, H. Bogardus, D. Fabbri, Vanderbilt University

Interoperability between Value Sets for Clinical Research and Healthcare: Mapping Value Sets between the Clinical Data Interchange Standards Consortium (CDISC) and Meaningful Use
R. Cholan, Oregon Health & Science University; O. Bodenreider, NLM

Evaluating a Practice-based Health IT Intervention Using Audit Log, Qualitative and Clinical Data
X. Yan, J. Jones, J. Delatorre-Reimer, H. Husby, C. Mosser, R. Nerlekar, S. Liang, S. Mudiganti, Z. Shen, W. Stewart, Sutter Health

10:30 a.m. – 12:00 p.m.

S41: Oral Presentations – Imaging

Comparison of Different Classifiers with Active Learning to Support Quality Control in Nucleus Segmentation in Pathology Images
S. Wen, T. Kurc, L. Hou, J. Saltz, R. Gupta, Stony Brook University; R. Batiste, T. Zhao, Stony Brook School of Medicine; V. Nguyen, D. Samaras, W. Zhu, Stony Brook University

Predicting Low Information Laboratory Diagnostic Tests
S. Roy, J. Hom, Stanford University; L. Mackey, Microsoft Research New England; N. Shah, J. Chen, Stanford University

Development of MRI-based Radiomics Signature for Predicting Molecular Subtypes in Medulloblastoma
Z. Wang, Stanford University/Zhejiang University; M. Zhou, E. Tranvinh, B. Lanzman, K. Shpanskaya, Stanford University; T. Poussaint, Harvard University; M. Iv, K. Yeom, O. Gevaert, Stanford University

Deciphering the Molecular Basis of Lung Adenocarcinoma Dedifferentiation and Prognosis by Integrating Omics and Histopathology
K. Yu, Harvard Medical School; G. Berry, D. Rubin, C. Re, R. Altman, M. Snyder, Stanford University

NegBio: A High-performance Tool for Negation and Uncertainty Detection in Radiology Reports
Y. Peng, X. Wang, L. Lu, M. Bagheri, R. Summers, Z. Lu, National Institutes of Health

S42: Oral Presentations – Standards and Models for Clinical Trial, Mobile Health and Population Data

CDISC SHARE, a Global, Cloud-based Resource of Machine-readable CDISC Standards for Clinical and Translational Research
S. Hume, A. Chow, CDISC; J. Evans, Samvit Solutions, LLC; F. Malfait, TransCelerate Biopharma; J. Chason, J. Wold, CDISC; W. Kubick, HL7; L. Becnel, CDISC/Baylor College of Medicine

Applying Probabilistic Decision Models to Clinical Trial Design
M. Phillips, W. Smith, University of Washington

Automatically Linking Registered Clinical Trials to their Published Results with Deep Highway Networks
T. Goodwin, University of Texas at Dallas; M. Skinner, University of Texas at Dallas/University of Texas Southwestern Medical Center; S. Harabagiu, University of Texas at Dallas

Open mHealth: Common Data Schemas and API for Mobile Health Data
S. Carini, University of California San Francisco/Open mHealth; E. Farrugia, D. Haddad, Open mHealth/Overlap Health, Inc; D. Estrin, Cornell Tech/Open mHealth; S. Kumar, University of Memphis; I. Sim, University of California San Francisco/Open mHealth

Data Science Approach to Monitoring Health Status for a Diabetes Population
A. Ford, Livongo Health; J. Bollyky, Livongo Health/Stanford University School of Medicine; J. Schneider, J. Bridgewater, Livongo Health

S43: Oral Presentations – Research Informatics Infrastructure

i2b2 Implemented Over SMART-on-FHIR
N. Paris, AP-HP/CNRS/INSERM; M. Mendis, Partners Healthcare; X. Tannier, INSERM; S. Murphy, Partners Healthcare; P. Zweigenbaum, CNRS

Feasibility of Homomorphic Encryption for Sharing i2b2 Aggregate-level Data in the Cloud
J. Raisaro, École Polytechnique Fédérale de Lausanne; J. Klann, K. Wagholikar, H. Estiri, Massachusetts General Hospital/Harvard Medical School/Partners Healthcare; J. Hubaux, École Polytechnique Fédérale de Lausanne; S. Murphy, Harvard Medical School/Massachusetts General Hospital/Partners Healthcare

The Ad-hoc Uncertainty Principle of Patient Privacy
J. Klann, Harvard University School of Medicine/Partners Healthcare/Massachusetts General Hospital; M. Joss, Partners Healthcare; R. Shirali, Boston Children's Hospital; M. Natter, Boston Children's Hospital/Harvard University School of Medicine; S. Schneeweiss, Brigham and Women's Hospital/Harvard University School of Medicine/Partners Healthcare; K. Mandl, Boston Children's Hospital/Harvard University School of Medicine; S. Murphy, Partners Healthcare/Massachusetts General Hospital/Harvard University School of Medicine

A Transparent System for Evaluating Data Completeness in the Accessible Research Commons for Health (ARCH) Network
H. Estiri, J. Klann, Harvard Medical School/Massachusetts General Hospital; S. Weiler, K. Mandl, Harvard Medical School; S. Murphy, Harvard Medical School/Massachusetts General Hospital

Exploring Hadoop-based Data Lakes for Research
R. Chandras, NYU Langone Health; M. Cantor, New York University Langone Health/New York University School of Medicine; J. Shein, New York University Langone Health

S45: Oral Presentations – Predictive Modeling for Clinical Outcomes and Beyond (Part 2)

Using Machine Learning Algorithms to Predict Risk for Development of Calciphylaxis in Patients with Chronic Kidney Disease
R. Kleiman, University of Wisconsin-Madison/Marshfield Clinic Research Institute ; E. LaRose, Marshfield Clinic Research Institute; J. Badger, Marshfield Clinic Research Institute/University of Wisconsin-Madison; D. Page, University of Wisconsin-Madison; M. Caldwell, J. Clay, Marshfield Clininc; P. Peissig, Marshfield Clinic Research Institute

What's in a Note? Unpacking Predictive Value in Clinical Note Representations
W. Boag, D. Doss, T. Naumann, P. Szolovits, Massachusetts Institute of Technology

Accurate and Interpretable Intensive Care Risk Adjustment for Fused Clinical Data ith Generalized Additive Models
B. Marafino, Stanford University; R. Dudley, University of California, San Francisco; N. Shah, J. Chen, Stanford University

Predicting Mortality in Diabetic ICU Patients Using Machine Learning and Severity Indices
R. Anand, P. Stey, S. Jain, D. Biron, H. Bhatt, K. Monteiro, E. Feller, M. Ranney, I. Sarkar, E. Chen, Brown University

Predicting Postoperative Bleeding Risk for Patients Undergoing Colorectal Surgery Using Machine Learning
D. Chen, N. Afzal, S. Sohn, E. Habermann, J. Naessens, D. Larson, Mayo Clinic; H. Liu, Mayo Clinic

S46: Oral Presentations – Clinical Data Mining and Machine Learning (Part 2)

Multi-task Learning to Identify Outcome-Specific Risk Factors that Distinguish Individual Micro and Macrovascular Complications of Type 2 Diabetes
E. Kim, University of Minnesota/Medical Research Institute; D. Pieczkiewicz, University of Minnesota; M. Castro, P. Caraballo, Mayo Clinic; G. Simon, University of Minnesota

A Network-theoretic Analysis of Hospital Admission, Transfer, and Discharge Data
J. Klobusicky, Rensselaer Polytechnic Institute; N. Ryan, M. Cioffi, N. Mukhtar, Bucknell Univeristy

Neighborhood Socioeconomic Status as a Predictor of Health Outcomes in Electronic Health Record Based Studies
N. Bhavsar, A. Gao, Duke University School of Medicine; N. Pagidipati, Duke University School of Medicine/Duke Clinical Research Institute; M. Phelan, Duke Clinical Research Institute; B. Goldstein, Duke University School of Medicine/Duke Clinical Research Institute

The Information Gap between Research Eligibility Criteria and EHR Data
A. Butler, W. Wei, C. Yuan, T. Kang, Columbia University; Y. Si, The University of Texas Health Science Center at Houston; C. Weng, Columbia University

Automated Detection of Diabetic Retinopathy Using Deep Learning
T. Lindsey, Stanford University

S47: Oral Presentations

Secure Reusable Linkage Between a EHR Patient Portal and REDCap for Population-based Survey Research
M. Habrat, L. Moriera, J. Clark, C. Jaruzel, J. Oates, J. Obeid, L. Lenert, Medical University of South Carolina

Application of Data Provenance in Healthcare Analytics Software: Information Visualization of User Activities
S. Xu, Kings College London/Imosphere Ltd.; T. Rogers, Imosphere Ltd.; E. Fairweather, Kings College London; A. Glenn, J. Curran, Imosphere Ltd.; V. Curcin, Kings College London

CHCi – A Dynamic Data Platform for Clinical Data Capture and Use
D. Wu, University of Michigan/University of Cincinnati; K. Zheng, University of Michigan/University of California; D. Bradley, University of Michigan

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