2017 Joint Summits Papers

Monday, March 27, 2017

10:30 a.m. – 12:00 p.m.

S03: Papers – Data Processing for Discovery

Towards Generation, Management, and Exploration of Combined Radiomics and Pathomics Datasets for Cancer Research 
J. Saltz, J. Almeida, Y. Gao, Stony Brook University; A. Sharma, Emory University; E. Bremer, T. DiPrima, T. Kurc,  M. Saltz, Stony Brook University; J. Kalpathy–Cramer, Massachusetts General Hospital

Development of a Framework for Large Scale Three-dimensional Pathology and Biomarker Imaging and Spatial Analytics 
Y. Liang, F. Wang, P. Zhang, J. Saltz, Stony Brook University; D. Brat, J. Kong, Emory University

Search Datasets in Literature: A Case Study of GWAS 
Y. Zhang, H. Xu, The University of Texas Health Science Center at Houston

Introducing a Comprehensive Informatics Framework to Promote Breast Cancer Risk Assessment and Chemoprevention in the Primary Care Setting 
J. Finkelstein, J. Wood, K. Crew, R. Kukafka, Columbia University

1:30 p.m. – 3:00 p.m.

S06: TBI Student Paper Competition

Interrogating Patient-level Genomics and Mouse Phenomics towards Understanding Cytokines in Colorectal Cancer Metastasis 
X. Cai, Y. Chen, C. Zheng, R. Xu, Case Western Reserve University

Design Recommendations for Pharmacogenomics Clinical Decision Support Systems 
M. Khelifi, P. Tarczy-Hornoch, B. Devine, W. Pratt, University of Washington

Integrative Network and Transcriptomics-based Approach Predicts Genotype-specific Drug Combinations for Melanoma 
K. Regan, The Ohio State University; P. Payne, Washington University; F. Li, The Ohio State University

Precision Diagnosis of Melanoma and Other Skin Lesions from Digital Images Using Deep Learning 
A. Bhattacharya, University of California, San Francisco/University of California, Santa Barbara; A. Young, A. Wong, D. Hadley, M. Wei, University of California, San Francisco

Tuesday, March 28, 2017

10:30 a.m. – 12:00 p.m.

S13: CRI Student Paper Competition – 1

Identifying Psychiatric Comorbidities for Obstructive Sleep Apnea in the Biomedical Literature and Electronic Health Record 
J. Haddad, E. Chen, Warren Alpert Medical School, Brown University

Populating Physician Biographical Pages Based on EMR Data 
F. Shen, S. Sohn, M. Rastegar-Mojarad, S. Liu, J. Pankratz, M. Hatton, N. Sowada, O. Shrestha, S. Shurson, H. Liu, Mayo Clinic

Classifying Supplement Use Status in Clinical Notes 
Y. Fan, L. He, S. Pakhomov, G. Melton, R. Zhang, University of Minnesota

Spatio-temporal Analysis for New York State SPARCS Data 
X. Chen, Y. Wang, Stony Brook University; E. Schoenfeld, M. Saltz, J. Saltz, Stony Brook School of Medicine; F. Wang, Stony Brook University

1:30 p.m. – 3:00 p.m.

S16: Papers – EHR-based Phenotyping

A Comparative Study of Different Methods for Automatic Identification of Clopidogrel-induced Bleedings in Electronic Health Records 
H. Lee, M. Jiang, Y. Wu, University of Texas Health Science Center at Houston; C. Shaffer, J. Cleator, J. Denny, E. Friedman, D. Roden, Vanderbilt University Vanderbilt University; J. Lewis, University of Maryland; H. Xu, University of Texas Health Science Center at Houston

Electronic Phenotyping with APHRODITE and the Observational Health Sciences and Informatics (OHDSI) Data Network 
J. Banda, Stanford University; Y. Halpern, D. Sontag, New York University; N. Shah, Stanford University

Reducing Clinical Noise for Body Mass Index Measures Due to Unit and Transcription Errors in the Electronic Health Record 
R. Goodloe, E. Farber-Eger, J. Boston, Vanderbilt University Medical Center; D. Crawford, W. Bush, Case Western Reserve University

Surveillance of Peripheral Arterial Disease Cases Using Natural Language Processing of Clinical Notes 
N. Afzal, S. Sohn, C. Scott, H. Liu, I. Kullo, A. Arruda-Olson, Mayo Clinic

S17: Papers – Clinical Integration

Integrating Medication Alert Data into a Clinical Data Repository to Enable Retrospective Study of Drug Interaction Alerts in Clinical Practice 
M. Liu, University of Kansas Medical Center; B. Melton, University of Kansas; G. Ator, R. Waitman, University of Kansas Medical Center

Incorporating Data Citation in a Biomedical Repository: An Implementation Description 
S. Gupta, C. Zabarovskaya, B. Romine, D. Vianello, Washington University School of Medicine; C. Vitale, Washington University; L. McIntosh, Washington University School of Medicine

Evolving Research Data Sharing Networks to Clinical App Sharing Networks 
K. Wagholikar, Harvard Medical School; R. Colas, R. Jain, E. Oliveira, P. Patil, K. Yadav, LPHI; J. Mandel, K. Mandl, Children's Hospital Boston; J. Klann, S. Murphy, Harvard Medical School

A Knowledge-based System for Intelligent Support in Pharmacogenomics Evidence Assessment: Ontology-driven Evidence Representation and Retrieval 
C. Lee, B. Devine, P. Tarczy-Hornoch, University of Washington

3:30 p.m. – 5:00 p.m.

S19: Papers – The EHR as a Resource for Discovery

Enhancing Electronic Health Record Data with Geospatial Information 
S. Xie, R. Greenblatt, M. Levy, B. Himes, University of Pennsylvania

Extracting Country-of-origin from Electronic Health Records for Gene-environment Studies as Part of the Epidemiologic Architecture for Genes Linked to Environment (EAGLE) Study 
E. Farber-Eger, R. Goodloe, J. Boston, Vanderbilt University Medical Center; W. Bush, D. Crawford, Case Western Reserve University

Extracting Geographic Locations from the Literature for Virus Phylogeography Using Supervised and Distant Supervision Methods 
D. Weissenbacher, A. Sarker, T. Tahsin, G. Gonzalez, M. Scotch, Arizona State University

Systematic Analysis of Free-text Family History in the Electronic Health Records 
Y. Wang, L. Wang, M. Rastegar-Mojarad, S. Liu, F. Shen, H. Liu, Mayo Clinic

S20: Papers – Machine Learning for Clinical Applications

Deep Learning from EEG Big Data for Inferring Underspecified Information 
T. Goodwin, S. Harabagiu, University of Texas at Dallas

Predicting Intervention Onset in the ICU with Switching State Space Models 
M. Ghassemi, Massachusetts Institute of Technology; M. Wu, Yale University; M. Hughes, F. Doshi-Velez, Harvard University

Combining Kernel and Model Based Learning for HIV Therapy Selection 
S. Parbhoo, University of Basel; J. Bogojeska, IBM Research Zurich; M. Zazzi, University of Siena; V. Roth, University of Basel; F. Doshi–Velez, Harvard University

SDT: A Tree Method for Detecting Patient Subgroups with Personalized Risk Factors 
X. Li, D. Zhu, M. Dong, M. Nezhad, A. Janke, P. Levy, Wayne State University

Wednesday, March 29, 2017

8:30 a.m. – 10:00 a.m.

S24: Student Paper Competition – 2

Triangulating Methodologies from Software, Medicine and Human Factors Industries to Measure Usability and Clinical Efficacy of Medication Data Visualization in an Electronic Health Record System 
B. Chang, M. Kanagaraj, Duke University School of Medicine; B. Neely, Duke University Health System ; N. Segall, Duke University School of Medicine; E. Huang, Duke University School of Medicine/Duke University Health System

High-risk Drug-drug Interactions Between Clinical Practice Guidelines for Management of Chronic Conditions 
G. Tso, Veterans Affairs/Stanford University; S. Tu, M. Musen, Stanford University; M. Goldstein, Veterans Affairs/Stanford University

Quantifying the Relative Change in Physical Activity after Total Knee Arthroplasty Using Accelerometer Based Measurements 
V. Agarwal, M. Smuck, N. Shah, Stanford University

Eye-tracking for Clinical Decision Support: A Method to Capture Automatically What Physicians are Viewing in the EMR 
A. King, H. Hochheiser, S. Visweswaran, G. Clermont, G. Cooper, University of Pittsburgh

10:30 a.m. – 12:00 p.m.

S26: Papers – Next-generation Pharmacology

Discovering Adverse Drug Events Combining Spontaneous Reports with Electronic Medical Records: A Case Study of Conventional DMARDs and Biologics for Rheumatoid Arthritis 
L. Wang, M. Rastegar–Mojarad, S. Liu, Mayo Clinic; H. Zhang, Chinese Pharmaceutical Association; H. Liu, Mayo Clinic

Enabling Comprehension of Patient Subgroups and Characteristics in Large Bipartite Networks: Implications for Precisions Medicine 
S. Bhavnani, J. Mathew, UTMB; T. Chen, University of Houston; S. Visweswaran, University of Pittsburgh; G. Bellala, HP Labs

Visualization of Molecular Structures Using HoloLens-based Augmented Reality 
M. Hoffman, Children's Mercy/University of Missouri Kansas City; J. Provance, University of Missouri Kansas City

Characterizing the Strength of Evidence in FDA Labels for Pharmacogenomic Biomarker-Guided Medication Use 
B. Devine, L. Chin, S. Baradaran, K. Keyloun, W. Canestaro, J. Pharm, University of Washington

1:30 p.m. – 3:00 p.m.

S31: Papers – Text Mining

A Fast Text Mining Approach for Predicting Pairwise Associations in Biomedical Applications 
F. Kuusisto, J. Steill, Morgridge Institute for Research; Z. Kuang, University of Wisconsin; J. Thomson, Morgridge Institute for Research/University of Wisconsin; D. Page, University of Wisconsin; R. Stewart, Morgridge Institute for Research

Ground Truth Creation for Complex Clinical NLP Tasks – an Iterative Vetting Approach and Lessons Learned 
J. Liang, C. Tsou, M. Devarakonda, IBM Research

Identifying Metastases Related Information from Pathology Reports of Lung Cancer Patients 
E. Soysal, The University of Texas Health Science Center at Houston; J. Warner, Vanderbilt University/Vanderbilt University Medical Center; J. Denny, Vanderbilt University; H. Xu, The University of Texas Health Science Center at Houston

Clinical Trials.Gov: A Topical Analyses 
V. Anand, A. Cahan, S. Ghosh, IBM T.J. Watson Research Center

Thursday, March 30, 2017

8:30 a.m. – 10:00 a.m.

S33: Papers – Data Harmonization and Visualization

Visualizing and Validating Metadata Traceability within the CDISC Standards 
S. Hume, Dakota State University/Clinical Data Interchange Standards Consortium; S. Sarnikar, California State University, East Bay; L. Becnel, Clinical Data Interchange Standards Consortium; D. Bennett, Dakota State University

D2Refine: A Platform for Clinical Research Study Data Element Harmonization and Standardization 
D. Sharma, H. Solbrig, Mayo Clinic; E. Prud’hommeaux, W3C/MIT; K. Lee, J. Pathak, Weill Cornell Medicine; G. Jiang, Mayo Clinic

Rapid and Reusable Text Visualization and Exploration Development with DELVE 
D. Harris, R. Kavuluru, J. Jaromczyk, University of Kentucky; T. Johnson, University of Texas Health Science Center at Houston

Generalizable Middleware to Support Use of REDCap Dynamic Data Pull for Integrating Clinical and Research Data 
T. Campion, Weill Cornell Medical College

S34: Papers – Data Mining and Discovery

Integrating Temporal Pattern Mining in Ischemic Stroke Prediction and Treatment Pathway Discovery for Atrial Fibrillation 
S. Guo, X. Li, H. Liu, IBM Research – China; P. Zhang, IBM T.J. Watson Research Center; X. Du, Beijing Anzhen Hospital; G. Xie, IBM Research – China; F. Wang, Cornell University

An Exploration of Latent Structure in Observational Huntington Disease Studies 
S. Ghosh, Z. Sun, Y. Li, Y. Cheng, IBM T.J. Watson Research Center; A. Mohan, C. Sampaio, CHDI Foundation; J. Hu, IBM T.J. Watson Research Center

Active Deep Learning-based Annotation of Electroencephalography Reports for Cohort Identification 
R. Maldonado, T. Goodwin, S. Harabagiu, The University of Texas at Dallas

Correlating Lab Test Results in Clinical Notes with Structured Lab Data: A Case Study in HbA1c and Glucose 
S. Liu, Mayo Clinic/University at Buffalo; L. Wang, D. Ihrke, Mayo Clinic; V. Chaudhary, University at Buffalo; C. Tao, University of Texas Health Science Center at Houston; C. Weng, Columbia University; H. Liu, Mayo Clinic

10:30 a.m. – 12:00 p.m.

S37: Papers – Clinical Decision Support

A Clinical Decision Support System for Monitoring Post-colonoscopy Patient Follow-up and Scheduling 
R. Wadia, M. Shifman, VA Connecticut Healthcare System/Yale University; F. Levin, VA Connecticut Healthcare System; L. Marenco, C. Brandt, K. Cheung, T. Taddei, M. Krauthammer, VA Connecticut Healthcare System/Yale University

SemanticFind: Locating What You Want in a Patient Record, Not Just What You Ask For 
J. Prager, J. Liang, M. Devarakonda, IBM T.J. Watson Research Center

Automated Prediction of Hepatic Arterial Stenosis 
J. Baraboo, D. Dinakarpandian, University of Missouri-Kansas City; S. Chan, CMH

Analyzing Electronic Medical Records to Predict Risk of DIT (Death, Intubation, or Transfer to ICU) in Pediatric Respiratory Failure or Related Conditions 
T. Viangteeravat, O. Akbilgic, R. Davis, University of Tennessee Health Science Center at Memphis

1:30 p.m. – 3:00 p.m.

S42: Papers – Supporting Systems for Clinical Research

PheKnow-Cloud: A Tool for Evaluating High-throughput Phenotype Candidates Using Online Medical Literature 
J. Henderson, The University of Texas at Austin; R. Bridges, Epic Systems; J. Ho, Emory University; B. Wallace, Northeastern University; J. Ghosh, The University of Texas at Austin

Monitoring Biomedical Literature for Post-market Safety Purposes by Analyzing Networks of Text-based Coded Information 
T. Botsis, M. Foster, K. Kreimeyer, A. Pandey, R. Forshee, Food and Drug Administration

A Data Capture Framework for Large-scale Interventional Studies with Survey Workflow Management. 
S. Tao, N. Zeng, X. Wu, University of Kentucky; W. Zhu, X. Li, Case Western Reserve University; L. Cui, G. Zhang, University of Kentucky