Center for Predictive Computational Phenotyping (CPCP): Training Plans May 15, 2015 Debora Treu and...
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Transcript of Center for Predictive Computational Phenotyping (CPCP): Training Plans May 15, 2015 Debora Treu and...
Center for Predictive Computational Phenotyping (CPCP): Training Plans
May 15, 2015
Debora Treu and Whitney SweeneyCenter for Predictive Computational Phenotyping (CPCP)
University of Wisconsin-Madison
What is CPCP?• The Center for Predictive Computational Phenotyping
(CPCP) promises to significantly advance the state of the art in computational methods for transforming large, heterogeneous, high-dimensional data sources into predictive models for biomedicine. Specifically, we are focusing on a broad range of problems that can be cast as computational phenotyping.
timenow
predict a clinically important phenotype before it is exhibited
prospective phenotyping
extract a relevant phenotype from a complex data source or collection of sources
retrospective phenotyping
?
The term phenotype refers to the observable properties of an organism that result from the interaction of its genotype and its environment. Some phenotypes are easily measured and interpreted, and are available in an accessible format. However, a wide range of scientifically and clinically important phenotypes do not satisfy these criteria. In such cases, computational phenotyping methods are required either to:
CPCP Aims• Aim 1
Develop, evaluate and disseminate computational and statistical algorithms, models and software packages that significantly advance the state of the art in predictive computational phenotyping.
• Aim 2
Develop, conduct and evaluate training activities that reach a broad set of audiences whose education, research and practice would significantly benefit from having state-of-the-art knowledge about data science, predictive models for biomedicine, and computational phenotyping. These audiences include:
• Biomedical scientists• Clinicians• Data scientists• Postdocs• Graduate students• Undergraduates• General public
biomedical informatics
computer science
biostatistics
engineering
biological sciences
bioethics & law
medicine
CPCP
The Center for Predictive Computational Phenotyping
Types of Events
• Weekly Center Meetings• Short courses• Tutorial Modules• “Boot camp” Tutorials• Seminars• Training in Undergraduate Research• TED-style talks• Annual Center Retreat
Summer Research Program in Computational Biology and Biostatistics (CBB)
• Nicholas Escanilla, Lake Forest College Mentor: David Page
• Vir Patel, Western Kentucky University Mentor: Sushmita Roy
• Emily Balczewski, Carleton College Mentor: Vikas Singh
Seminars on High-Throughput Computing Platforms
• The primary goal of these seminars are to help researchers make sense of what tools are
available for the analysis of large and complex data sets and how they are relevant to their
specific work.
• The Hadoop Ecosysytem: A Bird's-Eye Overview
Jignesh Patel, CS
This seminar addressed tools like Hadoop
and Hive. It was videotaped and will be
available on the CPCP website.
• CONDOR and the Center for High Throughput Computing Miron Livny, CS and Morgridge; Tim Cartwright, CS; Lauren Michael & Christina Koch, Morgridge
This seminar will specifically deal with the tools provided by the Center
for High Throughput Computing at the UW Madison. This seminar is tentatively
scheduled for June 2015. It will also be videotaped and available on the CPCP website.
Small Talks on Big Data• These “TED-style” talks have been created to introduce
some of the scientific questions and quantitative problems with which the CPCP is grappling. Our goals are to share the knowledge and innovations derived while working on these issues as well as to promote collaborations with other data and biomedical scientists.• Mark Craven, BMI
• Biomedical Big Data and the Computational Phenotyping Challenge
• Beth Burnside, Radiology• Personalizing Breast Cancer: Integrating Predictive Phenotypes into
Clinical Care
• David Page, BMI• Predicting Health Events from Electronic Health Records by Machine
Learning
First Annual Retreat
Center for Predictive Computational Phenotyping June 12, 2015
DeLuca Forum, The Discovery Building
8:00 – 8:30 continental breakfast and registration
8:30 – 8:45 Overview of the Center for Predictive Computational Phenotyping
Mark Craven, Professor, Dept. of Biostatistics & Medical Informatics (BMI)
Director, CPCP
8:45 – 9:00 welcoming remarks
Robert Golden, Dean of the School of Medicine and Public Health
9:00 – 10:15 keynote talk
Understanding Alzheimer’s via Neuroimage-Based Phenotyping
Barbara Bendlin, Assistant Professor, Dept. of Medicine
Sterling Johnson, Professor, Dept. of Medicine
Vikas Singh, Associate Professor, Dept. of BMI
10:15 – 11:00 poster session
11:00 – 12:00 Transcription-Based Cellular Phenotyping
Colin Dewey, Assoc. Professor, Dept. of BMI
Christina Kendziorski, Professor, Dept. of BMI
Epigenome-Based Phenotyping
Sunduz Keles, Professor, Dept. of BMI
Sushmita Roy, Assistant Professor, BMI
12:00 – 1:00 lunch
(continued)
1:00 – 1:15 welcoming remarks
Brad Schwartz, CEO of the Morgridge Institute for Research
1:15 – 2:45 Prioritization Strategies for Ranking, Selection and Data Integration in
Computational Phenotyping
Michael Newton, Professor, Dept. of BMI
Associate Director, CPCP
High-Throughput Computing in Support of High-Throughput Phenotyping
Miron Livny, Professor, Dept. of Computer Sciences
CTO, Morgridge Institute
Gary Pack, Postdoctoral Fellow, Marshfield Clinic Research Foundation
Yuriy Sverchkov, Postdoctoral Fellow, Dept. of BMI
Scaling up Inductive Logic Programming for EHR-Based Phenotyping
David Page, Professor, Dept. of BMI
Jignesh Patel, Professor, Dept. of Computer Sciences
2:45 – 3:30 poster session
3:30– 4:30 Active Learning from Human Experts and an Application to
EHR-Based Phenotyping
Rob Nowak, Professor, Dept. of Electrical and Computer Engineering
Peggy Peissig, Director, Biomedical Informatics Research Center
Marshfield Clinic Research Foundation
Building Entity Matching Management Systems for Big Data Problems in
Biomedicine
AnHai Doan, Professor, Dept. of Computer Sciences
4:30 – 4:45 closing comments
4:45 – reception
The CPCP partners with the Morgridge Institute for Research and the Marshfield Research Clinic, and receives additional support from the UW-Madison School of Medicine and Public Health and the Office of the Vice Chancellor for Research and Graduate Education at the University of Wisconsin-Madison with funding from the Wisconsin Alumni Research Foundation.
This research is supported by the National Institutes of Health under Award Number U54AI117924. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.