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CAFCW20 Program

The virtual Sixth Computational Approaches for Cancer Workshop (CAFCW20) was held on Friday, November 13, 2020, 10:00 a.m. to 6:30 p.m. ET, in conjunction with SC20: The International Conference on High Performance Computing, Networking, Storage and Analysis. You can still register for the standalone Workshop-only option, which gets you access to all Workshops proceedings on demand until May. Registration is required by Dec. 7, 2020, to access the on-demand content.

Friday, November 13, 2020, 10:00 a.m.–6:30 p.m.

(All times listed are Eastern Time)

Register here

View Presenter Bios

10:00 a.m.–10:10 a.m.

Welcome — Sixth Computational Approaches for Cancer Workshop (CAFCW20)

Eric Stahlberg, PhD, Frederick National Laboratory for Cancer Research

10:10 a.m.–11:00 a.m.

Keynote: Data Science Initiatives at the National Cancer Institute Norman “Ned” Sharpless, MD, National Cancer Institute Director Introduced by Sean Hanlon, PhD, National Cancer Institute

Watch the keynote

View Dr. Sharpless's slides.

11:00 a.m.–11:45 a.m.

Panel: HPC, Cancer and COVID-19

Organizer and Moderator: Patricia Kovatch, Icahn School of Medicine, Mount Sinai

Panel:

Jim Brase, Lawrence Livermore National Laboratory

Diane Del Valle, Icahn School of Medicine at Mount Sinai

Sacha Gnjatic, PhD, Icahn School of Medicine at Mount Sinai

Sharon Nirenberg, MD, Icahn School of Medicine at Mount Sinai

Carlos Simmerling, PhD, Stony Brook University

11:45 a.m.–12:00 p.m.

Scalable Human Pharmacokinetics Property Prediction for Cancer Drug Discovery at ATOM

Presenter: Benjamin Madej, PhD, Frederick National Laboratory for Cancer Research

12:00 p.m.–12:15 p.m.

CAFCW20 Morning Break

12:15 p.m.–12:30 p.m.

Scaffold-Induced Molecular Subgraphs (SIMSG): Effective Graph Sampling Methods for High-Throughput Computational Drug Discovery

Rick Stevens; Ashka Shah; Arvind Ramanathan, PhD; Max Zvyagin; Austin Clyde

Presenters: Ashka Shah, University of Chicago, and Max Zvyagin, Argonne National Laboratory

12:30 p.m.–12:45 p.m.

Causal Deconvolution of a Mechanistic Model of EGFR and ERK Signaling explains Adaptive and Genetic Resistance in Melanoma

Presenter: Fabian Fröhlich, PhD, Harvard Medical School

12:45 p.m.–1:00 p.m.

An Efficient, Data-Driven Approach to Model Specific Cancer Cell Lines

Peter Balogh, PhD; John Gounley, PhD; Amanda Randles, PhD

Presenter: Peter Balogh, PhD, Duke University

1:00 p.m.–1:15 p.m.

Deep Learning Based Prediction of the Temporal Behavior of RAS Protein Conformations on Simulated Cell Membrane Surfaces

Brian C. Van Essen, PhD; James Glosli, PhD; Sam Adé Jacobs. PhD; Timothy S. Carpenter, PhD; Peer-Timo Bremer, PhD; Harsh Bhatia, PhD; Helgi I. Ingólfsson, PhD; Gautham Dharuman, PhD; Adam Moody

Presenter: Adam Moody, Lawrence Livermore National Laboratory

1:15 p.m.–2:00 p.m.

Panel #2: Digital Twins for Cancer Care

Organizers: Emily Greenspan, PhD, National Cancer Institute and Eric Stahlberg, Frederick National Laboratory for Cancer Research

Moderator: Eric Stahlberg, PhD, Frederick National Laboratory for Cancer Research

Panel:

Richard Arthur, GE Research

Emily Greenspan, PhD, National Cancer Institute

Tina Hernandez-Boussard, PhD, Stanford University

2:00 p.m.–3:20 p.m.

Lunch Break

Networking and Informal Discussion via WebEx

Poster and Presenters (via virtualpostersession.org)

A Multistaged Hyperparallel Optimization of the Fuzzy-Logic Mechanistic Model of Molecular Regulation, Paul Aiyetan, MD, Frederick National Laboratory for Cancer Research

Analyzing Tracking Graphs to Better Understand RAS Diffusion, Torin McDonald, Scientific Computing and Imaging Institute, University of Utah

Analyzing Tumor Heterogeneity thru Advanced Proteogenomic Bioinformatic Approaches, Don Johann, MD, University of Arkansas for Medical Science

Bayesian Deep Learning for Robust Information Extraction from Cancer Pathology Reports, Devanshu Agrawal, University of Tennessee at Knoxville

Developing Predictive Random Forest Models of MRP3 and MRP4 Transporter Inhibition, Amanda Paulson, PhD, Accelerating Therapeutics for Opportunities in Medicine (ATOM) Consortium

Exploring Strengths and Weaknesses of PQSAR 2, Stewart He, PhD, Lawrence Livermore National Laboratory

Large-Scale Photoacoustic Tomography: A Trade-off Between Image Quality and Computational Cost, Gabriel Bordovský, Brno University of Technology

Leveraging a Hybrid and Multiscale Model to Assist Androgen Deprivation Therapy in Recurrent Prostate Cancer Patients, Mengdi Tao, University of Pennsylvania

Long Time Evolution of Lipid Membranes, Tomas Oppelstrup, Lawrence Livermore National Laboratory

Machine Learning for Detection of Circulating Tumor Cells by Optical Imaging without Label, Yaling Liu, PhD, Lehigh University

Making the Most of Genomic Data for Small and Medium-Sized Data Commons, Jong Cheol Jeong, PhD, University of Kentucky

Molecular Classification of Pediatric High-Risk Leukemias Using Expression Profiles of Multimodally Expressed Genes, Sneha Jariwala, University of California, Santa Cruz

Neural Collaborative Filtering Method for IC50 Prediction of drug compounds, Sookyung Kim, PhD, Lawrence Livermore National Laboratory

Performance Evaluation of Graph Convolutional Networks for Information Extraction from Cancer Pathology Reports, Hong-Jun Yoon, PhD, Oak Ridge National Laboratory

Probabilistic-based Interactive Machine Learning for Tomogram Segmentation and Annotation, Talita Perciano, PhD, Lawrence Berkeley National Laboratory

System for High Intensity Evaluation During Radiation Therapy (SHIELD-RT): A Prospective Randomized Study of Machine Learning-Directed Clinical Evaluations During Outpatient Cancer Radiation and Chemoradiation, Julian Hong, MD, University of California, San Francisco

Training Data Error Impacts on Deep Neural Networks for Classifying RNA-seq Gene Expressions, Rajeev Jain, Argonne National Laboratory

3:20 p.m.–3:25 p.m.

Afternoon Welcome

Patricia Kovatch, Icahn School of Medicine, Mount Sinai

3:25 p.m.–3:40 p.m.

Machine Learning Driven Importance Sampling Approach for Multiscale Simulations

Presenter: Harsh Bhatia, PhD, Lawrence Livermore National Laboratory

3:40 p.m.–3:55 p.m.

A Metapath Approach to Predicting Drug Response in Cancer Cell Lines

Judith D. Cohn, PhD, Los Alamos National Lab; Benjamin H. McMahon, PhD, Los Alamos National Lab; Nicholas W. Hengartner, PhD, Los Alamos National Lab; Marian Anghel, PhD, Los Alamos National Lab; Tudor Oprea, MD, PhD, University of New Mexico School of Medicine

Presenter: Judith D. Cohn, PhD, Los Alamos National Laboratory

3:55 p.m. – 4:10 p.m.

Towards a Data-Driven System for Personalized Cervical Cancer Screening

Presenter: Geir Severin Elvatun Rakh Langberg, Cancer Registry of Norway

4:10 p.m.–4:40 p.m.

Integration of Domain Knowledge Using Medical Knowledge Graph Deep Learning for Cancer Phenotyping

Presenter: Mohammed Alawad, PhD, Oak Ridge National Laboratory

4:40 p.m.–4:55 p.m.

Afternoon Break

4:55 p.m.–5:10 p.m.

Deciphering Hallmarks of Resistance in Breast Cancer

Presenter: Amrita Basu, PhD, University of California, San Francisco

5:10 p.m.–5:40 p.m.

Why I’m Not Answering: Understanding Determinants of Classification of an Abstaining Classifier for Cancer Pathology Reports

Sayera Dhaubhadel; Benjamin McMahon, PhD

Presenter: Sayera Dhaubhadel, Los Alamos National Laboratory

5:40 p.m.–6:25 p.m.

Panel #3: Translating Cancer Research Advances in Artificial Intelligence into Clinical Practice

Organizer and Moderator: Sally Ellingson, PhD, University of Kentucky

Panel:

Douglas W. Blayney, MD, Stanford University Medical Center

Cody Bumgardner, PhD, University of Kentucky

Stephanie Harmon, PhD, National Cancer Institute

Yaling Liu, PhD, Lehigh University

6:25 p.m.–6:30 p.m.

CAFCW20 Wrap-Up

Keynote

NCI Director Norman "Ned" Sharpless in front of an American flag

Norman “Ned” Sharpless, MD, National Cancer Institute

Dr. Ned Sharpless has served as the director of the National Cancer Institute since October 2017. Previously, Dr. Sharpless served as Acting Commissioner of the U.S. Food and Drug Administration, director of the University of North Carolina Lineberger Comprehensive Cancer Center and on the faculty of Harvard Medical School.

Dr. Sharpless earned his medical degree from UNC and completed his internal medicine residency at Massachusetts General Hospital and a hematology/oncology fellowship at Dana-Farber and Partners Cancer Care.

Dr. Sharpless is a member of the Association of American Physicians as well as the American Society for Clinical Investigation (ASCI), the nation’s oldest honor society for physician–scientists. He served on the ASCI council from 2011 to 2014. He has written more than 150 original scientific papers, reviews and book chapters and holds 10 patents. He co-founded two clinical-stage biotechnology companies: G1 Therapeutics and HealthSpan Diagnostics.

In addition to serving as director of NCI, Dr. Sharpless is chief of the Aging Biology and Cancer Section in the National Institute on Aging’s Laboratory of Genetics and Genomics, where he continues his research on the biology of the aging process that promotes the conversion of normal self-renewing cells into dysfunctional cancer cells. Dr. Sharpless has made pivotal contributions to the understanding of the relationship between aging and cancer, and in the preclinical development of novel therapeutics for melanoma, lung cancer and breast cancer.

 

Thank you to our CAFCW20 Program Committee:

Frank Alexander, PhD, Brookhaven National Laboratory

Orly Alter, PhD, University of Utah

John Baldoni, PhD, Integral Health, Inc.

Jeff Buchsbaum, MD, PhD, National Cancer Institute

Fernanda Foertter, BioTeam

Emily Greenspan, PhD, National Cancer Institute

Ryuji Hamamoto, PhD, National Cancer Center Japan/RIKEN, Tokyo

Abdul Hamid Halabi, NVIDIA

Florence Hudson, Northeast Big Data Innovation Hub, Columbia University

Steven Litster, PhD, Amazon Web Services

Michael McManus, PhD, Intel

William Richards, PhD, Brigham and Women's Hospital, Harvard Medical School

Ilya Shmulevich, PhD, Institute for Systems Biology

Thomas Steinke, PhD, Zuse Institute Berlin

Kristin Swanson, PhD, Mayo Clinic Arizona

George Zaki, PhD, Frederick National Laboratory

 

CAFCW20 Organizing Committee:

Eric Stahlberg, PhD, Frederick National Laboratory for Cancer Research

Sean Hanlon, PhD, National Cancer Institute

Sally Ellingson, PhD, University of Kentucky

Patricia Kovatch, Icahn School of Medicine, Mount Sinai

Petrina Hollingsworth, Frederick National Laboratory for Cancer Research

Lynn Borkon, Frederick National Laboratory for Cancer Research

 

Created by Petrina Hollingsworth Last Modified Fri November 20, 2020 11:36 am by Petrina Hollingsworth