CAFCW 122 Fusion of Structure Based Deep Learning to Accelerate Molecular Docking Predictions
09 Dec 2019 | Contributor(s):: Derek Jones
Modeling interactions with biological targets is a necessary step to begin reasoning about the therapeutic potential of a novel molecule in the drug discovery process. Molecular docking aids drug discovery researchers by searching over potential binding ‘poses’ of a drug molecule,...
CAFCW 104 Deep Kernel Learning for Information Extraction from Cancer Pathology Reports
09 Dec 2019 | Contributor(s):: Devanshu Agrawal, Abhishek Dubey, Georgia Tourassi, Jacob Hinkle
Cancer pathology reports comprise a rich source of data for surveilling cancer incidents and tracking cancer trends across the United States. Cancer registries manually extract key pieces of information from these reports including tumor site, histology, laterality, behavior, grade, and...
CAFCW 105 Acceleration of Hyperparameter Optimization via Task Parallelism for Information Extraction from Cancer Pathology Reports
09 Dec 2019 | Contributor(s):: John Gounley, Hong-Jun Yoon
Recent advances in high-performance computing systems for artificial intelligence enable large-scale training of information extraction models from free-form natural language texts. The development of these models is essential to the cancer surveillance research and automation. In this study, we...
CAFCW 120 Integrating High-Performance Simulations and Learning toward Improved Cancer Therapy
09 Dec 2019 | Contributor(s):: Austin Clyde, Dave Wright, Shantenu Jha
We develop a novel deep learning workflow to effectively combine expensive but accurate molecular dynamics (MD) based BFE calculations with fast machine learning models to predict the affinity of compounds. In this approach, candidates are sampled from a large billion-compound synthetically...
CAFCW 113 Digital Twins for Predictive Cancer Care: an HPC-Enabled Community Initiative
09 Dec 2019 | Contributor(s):: Emily Greenspan, Carolyn Lauzon, Amy Gryshuk, Jonathan Ozik, Nicholson Collier, Tanveer Syeda-Mahmood, Ilya Shmulevich, Tina Hernandez-Boussard, Paul Macklin
Cancer is a complex multiscale dynamical systems problem with interactions between the tumor and host at the molecular, cellular, tissue, and organism levels. Moreover, treatment occurs within a larger dynamical system that couples clinical care teams, hospital systems, industry, and government...