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Bioinformatics/IT and Data Sharing Working Group Update
21 Apr 2014 | Presentations | Contributor(s): Brad Erickson, Tom Casavant, John Freymann, Vyshak Chandra
Bioinformatics/IT and Data Sharing Working Group Update
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BioIT Call To Action
28 Apr 2022 | Publications | Contributor(s): Anil Srivastava, Nicholas Siebenlist, Jane J Yu, Bishen Singh
Call to action to join cancer patient digital twin consortium in advance of BioIT-World Conference, held May 3rd-5th.
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Biomedical Evidence Graph
03 Oct 2014 | Presentations | Contributor(s): Josh Stuart
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Biospecimen and Clinical Trials Educational Videos in Asian Languages
24 Nov 2015 | Teaching Materials | Contributor(s): Julie Dang
Culturally appropriate, ethnic specific, community tested biospecimen and clinical trials educational videos in multiple Asian American languages (Chinese, English, Hmong, Ilokano, Korean, Tagalog, and Vietnamese).
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Biospecimen NCI PPT
24 Nov 2015 | Teaching Materials | Contributor(s): NCI
This NCI presentation was originally used at the UNM Cancer Center by the NON/CHE (Maria Otero).
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Brain Cancer Imaging Analytics
02 Oct 2015 | Presentations | Contributor(s): Christos Davatzikos
The transition of oncologic imaging from its “industrial era” to it is “information era” demands analytical methods that 1) extract information from this data that is clinically and biologically relevant; 2) integrate imaging, clinical, and genomic data via rigorous...
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Breast Cancer Crossword
20 Nov 2015 | Teaching Materials | Contributor(s): Katelyn Schifano
This crossword is designed for use in social media as well as patient waiting areas.
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BRIDG 4.0 HTML.zip
08 Dec 2015 | Downloads | Contributor(s): Wendy Nan Ver Hoef, Smita Hastak, Lloyd Mckenzie, Julie Evans, Boris Brodsky
Download this file to save and install a local copy of the HLTML version of BRIDG 4.0. The Biomedical Research Integrated Domain Group (BRIDG) Model is a collaborative effort engaging stakeholders from the Clinical Data Interchange Standards Consortium (CDISC), the HL7 BRIDG Work Group, the US...
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BRIDG Imaging Project Description
25 Nov 2015 | Presentations | Contributor(s): Smita Hastak, Wendy Verhoef
11/25/2015 meeting slides
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Building Online Scientific Communities via NCIP Hub
17 Nov 2014 | Teaching Materials | Contributor(s): Ishwar Chandramouliswaran
Overview of how NCIP Hub can be used to build online scientific communities.
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Building the Knowledgebase of Biology using Citizen Science
12 Jun 2015 | Presentations | Contributor(s): Andrew Su
Andrew Su discusses Mark2Cure and how to build a knowledgebase of biology using citizen science.
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caCDE-QA: A quality assurance platform for cancer study common data elements
26 Mar 2015 | Presentations | Contributor(s): Guoqian Jiang
This is a presentation about an overview of a NCI ITCR U01 project - caCDE-QA: A quality assurance platform for cancer study common data elements (PI, Guoqian Jiang, Mayo Clinic). The goal of the project is to design, develop and evaluate an integrative platform known as caCDE-QA that implements...
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CAFCW 104 Deep kernel Learning for Information Extraction from Cancer Pathology Reports
05 Dec 2019 | Presentations | 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...
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CAFCW 104 Deep Kernel Learning for Information Extraction from Cancer Pathology Reports
09 Dec 2019 | Presentations | 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...
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CAFCW 105 Acceleration of Hyperparameter Optimization via Task Parallelism for Information Extraction from Cancer Pathology Reports
09 Dec 2019 | Presentations | 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...
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CAFCW 113 Digital Twins for Predictive Cancer Care: an HPC-Enabled Community Initiative
09 Dec 2019 | Presentations | 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...
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CAFCW 120 Integrating High-Performance Simulations and Learning toward Improved Cancer Therapy
09 Dec 2019 | Presentations | 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...
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CAFCW 122 Fusion of Structure Based Deep Learning to Accelerate Molecular Docking Predictions
09 Dec 2019 | Presentations | 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,...
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CAFCW109 Semi-Supervised Method for Countering Batch Effect
06 Dec 2019 | Presentations | Contributor(s): Stewart He
Predictive modeling of patient tumor growth response to drug treatment is severely limited by a lack of experimental data for training. Combining experimental data from several studies is an attractive approach, but presents two problems: batch effects and limited data for individual drugs and...
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CAFCW115 Massively Parallel Large-Scale Multi-Model Simulation of Tumor Development including Treatments
19 Dec 2019 | Presentations | Contributor(s): Marco Berghoff, Jakob Rosenbauer, Alexander Schug
The temporal and spatial resolution in the microscopy of tissues has increased significantly within the last years, yielding new insights into the dynamics of tissue development and the role of the single-cell within it. A thorough theoretical description of the connection of single-cell...