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HACKING
THE KIDNEY

GLOMERULI SEGMENTATION HACKATHON

HuBMap Kidney Segmentation

Join the May 21st Innovation Digi Conference Celebration of the "Hacking the Kidney" hackathon designed to advance the National Institute of Health HubMAP program, which is striving to map the human body at single cell and functional tissue unit resolution for the first time in history. The celebration is at 1:00 PM - 3:00 PM EST.

Anyone who is interested in participating in the Hacking the Kidney hackathon should complete the following form to receive more information.

THE HACKATHON IS BEING SPONSORED BY

TOTAL PRIZE MONEY $60,000 TO BE AWARDED TO THE WINNING TEAMS!

Moderator

Andrea deSouza

HuBMAP External Advisor
Senior Director
Eli Lilly and Company

SPEAKERS

DR RICHARD CONROY

PROGRAM LEADER, NIH

BOYD STEERE

Principal Research Scientist
Immunology Therapeutics, LILLY RESEARCH LABS

Claire bernard

Senior Director, Product Management, Data Sciences Platform at Broad Institute of MIT and Harvard

SCOTT penberthy

AI and Cloud CTO, Google

This HuBMAP hackathon aims to advance the detection of functional tissue units (FTUs) across different tissue preparation pipelines. An FTU is defined as a “three-dimensional block of cells centered around a capillary, such that each cell in this block is within diffusion distance from any other cell in the same block.” There are 1 million glomeruli in each human kidney. The goal of this hackathon is the implementation of a successful and robust glomeruli FTU detector.

DATA

The HuBMAP data used in this hackathon includes 11 fresh frozen and 9 Formalin Fixed Paraffin Embedded (FFPE) PAS kidney images. 

TASKS

Teams were invited to develop segmentation algorithms that identify glomeruli in the PAS stained microscopy data. They are welcome to use other external data and/or pretrained machine learning models in support of Functional Tissue Unit segmentation. All data and all code used must be released under Attribution 4.0 International (CC BY 4.0).

TIMELINE

  • November 5th, 2020 – Competition Opens
  • January 5th, 2021 -- First Submission deadline. A team must make at least one submission by this date in order to compete
  • January 15th, 2021 - Team Merger deadline. This is the last day competitors may join or merge teams
  • February 5th, 2021 - Final submission deadline
  • February 9th, 2021 – Teams with top-20 highest Kaggle scores present their solutions to Judges
  • February 12th, 2021 – Prize winner announcements
All deadlines are at 11:59 PM UTC on the corresponding day unless otherwise noted. The competition organizers reserve the right to update the contest timeline if they deem it necessary.

AWARDS

Winning teams will receive cash prizes. If desired, teams can choose to have their winnings donated to a charity foundation.

OUR ORGANIZERS

Katy Börner

Distinguished Professor of Engineering and Information Science
Indiana University, USA

Andrea deSouza

HuBMAP External Advisor
Senior Director
Eli Lilly and Company

Deepika Vuppalanchi

Senior Medical Director
Precision Value Health

Richard Holland

Enterprise Cloud Architect, Healthcare & Life Sciences
Google

Sandeep Allam

CEO
STLogics

Christine Drury

CEO
Conference Ventures

OUR JUDGES

Thomas Fuchs

Founder and CSO of Paige. or AI, Director at Memorial Sloan Kettering Cancer Center, Professor at Weill Cornell

Amy Bernard

Director, Science & Technology Strategy, Allen Institute

Maigan Brusko

Department of Pathology, Immunology, and Laboratory Medicine at the University of Florida

John Marioni

Research Group Leader,
EMBL-EBI

Zorina Galis

Chief, Vascular Biology and Hypertension, National Heart Lung and Blood Institute/National Institutes of Health, Bethesda, MD

Blue Lake

Integrative Genomics Group
Department of Bioengineering
University of California
at San Diego

David Van Valen

Division of Biology and Bioengineering, California Institute of Technology

Matt Nelson

Vice Precedent, Genetics and Genomics at Deerfield

Andy Palmer

CEO and co-founder of
Tamr Inc.

Lucy Colwell

Research Scientist at Google

Alex Wolf

Head of Applied Machine Learning at Cellarity

SUPPORT TEAM

Arkan Abadi

Translational Informatics Team
Eli Lilly

Lisel Record

CNS Associate Director Luddy School of Informatics, Computing, and Engineering, Indiana University

Leah Scherschel

CNS Research Assistant
Luddy School of Informatics, Computing, and Engineering, Indiana University

Ellen Quardokus

CNS Research Analyst
Luddy School of Informatics, Computing, and Engineering, Indiana University

Yingnan Ju

PhD Candidate
Luddy School of Informatics, Computing, and Engineering, Indiana University

Heath Patterson

Research Instructor
Vanderbilt School of Medicine

Marcos Novaes

Google Cloud Platform Solution Specialist for HPC, ML and IoT at Google

Yingnan Ju

PhD Candidate
Luddy School of Informatics, Computing, and Engineering, Indiana University

Heath Patterson

Research Instructor
Vanderbilt School of Medicine

OUR SPONSORS

Innovation Sponsor

cyber sponsor

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Dr. Richard Conroy is a Program Leader in the Office of Strategic Coordination at the National Institutes of Health, leading large-scale (>$200M) programs across NIH. Currently, Richard coordinates the Human BioMolecular Atlas Program (HuBMAP) and the Somatic Mosaicism and Retrotransposition (SMaRT) programs, and previously worked on the Single Cell Analysis and the 4D Nucleome programs.  Before joining the Office of the Director, Richard was the Director of the Division of Applied Science and Technology at the National Institute of Biomedical Imaging and Bioengineering, coordinating biomedical imaging research at the institute and leading initiatives in the development and use of decision support systems, understanding data from mobile health technologies to promote behavior change and promoting the use of quantification and standards in all imaging modalities.

Boyd Steere is a Principal Research Scientist at Lilly, where he works as a bioinformaticist in the Immunology therapeutic area, heads the biology effort of a drug discovery team, and leads Lilly Immunology’s single cell multi-omics program.  Dr. Steere graduated from UCLA in 2000 with a PhD in X-ray protein crystallography.  He then joined the pharmaceutical software company Simulations Plus, where he developed neural network models to predict small molecule properties.  After coming to Lilly in 2005, Dr. Steere was a scientific lead in the Discovery IT organization before transitioning in 2015 to the company’s drug research program in autoimmune diseases

Prior to joining the Broad, Clare led product and engineering at TAMR, a Cambridge-based software company that uses machine learning to integrate large datasets. She received her PhD from Boston University for research in particle physics conducted at the Large Hadron Collider

Scott is the Director of Applied AI at Google. In this role, he leads a team of AI engineers and PhDs who help VIPs reimagine the production of goods and services and how value is exchanged in free markets. His team applies current and upcoming AI technologies to materialize proofs of concept and drive long-term transformations.

Scott has a rich background in financial services and enterprise computing. He was recently Scott is the Director of Applied AI at Google. In this role, he leads a team of AI engineers and PhDs who help VIPs reimagine the production of goods and services and how value is exchanged in free markets. His team applies current and upcoming AI technologies to materialize proofs of concept and drive long-term transformations.