Collaboration and Impressive Skill Mark First HuBMAP Kaggle Competition
May 24, 2021
Hacking the Kidney harnesses community effort to automate detection of microscopic kidney structure. A combination of intense competition and expansive collaboration that reflected on HuBMAP’s own constitution marked Hacking the Kidney, what is likely to be the first but not the last Kaggle Competition sponsored by the Consortium. Held between Nov. 11, 2020, and May 10, 2021, the competition focused on mapping the human kidney at single-cell resolution by implementing a successful and robust machine-learning (ML) algorithm to automatically detect kidney glomeruli in three-dimensional microscopic images—a functional tissue unit, or FTU, detector. The awards ceremony for the competition capped a three-day HuBMAP Annual All-Hands Meeting reviewing consortium members’ work and achievements over the past year. HuBMAP “hope[s] to catalyze the development of an open global framework for comprehensively mapping the human body at cellular resolution,” said Katy Börner of Indiana University, one of the competition organizers and PI of the university’s HIVE mapping component. “So just like we used to have maps in large atlases but now we have Google Maps that we can run API queries against, we would like to have some of the anatomical atlases converted into a digital format that we can really run API queries against … Ultimately that means that we need to accelerate the development of the next generation of tools and techniques for constructing such a high-resolution, spatial-tissue-mapping atlas.” Kaggle, the product of an eponymous Google subsidiary, is a platform designed for finding and publishing scientific datasets in a collaborative, Web-based fashion. By powering exploration and creation of models and ML tools and publishing an open collection of “Kaggle workbooks” that lay out these tools and solutions, Kaggle creates a working environment that leverages cooperation for scientific discovery. Kaggle Competitions serve to popularize the platform and help new generations of scientists and coders to learn and use it to solve real-world problems. “The key behind the science and success of this competition was collaboration,” said competition support team member Leah Scherschel of Indiana University. “Kaggle is very unique in that it is part data science and part social media platform. Competitors … shared knowledge of the medical domain with one another because most of them only had machine-learning experience, not medical experience, and they showed each other how multiple AI frameworks such as TensorFlow, PyTorch and Keras could be applied to this challenge.” On May 21, 2021, staff from HuBMAP and sponsors presented a number of awards to Hacking the Kidney competitors, distributing a total of $60,000 in prize money. The awards were: Accuracy Prizes: