Background

Previously, the Broad Institute’s Hacohen Lab ran experiments testing the effects of 73 gene knockouts in T cells on mice with cancer. Given that it took months to test a fraction of the 20,000 potential gene knockouts, Broad researchers wanted a way to zero in on the most promising perturbations. Enter the Cancer Immunotherapy Machine Learning Competition.

In Part 1 of the competition, participants received gene expression data from 66 of the 73 T-cell-gene knockouts from the Hacohen Lab experiments as training data. They then had to develop an algorithm that could predict how knocking out the seven “held-out” genes would affect T cells.

Part 2 participants used their algorithms from the first part to propose new gene knockouts (picking from any of the 20K genes in the entire genome) to shift as many T cells as possible into a cancer-fighting state. In Part 3, participants proposed a metric for ranking how well a particular gene knockout would bring about this desired shift in T cells.

Winners

Part 1

First place: Marios Gavrielatos and Konstantinos Kyriakidis, Greece
Second place: Yuzhou Gu, Anzo Teh, Yanjun Han, and Brandon Wang, U.S. (MIT)
Third place: Peter Novotný, Poland

Part 2

First place: Brody Langille, Jordan Trajkovski, and Elizabeth Hudson
Second place: mglettig (username)*
Third place: Ai Vu Hong, researcher at Genethon, France
Fourth place: Saket Kunwar, independent researcher, Nepal
Fifth place: lxastro0 (username)*
Sixth place: John Gardner, freelance data scientist
Seventh place: agilsoft (username)*
Eighth place: Basak Eraslan, postdoctoral researcher holding a joint position at the Regev Lab in Genentech and Kundaje Lab at Stanford University
Ninth place: Haoyue Dai, Kun Zhang, Ignavier Ng, Yujia Zheng, Xinshuai Dong, and Yewen Fan from Carnegie Mellon University; Petar Stojanov, postdoctoral fellow at the Eric and Wendy Schmidt Center; Gongxu Luo, Mohamed bin Zayed University of Artificial Intelligence; and Biwei Huang, University of California, San Diego
Ninth place: Liu Xindi, freelance programmer
Ninth place: Johnson Zhou, Camille Sayoc, and Yi-Cheng Peng, Master’s students of the Faculty of Engineering and IT at the University of Melbourne, Victoria, Australia

Part 3

First place: Dariusz Brzeziński and Wojciech Kotlowski from Poznań University of Technology in Poland
Second place: Salil Bhate, postdoctoral fellow at the Eric and Wendy Schmidt Center
Third place: Irene Bonafonte Pardàs, Artur Szalata, and Benjamin Schubert from Helmholtz Center Munich and Miriam Lyzotte from Mila - Quebec AI Institute