NeurIPS 2023: Single-Cell Perturbation Prediction

Generalizing experimental interventions to unseen contexts, a NeurIPS 2023 competition

Single Cell Perturbation Prediction


Single-cell sequencing technologies have revolutionized our understanding of the heterogeneity and dynamics of cells and tissues. However, single-cell data analysis faces challenges such as high dimensionality, sparsity, noise, and limited ground truth.

In this 3rd installment in the Open Problems in Single-Cell Analysis competitions at NeurIPS, we challenge competitors to develop algorithms capable of predicting single-cell perturbation response across experimental conditions and cell types. We will provide a new benchmark dataset of human peripheral blood cells under chemical perturbations, which simulate drug discovery experiments. The objective is to develop methods to generalize to unseen perturbations and cell types to enable scientists to overcome the practical and economic limitations of single-cell perturbation studies.

The goal of this competition is to leverage advances in representation learning (in particular, self-supervised, multi-view, and transfer learning) to unlock new capabilities bridging data science, machine learning, and computational biology. We hope this effort will continue to foster collaboration between the computational biology and machine learning communities to advance the development of algorithms for biomedical data.


  • September 12, 2023 - Start Date.

  • November 23, 2023 - Entry Deadline. You must accept the competition rules before this date in order to compete.

  • November 23, 2023 - Team Merger Deadline. This is the last day participants may join or merge teams.

  • November 30, 2023 - Final Submission Deadline.

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.

Get Started

Saturn Cloud is proud to sponsor the NeurIPS for the third year in a row by providing free compute on their platform for the competition with 150 hours per month on A10 GPU instances with 25GB of GPU RAM!

To make it easy to get started, We’ve created a project template with all the competition data pre-loaded along with some commonly used tools for ML and single-cell analysis. All you need to do to start the project is click “Run in Saturn Cloud” 👇

This project will automatically download all competition data to ~/kaggle/inputs, and drop you into ~/kaggle/working to mirror the directory layout inside of Kaggle. We’ve also uploaded LINCS L4/L5 data to a public s3 bucket for easy access at s3://saturn-kaggle-datasets/open-problems-single-cell-perturbations-optional/.

If you message Saturn Cloud (look for chat in the lower right window) and say “I’m competing in NeurIPS 2023”, your account will be upgraded to allow access to A10 GPUs, more RAM, and more CPUs.

Happy modeling!