Virtual Cell Challenge
Join us in shaping the future of cellular biology through predictive modeling.
Solve One of Biology’s Biggest Challenges with AI
Understanding, predicting, and ultimately programming how cells respond to internal cues and external stimuli is a fundamental challenge in biology.
Advances in single-cell technologies now enable large-scale measurements of cellular responses to genetic and chemical perturbations, fueling this exciting era of predictive cellular modeling. Virtual Cell Challenge is a recurring, open, community-driven challenge aimed at evaluating and improving computational models that predict cellular responses to genetic or chemical perturbations.
In 2025, the challenge will focus on context generalization: participants must predict the effects of perturbation in a held out cell type—the H1 human embryonic steam cell line.
The top three models will win cash prizes of $100,000, $50,000, and $25,000.
Join us in shaping the future of cellular biology through predictive modeling.
Challenge in Cell
Challenge in Cell ↗
Why Participate?
World-class Benchmark Datasets
Significant Scientific Impact
Recognition and Awards
Global Community
Getting Started
Challenge Timeline
The Virtual Cell Challenge will be an annual challenge, with new data added each year to help improve model performance. The inaugural challenge will run from June to November 2025.
About the Data
Arc Institute has developed a new deeply sequenced, high cell coverage, large scale dataset of single cell perturbations. We are making these data available through the Virtual Cell Challenge challenge.
Learn more about the datasets ↗Arc’s Perturbation Data
Training data
Validation set
Public Training Data
scBaseCount ↗
Tahoe-100 ↗
Public Perturb-seq Datasets
Evaluation
While the challenge is open, predictions submitted to the Virtual Cell Challenge will be compared to known results from the validation data set to calculate an accuracy score. Participants’ scores will be shown on the live ranking leaderboard in real time as they are submitted.
We have designed three metrics to evaluate model performance—
- Differential expression score to measure differential gene expression prediction accuracy
- Perturbation discrimination score to rank predictions according to their similarity to the true perturbational effect
- Mean Absolute Error to capture overall predictive accuracy and capture performance across the entire gene expression profile
We use a combined score (Overall score) that appropriately weighs each component, and enforces minimum thresholds on all metrics to promote a balanced performance.
In October, we will release the final test set for final submissions to the challenge. Scoring against the final test set will not be revealed publicly until winners are announced in November.
Prizes
The top three models submitted to the challenge will win cash prizes. Winners will be announced in December 2025 after submission and evaluation of final scoring.
Winning submissions will be based on prediction accuracy on the final test set. The Virtual Cell Challenge will privately identify the top five submissions at the end of the challenge.
The top three scores will win prizes as follows —
Virtual Cell Challenge
