PerturbArena

Comprehensive benchmark for comparing single-cell perturbation prediction models. 12 models + 3 baselines across 25 datasets with 24 metrics. Three core tasks: unseen perturbations, combinatorial perturbations, and cell state transfer across conditions.

Composite

74.4

Experimental validation

None

Stages

Target ID

Modalities

chemical_perturbationgenetic_perturbationsingle_cell

Task types

perturbation_predictioncombinatorial_predictioncell_state_transfer

Size

models: 12
datasets: 25
metrics: 24

License

Unknown

First release

2024-12

Last updated

2025-06

Official site

→ project page

Leaderboard

→ leaderboard

Dataset

→ dataset

Code / GitHub

→ repository

HuggingFace

→ HF

Paper

PerturbArena: A Comprehensive Benchmark for Single-Cell Perturbation Prediction · · 2024 · paper · doi:10.1101/2024.12.23.630036 · 12 citations

Flags

virtual_cellmulti_metric

Experts

—

Groups

—

Hosted by

—

Related benchmarks

scPerturBench, Open Problems: Perturbation Prediction, PerturbBench

Rubric (7-criterion)

rigor

coverage

maintenance

adoption

quality

accessibility

industry_relevance

Notes

Complementary to scPerturBench. Emphasizes metric divergence analysis and practical method selection guidelines. Shows limited robustness to shifts across cellular contexts. Chinese research group.

← Back to all benchmarks

Compare:

Open comparison →