Perturbation prediction research benchmarks

Benchmarks

Dataset NameSOTA methodMetricTrendResultsLast Updated

Replogle

Squidiff

0.039DEOver

Mar 19, 2026

Tahoe100M

SCALE

0.806DEOver

Mar 19, 2026

PBMC

SCALE

81DE Overlap

Mar 19, 2026

PDO (OOD)

Energy

0.002MMD Distance

Mar 6, 2026

PDO (IID)

SWD

0.001MMD Distance (x100)

Mar 6, 2026

Perturb-seq double-gene perturbation

PerturbedVAE

0.447RMSE

May 20, 2026

PBMC-IFN

CellOT

0.99CD8T PCC

Apr 21, 2026

Norman2019 (double-gene)

PerturbedVAE

0.449RMSE (10 genes)

May 20, 2026

Norman 2019 (Single-gene)

PerturbedVAE

0.403RMSE (10 genes)

May 20, 2026

Tahoe compound perturbations (unseen interventions)

State

0.778Pearson Correlation

Mar 16, 2026

Parse signaling perturbations (unseen interventions)

C3TL

0.67Pearson Correlation

Mar 16, 2026

Replogle genetic perturbations (unseen interventions)

C3TL

0.491Pearson Correlation Coefficient

Mar 16, 2026