metadata
pretty_name: SubcellPert
language:
- en
tags:
- biology
- spatial-transcriptomics
- perturbation
- subcellular
configs:
- config_name: catalog
default: true
data_files:
- split: inventory
path: catalog/datasets.parquet
SubcellPert: Benchmarking Subcellular Perturbation Prediction
SubcellPert benchmarks perturbation-response prediction across 14 imaging datasets and eight baselines, extending virtual cell evaluation from gene counts to intracellular RNA organization.
Project page · Paper · Code
Dataset overview
This snapshot contains 14 datasets, 13,880,723 cells, and 3,653,986,724 retained RNA events, with frozen benchmark splits and intervention descriptors. Each physical dataset is counted once. Seeds, baselines, and oracle/joint settings reuse the observations.
| Dataset | Cells | RNA events | Genes |
|---|---|---|---|
| DSS-Colitis | 1,439,542 | 119,553,365 | 940 |
| ATM-RT | 790,166 | 147,722,071 | 298 |
| Kidney-IRI | 1,374,915 | 168,519,194 | 300 |
| Cardiac-MI | 225,023 | 61,134,068 | 475 |
| Ddx54-PD1 | 1,155,233 | 494,265,984 | 5,006 |
| Spinal-KO | 122,645 | 36,073,815 | 347 |
| Adipose | 13,972 | 1,907,755 | 477 |
| Breast-FUS | 880,565 | 102,102,171 | 1,000 |
| GBM-oHSV | 2,401,940 | 520,974,197 | 480 |
| Lung-Drug | 1,561,700 | 681,015,170 | 5,006 |
| Gut-Microbiota | 2,057,563 | 189,197,264 | 1,815 |
| Sickness | 1,765,443 | 1,101,298,121 | 941 |
| PF-Astro | 11,454 | 10,670,839 | 485 |
| UC-VDZ | 80,562 | 19,552,710 | 1,000 |