| --- |
| 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 |
| --- |
| |
| <h1 align="center">SubcellPert: Benchmarking Subcellular Perturbation Prediction</h1> |
|
|
| <p align="center">SubcellPert benchmarks perturbation-response prediction across 14 imaging datasets and eight baselines, extending virtual cell evaluation from gene counts to intracellular RNA organization.</p> |
|
|
| <p align="center"> |
| <a href="https://personal-page.wjh.app/SubcellPert/">Project page</a> · |
| <a href="https://www.biorxiv.org/content/10.64898/2026.10.11.758305v1">Paper</a> · |
| <a href="https://github.com/king159/SubcellPert">Code</a> |
| </p> |
|
|
| ## 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 | |
|
|
