Initial NeurIPS 2026 release: 4 paper-canonical splits + multiview tensors

.gitattributes

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+CRISPRa-norman/norman2019_gears_split.h5ad filter=lfs diff=lfs merge=lfs -text
+replogle_k562/replogle_k562.h5ad filter=lfs diff=lfs merge=lfs -text
+replogle_rpe1/replogle_rpe1.h5ad filter=lfs diff=lfs merge=lfs -text
+sciplex3/sciplex3.h5ad filter=lfs diff=lfs merge=lfs -text

CRISPRa-norman/norman2019_gears_split.h5ad

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README.md

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+# scFATE — NeurIPS 2026 datasets
+
+Paper-canonical splits and biological-descriptor multiview tensors for the four perturbation benchmarks evaluated in
+[`Angione-Lab/scFATE`](https://huggingface.co/Angione-Lab/scFATE).
+
+## Files
+
+| Path | Source | Use |
+|---|---|---|
+| `CRISPRa-norman/norman2019_gears_split.h5ad`     | Norman et al. 2019, GEARS split | CRISPRa (Norman) |
+| `replogle_k562/replogle_k562.h5ad`               | Replogle et al. 2022 | K562 CRISPRi |
+| `replogle_rpe1/replogle_rpe1.h5ad`               | Replogle et al. 2022 | RPE1 CRISPRi |
+| `sciplex3/sciplex3.h5ad`                          | Srivatsan et al. 2020 | SciPlex3 chemical |
+| `gene_embeddings/{norman,replogle_k562,replogle_rpe1}_multiview.pt` | precomputed | gene-descriptor multiview |
+| `drug_embeddings/sciplex3_multiview_v2.pt`        | precomputed (Morgan + RDKit + ChemBERTa) | drug-descriptor multiview |
+| `splits/sciplex3_split_v2b.json`                  | mechanism-of-action stratified | SciPlex3 25-drug OOD split |
+
+## Usage
+
+```python
+from huggingface_hub import snapshot_download
+data_dir = snapshot_download("Angione-Lab/scFATE-datasets", repo_type="dataset")
+# Then in scFATE training code, point --dataset_h5ad at e.g.
+# {data_dir}/replogle_k562/replogle_k562.h5ad
+```

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splits/sciplex3_split_v2b.json

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+{
+  "train_drugs": [
+    "2-Methoxyestradiol",
+    "A-366",
+    "ABT-737",
+    "AG-490",
+    "AMG-900",
+    "AR-42",
+    "AT9283",
+    "AZ",
+    "AZD1480",
+    "Abexinostat",
+    "Alisertib",
+    "Altretamine",
+    "Alvespimycin",
+    "Aminoglutethimide",
+    "Anacardic",
+    "Andarine",
+    "Aurora",
+    "Avagacestat",
+    "BMS-265246",
+    "BMS-536924",
+    "BMS-911543",
+    "BRD4770",
+    "Barasertib",
+    "Baricitinib",
+    "Bisindolylmaleimide",
+    "Bosutinib",
+    "Busulfan",
+    "CEP-33779",
+    "CUDC-907",
+    "CYC116",
+    "Capecitabine",
+    "Carmofur",
+    "Cediranib",
+    "Celecoxib",
+    "Cerdulatinib",
+    "Clevudine",
+    "Costunolide",
+    "Crizotinib",
+    "Curcumin",
+    "Cyclocytidine",
+    "Dacinostat",
+    "Danusertib",
+    "Dasatinib",
+    "Decitabine",
+    "Disulfiram",
+    "Divalproex",
+    "Droxinostat",
+    "EED226",
+    "ENMD-2076",
+    "Ellagic",
+    "Entacapone",
+    "Entinostat",
+    "Enzastaurin",
+    "Epothilone",
+    "FLLL32",
+    "Fasudil",
+    "Fedratinib",
+    "Filgotinib",
+    "Flavopiridol",
+    "Fluorouracil",
+    "Fulvestrant",
+    "G007-LK",
+    "GSK",
+    "GSK1070916",
+    "Gandotinib",
+    "Givinostat",
+    "Glesatinib?(MGCD265)",
+    "Hesperadin",
+    "IOX2",
+    "ITSA-1",
+    "Iniparib",
+    "Ivosidenib",
+    "JQ1",
+    "KW-2449",
+    "Ki16425",
+    "Ki8751",
+    "Lapatinib",
+    "Lenalidomide",
+    "Linifanib",
+    "Lomustine",
+    "Luminespib",
+    "M344",
+    "MC1568",
+    "MK-0752",
+    "MK-5108",
+    "Maraviroc",
+    "Meprednisone",
+    "Mercaptopurine",
+    "Mesna",
+    "Mocetinostat",
+    "Motesanib",
+    "Navitoclax",
+    "Nilotinib",
+    "Obatoclax",
+    "Ofloxacin",
+    "PCI-34051",
+    "PD173074",
+    "PD98059",
+    "PF-3845",
+    "PF-573228",
+    "PFI-1",
+    "PJ34",
+    "Panobinostat",
+    "Patupilone",
+    "Pelitinib",
+    "Pirarubicin",
+    "Pracinostat",
+    "Prednisone",
+    "Quercetin",
+    "Quisinostat",
+    "RG108",
+    "Ramelteon",
+    "Regorafenib",
+    "Resminostat",
+    "Resveratrol",
+    "Rigosertib",
+    "Roscovitine",
+    "Rucaparib",
+    "Ruxolitinib",
+    "S-Ruxolitinib",
+    "S3I-201",
+    "SGI-1776",
+    "SL-327",
+    "SNS-314",
+    "SRT1720",
+    "SRT2104",
+    "SRT3025",
+    "Selisistat",
+    "Sirtinol",
+    "Sorafenib",
+    "Streptozotocin",
+    "TAK-901",
+    "TG101209",
+    "TGX-221",
+    "Tacedinaline",
+    "Tanespimycin",
+    "Tazemetostat",
+    "Temsirolimus",
+    "Thalidomide",
+    "Thiotepa",
+    "Tie2",
+    "Tofacitinib",
+    "Tozasertib",
+    "Trametinib",
+    "Tranylcypromine",
+    "Triamcinolone",
+    "Trichostatin",
+    "Tubastatin",
+    "Tucidinostat",
+    "UNC0379",
+    "UNC0631",
+    "UNC1999",
+    "Valproic",
+    "Vandetanib",
+    "Veliparib",
+    "WHI-P154",
+    "WP1066",
+    "XAV-939",
+    "YM155",
+    "ZM",
+    "Zileuton"
+  ],
+  "ood_drugs": [
+    "AC480",
+    "AG-14361",
+    "AICAR",
+    "Alendronate",
+    "Amisulpride",
+    "Azacitidine",
+    "BMS-754807",
+    "Belinostat",
+    "CUDC-101",
+    "Cimetidine",
+    "Daphnetin",
+    "GSK-LSD1",
+    "INO-1001",
+    "JNJ-26854165",
+    "JNJ-7706621",
+    "MLN8054",
+    "Momelotinib",
+    "NVP-BSK805",
+    "Nintedanib",
+    "PHA-680632",
+    "Raltitrexed",
+    "Roxadustat",
+    "SB431542",
+    "TMP195",
+    "Toremifene"
+  ],
+  "seed": 1,
+  "n_train": 161,
+  "n_ood": 25,
+  "stratum_counts": {
+    "PKC signaling": {
+      "eligible": 3,
+      "ood": 1
+    },
+    "Epigenetic regulation": {
+      "eligible": 46,
+      "ood": 5
+    },
+    "Cell cycle regulation": {
+      "eligible": 21,
+      "ood": 3
+    },
+    "Other": {
+      "eligible": 6,
+      "ood": 1
+    },
+    "Tyrosine kinase signaling": {
+      "eligible": 29,
+      "ood": 3
+    },
+    "JAK/STAT signaling": {
+      "eligible": 22,
+      "ood": 2
+    },
+    "Focal adhesion signaling": {
+      "eligible": 2,
+      "ood": 0
+    },
+    "Protein folding & Protein degradation": {
+      "eligible": 7,
+      "ood": 0
+    },
+    "HIF signaling": {
+      "eligible": 3,
+      "ood": 1
+    },
+    "DNA damage & DNA repair": {
+      "eligible": 19,
+      "ood": 3
+    },
+    "Apoptotic regulation": {
+      "eligible": 5,
+      "ood": 1
+    },
+    "Nuclear receptor signaling": {
+      "eligible": 6,
+      "ood": 1
+    },
+    "Antioxidant": {
+      "eligible": 4,
+      "ood": 1
+    },
+    "TGF/BMP signaling": {
+      "eligible": 3,
+      "ood": 1
+    },
+    "Neuronal signaling": {
+      "eligible": 4,
+      "ood": 1
+    },
+    "Metabolic regulation": {
+      "eligible": 6,
+      "ood": 1
+    }
+  },
+  "swap_note": "v2b: swapped Belinostat (TRAIN->OOD) with SRT1720 (OOD->TRAIN). Both Epigenetic regulation stratum; iter169 plan named SRT2104 but that drug is in TRAIN under v2. Motivation: restore belinostat OOD to match the wet-lab narrative (MCF7 qPCR + microscopy)."
+}