TabBioMed camera-ready release

README.md

@@ -0,0 +1,97 @@
+---
+license: cc-by-4.0
+pretty_name: TOX_171
+task_categories:
+- tabular-classification
+tags:
+- tabular
+- biomedical
+- benchmark
+- TabBioMed
+- transcriptomics
+- classification
+size_categories:
+- n<1K
+configs:
+- config_name: default
+  data_files:
+  - split: fold_0_train
+    path: data/fold_0/train.parquet
+  - split: fold_0_validation
+    path: data/fold_0/val.parquet
+  - split: fold_0_test
+    path: data/fold_0/test.parquet
+  - split: fold_1_train
+    path: data/fold_1/train.parquet
+  - split: fold_1_validation
+    path: data/fold_1/val.parquet
+  - split: fold_1_test
+    path: data/fold_1/test.parquet
+  - split: fold_2_train
+    path: data/fold_2/train.parquet
+  - split: fold_2_validation
+    path: data/fold_2/val.parquet
+  - split: fold_2_test
+    path: data/fold_2/test.parquet
+  - split: fold_3_train
+    path: data/fold_3/train.parquet
+  - split: fold_3_validation
+    path: data/fold_3/val.parquet
+  - split: fold_3_test
+    path: data/fold_3/test.parquet
+  - split: fold_4_train
+    path: data/fold_4/train.parquet
+  - split: fold_4_validation
+    path: data/fold_4/val.parquet
+  - split: fold_4_test
+    path: data/fold_4/test.parquet
+---
+
+# TOX_171
+
+Part of **TabBioMed** (*TabBioMed: A Large-Scale Benchmark for Biomedical Tabular Learning*), a benchmark of 94 curated biomedical
+tabular datasets. Code, preprocessing and documentation: https://github.com/AI-sandbox/TabBioMed.
+
+Retrospective four-group classification of healthy controls, skin-cancer controls, limited-radiation-toxicity controls, and acute-radiation-toxicity cases. The 171 gene-expression profiles represent 57 donors, each measured in donor-derived lymphoblastoid cells under mock, ultraviolet, and ionizing-radiation conditions (GEO GDS968/GSE1725; Rieger et al., PNAS 2004). Five donor-grouped outer folds test every profile once; three donor-grouped inner folds select hyperparameters. The final-fit validation holdout is also donor-disjoint. Donor and GEO sample identifiers are split metadata, not features.
+
+| Domain | Task | Samples | Features | Classes |
+|---|---|---|---|---|
+| Transcriptomics | classification | 171 | 5,748 | 4 |
+
+**Splits.** 5 stored outer cross-validation folds (`data/fold_<i>/`), each with train/val/test files (fold 0: 117/18/36 rows). Every row appears in exactly one outer test fold. HPO in the paper uses inner folds drawn from each outer non-test pool.
+
+## Files
+
+- `data/**.parquet`: one row per sample. `row_idx` is the row index in the original
+  TabBioMed array; `f_<i>[_<name>]` are the features (in order); `target` (or `target_<j>`
+  for multi-target tasks) is the label. Categorical feature indices (0-based, among the
+  features): `[]`. Missing values are stored as nulls.
+- `metadata.json`: TabBioMed task metadata (task type, categorical indices, source, description).
+- `split_groups.json`: `groups[row_idx]` gives the sample group (e.g. patient, donor or strain) that must stay together in any re-split. Split metadata only, never a feature.
+- `sample_metadata.csv`: per-row provenance (identifiers, source annotations); not features.
+
+```python
+from datasets import load_dataset
+ds = load_dataset("TabBioMed/TOX_171")
+```
+
+A Croissant (1.1) description with Responsible-AI fields is distributed with the
+TabBioMed release.
+
+## Source and license
+
+Source: GEO_GDS968_GSE1725
+
+This derived dataset is distributed under CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/). Please also
+cite and respect the terms of the original source.
+
+## Citation
+
+```bibtex
+@inproceedings{tabbiomed2026,
+  title     = {TabBioMed: A Large-Scale Benchmark for Biomedical Tabular Learning},
+  author    = {Mateo Bernad{\'o}, Pau and Polapragada, Saivenkata Nagavyjayanthi and Bonet, David and Arbiol Rakuljic, Pol and Mogas Pladevall, Laia and Comajoan Cara, Mar{\c{c}}al and Gonzalez Ferrer, Jesus and Abante, Jordi and Mas Montserrat, Daniel and Haussler, David and Ioannidis, Alexander G.},
+  booktitle = {Advances in Neural Information Processing Systems (NeurIPS), Evaluations and Datasets Track},
+  year      = {2026}
+}
+```

data/fold_0/test.parquet

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metadata.json

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+{
+  "READY": true,
+  "name": "TOX_171",
+  "task": "classification",
+  "num_classes": 4,
+  "cat_idx": [],
+  "num_samples": 171,
+  "num_features": 5748,
+  "imbalance_ratio": 1.1538,
+  "description": "Retrospective four-group classification of healthy controls, skin-cancer controls, limited-radiation-toxicity controls, and acute-radiation-toxicity cases. The 171 gene-expression profiles represent 57 donors, each measured in donor-derived lymphoblastoid cells under mock, ultraviolet, and ionizing-radiation conditions (GEO GDS968/GSE1725; Rieger et al., PNAS 2004). Five donor-grouped outer folds test every profile once; three donor-grouped inner folds select hyperparameters. The final-fit validation holdout is also donor-disjoint. Donor and GEO sample identifiers are split metadata, not features.",
+  "source": "GEO_GDS968_GSE1725",
+  "label": "transcriptomics",
+  "split_strategy": "cv",
+  "distribution_source": "ProtoGate/scikit-feature TOX_171.mat",
+  "source_url": "https://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=GDS968",
+  "publication_doi": "10.1073/pnas.0307761101",
+  "num_donors": 57,
+  "class_names": [
+    "healthy control",
+    "skin cancer control",
+    "limited toxicity control",
+    "acute toxicity"
+  ],
+  "split_group": "donor",
+  "sample_metadata_file": "sample_metadata.csv",
+  "outer_split_protocol": "tox171_donor_outer_v1",
+  "donor_mapping_sha256": "3c55970c2b79253e671c4346dc3ba95fe14256e66b94a618ac7a571ccc5427a4"
+}

sample_metadata.csv

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+row,geo_sample,target,disease_state,agent,individual
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split_groups.json

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+{
+  "description": "Split metadata only: groups[row_idx] identifies the sample group; never use as a model feature.",
+  "groups": [
+    "NoCa1",
+    "NoCa1",
+    "NoCa1",
+    "NoCa2",
+    "NoCa2",
+    "NoCa2",
+    "NoCa3",
+    "NoCa3",
+    "NoCa3",
+    "NoCa4",
+    "NoCa4",
+    "NoCa4",
+    "NoCa5",
+    "NoCa5",
+    "NoCa5",
+    "NoCa6",
+    "NoCa6",
+    "NoCa6",
+    "NoCa7",
+    "NoCa7",
+    "NoCa7",
+    "NoCa8",
+    "NoCa8",
+    "NoCa8",
+    "NoCa9",
+    "NoCa9",
+    "NoCa9",
+    "NoCa10",
+    "NoCa10",
+    "NoCa10",
+    "NoCa11",
+    "NoCa11",
+    "NoCa11",
+    "NoCa12",
+    "NoCa12",
+    "NoCa12",
+    "NoCa13",
+    "NoCa13",
+    "NoCa13",
+    "NoCa14",
+    "NoCa14",
+    "NoCa14",
+    "NoCa15",
+    "NoCa15",
+    "NoCa15",
+    "SkCa1",
+    "SkCa1",
+    "SkCa1",
+    "SkCa2",
+    "SkCa2",
+    "SkCa2",
+    "SkCa3",
+    "SkCa3",
+    "SkCa3",
+    "SkCa4",
+    "SkCa4",
+    "SkCa4",
+    "SkCa5",
+    "SkCa5",
+    "SkCa5",
+    "SkCa6",
+    "SkCa6",
+    "SkCa6",
+    "SkCa7",
+    "SkCa7",
+    "SkCa7",
+    "SkCa8",
+    "SkCa8",
+    "SkCa8",
+    "SkCa9",
+    "SkCa9",
+    "SkCa9",
+    "SkCa10",
+    "SkCa10",
+    "SkCa10",
+    "SkCa11",
+    "SkCa11",
+    "SkCa11",
+    "SkCa12",
+    "SkCa12",
+    "SkCa12",
+    "SkCa13",
+    "SkCa13",
+    "SkCa13",
+    "SkCa14",
+    "SkCa14",
+    "SkCa14",
+    "SkCa15",
+    "SkCa15",
+    "SkCa15",
+    "RadC1",
+    "RadC1",
+    "RadC1",
+    "RadC2",
+    "RadC2",
+    "RadC2",
+    "RadC3",
+    "RadC3",
+    "RadC3",
+    "RadC4",
+    "RadC4",
+    "RadC4",
+    "RadC5",
+    "RadC5",
+    "RadC5",
+    "RadC6",
+    "RadC6",
+    "RadC6",
+    "RadC7",
+    "RadC7",
+    "RadC7",
+    "RadC8",
+    "RadC8",
+    "RadC8",
+    "RadC9",
+    "RadC9",
+    "RadC9",
+    "RadC10",
+    "RadC10",
+    "RadC10",
+    "RadC11",
+    "RadC11",
+    "RadC11",
+    "RadC12",
+    "RadC12",
+    "RadC12",
+    "RadC13",
+    "RadC13",
+    "RadC13",
+    "Rad1",
+    "Rad1",
+    "Rad1",
+    "Rad2",
+    "Rad2",
+    "Rad2",
+    "Rad3",
+    "Rad3",
+    "Rad3",
+    "Rad4",
+    "Rad4",
+    "Rad4",
+    "RadS5",
+    "RadS5",
+    "RadS5",
+    "RadS6",
+    "RadS6",
+    "RadS6",
+    "RadS7",
+    "RadS7",
+    "RadS7",
+    "RadS8",
+    "RadS8",
+    "RadS8",
+    "RadS9",
+    "RadS9",
+    "RadS9",
+    "RadS10",
+    "RadS10",
+    "RadS10",
+    "RadS11",
+    "RadS11",
+    "RadS11",
+    "RadS12",
+    "RadS12",
+    "RadS12",
+    "RadS13",
+    "RadS13",
+    "RadS13",
+    "RadS14",
+    "RadS14",
+    "RadS14"
+  ]
+}