Datasets:
Add paper link, GitHub link, and graph-ml task category
Browse filesHi! I'm Niels from the community science team at Hugging Face. I noticed this dataset card could be improved with additional metadata and links to the associated research.
This PR:
- Adds a link to the [accompanying paper](https://huggingface.co/papers/2605.15511).
- Adds a link to the [official GitHub repository](https://github.com/geometric-intelligence/ogbench).
- Updates the `task_categories` to include `graph-ml`.
- Adds a sample usage section with instructions on how to download the datasets and train models using the provided framework.
README.md
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---
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license: cc-by-4.0
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tags:
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- biology
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- genomics
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- graph-neural-networks
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- benchmarking
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- omics
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pretty_name: OgBench — Omics Graph Benchmark
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task_categories:
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- tabular-classification
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size_categories:
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- n<1K
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---
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# OgBench: Benchmarking Graph Neural Networks on Omics Data
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patient samples n is much smaller than the number of nodes (genes or
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proteins) p per graph.
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## Datasets
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This repository contains four preprocessed omics graph classification
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datasets:
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| Dataset | Modality | n | p | Task |
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| AddNeuroMed | Transcriptomics | 711 | 17,198 | Clinical diagnosis (3-class) |
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| BRCA | Epigenomics | 640 | 19,049 | Cancer subtype (4-class) |
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## Source Data
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- **HERITAGE**: Robbins et al. (2021), *Nature Metabolism*. Available
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- **AddNeuroMed**: Lovestone et al. (2009). Available via NCBI GEO
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(GSE63063) under GEO public data access policy.
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- **BRCA**: Yang et al. (2025), MLOmics, *Scientific Data*. Available
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on Figshare/Hugging Face under CC-BY 4.0.
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## Preprocessing
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All datasets are preprocessed with a consistent pipeline including
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probe-to-gene aggregation, normalization, and covariate adjustment.
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Full preprocessing details are provided in Appendix B of the
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accompanying paper. Graphs are split 70/15/15 (train/val/test) with
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a fixed random seed.
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---
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license: cc-by-4.0
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size_categories:
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- n<1K
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task_categories:
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- graph-ml
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pretty_name: OgBench — Omics Graph Benchmark
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tags:
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- biology
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- genomics
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- graph-neural-networks
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- benchmarking
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- omics
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# OgBench: Benchmarking Graph Neural Networks on Omics Data
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[**Paper**](https://huggingface.co/papers/2605.15511) | [**GitHub**](https://github.com/geometric-intelligence/ogbench)
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OgBench is the first benchmark suite for graph-level prediction in the **n ≪ p regime** characteristic of omics data, where the number of patient samples *n* is much smaller than the number of nodes (genes or proteins) *p* per graph.
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## Datasets
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This repository contains four preprocessed omics graph classification datasets:
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| Dataset | Modality | n | p | Task |
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|---|---|---|---|---|
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| AddNeuroMed | Transcriptomics | 711 | 17,198 | Clinical diagnosis (3-class) |
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| BRCA | Epigenomics | 640 | 19,049 | Cancer subtype (4-class) |
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## Usage
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After installing the [OgBench framework](https://github.com/geometric-intelligence/ogbench), you can download and process the datasets using the provided script:
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```bash
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# Download a specific dataset (e.g., motrpac/HERITAGE)
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python scripts/download_datasets.py motrpac
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# Download all datasets
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python scripts/download_datasets.py all
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```
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To train a model (e.g., GATv2) on one of the datasets:
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```bash
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python ogbench/run.py dataset=motrpac model=gatv2
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```
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## Source Data
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- **HERITAGE**: Robbins et al. (2021), *Nature Metabolism*. Available via MoTrPAC Data Hub (motrpac-data.org) under CC-BY 4.0.
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- **Parkinson's**: Shamir et al. (2017), *Neurology*. Available via NCBI GEO (GSE99039) under GEO public data access policy.
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- **AddNeuroMed**: Lovestone et al. (2009). Available via NCBI GEO (GSE63063) under GEO public data access policy.
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- **BRCA**: Yang et al. (2025), MLOmics, *Scientific Data*. Available on Figshare/Hugging Face under CC-BY 4.0.
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## Preprocessing
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All datasets are preprocessed with a consistent pipeline including probe-to-gene aggregation, normalization, and covariate adjustment. Full preprocessing details are provided in Appendix B of the accompanying paper. Graphs are split 70/15/15 (train/val/test) with a fixed random seed.
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