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Add paper link, GitHub link, and graph-ml task category

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Hi! 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.

Files changed (1) hide show
  1. README.md +32 -24
README.md CHANGED
@@ -1,5 +1,10 @@
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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
@@ -7,24 +12,17 @@ tags:
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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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- OgBench is the first benchmark suite for graph-level prediction in the
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- **n ≪ p regime** characteristic of omics data, where the number of
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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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  |---|---|---|---|---|
@@ -33,21 +31,31 @@ datasets:
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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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- 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
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- NCBI GEO (GSE99039) under GEO public data access policy.
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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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  ---
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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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+
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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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+
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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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+
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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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+
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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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+
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+ To train a model (e.g., GATv2) on one of the datasets:
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+
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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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+
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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.