| --- |
| license: cc-by-4.0 |
| tags: |
| - biology |
| - genomics |
| - proteomics |
| - graph-neural-networks |
| - benchmarking |
| - omics |
| pretty_name: OmicsGBench — Omics Graph Benchmark |
| task_categories: |
| - tabular-classification |
| size_categories: |
| - n<1K |
| --- |
| |
| # OmicsGBench: Benchmarking Graph Neural Networks on Omics Data |
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| OmicsGBench 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 six preprocessed omics graph classification datasets, grouped by modality: |
|
|
| | Dataset | Modality | n | p | Task | |
| | --- | --- | --- | --- | --- | |
| | HERITAGE | Proteomics | 654 | 4,976 | Exercise responder (binary) | |
| | Tuberculosis | Proteomics | 561 | 3,814 | Culture negative vs positive | |
| | Parkinson's | Transcriptomics | 535 | 21,755 | Cognitive status (binary) | |
| | AddNeuroMed | Transcriptomics | 711 | 17,197 | Clinical diagnosis (3-class) | |
| | Smoking | Epigenomics | 464 | 139,125 | Never- vs ever-smoker | |
| | BRCA | Epigenomics | 640 | 19,049 | Cancer subtype (4-class) | |
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| Tuberculosis is a full-proteome antibody microarray (immunoproteomics), where each feature is one *M. tuberculosis* protein. Smoking stores 139,125 TSS1500/TSS200 methylation probes; training keeps one probe per gene, about 20,763 genes. |
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| ## Source Data |
|
|
| - **HERITAGE**: Robbins et al. (2021), *Nature Metabolism*. Available via MoTrPAC Data Hub (motrpac-data.org) under CC-BY 4.0. |
| - **Tuberculosis**: Kunnath-Velayudhan et al. (2010), *PNAS*. Available via NCBI GEO (GSE19433) under GEO public data access policy. |
| - **Parkinson's**: Shamir et al. (2017), *Neurology*. Available via NCBI GEO (GSE99039) under GEO public data access policy. |
| - **AddNeuroMed**: Lovestone et al. (2009). Available via NCBI GEO (GSE63063) under GEO public data access policy. |
| - **Smoking**: Tsaprouni et al. (2014), *Epigenetics*. Available via NCBI GEO (GSE50660) under GEO public data access policy. |
| - **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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| Datasets share one ingest pipeline: probe-to-gene aggregation where the source is probe-level, and the normalization described in Appendix B of the accompanying paper. Matrices on the Hub are uncorrected. HERITAGE covariate adjustment, AddNeuroMed ComBat, and smoking promoter-probe selection plus median-centering are fit on the training split only. |
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| The default evaluation is stratified 5-fold. A 70/15/15 train/val/test split is available as `split_type=fixed`. Parkinson's and Tuberculosis keep each batch inside one fold: hybridization date for Parkinson's, country of serum collection for Tuberculosis. |
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