geometric-intelligence/ogbench
OgBench: Benchmarking Graph Neural Networks on Omics Data 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. Datasets This repository contains four preprocessed omics graph classification datasets: Dataset Modality n p Task HERITAGE Proteomics 654 4,977 Exercise responder… See the full description on the dataset page: https://huggingface.co/datasets/geometric-intelligence/ogbench.
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1{2 "dataset_name": "ov",3 "download_urls": {4 "OV_mRNA": "https://huggingface.co/datasets/AIBIC/MLOmics/resolve/main/Main_Dataset/Classification_datasets/GS-OV/Original/OV_mRNA.csv",5 "OV_label_num": "https://huggingface.co/datasets/AIBIC/MLOmics/resolve/main/Main_Dataset/Classification_datasets/GS-OV/Original/OV_label_num.csv"6 },7 "download_timestamp": "2026-06-01T13:48:09.093293",8 "statistics": {9 "num_samples": 284,10 "num_features": 14229,11 "target_stats": {12 "class_mapping": {13 "Immunoreactive": 0,14 "Mesenchymal": 1,15 "Proliferative": 2,16 "Differentiated": 317 },18 "num_classes": 4,19 "class_names": [20 "Immunoreactive",21 "Mesenchymal",22 "Proliferative",23 "Differentiated"24 ],25 "samples_per_class": {26 "Immunoreactive": 64,27 "Mesenchymal": 79,28 "Proliferative": 67,29 "Differentiated": 7430 }31 }32 },33 "preprocessing_notes": "MLOmics log-transformed FPKM values (no additional log transform). Dropped genes with >50% zero values in a random 70% training split. Duplicate gene symbols are dropped keeping first occurrence (1-Mar, 2-Mar). Parquet feature names replace dots with underscores; gene map string_id retains original HGNC symbols."34}