Align modality labels with paper table; uppercase HERITAGE; group by modality

README.md

@@ -1,17 +1,17 @@
 ---
 license: cc-by-4.0
 tags:
-- biology
-- genomics
-- proteomics
-- graph-neural-networks
-- benchmarking
-- omics
+  - biology
+  - genomics
+  - proteomics
+  - graph-neural-networks
+  - benchmarking
+  - omics
 pretty_name: OmicsGBench — Omics Graph Benchmark
 task_categories:
-- tabular-classification
+  - tabular-classification
 size_categories:
-- n<1K
+  - n<1K
 ---
 
 # OmicsGBench: Benchmarking Graph Neural Networks on Omics Data
@@ -20,30 +20,30 @@ OmicsGBench is the first benchmark suite for graph-level prediction in the **n
 
 ## Datasets
 
-This repository contains six preprocessed omics graph classification datasets:
+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) |
+| --- | --- | --- | --- | --- |
+| 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) |
-| Tuberculosis | Protein microarray | 561 | 3,814 | Culture negative vs positive |
-| Smoking | DNA methylation | 464 | 139,125 | Never- vs ever-smoker |
 
-Smoking stores 139,125 TSS1500/TSS200 probes. Training keeps one probe per gene, about 20,763 genes.
+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.
 
 ## Source Data
 
-- **Heritage**: Robbins et al. (2021), *Nature Metabolism*. Available via MoTrPAC Data Hub (motrpac-data.org) under CC-BY 4.0.
+- **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.
-- **BRCA**: Yang et al. (2025), MLOmics, *Scientific Data*. Available on Figshare/Hugging Face under CC-BY 4.0.
-- **Tuberculosis**: Kunnath-Velayudhan et al. (2010), *PNAS*. Available via NCBI GEO (GSE19433) 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.
 
 ## Preprocessing
 
 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.
 
-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.
+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.