Update README.md

README.md

@@ -43,16 +43,12 @@ non_coding = load_dataset("hf-carbon/clinvar-vep-final", "non_coding", split="te
 
 ## Coding subset — origin
 
-For the coding ClinVar benchmark, we use the ClinVar VEP subset from [`GenerTeam/variant-effect-prediction`](https://huggingface.co/datasets/GenerTeam/variant-effect-prediction), which was originally used in the GPN-MSA study ([Benegas et al., 2025](https://www.nature.com/articles/s41587-024-02511-w)). After annotating this dataset with ClinVar molecular consequence / region information, we found that it is overwhelmingly coding: among matched variants, **39,473 are coding and only 1,503 are non-coding**, with only **10 pathogenic non-coding variants** in the entire non-coding split — far too few and far too imbalanced for meaningful AUROC. We therefore keep this dataset as our coding ClinVar benchmark.
+For the coding ClinVar benchmark, we use the ClinVar VEP subset from [`GenerTeam/variant-effect-prediction`](https://huggingface.co/datasets/GenerTeam/variant-effect-prediction), which was originally used in the GPN-MSA study ([Benegas et al., 2025](https://www.nature.com/articles/s41587-024-02511-w)). However, wee found that it is largely coding:  **39,473 are coding and 1,503 are non-coding**. The non-coding subset is also highly label-imbalanced, with **10 pathogenic non-coding variants**. We therefore use this dataset as our coding ClinVar benchmark and construct a separate balanced non-coding subset from ClinVar.
 
-The coding parquet preserves all upstream baseline scores (CADD, phyloP-100v, phyloP-241m, phastCons-100v, GPN-MSA, NT, NT-v2, HyenaDNA, Evo2-1B-Base, Evo2-7B-Base, Evo2-7B, GENERator-1B/3B, GENERator-v2-1B/3B) along with `chrom`, `pos`, `ref`, `alt`, `label`, `type`, `refseq_id`.
 
 ## Non-coding subset — construction
 
 To construct a separate non-coding ClinVar benchmark, we start from the original ClinVar VCF and restrict to single-nucleotide variants on chromosomes 1–22, X, and Y with binary clinical labels, mapping benign / likely benign to `label = 0` and pathogenic / likely pathogenic to `label = 1`. We retain reviewed variants, annotate each variant using ClinVar consequence terms into broad region classes (`coding`, `non_coding`, `splice`, `unknown`) and finer subtypes (`intronic`, `utr_5_prime`, `utr_3_prime`, etc.), and then select the clean non-coding subset with `coding_status == "non_coding"`.
 
-This yields a **balanced non-coding benchmark of 15,258 variants: 7,629 benign and 7,629 pathogenic**, covering intronic (10,310) and UTR variants (4,948 total — 4,174 5′UTR + 774 3′UTR). Splice (250) and unknown-region variants (12,200) are kept separate from the main non-coding subset because they represent distinct or ambiguous categories, and live in the source repository [`hf-carbon/ClinVar-VEP`](https://huggingface.co/datasets/hf-carbon/ClinVar-VEP).
+This yields a **balanced non-coding benchmark of 15,258 variants: 7,629 benign and 7,629 pathogenic**, covering intronic (10,310) and UTR variants (4,948 total — 4,174 5′UTR + 774 3′UTR).
 
-## Citation
-
-If you use this benchmark, please cite GPN-MSA (Benegas et al., 2025) and the ClinVar database.