Datasets:
| { | |
| "READY": true, | |
| "name": "vep_pathogenic_coding", | |
| "task": "binary", | |
| "num_classes": 2, | |
| "cat_idx": [ | |
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| ], | |
| "num_samples": 37166, | |
| "num_features": 98, | |
| "imbalance_ratio": 1.1365, | |
| "description": "Classify coding single-nucleotide variants as pathogenic (ClinVar, label 1) or common (gnomAD MAF > 5%, label 0) from DNA sequence context only. Variants are strand-canonicalised (reverse-complemented when the reference allele is a purine, so it is always C or T). Features: GRCh38 reference bases at offsets -32..+32 around the variant (the central base is the reference allele) and the alternative allele (66 categorical), plus canonical 3-mer frequencies (k-mer and reverse complement merged) of the 513-bp reference window centred on the variant (32 numeric). Allele-frequency fields, annotation fields (VEP consequence, ClinVar IDs/review status) and genomic coordinates are excluded because they define or reveal the label. chrX/chrY variants (all pathogenic by construction) and two variants listed with both labels are removed. Split by whole chromosomes: test = chr1, chr4, chr21; validation = chr5, chr6, chr11; train = remaining autosomes.", | |
| "source": "InstaDeepAI/genomics-long-range-benchmark (Hugging Face), task variant_effect_pathogenic (ClinVar, coding SNVs): ClinVar pathogenic variants vs gnomAD v3.1.2 common variants (MAF > 5%, AN >= 25,000) (Kao et al., 2024). Sequence context from the UCSC hg38 (GRCh38) reference genome.", | |
| "label": "genomics" | |
| } |