Benchmarking DNA foundation models for genomic and genetic tasks
One-time benchmark study rather than a maintained benchmark suite.
6 benchmark-wide protocols · 8 benchmark-wide rows (not a task subtotal)D4 · Variant effect & evolution
Molecular functional or pathogenic variant interpretation
Restricted here to molecular/functional challenges; patient-level diagnosis and PRS are excluded.
Task definition
- Input granularity
- variant plus molecular context
- Biological target
- functional consequence/pathogenicity
- Output representation
- class or score
- ML formulation
- classification/ranking
- Counting notes
- NR
Benchmark coverage
2 benchmarks cover this task
CAGI molecular/functional challenges
Only molecular and functional variant challenges are in scope; phenotype-from-exome and patient-level tasks are excluded.
0 benchmark-wide protocols · 0 benchmark-wide rows (not a task subtotal)Evaluation protocols
2 protocol units
| Protocol | Track | Split / subset | Comparability |
|---|---|---|---|
PROT-B03-VARIANT-EFFECTS-DISEASE-OFFICIAL-ZE-9C85FF58-6CB6E8D4 | variant_effects_disease NR | official zero-shot disease-variant set variant effects disease | same_table_comparable inference_budget |
P-B08-PATHOGENIC | Benchmarking DNA foundation models for genomic and genetic tasks — Molecular functional or pathogenic variant interpretation B08-TR06 | nested chromosome-based held-out test groups pathogenic versus common SNP | same_table_comparable cross-work compute/hardware equivalence |