BEND
Human-genome tasks with biologically aligned splits; inspect each track for leakage controls.
7 benchmark-wide protocols · 105 benchmark-wide rows (not a task subtotal)D4 · Variant effect & evolution
Regulatory variant-effect prediction
Predict effects of non-coding variants on regulatory activity.
Task definition
- Input granularity
- reference/alternate sequence
- Biological target
- regulatory activity change
- Output representation
- delta score
- ML formulation
- regression/ranking
- Counting notes
- NR
Benchmark coverage
4 benchmarks cover this task
DART-Eval
Regulatory DNA evaluation across zero-shot, probing and fine-tuning regimes.
0 benchmark-wide protocols · 0 benchmark-wide rows (not a task subtotal)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)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
3 protocol units
| Protocol | Track | Split / subset | Comparability |
|---|---|---|---|
P-B08-SQTL | Benchmarking DNA foundation models for genomic and genetic tasks — Regulatory variant-effect prediction B08-TR05 | nested chromosome-based held-out test groups putative causal sQTL | same_table_comparable cross-work compute/hardware equivalence |
P-B08-IPAQTL | Benchmarking DNA foundation models for genomic and genetic tasks — Regulatory variant-effect prediction B08-TR05 | nested chromosome-based held-out test groups putative causal ipaQTL | same_table_comparable cross-work compute/hardware equivalence |
P-B08-EQTL | Benchmarking DNA foundation models for genomic and genetic tasks — Regulatory variant-effect prediction B08-TR05 | nested chromosome-based held-out test groups putative causal eQTL | same_table_comparable cross-work compute/hardware equivalence |