DaviBonetto/spectralbio-clinvar

SpectralBio Dataset Card

Public Hierarchy

SpectralBio separates manuscript-facing scientific centrality from frozen executable replay centrality.

• Flagship scientific result: BRCA2 covariance-aware augmentation against a stronger five-model ESM-1v baseline
• Validation anchor: TP53 is the only frozen public canonical replay surface
• Breadth surface: support-ranked top-25 feasible panel derived from the 15,752-gene ClinVar scan
• Boundary surfaces: protocol sweep and BRCA1 failure analysis
• Auxiliary executable surface: bounded transfer on a fixed BRCA1 subset (N=100) without retraining

This dataset card therefore describes both the released executable payloads and the broader scientific audit context in which they sit.

Frozen Executable Replay Contract

• Primary executable benchmark: TP53 canonical executable benchmark
• Auxiliary executable surface: bounded transfer on a fixed BRCA1 subset (N=100) without retraining
• Transfer framing: secondary transfer evaluation without retraining
• Repository framing: research reproducibility artifact
• Extension policy: adaptation recipe only
• Provenance-only data: BRCA1_full_filtered_v1.json is preserved for transparency and transfer-subset derivation only

TP53 remains the only canonical scored benchmark. BRCA1_transfer100 remains bounded auxiliary executable evidence without retraining.

The Hugging Face dataset payload mirrors the frozen benchmark JSONs directly, so the Hub viewer and downloadable files point at the same canonical records used by the release bundle.

Frozen Files

Surface	Role	File	Count	Label split	SHA256
TP53 canonical variants	Canonical executable benchmark	benchmarks/tp53/tp53_canonical_v1.json	255	pathogenic=115, benign=140 (1=pathogenic, 0=benign)	ba37cef10ef3a334932be0b0b7a7d4756d15ea7c6aaf29a777ef79c14e1d4fa6
TP53 score reference	Canonical companion file	benchmarks/tp53/tp53_scores_v1.json	255	aligned to TP53 canonical variants by name and order	a07066ca3d55cce98d81a04a30f71ab99e3c5cbb95d28a4a135d03229e809b28
BRCA1 transfer subset	Secondary transfer evaluation without retraining	benchmarks/brca1/brca1_transfer100_v1.json	100	pathogenic=29, benign=71 (1=pathogenic, 0=benign)	62c3bcc50d0258adb0af2fef77be00f763ff3c03f3adb27e52393d0ea49f2341
BRCA1 full filtered	Provenance-only source snapshot	benchmarks/brca1/brca1_full_filtered_v1.json	512	pathogenic=165, benign=347 (1=pathogenic, 0=benign)	4a4e911a226b4f5c5aa7069e39d5ccfc22be122678bf2d11275f70240d0d7a46

Public Scientific Audit Surfaces

The BRCA2 flagship result and the support-ranked breadth evidence are carried by the public scientific audit surfaces rather than by the frozen executable dataset payload itself.

• abstract.md
• content.md
• notebooks/final_accept_part3_esm1v_augmentation_A100.ipynb
• notebooks/final_accept_part4_brca2_canonicalization_A100.ipynb
• notebooks/final_accept_part1_support_panel.ipynb
• notebooks/final_accept_part5_protocol_sweep_A100.ipynb
• notebooks/final_accept_part6_panel25_brca1_failure_L4.ipynb

Official Metrics

Manuscript Scientific Audit Metrics

• BRCA2 ESM-1v baseline AUC: 0.6324
• BRCA2 covariance + ESM-1v AUC: 0.6890
• BRCA2 paired gain vs ESM-1v: 0.0566
• BRCA2 paired 95% bootstrap CI: [0.0131, 0.1063]
• BRCA2 empirical permutation p: 0.0010

Machine-Verified Executable Metrics

• TP53 canonical executable benchmark: 0.55 * frob_dist + 0.45 * ll_proper AUC = 0.7498
• Bounded transfer on a fixed BRCA1 subset (N=100) without retraining: ll_proper AUC = 0.9174
• Reproducibility delta: 0.0

Provenance Link

• brca1_transfer100_v1.json is the fixed first 100 records from brca1_full_filtered_v1.json.
• BRCA1_full_filtered_v1.json is preserved for provenance and migration safety only.
• Canonical truth lives in docs/truth_contract.md, benchmarks/manifests/*.json, and artifacts/expected/*.
• Scientific framing truth lives in abstract.md, content.md, and the BRCA2 / panel notebooks listed above.

References

• Truth contract: docs/truth_contract.md
• Reproducibility notes: docs/reproducibility.md
• Canonical benchmark manifest: benchmarks/manifests/tp53_canonical_manifest.json
• Transfer benchmark manifest: benchmarks/manifests/brca1_transfer_manifest.json
• Provenance manifest: benchmarks/manifests/source_snapshot.json
• Checksums: benchmarks/manifests/checksums.json