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fix(regen): score short-input oracles on their native window in multi-oracle report #94

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Merged
lucapinello merged 1 commit into from
Jun 17, 2026
Merged

fix(regen): score short-input oracles on their native window in multi-oracle report #94

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768 changes: 387 additions & 381 deletions ...ples/walkthroughs/validation/SORT1_rs12740374_multioracle/alphagenome_variant_report.json
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51 changes: 12 additions & 39 deletions examples/walkthroughs/validation/SORT1_rs12740374_multioracle/chrombpnet_variant_report.json
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Original file line number Diff line number Diff line change
Expand Up @@ -11,34 +11,7 @@
"gene_name": "SORT1",
"nearby_genes": [
"SORT1",
"PSRC1",
"CELSR2",
"MYBPHL",
"SARS1",
"ELAPOR1",
"PSMA5",
"CFAP276",
"TMEM167B",
"SYPL2",
"TAF13",
"ATXN7L2",
"CYB561D1",
"AMIGO1",
"WDR47",
"GPR61",
"GNAI3",
"GNAT2",
"AMPD2",
"CLCC1",
"GPSM2",
"AKNAD1",
"GSTM4",
"GSTM2",
"GSTM1",
"GSTM3",
"GSTM5",
"EPS8L3",
"STXBP3"
"CELSR2"
],
"report_title": "Multi-Layer Variant Effect Report",
"alleles": {
Expand All @@ -50,12 +23,12 @@
"assay_type": "DNASE",
"cell_type": "HepG2",
"layer": "chromatin_accessibility",
"ref_value": 255.6614961475134,
"alt_value": 605.572213485837,
"raw_score": 1.240812529069907,
"ref_value": 287.8572843968868,
"alt_value": 747.6530608385801,
"raw_score": 1.3739404259847205,
"description": "DNASE:HepG2",
"quantile_score": 0.9987,
"ref_signal_percentile": 0.8975
"quantile_score": 0.9995,
"ref_signal_percentile": 0.9059
}
]
},
Expand All @@ -65,12 +38,12 @@
"assay_type": "DNASE",
"cell_type": "HepG2",
"layer": "chromatin_accessibility",
"ref_value": 255.6614961475134,
"alt_value": 605.572213485837,
"raw_score": 1.240812529069907,
"ref_value": 287.8572843968868,
"alt_value": 747.6530608385801,
"raw_score": 1.3739404259847205,
"description": "DNASE:HepG2",
"quantile_score": 0.9987,
"ref_signal_percentile": 0.8975
"quantile_score": 0.9995,
"ref_signal_percentile": 0.9059
}
]
}
Expand All @@ -83,6 +56,6 @@
"tracks_requested": "1 tracks",
"cell_types": [],
"notes": [],
"generated_at": "2026-05-09 22:16 UTC"
"generated_at": "2026-06-17 15:28 UTC"
}
}
16 changes: 8 additions & 8 deletions examples/walkthroughs/validation/SORT1_rs12740374_multioracle/example_output.json
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Expand Up @@ -24,15 +24,15 @@
"layer": "chromatin_accessibility",
"oracles": {
"chrombpnet": {
"raw_score": 1.240812529069907,
"raw_score": 1.3739404259847205,
"assay_id": "DNASE:HepG2",
"cell_type": "HepG2",
"quantile_score": 0.9987,
"quantile_score": 0.9995,
"description": "DNASE:HepG2"
},
"legnet": null,
"alphagenome": {
"raw_score": 1.3359733411092043,
"raw_score": 1.3328380903453634,
"assay_id": "DNASE/EFO:0001187 DNase-seq/.",
"cell_type": "HepG2",
"quantile_score": 1.0,
Expand All @@ -46,7 +46,7 @@
"oracles": {
"chrombpnet": null,
"legnet": {
"raw_score": 6.079673767089844e-05,
"raw_score": 0.29897384718060493,
"assay_id": "LentiMPRA:HepG2",
"cell_type": "HepG2",
"quantile_score": null,
Expand All @@ -62,7 +62,7 @@
"chrombpnet": null,
"legnet": null,
"alphagenome": {
"raw_score": 2.777128004016167,
"raw_score": 2.7671279500219135,
"assay_id": "CHIP_TF/EFO:0001187 TF ChIP-seq CEBPA genetically modified (insertion) using CRISPR targeting H. sapiens CEBPA/.",
"cell_type": "HepG2",
"quantile_score": 1.0,
Expand All @@ -77,7 +77,7 @@
"chrombpnet": null,
"legnet": null,
"alphagenome": {
"raw_score": 1.2672761952097673,
"raw_score": 1.2638874528953854,
"assay_id": "CHIP_HISTONE/EFO:0001187 Histone ChIP-seq H3K27ac/.",
"cell_type": "HepG2",
"quantile_score": 1.0,
Expand All @@ -92,7 +92,7 @@
"chrombpnet": null,
"legnet": null,
"alphagenome": {
"raw_score": 1.5224982499093178,
"raw_score": 1.525278252854752,
"assay_id": "CAGE/hCAGE EFO:0001187/-",
"cell_type": "HepG2",
"quantile_score": 1.0,
Expand All @@ -110,6 +110,6 @@
"tracks_requested": "assay_ids as listed in each per-oracle request",
"cell_types": [],
"notes": [],
"generated_at": "2026-05-09 22:22 UTC"
"generated_at": "2026-06-17 15:29 UTC"
}
}
12 changes: 6 additions & 6 deletions examples/walkthroughs/validation/SORT1_rs12740374_multioracle/example_output.md
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Expand Up @@ -3,14 +3,14 @@
- **Variant:** chr1:109,274,968 G>T
- **Gene:** SORT1
- **Oracles:** chrombpnet, legnet, alphagenome
- **Generated:** 2026-05-09 22:22 UTC
- **Generated:** 2026-06-17 15:29 UTC

## Cross-oracle consensus

| Layer | chrombpnet | legnet | alphagenome | Agreement |
|---|---|---|---|---|
| Chromatin accessibility (DNASE/ATAC) (log2FC) | +1.241 · DNASE:HepG2 | — | +1.336 · DNASE:HepG2 | all ↑ |
| Promoter activity (MPRA) (Δ (alt−ref)) | — | +0.000 · LentiMPRA:HepG2 | — | only ↑ (n=1) |
| Transcription factor binding (ChIP-TF) (log2FC) | — | — | +2.777 · CHIP:CEBPA:HepG2 | only ↑ (n=1) |
| Histone modifications (ChIP-Histone) (log2FC) | — | — | +1.267 · CHIP:H3K27ac:HepG2 | only ↑ (n=1) |
| TSS activity (CAGE/PRO-CAP) (log2FC) | — | — | +1.522 · CAGE:HepG2 | only ↑ (n=1) |
| Chromatin accessibility (DNASE/ATAC) (log2FC) | +1.374 · DNASE:HepG2 | — | +1.333 · DNASE:HepG2 | all ↑ |
| Promoter activity (MPRA) (Δ (alt−ref)) | — | +0.299 · LentiMPRA:HepG2 | — | only ↑ (n=1) |
| Transcription factor binding (ChIP-TF) (log2FC) | — | — | +2.767 · CHIP:CEBPA:HepG2 | only ↑ (n=1) |
| Histone modifications (ChIP-Histone) (log2FC) | — | — | +1.264 · CHIP:H3K27ac:HepG2 | only ↑ (n=1) |
| TSS activity (CAGE/PRO-CAP) (log2FC) | — | — | +1.525 · CAGE:HepG2 | only ↑ (n=1) |
43 changes: 8 additions & 35 deletions examples/walkthroughs/validation/SORT1_rs12740374_multioracle/legnet_variant_report.json
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Original file line number Diff line number Diff line change
Expand Up @@ -11,34 +11,7 @@
"gene_name": "SORT1",
"nearby_genes": [
"SORT1",
"PSRC1",
"CELSR2",
"MYBPHL",
"SARS1",
"ELAPOR1",
"PSMA5",
"CFAP276",
"TMEM167B",
"SYPL2",
"TAF13",
"ATXN7L2",
"CYB561D1",
"AMIGO1",
"WDR47",
"GPR61",
"GNAI3",
"GNAT2",
"AMPD2",
"CLCC1",
"GPSM2",
"AKNAD1",
"GSTM4",
"GSTM2",
"GSTM1",
"GSTM3",
"GSTM5",
"EPS8L3",
"STXBP3"
"CELSR2"
],
"report_title": "Multi-Layer Variant Effect Report",
"alleles": {
Expand All @@ -50,9 +23,9 @@
"assay_type": "LentiMPRA",
"cell_type": "HepG2",
"layer": "promoter_activity",
"ref_value": -0.7386637330055237,
"alt_value": -0.7386029362678528,
"raw_score": 6.079673767089844e-05,
"ref_value": -0.04832424595952034,
"alt_value": 0.2506496012210846,
"raw_score": 0.29897384718060493,
"description": "LentiMPRA:HepG2"
}
]
Expand All @@ -63,9 +36,9 @@
"assay_type": "LentiMPRA",
"cell_type": "HepG2",
"layer": "promoter_activity",
"ref_value": -0.7386637330055237,
"alt_value": -0.7386029362678528,
"raw_score": 6.079673767089844e-05,
"ref_value": -0.04832424595952034,
"alt_value": 0.2506496012210846,
"raw_score": 0.29897384718060493,
"description": "LentiMPRA:HepG2"
}
]
Expand All @@ -79,6 +52,6 @@
"tracks_requested": "1 tracks",
"cell_types": [],
"notes": [],
"generated_at": "2026-05-09 22:19 UTC"
"generated_at": "2026-06-17 15:25 UTC"
}
}
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