genepropx-bgcn / training_report.json
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{
"trained_at": "2026-08-28T13:42:32.184957+00:00",
"device": "cpu",
"n_genes_total": 570,
"n_train_labeled": 199,
"n_test_labeled": 102,
"temporal_split": {
"train_total": 1504,
"test_total": 1415,
"leakage_prevented": 0,
"no_leak_verified": true
},
"baseline": {
"auroc": 0.1190368014538846,
"auprc": 0.547004870356739
},
"bgcn": {
"auroc": 0.9213993639254885,
"auprc": 0.9559666780818283
},
"calibration": {
"slope": 1.039452672944247,
"intercept": 0.14796603209583445,
"ece": 0.10702049929429502
},
"dca": {
"passes_gate": true,
"positive_range": [
0.01,
0.97
]
},
"lrp_fidelity": {
"mean_fidelity": -0.08218878777653914,
"median_fidelity": -0.013004715115331498,
"std_fidelity": 0.37249609903622566,
"min_fidelity": -1.4798435791581208,
"n_faithful": 4
},
"gates": {
"auroc_beats_baseline": true,
"auprc_beats_baseline_margin_0.02": true,
"calibration_slope_in_range": true,
"calibration_intercept_in_range": false,
"dca_net_benefit_positive": true,
"lrp_fidelity_ge_0.3": false
},
"release_status": "RESEARCH_ONLY_NOT_PROMOTED",
"meta": {
"n_genes": 570,
"gene_list": [
"14q partial distal trisomy syndrome",
"ABCA7",
"ABCC2",
"ABHD17B",
"ABHD3",
"ACD",
"ADAMTS1",
"ADAMTS9",
"ADAP2",
"AIMP2",
"AKAP11",
"AKT1",
"ALK",
"ALS2",
"ANG",
"ANKRD22",
"ANKRD26",
"AOPEP",
"APBA2",
"APC",
"APOB",
"APOB3'MAR",
"APOE",
"APP",
"AR",
"ARID1A",
"ASXL1",
"ATM",
"ATP13A2",
"ATR",
"ATRX",
"AXIN2",
"BAP1",
"BARD1",
"BAX",
"BCL10",
"BCL2",
"BCL6",
"BIVM-ERCC5",
"BRAF",
"BRCA1",
"BRCA2",
"BRIP1",
"BRK1",
"C10orf55",
"C6orf201",
"C9orf72",
"CARD11",
"CASP10",
"CASP8",
"CASR",
"CBL",
"CCND1",
"CCNF",
"CDH1",
"CDK4",
"CDK6",
"CDKN2A",
"CEBPA",
"CEP290",
"CFTR",
"CFTR-AS1",
"CFTR-AS2",
"CHCHD10",
"CHEK2",
"CHMP2B",
"CNTN1",
"COL18A1",
"COL4A4",
"CPSF2",
"CREBBP",
"CTAGE1",
"CTNNA1",
"CTNNB1",
"CYLD",
"Cardiovascular phenotype",
"DAXX",
"DCTN1",
"DDX41",
"DHCR7",
"DICER1",
"DIPK1A",
"DKC1",
"DMD",
"DNAJC6",
"DNAJC7",
"DNMT3A",
"EGFR",
"EGFR-AS1",
"EGFR-related lung cancer",
"EGLN1",
"ELANE",
"EP300",
"EPAS1",
"EPCAM",
"ERBB2",
"ERBB4",
"ERCC2",
"ERCC4",
"ESR1",
"ETV6",
"EVI2A",
"EWSR1",
"EZH2",
"FAN1",
"FANCA",
"FANCC",
"FANCD2",
"FANCE",
"FANCG",
"FANCI",
"FAS",
"FASLG",
"FBP2",
"FBXW7",
"FH",
"FLCN",
"FLT1",
"FLT3",
"FMR1",
"FOXA1",
"FOXL2",
"FRONTOTEMPORAL LOBAR DEGENERATION WITH TDP43 INCLUSIONS, TARDBP-RELATED",
"FUS",
"FXR2",
"G6PD",
"GALNT12",
"GATA2",
"GATA3",
"GBA",
"GBA1",
"GBE1",
"GLE1",
"GLI1",
"GLIS2",
"GNA11",
"GNAQ",
"GNAS",
"GPD1",
"GRN",
"H3-3B",
"H3F3A",
"HBB",
"HEATR3",
"HIF1A",
"HNRNPA2B1",
"HRAS",
"HTT",
"Hereditary nonpolyposis colorectal neoplasms",
"IDH1",
"IDH2",
"IDH3A",
"INVS",
"IQCB1",
"Inborn genetic diseases",
"Inherited MMR deficiency (Lynch syndrome)",
"Inherited breast cancer and ovarian cancer",
"Inherited ovarian cancer (without breast cancer)",
"JAK1",
"JAK2",
"KDM6A",
"KDR",
"KIF1A",
"KIF5A",
"KIT",
"KMT2A",
"KMT2D",
"KRAS",
"LALTOP",
"LDLR",
"LDLRAP1",
"LNCR-SMAL",
"LOC107303340",
"LOC108281125",
"LOC108281182",
"LOC108903148",
"LOC110806263",
"LOC110806306",
"LOC111674477",
"LOC114803469",
"LOC126806050",
"LOC126807526",
"LOC126861339",
"LOC126861451",
"LOC126862483",
"LOC126862571",
"LOC129390965",
"LOC129937550",
"LOC130007385",
"LOC130055403",
"LOC130062441",
"LOC132090298",
"LRRFIP2",
"LRRK2",
"LZTR1",
"Li-Fraumeni syndrome 1",
"MAP2K1",
"MAP2K2",
"MAPT",
"MATR3",
"MBD4",
"MDM2",
"MDM4",
"MEN1",
"MET",
"MIR6084",
"MLH1",
"MLH3",
"MONDO:0000507",
"MONDO:0002447",
"MONDO:0003582",
"MONDO:0004975",
"MONDO:0004976",
"MONDO:0005145",
"MONDO:0005180",
"MONDO:0005439",
"MONDO:0005575",
"MONDO:0005835",
"MONDO:0007039",
"MONDO:0007086",
"MONDO:0007088",
"MONDO:0007089",
"MONDO:0007103",
"MONDO:0007104",
"MONDO:0007105",
"MONDO:0007110",
"MONDO:0007356",
"MONDO:0007485",
"MONDO:0007488",
"MONDO:0007648",
"MONDO:0007750",
"MONDO:0007827",
"MONDO:0008018",
"MONDO:0008021",
"MONDO:0008192",
"MONDO:0008199",
"MONDO:0008200",
"MONDO:0008233",
"MONDO:0008243",
"MONDO:0008280",
"MONDO:0008453",
"MONDO:0008555",
"MONDO:0008667",
"MONDO:0008685",
"MONDO:0008734",
"MONDO:0008762",
"MONDO:0008840",
"MONDO:0008887",
"MONDO:0009061",
"MONDO:0009134",
"MONDO:0009213",
"MONDO:0009214",
"MONDO:0009215",
"MONDO:0009623",
"MONDO:0009694",
"MONDO:0009892",
"MONDO:0009897",
"MONDO:0010035",
"MONDO:0010133",
"MONDO:0010210",
"MONDO:0010214",
"MONDO:0010215",
"MONDO:0010216",
"MONDO:0010385",
"MONDO:0010459",
"MONDO:0010584",
"MONDO:0010820",
"MONDO:0010936",
"MONDO:0010953",
"MONDO:0010997",
"MONDO:0011014",
"MONDO:0011136",
"MONDO:0011158",
"MONDO:0011196",
"MONDO:0011369",
"MONDO:0011383",
"MONDO:0011405",
"MONDO:0011450",
"MONDO:0011537",
"MONDO:0011613",
"MONDO:0011632",
"MONDO:0011658",
"MONDO:0011706",
"MONDO:0011713",
"MONDO:0011743",
"MONDO:0011764",
"MONDO:0011797",
"MONDO:0011913",
"MONDO:0011951",
"MONDO:0012041",
"MONDO:0012075",
"MONDO:0012132",
"MONDO:0012153",
"MONDO:0012183",
"MONDO:0012186",
"MONDO:0012249",
"MONDO:0012565",
"MONDO:0012669",
"MONDO:0012790",
"MONDO:0012924",
"MONDO:0012933",
"MONDO:0012937",
"MONDO:0013196",
"MONDO:0013216",
"MONDO:0013248",
"MONDO:0013253",
"MONDO:0013264",
"MONDO:0013292",
"MONDO:0013308",
"MONDO:0013357",
"MONDO:0013398",
"MONDO:0013499",
"MONDO:0013521",
"MONDO:0013522",
"MONDO:0013565",
"MONDO:0013625",
"MONDO:0013669",
"MONDO:0013692",
"MONDO:0013699",
"MONDO:0013710",
"MONDO:0013725",
"MONDO:0013888",
"MONDO:0014025",
"MONDO:0014045",
"MONDO:0014048",
"MONDO:0014108",
"MONDO:0014178",
"MONDO:0014223",
"MONDO:0014231",
"MONDO:0014233",
"MONDO:0014252",
"MONDO:0014382",
"MONDO:0014536",
"MONDO:0014600",
"MONDO:0014612",
"MONDO:0014630",
"MONDO:0014641",
"MONDO:0014690",
"MONDO:0014796",
"MONDO:0014802",
"MONDO:0014809",
"MONDO:0014975",
"MONDO:0014979",
"MONDO:0014986",
"MONDO:0014987",
"MONDO:0015253",
"MONDO:0015356",
"MONDO:0015780",
"MONDO:0016063",
"MONDO:0016073",
"MONDO:0016248",
"MONDO:0016419",
"MONDO:0017276",
"MONDO:0017623",
"MONDO:0018150",
"MONDO:0018604",
"MONDO:0018630",
"MONDO:0018770",
"MONDO:0018874",
"MONDO:0018875",
"MONDO:0018881",
"MONDO:0018921",
"MONDO:0018975",
"MONDO:0018996",
"MONDO:0019005",
"MONDO:0021056",
"MONDO:0024537",
"MONDO:0024551",
"MONDO:0030690",
"MONDO:0030805",
"MONDO:0030872",
"MONDO:0031071",
"MONDO:0032865",
"MONDO:0033362",
"MONDO:0042490",
"MONDO:0044300",
"MONDO:0054750",
"MONDO:0100216",
"MONDO:0100553",
"MONDO:0700270",
"MONDO:0800444",
"MONDO:0859183",
"MONDO:0859246",
"MONDO:0859267",
"MONDO:0957530",
"MONDO:0975748",
"MONDO:0980991",
"MONDO:8000012",
"MPO",
"MSH2",
"MSH3",
"MSH6",
"MTOR",
"MUTYH",
"MYC",
"MYD88",
"NBN",
"NEFH",
"NEK1",
"NF1",
"NF2",
"NOTCH1",
"NOTCH3",
"NPHP1",
"NPHP3",
"NPHP3-ACAD11",
"NPHP4",
"NPM1",
"NRAS",
"NTHL1",
"OLR1",
"OPTN",
"OSBPL1A",
"PALB2",
"PARK7",
"PARN",
"PAX8",
"PBRM1",
"PCSK9",
"PDGFRA",
"PIK3C2G",
"PIK3CA",
"PIK3R1",
"PIKFYVE",
"PINK1",
"PMS1",
"PMS2",
"POLD1",
"POLE",
"POLH",
"PRKAG2",
"PRKAR1A",
"PRKN",
"PRPH",
"PSAP",
"PSEN1",
"PSEN2",
"PTCH1",
"PTEN",
"PTPN11",
"PTRH2",
"Partial 18p monosomy with 18q trisomy",
"RAB32",
"RAD51",
"RAD51C",
"RAD51D",
"RAF1",
"RB1",
"REL",
"RET",
"RHOT1",
"RPA1",
"RPS10",
"RPS17",
"RPS19",
"RPS20",
"RUNX1",
"SAMD9L",
"SDHB",
"SDHD",
"SEC23B",
"SETD2",
"SETX",
"SH2D1A",
"SHOC2",
"SLC52A3",
"SLX4",
"SMAD4",
"SMARCB1",
"SMN1",
"SMO",
"SNCA",
"SOCS1",
"SOD1",
"SORL1",
"SOS1",
"SPG11",
"SPRED1",
"SQSTM1",
"STAG2",
"STAT3",
"STK11",
"SUFU",
"SUPT16H",
"SYNJ1",
"See cases",
"TAF15",
"TARDBP",
"TBK1",
"TERT",
"TET2",
"TINF2",
"TNFAIP3",
"TP53",
"TP53BP1",
"TRPM7",
"TSC1",
"TSC2",
"TTC21B",
"Triple-negative breast cancer",
"UBQLN2",
"USB1",
"VAPB",
"VCP",
"VEGFA",
"VHL",
"VPS13C",
"VPS35",
"WT1",
"XIAP",
"XPA",
"XRCC1",
"XRCC2",
"ZCCHC8",
"not provided",
"not specified",
"tissue:Adipose_Subcutaneous",
"tissue:Adipose_Visceral_Omentum",
"tissue:Adrenal_Gland",
"tissue:Artery_Aorta",
"tissue:Artery_Coronary",
"tissue:Artery_Tibial",
"tissue:Bladder",
"tissue:Brain_Amygdala",
"tissue:Brain_Anterior_cingulate_cortex_BA24",
"tissue:Brain_Caudate_basal_ganglia",
"tissue:Brain_Cerebellar_Hemisphere",
"tissue:Brain_Cerebellum",
"tissue:Brain_Cortex",
"tissue:Brain_Frontal_Cortex_BA9",
"tissue:Brain_Hippocampus",
"tissue:Brain_Hypothalamus",
"tissue:Brain_Nucleus_accumbens_basal_ganglia",
"tissue:Brain_Putamen_basal_ganglia",
"tissue:Brain_Spinal_cord_cervical_c-1",
"tissue:Brain_Substantia_nigra",
"tissue:Breast_Mammary_Tissue",
"tissue:Cells_Cultured_fibroblasts",
"tissue:Cells_EBV-transformed_lymphocytes",
"tissue:Cervix_Ectocervix",
"tissue:Cervix_Endocervix",
"tissue:Colon_Sigmoid",
"tissue:Colon_Transverse",
"tissue:Esophagus_Gastroesophageal_Junction",
"tissue:Esophagus_Mucosa",
"tissue:Esophagus_Muscularis",
"tissue:Fallopian_Tube",
"tissue:Heart_Atrial_Appendage",
"tissue:Heart_Left_Ventricle",
"tissue:Kidney_Cortex",
"tissue:Kidney_Medulla",
"tissue:Liver",
"tissue:Lung",
"tissue:Minor_Salivary_Gland",
"tissue:Muscle_Skeletal",
"tissue:Nerve_Tibial",
"tissue:Ovary",
"tissue:Pancreas",
"tissue:Pituitary",
"tissue:Prostate",
"tissue:Skin_Not_Sun_Exposed_Suprapubic",
"tissue:Skin_Sun_Exposed_Lower_leg",
"tissue:Small_Intestine_Terminal_Ileum",
"tissue:Spleen",
"tissue:Stomach",
"tissue:Testis",
"tissue:Thyroid",
"tissue:Uterus",
"tissue:Vagina",
"tissue:Whole_Blood"
],
"n_positive": 226,
"n_negative": 93,
"n_unlabeled": 251,
"seed_genes": [
"TP53",
"BRCA1",
"BRCA2",
"PTEN",
"EGFR",
"KRAS",
"APC",
"VHL"
],
"layers": {
"L1": {
"nodes": 158,
"edges": 3833
},
"L2": {
"nodes": 196,
"edges": 7668
},
"L3": {
"nodes": 412,
"edges": 342
},
"L4": {
"nodes": 0,
"edges": 0
}
},
"l4_status": "BLOCKED (CELLxGENE SIGILL in sandbox) \u2014 empty, no fabricated data",
"sources": [
"STRING v12.0 (real)",
"ClinVar esummary (real, dated)",
"GTEx Portal API v2 (real)",
"Gene Ontology (real, term-only, not gene-linked)"
],
"panel_genes": [
"AKT1",
"ALK",
"APC",
"APOE",
"APP",
"AR",
"ARID1A",
"ASXL1",
"ATM",
"ATR",
"ATRX",
"AXIN2",
"BAP1",
"BARD1",
"BAX",
"BCL10",
"BCL2",
"BCL6",
"BRAF",
"BRCA1",
"BRCA2",
"BRIP1",
"C9orf72",
"CARD11",
"CASP8",
"CASR",
"CBL",
"CCND1",
"CDH1",
"CDK4",
"CDK6",
"CDKN2A",
"CEBPA",
"CFTR",
"CHEK2",
"CREBBP",
"CTNNB1",
"DAXX",
"DMD",
"DNMT3A",
"EGFR",
"EGLN1",
"EP300",
"EPAS1",
"EPCAM",
"ERBB2",
"ERCC2",
"ESR1",
"EZH2",
"FBXW7",
"FH",
"FLT1",
"FLT3",
"FMR1",
"FOXA1",
"FOXL2",
"FUS",
"G6PD",
"GATA3",
"GBA",
"GLI1",
"GNA11",
"GNAQ",
"GNAS",
"GRN",
"H3F3A",
"HBB",
"HIF1A",
"HRAS",
"HTT",
"IDH1",
"IDH2",
"IDH3A",
"JAK1",
"JAK2",
"KDM6A",
"KDR",
"KIT",
"KMT2A",
"KMT2D",
"KRAS",
"LDLR",
"LRRK2",
"LZTR1",
"MAP2K1",
"MAP2K2",
"MAPT",
"MDM2",
"MDM4",
"MEN1",
"MET",
"MLH1",
"MSH2",
"MSH3",
"MSH6",
"MTOR",
"MYC",
"MYD88",
"NF1",
"NF2",
"NOTCH1",
"NPM1",
"NRAS",
"PALB2",
"PARK7",
"PAX8",
"PBRM1",
"PCSK9",
"PDGFRA",
"PIK3CA",
"PIK3R1",
"PINK1",
"PMS2",
"POLD1",
"POLE",
"PRKAR1A",
"PSEN1",
"PSEN2",
"PTCH1",
"PTEN",
"PTPN11",
"RAD51C",
"RAD51D",
"RAF1",
"RB1",
"RET",
"RUNX1",
"SDHB",
"SDHD",
"SETD2",
"SHOC2",
"SMAD4",
"SMARCB1",
"SMN1",
"SMO",
"SNCA",
"SOCS1",
"SOD1",
"SOS1",
"SPRED1",
"STAG2",
"STAT3",
"STK11",
"SUFU",
"TARDBP",
"TERT",
"TET2",
"TNFAIP3",
"TP53",
"TP53BP1",
"TSC1",
"TSC2",
"VEGFA",
"VHL",
"WT1",
"XRCC1"
]
}
}