benchmark_registry.json

{
  "project": {
    "title": "Blood-Brain Omics Benchmark",
    "description": "Benchmarking blood omics platforms for predicting brain molecular phenotypes",
    "cohort": "ROSMAP",
    "version": "1.0.0",
    "last_updated": "2026-05-01",
    "git_sha": "be3c622"
  },
  "blood_platforms": {
    "SomaScan": {
      "display_name": "SomaScan",
      "type": "proteomics",
      "n_features": 7289,
      "color": "#E64B35"
    },
    "TMT": {
      "display_name": "TMT",
      "type": "proteomics",
      "n_features": 1882,
      "color": "#4DBBD5"
    },
    "Metabolon": {
      "display_name": "Metabolon",
      "type": "metabolomics",
      "n_features": 1595,
      "color": "#00A087"
    },
    "Plasma_Tau": {
      "display_name": "Plasma Tau",
      "type": "biomarker",
      "n_features": 2,
      "color": "#3C5488"
    },
    "Biocrates_P180": {
      "display_name": "Biocrates P180",
      "type": "metabolomics",
      "n_features": 167,
      "color": "#F39B7F"
    },
    "Biocrates_P400": {
      "display_name": "Biocrates P400",
      "type": "metabolomics",
      "n_features": 292,
      "color": "#8491B4"
    },
    "ClinLabs": {
      "display_name": "ClinLabs",
      "type": "clinical",
      "n_features": 27,
      "color": "#91D1C2"
    },
    "Olink_Inflammation": {
      "display_name": "Olink Inflammation",
      "type": "proteomics",
      "n_features": 92,
      "color": "#DC0000"
    },
    "NULISA_CNS": {
      "display_name": "NULISA CNS",
      "type": "proteomics",
      "n_features": 131,
      "color": "#7E6148"
    },
    "NULISA_Inflammation": {
      "display_name": "NULISA Inflammation",
      "type": "proteomics",
      "n_features": 249,
      "color": "#B09C85"
    },
    "NULISA_Integrated": {
      "display_name": "NULISA Integrated",
      "type": "proteomics",
      "n_features": 328,
      "color": "#E64B35"
    },
    "Covariates": {
      "display_name": "Covariates",
      "type": "baseline",
      "n_features": 2,
      "color": "#9CA3AF"
    }
  },
  "brain_targets": {
    "bulkrnaseq_dlpfc": {
      "display_name": "Bulkrnaseq Dlpfc",
      "category": "transcriptomics",
      "n_modules": 41
    },
    "h3k9ac_dlpfc": {
      "display_name": "H3K9Ac Dlpfc",
      "category": "epigenomics",
      "n_modules": 34
    },
    "epicv2_dlpfc": {
      "display_name": "Epicv2 Dlpfc",
      "category": "methylation",
      "n_modules": 26
    },
    "tmt_dlpfc": {
      "display_name": "Tmt Dlpfc",
      "category": "proteomics",
      "n_modules": 27
    },
    "hmC_dlpfc": {
      "display_name": "Hmc Dlpfc",
      "category": "transcriptomics",
      "n_modules": 16
    },
    "tmt_dlpfc_proteins": {
      "display_name": "Tmt Dlpfc Proteins",
      "category": "proteomics",
      "n_modules": 905
    },
    "mofa_7omics": {
      "display_name": "Mofa 7Omics",
      "category": "multi-omics",
      "n_modules": 50
    },
    "pseudobulk_astrocyte": {
      "display_name": "Pseudobulk Astrocyte",
      "category": "single-cell",
      "n_modules": 44
    },
    "pseudobulk_endothelial": {
      "display_name": "Pseudobulk Endothelial",
      "category": "single-cell",
      "n_modules": 22
    },
    "pseudobulk_excitatory_neurons": {
      "display_name": "Pseudobulk Excitatory Neurons",
      "category": "single-cell",
      "n_modules": 42
    },
    "pseudobulk_inhibitory_neurons": {
      "display_name": "Pseudobulk Inhibitory Neurons",
      "category": "single-cell",
      "n_modules": 41
    },
    "pseudobulk_microglia": {
      "display_name": "Pseudobulk Microglia",
      "category": "single-cell",
      "n_modules": 33
    },
    "pseudobulk_oligodendrocytes": {
      "display_name": "Pseudobulk Oligodendrocytes",
      "category": "single-cell",
      "n_modules": 49
    },
    "pseudobulk_opcs": {
      "display_name": "Pseudobulk Opcs",
      "category": "single-cell",
      "n_modules": 31
    },
    "neuropathology": {
      "display_name": "Neuropathology",
      "category": "phenotype",
      "n_modules": 3,
      "variables": [
        "amylsqrt_est_8reg",
        "tangsqrt_est_8reg",
        "gpath"
      ]
    },
    "pheno_neuropath_ext": {
      "display_name": "Neuropath Ext",
      "category": "phenotype",
      "n_modules": 93,
      "temporal": false
    },
    "pheno_cognitive_slopes": {
      "display_name": "Cognitive Slopes",
      "category": "phenotype",
      "n_modules": 13,
      "temporal": false
    },
    "pheno_clinical": {
      "display_name": "Clinical",
      "category": "phenotype",
      "n_modules": 32,
      "temporal": false
    },
    "pheno_cognition": {
      "display_name": "Cognition",
      "category": "phenotype",
      "n_modules": 7,
      "temporal": true
    },
    "pheno_motor": {
      "display_name": "Motor",
      "category": "phenotype",
      "n_modules": 38,
      "temporal": true
    },
    "pheno_medical": {
      "display_name": "Medical",
      "category": "phenotype",
      "n_modules": 40,
      "temporal": true
    },
    "pheno_medications": {
      "display_name": "Medications",
      "category": "phenotype",
      "n_modules": 22,
      "temporal": true
    },
    "pheno_wellbeing": {
      "display_name": "Wellbeing",
      "category": "phenotype",
      "n_modules": 14,
      "temporal": true
    },
    "pheno_decision": {
      "display_name": "Decision",
      "category": "phenotype",
      "n_modules": 14,
      "temporal": true
    },
    "pheno_sleep": {
      "display_name": "Sleep",
      "category": "phenotype",
      "n_modules": 10,
      "temporal": true
    },
    "pheno_lifestyle": {
      "display_name": "Lifestyle",
      "category": "phenotype",
      "n_modules": 15,
      "temporal": true
    },
    "pheno_imaging": {
      "display_name": "Imaging",
      "category": "phenotype",
      "n_modules": 8,
      "temporal": true
    },
    "pheno_disability": {
      "display_name": "Disability",
      "category": "phenotype",
      "n_modules": 3,
      "temporal": true
    },
    "pheno_personality": {
      "display_name": "Personality",
      "category": "phenotype",
      "n_modules": 5,
      "temporal": true
    },
    "pheno_genetics": {
      "display_name": "Genetics",
      "category": "phenotype",
      "n_modules": 2,
      "temporal": true
    },
    "pheno_age": {
      "display_name": "Age",
      "category": "phenotype",
      "n_modules": 1,
      "temporal": true
    },
    "pheno_diagnosis": {
      "display_name": "Diagnosis",
      "category": "phenotype",
      "n_modules": 3,
      "temporal": true
    }
  },
  "phases": {
    "maxn": {
      "label": "1a",
      "description": "MaxN blood-only"
    },
    "maxn_covonly": {
      "label": "1b",
      "description": "MaxN covariates-only (age + sex baseline)"
    },
    "maxn_withcov": {
      "label": "1c",
      "description": "MaxN blood + covariates"
    },
    "h2h_blood": {
      "label": "2a",
      "description": "Blood H2H blood-only"
    },
    "h2h_blood_withcov": {
      "label": "2b",
      "description": "Blood H2H blood + covariates"
    },
    "h2h_brain": {
      "label": "3a",
      "description": "Brain H2H blood-only"
    },
    "h2h_brain_withcov": {
      "label": "3b",
      "description": "Brain H2H blood + covariates"
    },
    "temporal": {
      "label": "4a",
      "description": "Temporal blood-only"
    },
    "temporal_withcov": {
      "label": "4b",
      "description": "Temporal blood + covariates"
    }
  },
  "models": {
    "TabPFN": {
      "version": "2.0.0",
      "method": "CatBoost"
    }
  },
  "data_files": {
    "benchmark_results": "benchmark_results.parquet",
    "feature_importance": "feature_importance.parquet"
  }
}