{
  "n_genes": 13389,
  "raw_feature_dim": 1109,
  "pca_dim": 256,
  "explained_variance_ratio_sum": 0.5395395755767822,
  "channels": {
    "teacher": {
      "channel": "teacher",
      "geneformer_dim": 768,
      "pinnacle_dim": 128,
      "geneformer_hits": 13391,
      "pinnacle_hits": 13389,
      "n_genes": 13389
    },
    "regulation": {
      "channel": "regulation",
      "n_genes": 13389,
      "feature_dim": 86,
      "tf_count_in_universe": 1191,
      "dorothea_tfs": 367,
      "trrust_tfs": 748,
      "motif_count": 5876,
      "motif_target_genes": 13132
    },
    "network_ontology": {
      "channel": "network_ontology",
      "n_genes": 13389,
      "feature_dim": 64,
      "string_edge_count": 684790,
      "reactome_group_count": 2450,
      "complex_group_count": 1039
    },
    "expression": {
      "channel": "expression",
      "n_genes": 13389,
      "feature_dim": 63,
      "source_cells": {
        "gse174554_counts": 159625,
        "gse131928_smartseq2_tpm": 7930,
        "gse131928_10x_tpm": 16201,
        "gse70630_oligodendroglioma_processed": 4347,
        "gse89567_idh_processed": 6341,
        "gse57872_gbm_processed_signed": 543,
        "gse84465_gbm_counts": 3520
      },
      "sources": {
        "gse174554_counts": {
          "normalization": "raw_counts_to_cp10k_log1p",
          "description": "GSE174554 matched primary/recurrent GBM raw counts",
          "present_genes": 13106,
          "compendium_manifest": "sources/gse174554_counts/manifest.json",
          "approved_exclusions": [
            {
              "sample_name": "GSM5319529_SF8963",
              "reason": "approved upstream corruption exclusion",
              "evidence": {
                "md5": "aaad42216f6818980171343e1cc57857",
                "declared_nnz": 4855174,
                "parseable_coordinate_lines": 4648192,
                "missing_coordinate_lines_vs_declared": 206982,
                "nul_byte_line": 1396122
              }
            }
          ]
        },
        "gse131928_smartseq2_tpm": {
          "normalization": "tpm_to_log1p",
          "description": "GSE131928 Smart-seq2",
          "present_genes": 12825,
          "compendium_manifest": "sources/gse131928_smartseq2_tpm/manifest.json",
          "approved_exclusions": []
        },
        "gse131928_10x_tpm": {
          "normalization": "tpm_to_log1p",
          "description": "GSE131928 10x",
          "present_genes": 12888,
          "compendium_manifest": "sources/gse131928_10x_tpm/manifest.json",
          "approved_exclusions": []
        },
        "gse70630_oligodendroglioma_processed": {
          "normalization": "log_space_passthrough",
          "description": "GSE70630 oligodendroglioma processed",
          "present_genes": 12825,
          "compendium_manifest": "sources/gse70630_oligodendroglioma_processed/manifest.json",
          "approved_exclusions": []
        },
        "gse89567_idh_processed": {
          "normalization": "log_space_passthrough",
          "description": "GSE89567 IDH diffuse glioma processed",
          "present_genes": 12825,
          "compendium_manifest": "sources/gse89567_idh_processed/manifest.json",
          "approved_exclusions": []
        },
        "gse57872_gbm_processed_signed": {
          "normalization": "log_space_passthrough",
          "description": "GSE57872 GBM processed signed",
          "present_genes": 4874,
          "compendium_manifest": "sources/gse57872_gbm_processed_signed/manifest.json",
          "approved_exclusions": []
        },
        "gse84465_gbm_counts": {
          "normalization": "raw_counts_to_cp10k_log1p",
          "description": "GSE84465 GBM raw counts",
          "present_genes": 12580,
          "compendium_manifest": "sources/gse84465_gbm_counts/manifest.json",
          "approved_exclusions": []
        }
      },
      "compendium_manifest": "processed/stage_a/expression_compendium/compendium_manifest.json",
      "input_policy": "loads only processed Stage A compendium artifacts; does not read raw GEO matrices directly",
      "notes": {
        "normalization_contract": "raw counts -> CP10K + log1p; TPM -> log1p; already log-space -> passthrough; Stage A compendium also stores global gene-wise z-score moments for training-time standardization",
        "gse57872": "signed processed matrix is passthrough in the compendium; only descriptor statistics that require nonnegative support use per-gene minimum shift inside this H-GFB summary builder",
        "approved_exclusion": []
      }
    }
  },
  "manifest_path": "data/processed/hgfb/hgfb_manifest.json"
}