| { |
| "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" |
| } |
