Datasets:
update on 2026-03-28: rerun-confirmed hgfb artifacts
Browse files- data/processed/hgfb/channels/expression.npz +3 -0
- data/processed/hgfb/channels/network_ontology.npz +3 -0
- data/processed/hgfb/channels/regulation.npz +3 -0
- data/processed/hgfb/channels/teacher.npz +3 -0
- data/processed/hgfb/hgfb_manifest.json +130 -0
- data/processed/hgfb/raw_hgfb.npz +3 -0
- data/processed/hgfb/summary.json +119 -0
data/processed/hgfb/channels/expression.npz
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version https://git-lfs.github.com/spec/v1
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oid sha256:7b5da9cdfcdb6825dcd47d27738884551fd4d088ec4a219f02d452dd003bd599
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size 2539739
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data/processed/hgfb/channels/network_ontology.npz
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version https://git-lfs.github.com/spec/v1
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oid sha256:26c25cf41a594aaa67031a0fd877bbb73d20794dad3cf3ed9801e0737d7f45b6
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size 1244291
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data/processed/hgfb/channels/regulation.npz
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version https://git-lfs.github.com/spec/v1
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oid sha256:fe4adaeb229b4a1c5c503d468d273f389ae4ec4b16272c078d7a72d04c89b746
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size 1808652
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data/processed/hgfb/channels/teacher.npz
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version https://git-lfs.github.com/spec/v1
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oid sha256:825da302cbfae94225b4fc2c3a2ca3124e915755f6d07f86c081f7865fdb2b4a
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size 44750553
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data/processed/hgfb/hgfb_manifest.json
ADDED
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@@ -0,0 +1,130 @@
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{
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"artifact": "H-GFB",
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"raw_feature_path": "data/processed/hgfb/raw_hgfb.npz",
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"embedding_path": "data/processed/embeddings/hgfb.npz",
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| 5 |
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"channel_files": {
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"teacher": "data/processed/hgfb/channels/teacher.npz",
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| 7 |
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"regulation": "data/processed/hgfb/channels/regulation.npz",
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| 8 |
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"network_ontology": "data/processed/hgfb/channels/network_ontology.npz",
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"expression": "data/processed/hgfb/channels/expression.npz"
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},
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| 11 |
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"input_policy": {
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| 12 |
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"expression_channel_uses_processed_stage_a_only": true,
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| 13 |
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"raw_geo_direct_loading_allowed_downstream": false
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| 14 |
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},
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| 15 |
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"approved_exclusions": [],
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| 16 |
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"channels": {
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"teacher": {
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| 18 |
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"channel": "teacher",
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| 19 |
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"geneformer_dim": 768,
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| 20 |
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"pinnacle_dim": 128,
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| 21 |
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"geneformer_hits": 13391,
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| 22 |
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"pinnacle_hits": 13389,
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| 23 |
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"n_genes": 13389
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| 24 |
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},
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| 25 |
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"regulation": {
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| 26 |
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"channel": "regulation",
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| 27 |
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"n_genes": 13389,
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| 28 |
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"feature_dim": 86,
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| 29 |
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"tf_count_in_universe": 1191,
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| 30 |
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"dorothea_tfs": 367,
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| 31 |
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"trrust_tfs": 748,
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| 32 |
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"motif_count": 5876,
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| 33 |
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"motif_target_genes": 13132
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| 34 |
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},
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"network_ontology": {
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| 36 |
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"channel": "network_ontology",
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| 37 |
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"n_genes": 13389,
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| 38 |
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"feature_dim": 64,
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| 39 |
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"string_edge_count": 684790,
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| 40 |
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"reactome_group_count": 2450,
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| 41 |
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"complex_group_count": 1039
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| 42 |
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},
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| 43 |
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"expression": {
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| 44 |
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"channel": "expression",
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| 45 |
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"n_genes": 13389,
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| 46 |
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"feature_dim": 63,
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| 47 |
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"source_cells": {
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| 48 |
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"gse174554_counts": 159625,
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| 49 |
+
"gse131928_smartseq2_tpm": 7930,
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| 50 |
+
"gse131928_10x_tpm": 16201,
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| 51 |
+
"gse70630_oligodendroglioma_processed": 4347,
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| 52 |
+
"gse89567_idh_processed": 6341,
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| 53 |
+
"gse57872_gbm_processed_signed": 543,
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| 54 |
+
"gse84465_gbm_counts": 3520
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| 55 |
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},
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| 56 |
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"sources": {
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| 57 |
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"gse174554_counts": {
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| 58 |
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"normalization": "raw_counts_to_cp10k_log1p",
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| 59 |
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"description": "GSE174554 matched primary/recurrent GBM raw counts",
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| 60 |
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"present_genes": 13106,
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| 61 |
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"compendium_manifest": "sources/gse174554_counts/manifest.json",
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| 62 |
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"approved_exclusions": [
|
| 63 |
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{
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| 64 |
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"sample_name": "GSM5319529_SF8963",
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| 65 |
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"reason": "approved upstream corruption exclusion",
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| 66 |
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"evidence": {
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| 67 |
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"md5": "aaad42216f6818980171343e1cc57857",
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| 68 |
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"declared_nnz": 4855174,
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| 69 |
+
"parseable_coordinate_lines": 4648192,
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| 70 |
+
"missing_coordinate_lines_vs_declared": 206982,
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| 71 |
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"nul_byte_line": 1396122
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| 72 |
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}
|
| 73 |
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}
|
| 74 |
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]
|
| 75 |
+
},
|
| 76 |
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"gse131928_smartseq2_tpm": {
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| 77 |
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"normalization": "tpm_to_log1p",
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| 78 |
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"description": "GSE131928 Smart-seq2",
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| 79 |
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"present_genes": 12825,
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| 80 |
+
"compendium_manifest": "sources/gse131928_smartseq2_tpm/manifest.json",
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| 81 |
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"approved_exclusions": []
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| 82 |
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},
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| 83 |
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"gse131928_10x_tpm": {
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| 84 |
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"normalization": "tpm_to_log1p",
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| 85 |
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"description": "GSE131928 10x",
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| 86 |
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"present_genes": 12888,
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| 87 |
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"compendium_manifest": "sources/gse131928_10x_tpm/manifest.json",
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| 88 |
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"approved_exclusions": []
|
| 89 |
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},
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| 90 |
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"gse70630_oligodendroglioma_processed": {
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| 91 |
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"normalization": "log_space_passthrough",
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| 92 |
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"description": "GSE70630 oligodendroglioma processed",
|
| 93 |
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"present_genes": 12825,
|
| 94 |
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"compendium_manifest": "sources/gse70630_oligodendroglioma_processed/manifest.json",
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| 95 |
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"approved_exclusions": []
|
| 96 |
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},
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| 97 |
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"gse89567_idh_processed": {
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| 98 |
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"normalization": "log_space_passthrough",
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| 99 |
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"description": "GSE89567 IDH diffuse glioma processed",
|
| 100 |
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"present_genes": 12825,
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| 101 |
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"compendium_manifest": "sources/gse89567_idh_processed/manifest.json",
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| 102 |
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"approved_exclusions": []
|
| 103 |
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},
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| 104 |
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"gse57872_gbm_processed_signed": {
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| 105 |
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"normalization": "log_space_passthrough",
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| 106 |
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"description": "GSE57872 GBM processed signed",
|
| 107 |
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"present_genes": 4874,
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| 108 |
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"compendium_manifest": "sources/gse57872_gbm_processed_signed/manifest.json",
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| 109 |
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"approved_exclusions": []
|
| 110 |
+
},
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| 111 |
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"gse84465_gbm_counts": {
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| 112 |
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"normalization": "raw_counts_to_cp10k_log1p",
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| 113 |
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"description": "GSE84465 GBM raw counts",
|
| 114 |
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"present_genes": 12580,
|
| 115 |
+
"compendium_manifest": "sources/gse84465_gbm_counts/manifest.json",
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| 116 |
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"approved_exclusions": []
|
| 117 |
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}
|
| 118 |
+
},
|
| 119 |
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"compendium_manifest": "processed/stage_a/expression_compendium/compendium_manifest.json",
|
| 120 |
+
"input_policy": "loads only processed Stage A compendium artifacts; does not read raw GEO matrices directly",
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| 121 |
+
"notes": {
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| 122 |
+
"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",
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| 123 |
+
"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",
|
| 124 |
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"approved_exclusion": []
|
| 125 |
+
}
|
| 126 |
+
}
|
| 127 |
+
},
|
| 128 |
+
"pca_dim": 256,
|
| 129 |
+
"explained_variance_ratio_sum": 0.5395395755767822
|
| 130 |
+
}
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data/processed/hgfb/raw_hgfb.npz
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version https://git-lfs.github.com/spec/v1
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oid sha256:65934986118683ddb8ec84ebb23b68c530e41273faa213793dd4eee0a7ee5197
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size 101160722
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data/processed/hgfb/summary.json
ADDED
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@@ -0,0 +1,119 @@
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{
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| 2 |
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"n_genes": 13389,
|
| 3 |
+
"raw_feature_dim": 1109,
|
| 4 |
+
"pca_dim": 256,
|
| 5 |
+
"explained_variance_ratio_sum": 0.5395395755767822,
|
| 6 |
+
"channels": {
|
| 7 |
+
"teacher": {
|
| 8 |
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"channel": "teacher",
|
| 9 |
+
"geneformer_dim": 768,
|
| 10 |
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"pinnacle_dim": 128,
|
| 11 |
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"geneformer_hits": 13391,
|
| 12 |
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"pinnacle_hits": 13389,
|
| 13 |
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"n_genes": 13389
|
| 14 |
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},
|
| 15 |
+
"regulation": {
|
| 16 |
+
"channel": "regulation",
|
| 17 |
+
"n_genes": 13389,
|
| 18 |
+
"feature_dim": 86,
|
| 19 |
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"tf_count_in_universe": 1191,
|
| 20 |
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"dorothea_tfs": 367,
|
| 21 |
+
"trrust_tfs": 748,
|
| 22 |
+
"motif_count": 5876,
|
| 23 |
+
"motif_target_genes": 13132
|
| 24 |
+
},
|
| 25 |
+
"network_ontology": {
|
| 26 |
+
"channel": "network_ontology",
|
| 27 |
+
"n_genes": 13389,
|
| 28 |
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"feature_dim": 64,
|
| 29 |
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"string_edge_count": 684790,
|
| 30 |
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"reactome_group_count": 2450,
|
| 31 |
+
"complex_group_count": 1039
|
| 32 |
+
},
|
| 33 |
+
"expression": {
|
| 34 |
+
"channel": "expression",
|
| 35 |
+
"n_genes": 13389,
|
| 36 |
+
"feature_dim": 63,
|
| 37 |
+
"source_cells": {
|
| 38 |
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"gse174554_counts": 159625,
|
| 39 |
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"gse131928_smartseq2_tpm": 7930,
|
| 40 |
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"gse131928_10x_tpm": 16201,
|
| 41 |
+
"gse70630_oligodendroglioma_processed": 4347,
|
| 42 |
+
"gse89567_idh_processed": 6341,
|
| 43 |
+
"gse57872_gbm_processed_signed": 543,
|
| 44 |
+
"gse84465_gbm_counts": 3520
|
| 45 |
+
},
|
| 46 |
+
"sources": {
|
| 47 |
+
"gse174554_counts": {
|
| 48 |
+
"normalization": "raw_counts_to_cp10k_log1p",
|
| 49 |
+
"description": "GSE174554 matched primary/recurrent GBM raw counts",
|
| 50 |
+
"present_genes": 13106,
|
| 51 |
+
"compendium_manifest": "sources/gse174554_counts/manifest.json",
|
| 52 |
+
"approved_exclusions": [
|
| 53 |
+
{
|
| 54 |
+
"sample_name": "GSM5319529_SF8963",
|
| 55 |
+
"reason": "approved upstream corruption exclusion",
|
| 56 |
+
"evidence": {
|
| 57 |
+
"md5": "aaad42216f6818980171343e1cc57857",
|
| 58 |
+
"declared_nnz": 4855174,
|
| 59 |
+
"parseable_coordinate_lines": 4648192,
|
| 60 |
+
"missing_coordinate_lines_vs_declared": 206982,
|
| 61 |
+
"nul_byte_line": 1396122
|
| 62 |
+
}
|
| 63 |
+
}
|
| 64 |
+
]
|
| 65 |
+
},
|
| 66 |
+
"gse131928_smartseq2_tpm": {
|
| 67 |
+
"normalization": "tpm_to_log1p",
|
| 68 |
+
"description": "GSE131928 Smart-seq2",
|
| 69 |
+
"present_genes": 12825,
|
| 70 |
+
"compendium_manifest": "sources/gse131928_smartseq2_tpm/manifest.json",
|
| 71 |
+
"approved_exclusions": []
|
| 72 |
+
},
|
| 73 |
+
"gse131928_10x_tpm": {
|
| 74 |
+
"normalization": "tpm_to_log1p",
|
| 75 |
+
"description": "GSE131928 10x",
|
| 76 |
+
"present_genes": 12888,
|
| 77 |
+
"compendium_manifest": "sources/gse131928_10x_tpm/manifest.json",
|
| 78 |
+
"approved_exclusions": []
|
| 79 |
+
},
|
| 80 |
+
"gse70630_oligodendroglioma_processed": {
|
| 81 |
+
"normalization": "log_space_passthrough",
|
| 82 |
+
"description": "GSE70630 oligodendroglioma processed",
|
| 83 |
+
"present_genes": 12825,
|
| 84 |
+
"compendium_manifest": "sources/gse70630_oligodendroglioma_processed/manifest.json",
|
| 85 |
+
"approved_exclusions": []
|
| 86 |
+
},
|
| 87 |
+
"gse89567_idh_processed": {
|
| 88 |
+
"normalization": "log_space_passthrough",
|
| 89 |
+
"description": "GSE89567 IDH diffuse glioma processed",
|
| 90 |
+
"present_genes": 12825,
|
| 91 |
+
"compendium_manifest": "sources/gse89567_idh_processed/manifest.json",
|
| 92 |
+
"approved_exclusions": []
|
| 93 |
+
},
|
| 94 |
+
"gse57872_gbm_processed_signed": {
|
| 95 |
+
"normalization": "log_space_passthrough",
|
| 96 |
+
"description": "GSE57872 GBM processed signed",
|
| 97 |
+
"present_genes": 4874,
|
| 98 |
+
"compendium_manifest": "sources/gse57872_gbm_processed_signed/manifest.json",
|
| 99 |
+
"approved_exclusions": []
|
| 100 |
+
},
|
| 101 |
+
"gse84465_gbm_counts": {
|
| 102 |
+
"normalization": "raw_counts_to_cp10k_log1p",
|
| 103 |
+
"description": "GSE84465 GBM raw counts",
|
| 104 |
+
"present_genes": 12580,
|
| 105 |
+
"compendium_manifest": "sources/gse84465_gbm_counts/manifest.json",
|
| 106 |
+
"approved_exclusions": []
|
| 107 |
+
}
|
| 108 |
+
},
|
| 109 |
+
"compendium_manifest": "processed/stage_a/expression_compendium/compendium_manifest.json",
|
| 110 |
+
"input_policy": "loads only processed Stage A compendium artifacts; does not read raw GEO matrices directly",
|
| 111 |
+
"notes": {
|
| 112 |
+
"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",
|
| 113 |
+
"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",
|
| 114 |
+
"approved_exclusion": []
|
| 115 |
+
}
|
| 116 |
+
}
|
| 117 |
+
},
|
| 118 |
+
"manifest_path": "data/processed/hgfb/hgfb_manifest.json"
|
| 119 |
+
}
|