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outputs/runs/single_085_090_human_only_20260306_032339/subset090/reports/confound/gnn_structlite_confound_subset090.md
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# Mesh vs GSE Confound Check
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- embedding: `/home/zzz0054/deliverables/outputs/runs/single_085_090_human_only_20260306_032339/subset090/features/text_structlite_gnn_holdout_subset090.npz`
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- enriched metadata: `/home/zzz0054/deliverables/data/human_only_085_090/subset090/enriched_gs_metadata_subset090_human.csv`
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- seed: 11 | k: 10 | N: 1626
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- min_support: 5 | fdr_q: 0.05
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## Confound Association (Primary Labels)
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- primary GSE: items=1626 | unique=406 | NMI=0.358 | ARI=0.018
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- primary platform: items=1626 | unique=23 | NMI=0.070 | ARI=0.017
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## Cluster Summary
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| cluster | size | top_gse | gse_purity | mesh_sig | best_mesh (q,ER) | gse_sig | best_gse (q,ER) | plat_sig | best_plat (q,ER) |
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|---:|---:|---|---:|---:|---|---:|---|---:|---|
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| 0 | 221 | GSE213142 | 0.072 | 21 | Proteins (8.9e-04,1.42) | 0 | | 2 | "GPL21290" (2.1e-02,2.94) |
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| 1 | 241 | GSE213142 | 0.066 | 23 | Hepatocellular (9.8e-05,3.89) | 4 | GSE136711 (3.2e-04,5.06) | 1 | GPL21290 (8.4e-03,3.86) |
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| 2 | 88 | GSE219208 | 0.136 | 6 | Ribosomal (1.1e-02,10.56) | 4 | GSE219208 (3.5e-09,11.67) | 2 | "GPL21697" (2.4e-04,4.29) |
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| 3 | 67 | GSE184029 | 0.104 | 58 | CX3C (1.4e-05,20.80) | 8 | GSE159759 (9.2e-07,24.27) | 1 | "GPL15520" (4.0e-06,20.80) |
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| 4 | 228 | GSE213142 | 0.114 | 40 | Skin (5.7e-06,2.31) | 9 | GSE229066 (5.0e-06,5.35) | 2 | "GPL23227" (1.3e-05,5.94) |
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| 5 | 320 | GSE216249 | 0.087 | 32 | Liposomes (1.0e-09,3.85) | 7 | GSE216249 (6.5e-11,3.85) | 3 | GPL15520 (5.1e-10,3.32) |
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| 6 | 226 | GSE213142 | 0.053 | 13 | Cell (1.4e-03,1.41) | 0 | | 1 | "GPL18573" (8.3e-04,1.57) |
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| 7 | 120 | GSE218585 | 0.050 | 33 | Adult (7.5e-08,4.34) | 3 | GSE214921 (1.2e-05,13.55) | 1 | GPL24247 (8.4e-03,5.81) |
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| 8 | 28 | GSE219208 | 0.250 | 1 | Prognosis (2.9e-02,14.52) | 1 | GSE219208 (1.7e-06,21.39) | 1 | "GPL21697" (1.6e-04,8.30) |
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| 9 | 87 | GSE213142 | 0.184 | 40 | Bacteria (8.9e-04,8.18) | 7 | GSE232107 (4.2e-04,8.18) | 2 | GPL21273 (2.1e-02,8.31) |
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## Interpretation Guide
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- High `mesh_sig` with moderate/low `gse_purity` suggests biology-like themes not tied to one study.
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- Very high `gse_purity` and strong `best_gse` indicates a study/batch-driven cluster (still real structure, but a confound for cross-study biology).
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- Platform enrichment is a common technical confound; treat strong `best_plat` similarly.
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