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results/cellpaint_posh_summary.md
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# CellPaint-POSH External Morphology-Feature Replication
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## Dataset
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- **Dataset**: CellPaint-POSH POC
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- **Cell line**: A549
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- **Genes**: 116
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- **sgRNAs**: 1145 (median 10/gene)
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- **Cells**: 95,015
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- **Features**: 1278 CellStats morphology features
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- **Classes**: 6 pathway groups
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## Results
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| Method | Split | Gene overlap | Macro-F1 |
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|--------|-------|-------------|----------|
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| Morphology PCA+LR | Gene-disjoint | 0% | 0.466 ± 0.046 |
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| Morphology PCA+LR | Random sgRNA | 100% | 0.501 ± 0.014 |
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| Morphology 1-NN | Gene-disjoint | 0% | 0.384 ± 0.024 |
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| Morphology 1-NN | Random sgRNA | 100% | 0.450 ± 0.045 |
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| Metadata-only | Gene-disjoint | 0% | 0.219 ± 0.024 |
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| Metadata-only | Random sgRNA | 100% | 0.213 ± 0.017 |
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| Label shuffle | Gene-disjoint | 0% | 0.161 ± 0.037 |
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| Label shuffle | Random sgRNA | 100% | 0.150 ± 0.047 |
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## Mechanism Checks
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- Same-gene NN rate: 9.5%
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- Correct when same gene: 100.0%
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- Correct when diff gene: 43.6%
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- kNN without same-gene neighbors: F1 = 0.383 ± 0.039
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## Inclusion Decision
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- structural_leakage: PASS
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- practical_inflation_absolute: FAIL
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- practical_inflation_relative: FAIL
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- mechanism_confirmed: FAIL
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- controls_valid: FAIL
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**Include in main paper: NO**
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