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v1.0.0: VGAE applied to GM12878 vs IMR90 chr21 Hi-C at 25kb

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Full reproducible pipeline: .mcool + ChIP-seq bigwigs → latent
  embeddings → A/B compartment calls → cross-cell comparison.

  Key results (chr21, 25 kb, latent dim=32):
  - Test AUC=0.777, AP=0.759 (converged epoch 31/300)
  - GM12878 A/B silhouette (cosine) = 0.775
  - IMR90 zero-shot silhouette = 0.443
  - A-compartment bins stable across cell types (mean cosine Δ=0.042)
  - B-compartment bins shift substantially (mean cosine Δ=0.451)
  - 101 B→A and 70 A→B compartment switches GM12878→IMR90
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aman
2026-05-15 01:53:04 +02:00
parent 6c91af655d
commit acadbd780c
27 changed files with 6764 additions and 201 deletions
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results/figures/umap_stats.csv Normal file
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label,n_bins,latent_dim,mean_embedding_norm,std_embedding_values,silhouette_AB_cosine
GM12878,1869,32,0.6679670810699463,0.1371903121471405,0.7748898267745972
IMR90,1869,32,0.7111130356788635,0.14772675931453705,0.4431541860103607
1 label n_bins latent_dim mean_embedding_norm std_embedding_values silhouette_AB_cosine
2 GM12878 1869 32 0.6679670810699463 0.1371903121471405 0.7748898267745972
3 IMR90 1869 32 0.7111130356788635 0.14772675931453705 0.4431541860103607