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

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

scripts/compare_embeddings.py

@@ -50,7 +50,8 @@ def main():
     if emb1.shape != emb2.shape:
         raise ValueError(f"Shape mismatch: {emb1.shape} vs {emb2.shape}")
 
-    os.makedirs(os.path.dirname(args.prefix), exist_ok=True)
+    prefix_dir = os.path.dirname(os.path.abspath(args.prefix))
+    os.makedirs(prefix_dir, exist_ok=True)
     n_bins, n_dim = emb1.shape
     print(f"Loaded embeddings: {n_bins} bins × {n_dim} dims")