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

.gitignore

@@ -1,30 +1,30 @@
+# Raw sequencing and contact data (large files; download via run_pipeline.sh)
+data/raw/
+
 # Python
 __pycache__/
-*.pyc
+*.py[cod]
+*.pyo
+.pytest_cache/
+*.egg-info/
+dist/
+build/
 
-# Conda / mamba envs
-.env/
-*.yml.lock
+# Environments
+.env
+*.env
+.venv/
 
-# Data
-*.hic
-*.mcool
-*.cool
-*.bam
-*.bw
-*.bigwig
-*.bed
-*.pairs*
-*.pt
-*.npy
-*.csv
-*.png
+# Editors
+.vscode/
+.idea/
+*.swp
+*~
 
-# Jupyter and logs
-*.ipynb_checkpoints/
-*.log
+# Jupyter
+.ipynb_checkpoints/
+*.ipynb
+
+# OS
 .DS_Store
-
-# Results / temp
-results/
-data/
+Thumbs.db