251254f5a9
added the complete work on the 3 hypotheses
2026-05-17 23:38:28 +02:00
cab92e67ae
updated README
2026-05-15 03:41:47 +02:00
a081f29e12
fix: three silent bugs in training and inference
...
- Edge weights (ICE log1p) were computed but never passed to GCNConv
- encode_graph.py hardcoded GCNEncoder regardless of saved model type
- Inference graph lacked to_undirected + edge_weight pipeline from training
2026-05-15 03:37:20 +02:00
acadbd780c
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
2026-05-15 01:53:04 +02:00
Aman Nalakath
6c91af655d
Add MIT License to the project
2026-04-12 01:09:35 +02:00
bdd3516e9d
readme update
2025-10-23 09:13:46 +02:00
430e0a10ba
initial framework; to be extended
2025-10-23 08:56:46 +02:00
32228496d2
initial framework; to be extended
2025-10-23 08:46:48 +02:00
