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

CITATION.cff

@@ -0,0 +1,60 @@
+cff-version: 1.2.0
+message: >-
+  If you use this software in your research, please cite it using the
+  following metadata.
+type: software
+title: >-
+  chromatin-gnn: Variational Graph Autoencoder for learning latent
+  representations of chromatin topology from Hi-C data
+authors:
+  - family-names: Okada
+    given-names: Toru
+    alias: ToruOkadaOi
+    # orcid: "https://orcid.org/XXXX-XXXX-XXXX-XXXX"   # add your ORCID
+version: "1.0.0"
+date-released: "2024-01-01"   # update to actual release date
+doi: "10.5281/zenodo.XXXXXXX" # replace with actual Zenodo DOI after deposit
+repository-code: "https://github.com/ToruOkadaOi/chromatin-gnn"
+url: "https://github.com/ToruOkadaOi/chromatin-gnn"
+license: MIT
+abstract: >-
+  A Variational Graph Autoencoder (VGAE) applied to Hi-C chromatin contact
+  data to learn unsupervised latent representations of chromatin topology.
+  Genomic bins are modelled as graph nodes with ChIP-seq features (CTCF,
+  H3K27me3); normalised contact frequencies define weighted edges.
+  The model is trained on GM12878 lymphoblastoid cells and evaluated on
+  both link-prediction (AUROC/AP) and the biological interpretability of
+  the latent space against known A/B compartments.
+keywords:
+  - chromatin
+  - Hi-C
+  - graph neural network
+  - variational autoencoder
+  - VGAE
+  - A/B compartments
+  - topologically associating domains
+  - TAD
+  - epigenomics
+  - 3D genome organisation
+references:
+  - type: article
+    title: >-
+      A 3D Map of the Human Genome at Kilobase Resolution Reveals
+      Principles of Chromatin Looping
+    authors:
+      - family-names: Rao
+        given-names: "Suhas S. P."
+      - family-names: Huntley
+        given-names: "Miriam H."
+    year: 2014
+    journal: Cell
+    doi: 10.1016/j.cell.2014.11.021
+  - type: article
+    title: "Variational Graph Auto-Encoders"
+    authors:
+      - family-names: Kipf
+        given-names: "Thomas N."
+      - family-names: Welling
+        given-names: Max
+    year: 2016
+    url: "https://arxiv.org/abs/1611.07308"