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: "1.1.0"
date-released: "2026-05-15"
doi: "10.5281/zenodo.XXXXXXX" # replace with actual Zenodo DOI after deposit
repository-code: "https://gitea.nalakath.org/aman/chromatin-vgae"
url: "https://gitea.nalakath.org/aman/chromatin-vgae"
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, H3K27ac, H3K4me3); normalised contact frequencies define
  weighted edges. v1.0.0 trains on GM12878 lymphoblastoid cells and
  evaluates zero-shot transfer to IMR90 fibroblasts against known A/B
  compartments. v1.1.0 extends to a perturbation experiment — training on
  the control condition of Rao et al. 2017 RAD21-AID degron in HCT-116 cells
  and detecting long-range chromatin contact rewiring from latent embedding
  drift.
keywords:
  - chromatin
  - Hi-C
  - graph neural network
  - variational autoencoder
  - VGAE
  - A/B compartments
  - topologically associating domains
  - TAD
  - epigenomics
  - 3D genome organisation
  - perturbation analysis
  - cohesin
  - RAD21
  - loop domains
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: "Cohesin Loss Eliminates All Loop Domains"
    authors:
      - family-names: Rao
        given-names: "Suhas S. P."
      - family-names: Huang
        given-names: "Su-Chen"
      - family-names: Glenn St Hilaire
        given-names: "Brian"
    year: 2017
    journal: Cell
    volume: 171
    issue: 2
    doi: 10.1016/j.cell.2017.09.026
  - 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"