aman
acadbd780c
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
61 lines
2.0 KiB
YAML
61 lines
2.0 KiB
YAML
cff-version: 1.2.0
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message: >-
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If you use this software in your research, please cite it using the
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following metadata.
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type: software
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title: >-
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chromatin-gnn: Variational Graph Autoencoder for learning latent
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representations of chromatin topology from Hi-C data
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authors:
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- family-names: Okada
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given-names: Toru
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alias: ToruOkadaOi
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# orcid: "https://orcid.org/XXXX-XXXX-XXXX-XXXX" # add your ORCID
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version: "1.0.0"
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date-released: "2024-01-01" # update to actual release date
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doi: "10.5281/zenodo.XXXXXXX" # replace with actual Zenodo DOI after deposit
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repository-code: "https://github.com/ToruOkadaOi/chromatin-gnn"
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url: "https://github.com/ToruOkadaOi/chromatin-gnn"
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license: MIT
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abstract: >-
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A Variational Graph Autoencoder (VGAE) applied to Hi-C chromatin contact
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data to learn unsupervised latent representations of chromatin topology.
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Genomic bins are modelled as graph nodes with ChIP-seq features (CTCF,
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H3K27me3); normalised contact frequencies define weighted edges.
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The model is trained on GM12878 lymphoblastoid cells and evaluated on
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both link-prediction (AUROC/AP) and the biological interpretability of
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the latent space against known A/B compartments.
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keywords:
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- chromatin
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- Hi-C
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- graph neural network
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- variational autoencoder
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- VGAE
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- A/B compartments
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- topologically associating domains
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- TAD
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- epigenomics
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- 3D genome organisation
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references:
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- type: article
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title: >-
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A 3D Map of the Human Genome at Kilobase Resolution Reveals
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Principles of Chromatin Looping
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authors:
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- family-names: Rao
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given-names: "Suhas S. P."
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- family-names: Huntley
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given-names: "Miriam H."
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year: 2014
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journal: Cell
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doi: 10.1016/j.cell.2014.11.021
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- type: article
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title: "Variational Graph Auto-Encoders"
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authors:
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- family-names: Kipf
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given-names: "Thomas N."
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- family-names: Welling
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given-names: Max
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year: 2016
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url: "https://arxiv.org/abs/1611.07308"
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