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Published 20 hours ago • verified publisher icon scverse

Some suggestion about GNN

Open HuangDDU opened this issue 3 years ago • 3 comments

Is your feature request related to a problem? Please describe. I want to develop a new model with Pytorch Geometric which is a GNN library based on Pytorch. I hope you can develop some api to make it more easier.

Describe the solution you'd like

  1. Please develop a obsm_field for AnnDataManager to register obsm(n_obs*n_obs) attribute. Because scanpy neighbors save the graph adjacency matrix in obsm as key "connectivities".
  2. DataSplitter in scvi.dataloaders maybe also should be updated to support minibatch operation. This minibatch operation is similar to subgraph extraction.

HuangDDU avatar Nov 16 '22 07:11 HuangDDU

Thank you for the request.

We are interested in this but have no estimated timeline for when this would be available.

adamgayoso avatar Apr 24 '23 16:04 adamgayoso