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scverse / scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data
http://scvi-tools.org/
BSD 3-Clause "New" or "Revised" License
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Some suggestion about GNN #1789

Open HuangDDU opened 2 years ago

HuangDDU commented 2 years ago

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_obsn_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.
adamgayoso commented 1 year ago

Thank you for the request.

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

HuangDDU commented 1 month ago

Is there anyone involved in solving this problem? If not, can I join this project and solve this problem? I am interested in graph deep learning and hope to integrate this technology into scvi-tools.

canergen commented 1 week ago

Hi, happy to discuss further. Especially with spatial data graphs are critical but also for single-cell it would be cool. I think best way to get started would be to implement a model in external that uses graph. E.g. https://brbiclab.epfl.ch/projects/stellar/ could be a nice start.