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Is there a pre-trained cell type annotation model available with weights that can be directly used on the MS dataset? #16

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noob000007 opened this issue Aug 29, 2024 · 1 comment

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@noob000007
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Is there a pre-trained cell type annotation model available with weights that can be directly used on the MS dataset?

elif DATASET == 'MS':
data_train = ad.read_h5ad(f'../data/c_data.h5ad')
data_test = ad.read_h5ad(f'../data/filtered_ms_adata.h5ad')
data_train.var = data_train.var.set_index('index_column')
data_test.var = data_test.var.set_index('index_column')
train_num = data_train.shape[0]
data = ad.concat([data_train, data_test])
data.var_names_make_unique()

@noob000007
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I'm comparing the performance of CellPLM and scGPT for cell type annotation on other datasets. scGPT provides a pre-trained model that can be directly used, but unfortunately, CellPLM does not offer a pre-trained model that can be used in the same way.

Therefore, I plan to use the cell_type_annotation.ipynb code to train on the DATASET == 'MS' and then compare the results. Is there a fairer method for comparison? I would appreciate it if you could provide a pre-trained model with weights for direct comparison as soon as possible. Thank you.

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