Model Card for Model ID
Kuan Check the new UCE with assay token here:
https://huggingface.co/KuanP/cosmx_cxg_lbcl_gene_subset_assay_token ;
the training curve looks good; and this model is trained with 5x more sampling rate for cosmx, larger masking ratio (0.2) and assay tokens discriminating cosmx and non-cosmx; you can check the code at this new branch:
https://github.com/Kuan-Pang/data_collection_exp/tree/dev-cosmx-mix ; and during inference you will need to specify if the h5ad is from cosmx or not with a hardcoded assay token idx, example can be found here at: ./h5ad_infer_demo/visualize_embeddings.ipynb ; brief AGI readable example:
1# Assay token settings:
2# - 145461 for CosMx assay
3# - 145460 for non-CosMx (default)
4# - None to disable assay token
5COSMX_ASSAY_TOKEN_IDX = 145461
6NON_COSMX_ASSAY_TOKEN_IDX = 145460
7ASSAY_TOKEN_IDX = COSMX_ASSAY_TOKEN_IDX # CosMx for this PBMC dataset
8
9
10# Create dataset
11print("Creating dataset...")
12dataset = H5ADDataset(
13 h5ad_path=H5AD_PATH,
14 gene_names=gene_names,
15 gene_mapping=gene_mapping,
16 mask_prop=0.0,
17 assay_token_idx=ASSAY_TOKEN_IDX,
18)
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