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Update README.md
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ttgump authored Jan 1, 2024
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Expand Up @@ -80,7 +80,7 @@ python run_spaMultiVAE.py --data_file Multiomics_Spatial_Human_tonsil_SVG_data.h
**--select_genes:** number of selected genes for analysis, default = 0 means no filtering. It will use the mean-variance relationship to select informative genes.<br/>
**--batch_size:** mini-batch size, default = "auto", which means if sample size <= 1024 then batch size = 128, if 1024 < sample size <= 2048 then batch size = 256, if sample size > 2048 then batch size = 512.<br/>
**--maxiter:** number of max training iterations, default = 5000.<br/>
**--train_size:** proportion of training set, others will be validating set, default = 0.95.<br/>
**--train_size:** proportion of training set, others will be validating set, default = 0.95. In small datasets, e.g. there are only hundreds of spots, we recommend to set train_size to 1, and fix the maxiter to 1000.<br/>
**--patience:** patience of early stopping when using validating set, default = 200.<br/>
**--lr:** learning rate, default = 1e-3 for spaVAE and spaPeakVAE, and defualt = 5e-3 for spaMultiVAE.<br/>
**--weight_decay:** weight decay coefficient, default = 1e-6.<br/>
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