diff --git a/src/multivelo/dynamical_chrom_func.py b/src/multivelo/dynamical_chrom_func.py index 5c66d8a..193576c 100644 --- a/src/multivelo/dynamical_chrom_func.py +++ b/src/multivelo/dynamical_chrom_func.py @@ -3910,7 +3910,24 @@ def recover_dynamics_chrom(adata_rna, `'grid'`: grid search the best set of switch times. `'simple'`: simply initialize switch times to be 5, 10, and 15. device: `str` (default: `'cpu'`) - The device that pytorch tensor calculations will be run on. + The CUDA device that pytorch tensor calculations will be run on. Only + to be used with Adam. + adam: `bool` (default: `False`) + Whether MSE minimization is handled by the Adam algorithm or not. When + set to the default of False, function uses Nelder-Mead instead. + adam_lr: `float` (default: `None`) + The learning rate to use the Adam algorithm. If adam is False, this + value is ignored. + adam_beta1: `float` (default: `None`) + The beta1 parameter for the Adam algorithm. If adam is False, this + value is ignored. + adam_beta2: `float` (default: `None`) + The beta2 parameter for the Adam algorithm. If adam is False, this + value is ignored. + batch_size: `int` (default: `None`) + Speeds up performance using minibatch training. Specifies number of + cells to use per run of MSE when running the Adam algorithm. Ignored + if Adam is set to False. model_to_run: `int` or list of `int` (default: `None`) User specified models for each genes. Possible values are 1 are 2. If `None`, the model