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Config

helical.models.scgpt.scGPTConfig

Configuration class to use the scGPT Model.

Parameters:

Name Type Description Default
pad_token str

The padding token

 "<pad>"
batch_size int

The batch size

 24
fast_transformer bool

Whether to use fast transformer or not

 True
nlayers int

The number of layers

 12
nheads int

The number of heads

 8
embsize int

The embedding size

 512
d_hid int

The hidden dimension

 512
dropout float

The dropout rate

 0.2
n_layers_cls int

The number of classification layers

 3
mask_value int

The mask value

 -1
pad_value int

The padding value

 -2
world_size int

The world size

 8
accelerator bool

The accelerator configuration. By default same device as model.

 False
device Literal['cpu', 'cuda']

The device to use. Either use "cuda" or "cpu".

 "cpu"
use_fast_transformer bool

Wheter to use fast transformer or nots

 False

Returns:

Type Description
scGPTConfig

The scGPT configuration object
Notes

This configuration contains all the default parameteres that have been used in the original scGPT repository.

Source code in helical/models/scgpt/scgpt_config.py 
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class scGPTConfig:
    """
    Configuration class to use the scGPT Model.

    Parameters
    ----------
    pad_token : str, optional, default="<pad>"
        The padding token
    batch_size : int, optional, default=24
        The batch size
    fast_transformer : bool, optional, default=True
        Whether to use fast transformer or not
    nlayers : int, optional, default=12
        The number of layers
    nheads : int, optional, default=8
        The number of heads
    embsize : int, optional, default=512
        The embedding size
    d_hid : int, optional, default=512
        The hidden dimension
    dropout : float, optional, default=0.2
        The dropout rate
    n_layers_cls : int, optional, default=3
        The number of classification layers
    mask_value : int, optional, default=-1
        The mask value
    pad_value : int, optional, default=-2
        The padding value
    world_size : int, optional, default=8
        The world size
    accelerator : bool, optional, default=False
        The accelerator configuration. By default same device as model.
    device : Literal["cpu", "cuda"], optional, default="cpu"
        The device to use. Either use "cuda" or "cpu".
    use_fast_transformer : bool, optional, default=False
        Wheter to use fast transformer or nots

    Returns
    -------
    scGPTConfig
        The scGPT configuration object

    Notes
    -----
    This configuration contains all the default parameteres that have been used in the original scGPT repository.

    """

    def __init__(
        self,
        pad_token: str = "<pad>",
        batch_size: int = 24,
        emb_mode: Literal["cls", "cell", "gene"] = "cls",
        fast_transformer: bool = True,
        nlayers: int = 12,
        nheads: int = 8,
        embsize: int = 512,
        d_hid: int = 512,
        dropout: float = 0.2,
        n_layers_cls: int = 3,
        mask_value: int = -1,
        pad_value: int = -2,
        world_size: int = 8,
        accelerator: Optional[bool] = False,
        device: Literal["cpu", "cuda"] = "cpu",
        use_fast_transformer: bool = False,
        binning_seed: int = 123,
    ):

        model_name = "best_model"  # TODO: Include more models
        list_of_files_to_download = [
            "scgpt/scGPT_CP/vocab.json",
            f"scgpt/scGPT_CP/{model_name}.pt",
        ]
        model_path = Path(CACHE_DIR_HELICAL, "scgpt/scGPT_CP", f"{model_name}.pt")

        self.config = {
            "model_path": model_path,
            "list_of_files_to_download": list_of_files_to_download,
            "pad_token": pad_token,
            "batch_size": batch_size,
            "emb_mode": emb_mode,
            "fast_transformer": fast_transformer,
            "nlayers": nlayers,
            "nheads": nheads,
            "embsize": embsize,
            "d_hid": d_hid,
            "dropout": dropout,
            "n_layers_cls": n_layers_cls,
            "mask_value": mask_value,
            "pad_value": pad_value,
            "world_size": world_size,
            "accelerator": accelerator,
            "device": device,
            "use_fast_transformer": use_fast_transformer,
            "MAX_LENGTH": 1200,
            "binning_seed": binning_seed,
        }