from dataclasses import dataclass from typing import Tuple from transformers import PretrainedConfig @dataclass class sCTConfig(PretrainedConfig): # noqa: N801 model_type = "sCT" def __init__(self, **kwargs): # type: ignore self.alphabet_size = kwargs.get("alphabet_size", 7) self.pad_token_id = kwargs.get("pad_token_id", 5) self.mask_token_id = kwargs.get("mask_token_id", 6) self.cell_len = kwargs.get("cell_len", 19968) self.num_downsamples = kwargs.get("num_downsamples", 8) self.attention_heads = kwargs.get("attention_heads", 16) self.key_size = kwargs.get("key_size", None) self.token_embed_dim = kwargs.get("token_embed_dim", 16) self.embed_dim = kwargs.get("embed_dim", 1024) self.ffn_embed_dim = kwargs.get("ffn_embed_dim", 2048) self.num_layers = kwargs.get("num_layers", 4) self.layer_norm_eps = kwargs.get("layer_norm_eps", 1e-5) self.interpolation_method = kwargs.get("interpolation_method", "nearest") # bad hack to satisfy cellnt_celltype_annotation.py:312 self.max_positions: int = kwargs.get("max_positions", 20480) self.num_cells: int = kwargs.get("num_cells", 50) self.num_hidden_layers_head: int = kwargs.get("num_hidden_layers_head", 1) self.use_skip_connection: bool = kwargs.get("use_skip_connection", True) # logging self.use_gradient_checkpointing: bool = False # return self.embeddings_layers_to_save: Tuple[int, ...] = kwargs.get( "embeddings_layers_to_save", () ) self.attention_maps_to_save: list[tuple[int, int]] = kwargs.get( "attention_maps_to_save", [] ) # Spatial info configuration self.use_spatial_information: bool = kwargs.get( "use_spatial_information", False ) self.num_scales: int = kwargs.get("num_scales", 10) self.sigma_min: float = kwargs.get("sigma_min", 1.0) self.sigma_max: float = kwargs.get("sigma_max", 10.0) super().__init__(**kwargs) def __post_init__(self) -> None: # type: ignore # noqa: N807 """ Checks that the given values are compatible. """ if self.key_size is None: if not self.embed_dim % self.attention_heads == 0: raise ValueError( f"When no key size is provided, the embedding dimension" f"should be divisible by the number of heads, however " f"provided embedding dimension is {self.embed_dim} and " f"the number of heads is {self.attention_heads}." ) self.key_size = self.embed_dim // self.attention_heads