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import math
import os
from dataclasses import dataclass, field
from typing import Dict, List
dirname, _ = os.path.split(os.path.dirname(__file__))
@dataclass
class GeneEmbeddModelConfig:
model_input: str = "" #will be infered
num_embed_hidden: int = 100 #30 for exp, 100 for rest
ff_input_dim:int = 0 #is infered later, equals gene expression len
ff_hidden_dim: List = field(default_factory=lambda: [300]) #300 for exp hico
feed_forward1_hidden: int = 256
num_attention_project: int = 64
num_encoder_layers: int = 1
dropout: float = 0.2
n: int = 121
relative_attns: List = field(default_factory=lambda: [29, 4, 6, 8, 10, 11])
num_attention_heads: int = 5
window: int = 2
tokens_len: int = math.ceil(max_length / window)
second_input_token_len: int = 0 # is infered during runtime
vocab_size: int = 0 # is infered during runtime
second_input_vocab_size: int = 0 # is infered during runtime
tokenizer: str = (
"overlap" # either overlap or no_overlap or overlap_multi_window
)
clf_target:str = 'm' # sub_class_hico or major_class_hico. hico = high confidence
num_classes: int = 0 #will be infered during runtime
class_mappings:List = field(default_factory=lambda: [])#will be infered during runtime
class_weights :List = field(default_factory=lambda: [])
# how many extra window sizes other than deafault window
temperatures: List = field(default_factory=lambda: [0,10])
tokens_mapping_dict: Dict = None
false_input_perc:float = 0.0
@dataclass
class GeneEmbeddTrainConfig:
dataset_path_train: str = 'path/to/anndata.h5ad'
precursor_file_path: str = 'path/to/precursor_file.csv' #if not provided, sampling from the precurosr will not be done
mapping_dict_path: str = 'path/to/mapping_dict.json' #required for mapping sub class to major class, i.e: mir-568-3p to miRNA
device: str = "cuda"
l2_weight_decay: float = 0.05
batch_size: int = 512
batch_per_epoch:int = 0 # is infered during runtime
label_smoothing_sim:float = 0.2
label_smoothing_clf:float = 0.0
# learning rate
learning_rate: float = 1e-3 # final learning rate ie 'lr annealed to'
lr_warmup_start: float = 0.1 # start of lr before initial linear warmup section
lr_warmup_end: float = 1 # end of linear warmup section , annealing begin
# TODO: 122 is the number of train batches per epoch, should be infered and set
# warmup batch should be during the form epoch*(train batch per epoch)
warmup_epoch: int = 10 # how many batches linear warm up for
final_epoch: int = 20 # final batch of training when want learning rate
top_k: int = 10#int(0.1 * batch_size) # if the corresponding rna/GE appears during the top k, the correctly classified
cross_val: bool = False
labels_mapping_path: str = None
filter_seq_length:bool = False
num_augment_exp:int = 20
shuffle_exp: bool = False
max_epochs: int = 3000
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