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import os
import wandb
import numpy as np
import torch
import torch.nn as nn
from datetime import datetime
from sklearn.model_selection import train_test_split
from sklearn.utils.class_weight import compute_class_weight
from sklearn.metrics import accuracy_score, precision_recall_fscore_support, roc_auc_score, matthews_corrcoef
from transformers import AutoModelForTokenClassification, AutoTokenizer, DataCollatorForTokenClassification, TrainingArguments, Trainer
from datasets import Dataset
from accelerate import Accelerator
from peft import get_peft_config, PeftModel, PeftConfig, get_peft_model, LoraConfig, TaskType
import pickle
# Initialize accelerator and Weights & Biases
accelerator = Accelerator()
os.environ["WANDB_NOTEBOOK_NAME"] = 'train.py'
wandb.init(project='binding_site_prediction')
# Helper Functions and Data Preparation
def save_config_to_txt(config, filename):
"""Save the configuration dictionary to a text file."""
with open(filename, 'w') as f:
for key, value in config.items():
f.write(f"{key}: {value}\n")
def truncate_labels(labels, max_length):
return [label[:max_length] for label in labels]
def compute_metrics(p):
predictions, labels = p
predictions = np.argmax(predictions, axis=2)
predictions = predictions[labels != -100].flatten()
labels = labels[labels != -100].flatten()
accuracy = accuracy_score(labels, predictions)
precision, recall, f1, _ = precision_recall_fscore_support(labels, predictions, average='binary')
auc = roc_auc_score(labels, predictions)
mcc = matthews_corrcoef(labels, predictions)
return {'accuracy': accuracy, 'precision': precision, 'recall': recall, 'f1': f1, 'auc': auc, 'mcc': mcc}
def compute_loss(model, logits, inputs):
# logits = model(**inputs).logits
labels = inputs["labels"]
loss_fct = nn.CrossEntropyLoss(weight=class_weights)
active_loss = inputs["attention_mask"].view(-1) == 1
active_logits = logits.view(-1, model.config.num_labels)
active_labels = torch.where(
active_loss, labels.view(-1), torch.tensor(loss_fct.ignore_index).type_as(labels)
)
loss = loss_fct(active_logits, active_labels)
return loss
# Load data from pickle files
with open("770K_data/train_sequences_chunked_by_family.pkl", "rb") as f:
train_sequences = pickle.load(f)
with open("770K_data/test_sequences_chunked_by_family.pkl", "rb") as f:
test_sequences = pickle.load(f)
with open("770K_data/train_labels_chunked_by_family.pkl", "rb") as f:
train_labels = pickle.load(f)
with open("770K_data/test_labels_chunked_by_family.pkl", "rb") as f:
test_labels = pickle.load(f)
# Tokenization
tokenizer = AutoTokenizer.from_pretrained("facebook/esm2_t12_35M_UR50D")
# Set max_sequence_length to the tokenizer's max input length
max_sequence_length = tokenizer.model_max_length
train_tokenized = tokenizer(train_sequences, padding=True, truncation=True, max_length=max_sequence_length, return_tensors="pt", is_split_into_words=False)
test_tokenized = tokenizer(test_sequences, padding=True, truncation=True, max_length=max_sequence_length, return_tensors="pt", is_split_into_words=False)
# Directly truncate the entire list of labels
train_labels = truncate_labels(train_labels, max_sequence_length)
test_labels = truncate_labels(test_labels, max_sequence_length)
train_dataset = Dataset.from_dict({k: v for k, v in train_tokenized.items()}).add_column("labels", train_labels)
test_dataset = Dataset.from_dict({k: v for k, v in test_tokenized.items()}).add_column("labels", test_labels)
# Compute Class Weights
classes = [0, 1]
flat_train_labels = [label for sublist in train_labels for label in sublist]
class_weights = compute_class_weight(class_weight='balanced', classes=classes, y=flat_train_labels)
class_weights = torch.tensor(class_weights, dtype=torch.float32).to(accelerator.device)
# Define Custom Trainer Class
class WeightedTrainer(Trainer):
def compute_loss(self, model, inputs, return_outputs=False):
outputs = model(**inputs)
logits = outputs.logits
loss = compute_loss(model, logits, inputs)
return (loss, outputs) if return_outputs else loss
# Define and run training function
def train_function_no_sweeps(train_dataset, test_dataset):
# Directly set the config
config = {
"lora_alpha": 1,
"lora_dropout": 0.5,
"lr": 3.701568055793089e-04,
"lr_scheduler_type": "cosine_with_restarts",
"max_grad_norm": 0.5,
"num_train_epochs": 3,
"per_device_train_batch_size": 6,
"r": 2,
"weight_decay": 0.2,
# Add other hyperparameters as needed
}
# Log the config to W&B
wandb.config.update(config)
# Save the config to a text file
timestamp = datetime.now().strftime('%Y-%m-%d_%H-%M-%S')
config_filename = f"esm2_t12_35M_lora_config_{timestamp}.txt"
save_config_to_txt(config, config_filename)
model_checkpoint = "facebook/esm2_t12_35M_UR50D"
# Define labels and model
id2label = {0: "No binding site", 1: "Binding site"}
label2id = {v: k for k, v in id2label.items()}
model = AutoModelForTokenClassification.from_pretrained(model_checkpoint, num_labels=len(id2label), id2label=id2label, label2id=label2id)
# Convert the model into a PeftModel
peft_config = LoraConfig(
task_type=TaskType.TOKEN_CLS,
inference_mode=False,
r=config["r"],
lora_alpha=config["lora_alpha"],
target_modules=["query", "key", "value"],
lora_dropout=config["lora_dropout"],
bias="none", # or "all" or "lora_only"
modules_to_save=["classifier"]
)
model = get_peft_model(model, peft_config)
# Use the accelerator
model = accelerator.prepare(model)
train_dataset = accelerator.prepare(train_dataset)
test_dataset = accelerator.prepare(test_dataset)
timestamp = datetime.now().strftime('%Y-%m-%d_%H-%M-%S')
# Training setup
training_args = TrainingArguments(
output_dir=f"esm2_t12_35M_lora_binding_sites_{timestamp}",
learning_rate=config["lr"],
lr_scheduler_type=config["lr_scheduler_type"],
gradient_accumulation_steps=1,
max_grad_norm=config["max_grad_norm"],
per_device_train_batch_size=config["per_device_train_batch_size"],
per_device_eval_batch_size=config["per_device_train_batch_size"],
num_train_epochs=config["num_train_epochs"],
weight_decay=config["weight_decay"],
evaluation_strategy="epoch",
save_strategy="epoch",
load_best_model_at_end=True,
metric_for_best_model="f1",
greater_is_better=True,
push_to_hub=False,
logging_dir=None,
logging_first_step=False,
logging_steps=200,
save_total_limit=7,
no_cuda=False,
seed=8893,
fp16=True,
report_to='wandb'
)
# Initialize Trainer
trainer = WeightedTrainer(
model=model,
args=training_args,
train_dataset=train_dataset,
eval_dataset=test_dataset,
tokenizer=tokenizer,
data_collator=DataCollatorForTokenClassification(tokenizer=tokenizer),
compute_metrics=compute_metrics
)
# Train and Save Model
trainer.train()
save_path = os.path.join("lora_binding_sites", f"best_model_esm2_t12_35M_lora_{timestamp}")
trainer.save_model(save_path)
tokenizer.save_pretrained(save_path)
# Call the training function
if __name__ == "__main__":
train_function_no_sweeps(train_dataset, test_dataset)
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