train_genomics_lora.py

# /// script
# dependencies = [
#     "trl>=0.12.0",
#     "peft>=0.7.0",
#     "trackio",
#     "torch",
#     "transformers>=4.44.0",
#     "datasets",
#     "accelerate",
# ]
# ///

"""
LoRA Fine-tuning for Qwen2.5-72B on Consumer Genomics Data
Trains model to interpret SNP data and provide health insights
"""

from datasets import load_dataset
from peft import LoraConfig
from trl import SFTTrainer, SFTConfig
import trackio
import torch

print("="*80)
print("Qwen2.5-72B LoRA Fine-tuning for Genomics Interpretation")
print("="*80)

# Load dataset from Hub
print("\n[1/4] Loading dataset...")
dataset = load_dataset("mattPearce/genellm-genomics-finetune", split="train")
print(f"✓ Loaded {len(dataset)} training examples")

# Create train/eval split for monitoring training progress
print("\n[2/4] Creating train/eval split...")
dataset_split = dataset.train_test_split(test_size=0.05, seed=42)  # 5% for eval (25 examples)
print(f"✓ Train: {len(dataset_split['train'])} examples")
print(f"✓ Eval: {len(dataset_split['test'])} examples")

# LoRA configuration optimized for 72B model
print("\n[3/4] Configuring LoRA...")
peft_config = LoraConfig(
    r=32,                          # Rank - higher for better quality on large models
    lora_alpha=64,                 # Scaling factor (typically 2x rank)
    target_modules=[               # Apply LoRA to all attention layers
        "q_proj",
        "k_proj",
        "v_proj",
        "o_proj",
        "gate_proj",
        "up_proj",
        "down_proj"
    ],
    lora_dropout=0.05,
    bias="none",
    task_type="CAUSAL_LM"
)
print(f"✓ LoRA config: r={peft_config.r}, alpha={peft_config.lora_alpha}")
print(f"✓ Target modules: {len(peft_config.target_modules)} layer types")

# Training configuration
print("\n[4/4] Setting up training...")
training_args = SFTConfig(
    # Model output
    output_dir="qwen2.5-72b-genomics-lora",

    # Hub configuration - CRITICAL for saving results
    push_to_hub=True,
    hub_model_id="mattPearce/qwen2.5-72b-genomics-lora",
    hub_strategy="every_save",     # Push checkpoints to Hub
    hub_private_repo=False,

    # Training hyperparameters
    num_train_epochs=3,
    per_device_train_batch_size=1,   # Small batch for 72B model
    gradient_accumulation_steps=16,  # Effective batch size = 16
    learning_rate=2e-4,              # Standard for LoRA
    lr_scheduler_type="cosine",
    warmup_steps=50,

    # Optimization for memory efficiency
    gradient_checkpointing=True,
    bf16=True,                       # Use bfloat16 for better stability

    # Evaluation strategy
    eval_strategy="steps",
    eval_steps=25,                   # Evaluate every 25 steps

    # Checkpointing
    save_strategy="steps",
    save_steps=50,                   # Save every 50 steps
    save_total_limit=3,              # Keep only 3 most recent checkpoints

    # Logging and monitoring
    logging_steps=5,
    report_to="trackio",
    run_name="qwen2.5-72b-genomics-v1",

    # Misc
    seed=42,
    remove_unused_columns=True,
)

print(f"✓ Training config:")
print(f"  Epochs: {training_args.num_train_epochs}")
print(f"  Effective batch size: {training_args.per_device_train_batch_size * training_args.gradient_accumulation_steps}")
print(f"  Learning rate: {training_args.learning_rate}")
print(f"  Hub model ID: {training_args.hub_model_id}")

# Initialize trainer
print("\n[Starting Training]")
print("Model: Qwen/Qwen2.5-72B")
print("Method: LoRA fine-tuning")
print("Trackio monitoring: https://huggingface.co/spaces/mattPearce/trackio")
print("="*80)

trainer = SFTTrainer(
    model="Qwen/Qwen2.5-72B",
    train_dataset=dataset_split["train"],
    eval_dataset=dataset_split["test"],
    peft_config=peft_config,
    args=training_args,
)

# Train the model
trainer.train()

# Save final model to Hub
print("\n[Finalizing]")
print("Pushing final model to Hub...")
trainer.push_to_hub()

print("\n" + "="*80)
print("✓ Training completed successfully!")
print(f"✓ Model saved to: https://huggingface.co/mattPearce/qwen2.5-72b-genomics-lora")
print("="*80)