training/setup_mac.md

Mac Local Training Setup

This guide sets up a Mac-friendly Python environment for local DNABERT-2 experiments.

Full DNABERT-2 training can be slow on a Mac, especially on CPU. Start with small smoke tests before running larger jobs.

CSV File Locations

Training scripts should look for sequence CSVs in this order:

1. data/processed/
2. training/csv_files/

Your current CSV files are in:

training/csv_files/train_with_sequences.csv
training/csv_files/val_with_sequences.csv
training/csv_files/test_with_sequences.csv

That location is supported.

1. Create Virtual Environment

Run this from the project root:

python3 -m venv .venv

2. Activate It

source .venv/bin/activate

Your terminal prompt should now show .venv.

3. Upgrade pip

python -m pip install --upgrade pip

4. Install Requirements

pip install -r training/requirements-mac.txt

5. Check PyTorch Device

python training/check_device.py

Expected output includes one of:

Using device: mps

or:

Using device: cpu

If you see Using device: cpu, the project will still work, but local training will be slow. Use very small smoke tests locally and use a GPU environment for full model training.

6. Check Dataset

Before training, verify the CSV files:

python training/check_dataset.py

This confirms that the sequence and label columns exist, labels are encoded as 0 and 1, sequence values are present, and class balance is reasonable.