https://github.com/baderlab/apa-net

https://github.com/baderlab/apa-net

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• Host: GitHub
• URL: https://github.com/baderlab/apa-net
• Owner: BaderLab
• License: mit
• Created: 2024-01-02T21:33:53.000Z (12 months ago)
• Default Branch: main
• Last Pushed: 2024-11-14T19:56:39.000Z (about 1 month ago)
• Last Synced: 2024-11-14T20:35:21.319Z (about 1 month ago)
• Language: Python
• Size: 8.79 KB
• Stars: 0
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# APA-Net

APA-Net is a deep learning model designed for learning context specific APA usage. This guide covers the steps necessary to set up and run APA-Net.

## Installation

Before running APA-Net, ensure you have Python installed on your system. Clone this repository to your local machine:

```bash

git clone https://github.com/BaderLab/APA-Net.git

cd APA-Net

pip install .

```

# Usage

To train the APA-Net model, use the train_script.py script with the necessary command-line arguments:

```bash

python train_script.py \

--train_data "/path/to/train_data.npy" \

--train_seq "/path/to/train_seq.npy" \

--valid_data "/path/to/valid_data.npy" \

--valid_seq "/path/to/valid_seq.npy" \

--profiles "/path/to/celltype_profiles.tsv" \

--modelfile "/path/to/model_output.pt" \

--batch_size 64 \

--epochs 200 \

--project_name "APA-Net_Training" \

--device "cuda:1" \

--use_wandb "True"

```

# Arguments

- `--train_data`: Path to the training data file.

- `--train_seq`: Path to the training sequence data file.

- `--valid_data`: Path to the validation data file.

- `--valid_seq`: Path to the validation sequence data file.

- `--profiles`: Path to the cell type profiles file.

- `--modelfile`: Path where the trained model will be saved.

- `--batch_size`: Batch size for training (default: 64).

- `--epochs`: Number of training epochs (default: 200).

- `--project_name`: Name of the project for wandb logging.

- `--device`: Device to run the training on (e.g., 'cuda:1').

- `--use_wandb`: Flag to enable or disable wandb logging ('True' or 'False').