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A Modular Architecture for Deep Learning Systems

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# A Modular Architecture for Deep Learning Systems

## Notice: Alpha Release
This is an alpha release. The API is subject to change and the documentation is incomplete.

## What is `cortex`?

The `cortex` library provides a modular framework for neural network model composition for advanced use cases like multitask models, guided generative models, and multi-modal models.
Rather than tack on auxiliary abstractions to a single input --> single task model, `cortex` is built from the ground up to make adding new inputs or tasks to the model as seamless as possible.

## Installation

Note: conda/mamba are no longer actively supported. We recommend using `uv` for package management.

```bash
uv sync
source ~/.venv/cortex/bin/activate
```

## Running

Use `cortex_train_model --config-name <CONFIG_NAME>` to train, e.g.:

```bash
cortex_train_model --config-name train_protein_model wandb_mode=offline
```

## How to launch a WANDB sweep

1. Configure the sweep `.yaml`, e.g. `./config/wandb/protein_model_sweep.yaml`
2. Run `wandb sweep ./config/wandb/protein_model_sweep.yaml`
3. Launch the wandb agents using a scheduler of your choice, e.g. SLURM or LSF

## Contributing

Contributions are welcome!

### Install dev requirements and pre-commit hooks

```bash
uv sync --dev
uv run pre-commit install
```

### Testing

```bash
uv run pytest -v --cov-report term-missing --cov=./cortex ./tests
```

### Build and browse docs locally

```bash
make -C docs html
cd docs/build/html
python -m http.server
```

Then open `http://localhost:8000` in your browser.

### Citation

A standalone whitepaper is in progress, in the meantime please cite the following paper if you use `cortex` in your research:

```
@article{gruver2024protein,
  title={Protein design with guided discrete diffusion},
  author={Gruver, Nate and Stanton, Samuel and Frey, Nathan and Rudner, Tim GJ and Hotzel, Isidro and Lafrance-Vanasse, Julien and Rajpal, Arvind and Cho, Kyunghyun and Wilson, Andrew G},
  journal={Advances in Neural Information Processing Systems},
  volume={36},
  year={2024}
}
```

## What's in the name?

The cerebral cortex is the outer layer of the brain (i.e. the grey matter). Different parts of the cortex are responsible for different functions, including sensation, motor function, and reasoning. The cortex is supported and interconnected by subcortical structures (i.e. the white matter). Similarly the `cortex` package provides modular neural network components for different functions, such as extracting features from different types of inputs, or making predictions for different tasks.
`cortex` also provides a flexible superstructure to compose those modules into advanced architectures and route signals between them.

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