deepuq 0.1.6
a package for investigating and comparing the predictive uncertainties from deep learning models
License: MIT
Requires Python: <3.11,>=3.10

# DeepUQ
DeepUQ is a package for injecting and measuring different types of uncertainty in ML models.

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## Installation

### Install the deepuq package via venv and pypi
> python3.10 -m venv name_of_your_virtual_env

> source name_of_your_virtual_env/bin/activate

> pip install deepuq

Now you can run some of the scripts!
> UQensemble --generatedata --save_final_checkpoint --save_all_checkpoints --plot_savefig --overwrite_model

^`--generatedata` is required if you don't have any saved data. 

The default behavior is to train the model without saving any checkpoints. By specifying the `--save_final_checkpoint` flag, the script will save a pytorch checkpoint for the final epoch with the model weights as well as diagnostics like the MSE metric and the model loss. This checkpoint will be stored in a folder at the path specified by `--out_dir` flag, the default location is `./DeepUQResources/checkpoints/`.

To additionally save all checkpoints, use the `--save_all_checkpoints` flag.

To save diagnostic plots of the true and predicted model outputs as well as the model residuals, specify `--plot_inline` and `--plot_savefig` (to plot inline and save as a png, respectively).

The `--overwrite_model` flag will retrain and overwrite a previously existing version of the model.

It's also possible to verify the install works by running:
> pytest

### Preferred dev install option: Poetry
If you'd like to contribute to the package development, please follow these instructions.

First, navigate to where you'd like to put this repo and type:
> git clone https://github.com/deepskies/DeepUQ.git

Then, cd into the repo:
> cd DeepUQ

Poetry is our recommended method of handling a package environment as publishing and building is handled by a toml file that handles all possibly conflicting dependencies. 
Full docs can be found [here](https://python-poetry.org/docs/basic-usage/).

Install instructions: 

Add poetry to your python install 
> pip install poetry

Then, from within the DeepUQ repo, run the following:

Install the pyproject file
> poetry install 

Begin the environment
> poetry shell

Now you have access to all the dependencies necessary to run the package.

## Package structure
```
DeepUQ/
├── CHANGELOG.md
├── LICENSE.txt
├── README.md
├── DeepUQResources/
├── data/
├── notebooks/
├── poetry.lock
├── pyproject.toml
├── deepuq/
│   ├── __init__.py
│   ├── analyze/
│   │   ├── __init__.py
│   │   ├── analyze.py
│   ├── data/
│   │   ├── __init__.py
│   │   ├── data.py
│   ├── models/
│   │   ├── __init__.py
│   │   ├── models.py
│   ├── scripts/
│   │   ├── __init__.py
│   │   ├── DeepEnsemble.py
│   │   ├── DeepEvidentialRegression.py
│   ├── train/
│   │   ├── __init__.py
│   │   ├── train.py
│   └── utils/
│   │   ├── __init__.py
│   │   ├── defaults.py
│   │   ├── config.py
├── test/
│   ├── DeepUQResources/
│   ├── data/
│   ├── test_DeepEnsemble.py
│   └── test_DeepEvidentialRegression.py
```
The `deepuq/` folder contains the relevant modules for config settings, data generation, model parameters, training, and the two scripts for training the Deep Ensemble and the Deep Evidential Regression models. It also includes tools for loading and analyzing the saved checkpoints in `analysis/`.

Example notebooks for how to train and analyze the results of the models can be found in the `notebooks/` folder.

The `DeepUQResources/` folder is the default location for saving checkpoints and diagnostic plots from the trained model and the `data/` folder is where the training and validation set are saved.

## How to run the workflow
The scripts can be accessed via the ipython example notebooks in the `notebooks/` folder or via the model modules (ie `deepuq/scripts/DeepEnsemble.py`). For example, to ingest data and train a Deep Ensemble from the DeepUQ/ directory:

> python deepuq/scripts/DeepEnsemble.py

The equivalent shortcut command:
> UQensemble

With no config file specified, this command will pull settings from the `default.py` file within `utils`. For the `DeepEnsemble.py` script, it will automatically select the `DefaultsDE` dictionary.

Another option is to specify your own config file:

> python deepuq/scripts/DeepEnsemble.py --config "path/to/config/myconfig.yaml"

Where you would modify the "path/to/config/myconfig.yaml" to specify where your own yaml lives.

The third option is to input settings on the command line. These choices are then combined with the default settings and output in a temporary yaml.

> python deepuq/scripts/DeepEnsemble.py --noise_level "low" --n_models 10 --out_dir ./DeepUQResources/ --save_final_checkpoint --save_all_checkpoints --plot_savefig --n_epochs 10

This command will train a 10 network, 10 epoch ensemble on the low noise data and will save figures and all checkpoints to the specified directory.

For more information on the arguments:
> python deepuq/scripts/DeepEnsemble.py --help

The other available script is the `DeepEvidentialRegression.py` script:
> python deepuq/scripts/DeepEvidentialRegression.py --help

The shortcut:
> UQder