matbench-genmetrics 0.4.0

Generative materials benchmarking metrics, inspired by CDVAE.

NOTE: This is a WIP repository (as of 2022-06-21) being developed in parallel with xtal2png. Feedback and contributions welcome!

matbench-genmetrics

Generative materials benchmarking metrics, inspired by guacamol and CDVAE.

This repository provides standardized benchmarks for benchmarking generative models for crystal structure. Each benchmark has a fixed dataset, a predefined split, and a notion of best (i.e. metric) associated with it.

Getting Started

Installation, a dummy example, output metrics for the example, and descriptions of the benchmark metrics.

Installation

Create a conda environment with the matbench-genmetrics package installed from the conda-forge channel. Then activate the environment.

**NOTE: not available on conda-forge as of 2022-07-30, recipe under review by conda-forge team. So use pip install matbench-genmetrics for now

conda create --name matbench-genmetrics --channel conda-forge python==3.9.* matbench-genmetrics
conda activate matbench-genmetrics

NOTE: It doesn't have to be Python 3.9; you can remove python==3.9.* altogether or change this to e.g. python==3.8.*. See Advanced Installation

Example

NOTE: be sure to set dummy=False for the real/full benchmark run. MPTSMetrics10 is intended for fast prototyping and debugging, as it assumes only 10 generated structures.

>>> from tqdm import tqdm
>>> from mp_time_split.utils.gen import DummyGenerator
>>> from matbench_genmetrics.core import MPTSMetrics10, MPTSMetrics100, MPTSMetrics1000, MPTSMetrics10000
>>> mptm = MPTSMetrics10(dummy=True)
>>> for fold in mptm.folds:
>>>     train_val_inputs = mptm.get_train_and_val_data(fold)
>>>     dg = DummyGenerator()
>>>     dg.fit(train_val_inputs)
>>>     gen_structures = dg.gen(n=mptm.num_gen)
>>>     mptm.record(fold, gen_structures)

Output

print(mptm.recorded_metrics)

{
    0: {
        "validity": 0.4375,
        "coverage": 0.0,
        "novelty": 1.0,
        "uniqueness": 0.9777777777777777,
    },
    1: {
        "validity": 0.4390681003584229,
        "coverage": 0.0,
        "novelty": 1.0,
        "uniqueness": 0.9333333333333333,
    },
    2: {
        "validity": 0.4401197604790419,
        "coverage": 0.0,
        "novelty": 1.0,
        "uniqueness": 0.8222222222222222,
    },
    3: {
        "validity": 0.4408740359897172,
        "coverage": 0.0,
        "novelty": 1.0,
        "uniqueness": 0.8444444444444444,
    },
    4: {
        "validity": 0.4414414414414415,
        "coverage": 0.0,
        "novelty": 1.0,
        "uniqueness": 0.9111111111111111,
    },
}

Metrics

Metric	Description
Validity	One minus (Wasserstein distance between distribution of space group numbers for train and generated structures divided by distance of dummy case between train and space_group_number == 1).
Coverage	Match counts between held-out test structures and generated structures divided by number of test structures ("predict the future").
Novelty	One minus (match counts between train structures and generated structures divided by number of generated structures).
Uniqueness	One minus (non-self-comparing match counts within generated structures divided by total possible non-self-comparing matches).

A match is when StructureMatcher(stol=0.5, ltol=0.3, angle_tol=10.0).fit(s1, s2) evaluates to True.

Advanced Installation

Anaconda (conda) installation (recommended)

(2022-07-30, conda-forge installation pending, fallback to pip install xtal2png as separate command)

Create and activate a new conda environment named xtal2png (-n) that will search for and install the xtal2png package from the conda-forge Anaconda channel (-c).

conda env create -n xtal2png -c conda-forge xtal2png
conda activate xtal2png

Alternatively, in an already activated environment:

conda install -c conda-forge xtal2png

If you run into conflicts with packages you are integrating with xtal2png, please try installing all packages in a single line of code (or two if mixing conda and pip packages in the same environment) and installing with mamba (source).

PyPI (pip) installation

Create and activate a new conda environment named matbench-genmetrics (-n) with python==3.9.* or your preferred Python version, then install matbench-genmetrics via pip.

conda create -n xtal2png python==3.9.*
conda activate xtal2png
pip install xtal2png

Editable installation

In order to set up the necessary environment:

1. clone and enter the repository via:

   git clone https://github.com/sparks-baird/matbench-genmetrics.git
   cd matbench-genmetrics
   

2. create and activate a new conda environment (optional, but recommended)

   conda env create --name matbench-genmetrics python==3.9.*
   conda activate matbench-genmetrics
   

3. perform an editable (-e) installation in the current directory (.):

   pip install -e .
   

NOTE: Some changes, e.g. in setup.cfg, might require you to run pip install -e . again.

Optional and needed only once after git clone:

3. install several pre-commit git hooks with:

   pre-commit install
   # You might also want to run `pre-commit autoupdate`
   

   and checkout the configuration under .pre-commit-config.yaml. The -n, --no-verify flag of git commit can be used to deactivate pre-commit hooks temporarily.

4. install nbstripout git hooks to remove the output cells of committed notebooks with:

   nbstripout --install --attributes notebooks/.gitattributes
   

   This is useful to avoid large diffs due to plots in your notebooks. A simple nbstripout --uninstall will revert these changes.

Then take a look into the scripts and notebooks folders.

Dependency Management & Reproducibility

1. Always keep your abstract (unpinned) dependencies updated in environment.yml and eventually in setup.cfg if you want to ship and install your package via pip later on.
2. Create concrete dependencies as environment.lock.yml for the exact reproduction of your environment with:

   conda env export -n matbench-genmetrics -f environment.lock.yml
   

   For multi-OS development, consider using --no-builds during the export.
3. Update your current environment with respect to a new environment.lock.yml using:

   conda env update -f environment.lock.yml --prune
   

Project Organization

├── AUTHORS.md              <- List of developers and maintainers.
├── CHANGELOG.md            <- Changelog to keep track of new features and fixes.
├── CONTRIBUTING.md         <- Guidelines for contributing to this project.
├── Dockerfile              <- Build a docker container with `docker build .`.
├── LICENSE.txt             <- License as chosen on the command-line.
├── README.md               <- The top-level README for developers.
├── configs                 <- Directory for configurations of model & application.
├── data
│   ├── external            <- Data from third party sources.
│   ├── interim             <- Intermediate data that has been transformed.
│   ├── processed           <- The final, canonical data sets for modeling.
│   └── raw                 <- The original, immutable data dump.
├── docs                    <- Directory for Sphinx documentation in rst or md.
├── environment.yml         <- The conda environment file for reproducibility.
├── models                  <- Trained and serialized models, model predictions,
│                              or model summaries.
├── notebooks               <- Jupyter notebooks. Naming convention is a number (for
│                              ordering), the creator's initials and a description,
│                              e.g. `1.0-fw-initial-data-exploration`.
├── pyproject.toml          <- Build configuration. Don't change! Use `pip install -e .`
│                              to install for development or to build `tox -e build`.
├── references              <- Data dictionaries, manuals, and all other materials.
├── reports                 <- Generated analysis as HTML, PDF, LaTeX, etc.
│   └── figures             <- Generated plots and figures for reports.
├── scripts                 <- Analysis and production scripts which import the
│                              actual PYTHON_PKG, e.g. train_model.
├── setup.cfg               <- Declarative configuration of your project.
├── setup.py                <- [DEPRECATED] Use `python setup.py develop` to install for
│                              development or `python setup.py bdist_wheel` to build.
├── src
│   └── matbench_genmetrics <- Actual Python package where the main functionality goes.
├── tests                   <- Unit tests which can be run with `pytest`.
├── .coveragerc             <- Configuration for coverage reports of unit tests.
├── .isort.cfg              <- Configuration for git hook that sorts imports.
└── .pre-commit-config.yaml <- Configuration of pre-commit git hooks.

Note

This project has been set up using PyScaffold 4.2.2.post1.dev2+ge50b5e1 and the dsproject extension 0.7.2.post1.dev2+geb5d6b6.