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Guide

External Resources

Terminologies used in this project

  • Categories: are of following types Artificial Intelligence (AI), Electronic Structure (ES), Force-field (FF), Quantum Computation (QC) and Experiments (EXP). Each of these categories are divided into sub-categories. These sub-categories include single-property-prediction, single-property-classification, machine-learning force-fields, text-classification, text-token classification, text-generation, image classification, image-segmentation, image-generation, spectra-prediction, and eigensolver. These categories and sub-categories are highly flexible and new entries can be easily added.

  • Sub-categories: include 1) SinglePropertyPrediction (where the output of a model/experiment is one single number for an entry), 2) SinglePropertyClass (where the output is class-ids, e.g., 0,1,.. instead of floating values), 3) ImageClass (for multi-class image classification), 4) textClass (for multi-label text classification), 5) MLFF (machine learning force-field), 6) Spectra (for multi-value data) and 7) EigenSolver (for Hamiltonian simulation).

  • Benchmarks: are ground truth data used to calculate metrics for each specific task (e.g a json.zip file).

  • Methods: are a set of precise specifications for evaluation against a benchmark. For example, within ES category, DFT with VASP-GGA-PAW-PBE are specifications, hence a method. Similarly, within AI category, descriptor/feature based models with MatMiner-chemical features and LightGBM software are specifications, hence a method.

  • Contributions: are individual data in form of csv.zip files for each benchmark and specific method. Each contribution has six components: method (e.g. AI), category (e.g. SinglePropertyPrediction), property (e.g. formation energy), dataset (e.g. dft_3d), data-split (e.g. test), metric (e.g. mae).

A tree diagram for directory and file structure

Tree

How to contribute

1. How to add a contribution (csv.zip):

For a short demo, checkout this google colab-notebook

Prerequisites (for those not familiar with GitHub):

A GitHub username and a basic familiarity with GitHub is needed to work with the JARVIS-Leaderboard. See below:

If you do not have a GitHub account, sign up for one at: https://github.com/signup Related article: https://www.toolsqa.com/git/how-to-create-github-account/

GitHub

Suppose you choose your username as “knc6”, you’ll have a webpage at https://github.com/knc6 . Ofcourse, choose some other username of your choice, but for the following demo, we will use the “knc6” as an example username.

Once you have the GitHub account, go to the website https://github.com/usnistgov/jarvis_leaderboard. Here Fork (make your own copy) of the JARVIS-Leaderbord repo by clicking on the “Fork” button. Also, feel free to click on the “Star” button if you like the JARVIS-Leaderboard project.

GitHub

Now, go to your forked version of the JARVIS-Leaderboard. For a username “knc6”, you’ll have a repo at https://github.com/knc6/jarvis_leaderboard. Notice, we have “knc6” in the URL instead of usnistgov. Ofcourse, use your own username instead of knc6.

GitHub

Now, we will make a pull request (request to contribute your edits in the main repo). If you are not familiar with pull requests checkout this link

GitHub

If successful with basic GitHub setup, follow the guidelines:

  1. Go to your forked jarvis_leaderboard repo.

  2. git clone https://github.com/USERNAME/jarvis_leaderboard. NOTE: use your own GitHub USERNAME, e.g. knc6, instead of usnistgov

    Note if you do not use forked version, you won't be able to make a pull request

  3. cd jarvis_leaderboard

  4. conda create --name leaderboard python=3.8
  5. source activate leaderboard
  6. Install the package: python setup.py develop
  7. Let's add a contribution for Silicon bandgap using DFT PBE (an Electronic structure approach)

cd jarvis_leaderboard/contributions/

mkdir vasp_pbe_teamX , you can give any reaosnable name to the benchmark folder in place of vasp_pbe_teamX

cd vasp_pbe_teamX

cp ../vasp_optb88vdw/ES-SinglePropertyPrediction-bandgap_JVASP_1002_Si-dft_3d-test-mae.csv.zip .

vi ES-SinglePropertyPrediction-bandgap_JVASP_1002_Si-dft_3d-test-mae.csv.zip

Note: do not change filenames, e.g., replace dft with qmc etc., which will cause errors

After pressing eneter twice, you'll see the file content as id,prediction

Just modify the predicting value to your model/measurement value

Save the file (":wq!" and ":q!")

Add metadata.json and run.sh files to capture metadata and enhance reproducibility. The metadata file must have at least your project_url and model_name info. The project_url couls be a publication/GitHub page etc.

Note: An admin will run your run.sh to check if he/she can reproduce your benchmark

Now, cd ../../../

python jarvis_leaderboard/rebuild.py

which will compile all data, compare with reference dataset and calculate metrices

Hoping there's no error, try: mkdocs serve

Ensure vasp_pbe_teamX row exists at:

http://127.0.0.1:8000/usnistgov/jarvis_leaderboard/ES/SinglePropertyPrediction/bandgap_JVASP_1002_Si/

Now add changes, git add jarvis_leaderboard/contributions/vasp_pbe_teamX

Commit your changes, git commit -m 'Adding my PBE Si result.'

git push

Now go to your forked github repo and make a pull reuqest (PR) to usnistgov/jarvis_leaderboard in develop branch

If you are not familiar with pull requests checkout this link

Note: only admins are allowed to make pull requests to main branch

Once an admin approve the PR, you'll see your results on the official leaderboard

  1. Another example for AI mode as follows:

Populate the dataset for a benchmark, e.g.:

python jarvis_leaderboard/populate_data.py --benchmark_file AI-SinglePropertyPrediction-exfoliation_energy-dft_3d-test-mae --output_path=Out

Currently, this script works for atomistic tasks only, addition of other tasks will be available soon.

Train you model(s), e.g.:

pip install alignn

wget https://raw.githubusercontent.com/usnistgov/alignn/main/alignn/examples/sample_data/config_example.json

train_folder.py --root_dir "Out" --config "config_example.json" --output_dir="temp"

Create a folder in the jarvis_leaderboard/contributions folder under respective submodule, e.g.:

mkdir contributions/my_awesome_model

Add comma-separated zip file (.csv.zip) file(s) corresponding to benchmark(s), e.g.:

cp temp/prediction_results_test_set.csv .

mv prediction_results_test_set.csv AI-SinglePropertyPrediction-exfoliation_energy-dft_3d-test-mae.csv

zip AI-SinglePropertyPrediction-exfoliation_energy-dft_3d-test-mae.csv AI-SinglePropertyPrediction-exfoliation_energy-dft_3d-test-mae.csv.zip

mv AI-SinglePropertyPrediction-exfoliation_energy-dft_3d-test-mae.csv.zip jarvis_leaderboard/contributions/my_awesome_model

Add metadata info in the metadata.json file, e.g.:

cp jarvis_leaderboard/contributions/alignn_models/metadata.json jarvis_leaderboard/contributions/my_awesome_model

Also, add a run.py, run.sh and Dockerfile scripts to reproduce the model predictions.

Run python jarvis_leaderboard/rebuild.py to check there are no errors

Run mkdocs serve to check if the new benchmark exists, e.g. at page http://127.0.0.1:8000/usnistgov/jarvis_leaderboard/AI/SinglePropertyPrediction/exfoliation_energy/

Add. commit and push your changes, e.g.:

git add jarvis_leaderboard/contributions/my_awesome_model

git commit -m 'Adding my awesome_model to jarvis_leaderboard

git push origin main

Make a pull request from your fork to the source repo at usnistgov/jarvis_leaderboard develop branch

Notes:

  1. The word: SinglePropertyPrediction: task type, test, property: exfoliation_energy, dataset: dft_3d, method: AI, metric: mae have been joined with '-' sign. This format should be used for consistency in webpage generation.

  2. The test data splits are pre-determined, if the exact test IDs are not used, then the code might result in errors.

2. How to add a new benchmark (json.zip):

  1. Create a json.zip file in the jarvis_leaderboard/benchmarks folder under respective sub-category, e.g.:

    e.g. jarvis_leaderboard/benchmarks/AI/SinglePropertyPrediction/dft_3d_exfoliation_energy.json.zip.

    An example of a new json.zip (mydb_myprop.json) file can be found here as well.

  2. In the .json file should have train, val, test keys with array of ids and their values.

    Note train and val can be empty dictionaries if the benchmarks are other than AI method

  3. Add a .md file, e.g.: jarvis_leaderboard/docs/AI/SinglePropertyPrediction/exfoliation_energy.md. This is where contributions performers will be kept and website info will be generated.

  4. An example for creating such a file is provided in: jarvis_leaderboard/benchmarks/AI/SinglePropertyPrediction/transform_from_figshare.py

  5. Then follow the instructions for "Adding model benchmarks to existing dataset"

Notes: A new benchmark must be linked with a peer-reviewed article and must have a DOI to ensure a minimum quality assurance for the data. We recommend adding your large dataset in Figshare or similar repository and then integrate it in JARVIS-Tools We also recommend to use JARVIS-Tools for generating dataset/models/benchmarks which can help us maintain the benchmark for long term.
Methods used for generating the data and referece are given below:

Method used for results Methods for comparison
EXP EXP/ES/analytical results
ES ES/EXP
FF ES/EXP
QC Classical/analytical results
AI Test set data

Acronyms

  1. MAE: Mean Absolute Error
  2. ACC: Classification accuracy
  3. MULTIMAE: MAE sum of multple entries, Euclidean distance
  4. For names of datasets and associated propertiesm refer to datasets in JARVIS-Tools

Help

Ask a question/raise an issue on GitHub. You can also email Kamal Choudhary if needed (kamal.choudhary@nist.gov). However, we recommend using the GitHub issues for any questions/concerns.

Citation

Large Scale Benchmark of Materials Design Methods

License

This template is served under the NIST license.
Read the [LICENSE] file for more info.