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ROBERT (Refiner and Optimizer of a Bunch of Existing Regression Tools)

CircleCI Codecov Downloads Read the Docs PyPI

Documentation

Full documentation with installation instructions, technical details and examples can be found in Read the Docs.

Don't miss out the latest hands-on tutorials from our YouTube channel!

Recommended installation

  1. (Only once) Create new conda environment: conda create -n robert python=3.10
  2. Activate conda environment: conda activate robert
  3. Install ROBERT using pip: pip install robert
  4. Install libraries for the PDF report conda install -y -c conda-forge glib gtk3 pango mscorefonts
  5. (Only for compatible devices) Install Intelex accelerator: pip install scikit-learn-intelex
  • Inexperienced users should visit the Users with no Python experience section in Read the Docs.

Update the program

  1. Update to the latest version: pip install robert --upgrade

Developers and help desk

List of main developers and contact emails:

For suggestions and improvements of the code (greatly appreciated!), please reach out through the issues and pull requests options of Github.

License

ROBERT is freely available under an MIT License

Special acknowledgements

J.V.A.R. - The acronym ROBERT is dedicated to ROBERT Paton, who was a mentor to me throughout my years at Colorado State University and who introduced me to the field of cheminformatics. Cheers mate!

D.D.G. - The style of the ROBERT_report.pdf file was created with the help of Oliver Lee (2023, Zysman-Colman group at University of St Andrews).

J.V.A.R. and D.D.G. - The improvements from v1.0 to v1.2 are largely the result of insightful discussions with Matthew Sigman and his students, Jamie Cadge and Simone Gallarati (2024, University of Utah).

We really THANK all the testers for their feedback and for participating in the reproducibility tests, including:

  • David Valiente (2022-2023, Universidad Miguel Hernández)
  • Heidi Klem (2023, Paton group at Colorado State University)
  • Iñigo Iribarren (2023, Trujillo group at Trinity College Dublin)
  • Guilian Luchini (2023, Paton group at Colorado State University)
  • Alex Platt (2023, Paton group at Colorado State University)
  • Oliver Lee (2023, Zysman-Colman group at University of St Andrews)
  • Xinchun Ran (2023, Yang group at Vanderbilt University)

How to cite ROBERT

If you use any of the ROBERT modules, please include this citation:

  • Dalmau, D.; Alegre Requena, J. V. ROBERT: Bridging the Gap between Machine Learning and Chemistry. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2024, accepted. DOI: 10.1002/WCMS.1733.

If you use the AQME module, please include this citation:

  • Alegre-Requena et al., AQME: Automated Quantum Mechanical Environments for Researchers and Educators. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2023, 13, e1663.

Additionally, please include the corresponding reference for Scikit-learn and SHAP:

  • Pedregosa et al., Scikit-learn: Machine Learning in Python. J. Mach. Learn. Res. 2011, 12, 2825-2830.
  • Lundberg et al., From local explanations to global understanding with explainable AI for trees. Nat. Mach. Intell. 2020, 2, 56–67.