GuacaMol, benchmarking models.
Comparison of different algorithms is an under researched area, this publication looks like a useful starting point.
De novo design seeks to generate molecules with required property profiles by virtual design-make-test cycles. With the emergence of deep learning and neural generative models in many application areas, models for molecular design based on neural networks appeared recently and show promising results. However, the new models have not been profiled on consistent tasks, and comparative studies to well-established algorithms have only seldom been performed. To standardize the assessment of both classical and neural models for de novo molecular design, we propose an evaluation framework, GuacaMol, based on a suite of standardized benchmarks. The benchmark tasks encompass measuring the fidelity of the models to reproduce the property distribution of the training sets, the ability to generate novel molecules, the exploration and exploitation of chemical space, and a variety of single and multi-objective optimization tasks. The benchmarking framework is available as an open-source Python package.
Source code : https://github.com/BenevolentAI/guacamol.
The easiest way to install guacamol is with pip:
pip install git+https://github.com/BenevolentAI/guacamol.git#egg=guacamol --process-dependency-links
guacamol requires the RDKit library (version 2018.09.1.0 or newer).