--- a +++ b/doc/source/benchmark/generation.rst @@ -0,0 +1,29 @@ +Molecule Generation +=================== + +.. include:: ../bibliography.rst + +This page contains benchmarks of graph generative models for goal-directed property +optimization, which is aimed at generating novel molecules with optimized chemical +properties. We first pretrain the models on `ZINC250k`_ dataset, and then apply the +reinforcement learning algorithms to finetune the networks towards desired chemical +properties. + +We choose penalized logP and QED score as our target property. + +- Penalized logP score is the octanol-water partition coefficient penalized by the + synthetic accessibility score and the number of long cycles. +- QED score measures the drug-likeness of the molecule. + +We report the top-1 property scores of generated molecules by different models in +the following table. We also report the top-1 property scores of molecules in +`ZINC250k`_ dataset for reference. The maximum graph size is set as 38, which is the +same as the maximum graph size of molecules in `ZINC250k`_. + ++----------------+-----------------------+---------+------------+ +| | `ZINC250k`_ (Dataset) | `GCPN`_ | `GraphAF`_ | ++================+=======================+=========+============+ +| Penalized LogP | 4.52 | 6.560 | 5.630 | ++----------------+-----------------------+---------+------------+ +| QED | 0.948 | 0.948 | 0.948 | ++----------------+-----------------------+---------+------------+