From e396dbaf43f9d4ac2ee2568a4d5f93ad9e78b767 Mon Sep 17 00:00:00 2001 From: Wengong Jin Date: Wed, 28 Apr 2021 18:45:38 -0400 Subject: [PATCH] Update README.md --- README.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/README.md b/README.md index 878f9a3..48b51c1 100644 --- a/README.md +++ b/README.md @@ -51,9 +51,13 @@ mkdir ckpt/finetune python finetune_generator.py --train ${ACTIVE_MOLECULES} --vocab data/chembl/vocab.txt --generative_model ckpt/chembl-pretrained/model.ckpt --chemprop_model ${YOUR_PROPERTY_PREDICTOR} --min_similarity 0.1 --max_similarity 0.5 --nsample 10000 --epoch 10 --threshold 0.5 --save_dir ckpt/finetune ``` Here `${ACTIVE_MOLECULES}` should contain a list of experimentally verified active molecules. + `${YOUR_PROPERTY_PREDICTOR}` should be a directory containing saved chemprop model checkpoint. + `--max_similarity 0.5` means any novel molecule should have nearest neighbor similarity lower than 0.5 to any known active molecules in ${ACTIVE_MOLECULES}` file. + `--nsample 10000` means to sample 10000 molecules in each epoch. + `--threshold 0.5` is the activity threshold. A molecule is considered as active if its predicted chemprop score is greater than 0.5. In each epoch, generated active molecules are saved in `ckpt/finetune/good_molecules.${epoch}`. All the novel active molecules are saved in `ckpt/finetune/new_molecules.${epoch}`