Requires python<=3.11
To access model & dataset modules:
pip install chemprobe
To access scripts for preprocessing/training/inference you must install from source:
git clone https://github.com/keiserlab/chemprobe.git
cd chemprobe
# use a virutal env...
# conda activate env
pip install .
Required to run inference
bash download_data.sh
Required to run inference
python preprocess.py \
--data_path ../data
python train.py \
--name TEST \
--exp film \
--fold 0 \
--n_blocks 4 \
--data_path ../data/preprocessed \
--batch_size 16384 \
--gpus 0,1,2,3 \
--num_workers 4 \
--lr 1e-3
permuted label model
python train.py \
--study_path /scratch/wconnell/danger/chemprobe/optuna/exp=film/fold=0/ \
--data_path ../data/preprocessed \
--name perm-fold=0 \
--exp film \
--fold 0 \
--max_epochs 5 \
--batch_size 16384 \
--gpus 3, \
--permute_labels
python optimize.py \
--study_path /srv/danger/scratch/wconnell/chemprobe/optuna/ \
--data_path ../data/preprocessed \
--exp film \
--fold 0 \
--n_trials 20 \
--prune \
--batch_size 16384 \
--gpus 1,
python predict.py \
--cpds neratinib \ # Do not specify to run on all compounds
--data_path ../data/your_data/ \
--attribute \ # optional to run attribution
--batch_size 128 \
--gpus 2,
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