chemprobe 0.1.1

A package for chemprobe

chemprobe

installation

pip install chemprobe

download data

bash download_data.sh

preprocess

python preprocess.py \
    --data_path ../data

train

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

optimize

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,

predict

python predict.py \
    --cpds ceranib-2 CAY10618 \
    --data_path ../data/hani \
    --batch_size 128 \
    --gpus 2,