Revision

.gitignore

@@ -139,3 +139,5 @@ slurm*
 
 # smiles files
 *.smi
+
+bace

README.md

@@ -1,5 +1,6 @@
 [![Build Status](https://github.com/PaccMann/toxsmi/actions/workflows/build.yml/badge.svg)](https://github.com/PaccMann/toxsmi/actions/workflows/build.yml)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
 # toxsmi
 

data/cytotoxicity/README.md

@@ -17,42 +17,3 @@ Similar to what exists in the `data` folder, this subfolder should contain:
 Moreover,
 
 - `10_fold_stratified_cross_validation/`: A subfolder which contains the train / test split using 10-fold stratified cross-validation, of the form `cytotox_train0-10.csv` and `cytotox_test0-10.csv`.
-
-### 10-fold CV
-In order to run the 10-fold stratified cross-validation on the cluster of the Freie Universität Berlin, use the bash script below called `cytotox_10_fold_cross_validation.sh` (by adapting your email):
-
-```bash
-#!/bin/bash
-#SBATCH --job-name=cytotox_model_10_fold
-#SBATCH --mail-user=XXX
-#SBATCH --mail-type=end
-#SBATCH --partition=gpu
-#SBATCH --gres=gpu:1
-#SBATCH --mem=4G
-#SBATCH --time=8:00:00
-#SBATCH --qos=standard
-
-declare -a combinations
-index=0
-
-K=10 # K-fold cross-validation
-
-for fold in {0..9}
-do
-	combinations[$index]="$fold"
-	index=$((index + 1))
-done
-
-parameters=(${combinations[${SLURM_ARRAY_TASK_ID}]})
-fold=${parameters[0]}
-
-python3 scripts/train_tox.py data/cytotoxicity/10_fold_stratified_cross_validation/cytotox_train${fold}-$K.csv \
-data/cytotoxicity/10_fold_stratified_cross_validation/cytotox_test${fold}-$K.csv data/cytotoxicity/cytotox.smi data/smiles_language_tox21.pkl \
-models${fold}-$K params/mca.json test --embedding_path data/smiles_vae_embeddings.pkl
-```
-
-And execute the bash script by running the following:
-
-```console
-sbatch --array=0-9 cytotox_10_fold_cross_validation.sh
-```