<commit_before># ChEMBL Net

Python tools for building ChEMBL network.

# Installation
```
python setup.py install --user
```

You also need to install TensorFlow for running the models in this package.

## Installation in Conda

```
conda create --name chemblnet python=3
source activate chemblnet
conda install numpy scipy matplotlib
conda install ipython
conda install -c conda-forge tensorflow
```

# Model training example
First you need to download IC50 data and ECFP features:
```
wget http://homes.esat.kuleuven.be/~jsimm/chembl-IC50-346targets.mm
wget http://homes.esat.kuleuven.be/~jsimm/chembl-IC50-compound-feat.mm
```

Model directory contains several models, which you can then easily train:
```
python models/deep_macau.py --reg 1e-3 --zreg 1e-4 --hsize 100 \
  --model non_linear_z \
  --y chembl-IC50-346targets.mm \
  --side chembl-IC50-compound-feat.mm
```

Another example is `models/mlp_multi3.py` which uses multi-task MLP (multi-layer perceptron) with 1 hidden layer.
<commit_msg>using pip to install<commit_after># ChEMBL Net

Python tools for building ChEMBL network.

# Installation
```
pip install .
```

You also need to install TensorFlow for running the models in this package.

## Installation in Conda

```
conda create --name chemblnet python=3
source activate chemblnet
conda install numpy scipy matplotlib
conda install ipython
conda install -c conda-forge tensorflow
```

# Model training example
First you need to download IC50 data and ECFP features:
```
wget http://homes.esat.kuleuven.be/~jsimm/chembl-IC50-346targets.mm
wget http://homes.esat.kuleuven.be/~jsimm/chembl-IC50-compound-feat.mm
```

Model directory contains several models, which you can then easily train:
```
python models/deep_macau.py --reg 1e-3 --zreg 1e-4 --hsize 100 \
  --model non_linear_z \
  --y chembl-IC50-346targets.mm \
  --side chembl-IC50-compound-feat.mm
```

Another example is `models/mlp_multi3.py` which uses multi-task MLP (multi-layer perceptron) with 1 hidden layer.

{'fraction_non_alphanumeric': 0.10420841683366733, 'fraction_numerical': 0.026052104208416832, 'mean_word_length': 4.081424936386768, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '7670342', 'n_tokens_mistral': 733, 'n_tokens_neox': 667, 'n_words': 215}