cxhernandez / Molencoder
Licence: mit
Molecular AutoEncoder in PyTorch
Stars: ✭ 69
Programming Languages
python
139335 projects - #7 most used programming language
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MolEncoder
Molecular AutoEncoder in PyTorch
Install
$ git clone https://github.com/cxhernandez/molencoder.git && cd molencoder
$ python setup.py install
Download Dataset
$ molencoder download --dataset chembl22
Train
$ molencoder train --dataset data/chembl22.h5
Add --cuda flag to enable CUDA. Add --cont to continue training a model from a checkpoint file.
Pre-Trained Model
A pre-trained reference model is available in the ref/ directory. Currently, it performs with ~98% accuracy on the validation set after 100 epochs of training. However, if you succeed at training a better model, feel free to submit a pull request!
TODO
- [x] Implement encoder
- [x] Implement decoder
- [x] Add download command
- [x] Add train command
- [ ] Add encode command
- [ ] Add decode command
- [x] Add pre-trained model
Shoutouts
- Original paper by Gómez-Bombarelli, et al.
- keras-molecules by Max Hodak
- DeepChem
- PyTorch
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