keras-molecules
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maxhodak
Autoencoder network for learning a continuous representation of molecular structures.
i.e. list of outputs from the VAE. If not, are you aware of any other resources that might have molecular candidates via a generative algorithm? (VAE, GAN, etc.)
I receive the following error when trying to train the model. ImportError: libcudart.so.8.0: cannot open shared object file: No such file or directory I am using cuda 10.0, python 2.7.15,...
Hello, I've been trying to test out the autoencoder using the pre-trained model and examples in the readme. I pre-processed both the 50k and 500k datasets and get the same...
Hi, I am trying to run preprocess.py and there is an unresolved reference to reduce: `charset = list(reduce(lambda x, y: set(y) | x, structures, set()))` however, if I: `from functools...
Hi, it looks like that this code actually train not VAE model but simple auto-encoder model. Here are reasons: 1) Epsilon std is 0.01 https://github.com/maxhodak/keras-molecules/blob/master/molecules/model.py#L58 when it should be 1....
python preprocess.py data/smiles_50k.h5 data/processed_50k.h5 Traceback (most recent call last): File "preprocess.py", line 85, in main() File "preprocess.py", line 72, in main apply_fn=lambda ch: np.array(map(one_hot_encoded_fn, File "preprocess.py", line 63, in create_chunk_dataset...
When I tried to run a program by executing python preprocess.py data/smiles_50k.h5 data/processed.h5. it is generating an error. The detailed error is attached in the image. How to correct this?...
The loss function for the autoencoder is calculated here using `kl_loss = - 0.5 * K.mean(1 + z_log_var - K.square(z_mean) - K.exp(z_log_var), axis = -1) ` taking the mean over...
Dear author, I download your codes and pre-trained model (model_500k.h5) and tried out the following commands: python preprocess.py data/smiles_500k.h5 data/processed_500k.h5 python sample.py data/processed_500k.h5 data/model_500k.h5 --target autoencoder Then it outputs: NC(=O)c1nc(cnc1N)c2ccc(Cl)c(c2)S(=O)(=O)Nc3cccc(Cl)c3...
