Comments (4)
One problem I foresee is that if you don't train jointly the VAE with the property predictor, then the latent-space
will not be organized according to the property. So, you are doing something quite different from what is reported in their paper.
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Hello, do you figure out this question? Many thanks.
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from chemical_vae.
Hi all,
I also encounter the same problem, so I modified the code by myself. Please take it for your reference.
After finishing training the VAE itself by a large number of Molecules with SMILES and without properties,
I create a model which is composed of only the trained encoder and the property predictor and subsequently train the model by a limited number of Molecules with SMILES and properties.
the whole parameter setting
https://github.com/AustinApple/modified_chemvae/blob/master/exp_property_training.json
In order to train the property predictor separately, I made some modifications in the train_vae.py
https://github.com/AustinApple/modified_chemvae/blob/master/train_prop.py
However, in this way we need to freeze the weighting of encoder to train our property predictor or we will destroy the system of the trained auto-encoder. We can expect that the performance of property predictor would be worse than one training with encoder together.
If there is any question. please let me know.
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Related Issues (20)
- ...For time-series...
- Exact Python package versions
- I am trying to use your model to get the encoded representation of the smiles. HOT 1
- name 'vae' is not defined
- Is the Gaussian process for optimization of molecules included in the repository? HOT 1
- trying using the conda method HOT 3
- intro_to_chemvae.ipynb loading model AttributeError: 'str' object has no attribute 'decode' HOT 3
- Dense layer in variational_layers is not saved and cannot be used to generate latent variables
- AttributeError: 'TerminalGRU' object has no attribute 'preprocess_input' HOT 1
- GPU Support
- FileNotFoundError: [Errno 2] No such file or directory: 'zinc.json' HOT 1
- Hello
- updated version of this VAE?
- Paper
- Where can I find the model prediction result?
- Which RDkit version is used in this project?
- Version incompatible
- Metaclass conflict HOT 1
- Trouble Setting up Chemvae
- I am working in a new version of this project HOT 5
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