How to train your VAE

[xuzhang5788]

If I have a new dataset, how can I use your code to train? It will be great if you could provide a procedure. Do you have any documentations on this code? Many thanks.

[jnwei-zz]

Hi,

I'll write up a more thorough procedure and fix some documentation later, but to answer your question quickly:

1. Have your data prepared as a csv file. One of these columns should contain SMILES, the other should contain the properties you want to predict. This will be read later by mol_utils.load_smiles_and_data_df
2. Create a json containing the characters found in the SMILES strings of this file. mol_utils.make_charset can help you do that.
3. Copy the exp.json from models>zinc>exp.json, and change the data_file, char_file fields to match your experiment.
4. Run chem.train_vae from the directory containing the exp.json.

Let me know if you have more questions.

On Thu, May 17, 2018 at 7:59 PM xuzhang5788 [email protected] wrote:

If I have a new dataset, how can I use your code to train? It will be great if you could provide a procedure. Do you have any documentations on this code? Many thanks.

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[zealseeker]

Hi @jnwei I wonder is it possible to first feed a large dataset such as ZINC without the properties and then feed a much small one with the property such as the bioacitivity to a target. So that I can generate compounds with the bioactivity?

update

It seems that the issue has been created in #5, however no one replies.

[muammar]

Hi @jnwei I wonder is it possible to first feed a large dataset such as ZINC without the properties and then feed a much small one with the property such as the bioacitivity to a target. So that I can generate compounds with the bioactivity?

update

It seems that the issue has been created in #5, however no one replies.

Did you get to solve this?