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HIPS / molecule-autoencoder

A project to enable optimization of molecules by transforming them to and from a continuous representation.
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How to choose inducing point of the latent space and sample from the latent space? #7

Closed yangxiufengsia closed 7 years ago

yangxiufengsia commented 7 years ago

Hi, I tried to perform bayesian optimization on decoded smiles from 292 dimensional vectors. Following your paper, I first used the latent vector of this smile 'CCN(CC)C(=O)Cc1ccc(S(=O)(=O)N2CCCc3ccccc32)cc1' as inducing point. And I modified five dimensions of this vector(with value range [-0.8,1]) to obtain new smiles. But the following smiles I got are not valid ones. Do you any suggestions about how to modify the vectors in order to get new smiles? Thanks a lot [['CCN(CC)C(=O)Cc1ccc(S(=O)(=O)N2CCCc3ccccc32)cc1'], ['CCN(CC)(=O)CSc1ccc(S(=O)(=O)N2CCCc3ccccc33)cc1C'], ['CCN(CC(C(=O)Oc1cccc1S(])(==)NCCCcc2ccccc2)2C1'], ['CC1CCN1C(=O)Nc2cccc1C((=O)=O)N1CCc2ccccc3)cc1'], ['CCCCCN1C(=O)Nc2cccc1S(C)((=O)N(CCc2ccccc3))c21']]