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I am wondering if anyone has experience with generating molecules using machine learning in Mathematica. There are a bunch of papers these days with such applications/developments. For example, https://pubs.acs.org/doi/10.1021/acs.jcim.0c01496. Another example on Medium is https://medium.com/@sunitachoudhary103/generating-molecules-using-a-char-rnn-in-pytorch-16885fd9394b

I know about Molecule and associated chemistry functions. I am interested in how SMILES strings could be generated, perhaps, by adapting some neural networks that work for such kinds of applications.

If someone's aware of examples/tutorials that cover this, it would be great, if you could share.

Cheers!

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    $\begingroup$ A challenge with SMILES is guaranteeing semantic structure. Arguably, methods for representing molecular graphs like SELFIES github.com/aspuru-guzik-group/selfies might be easier to implement, as ANY generated string is valid. (These can always be translated into a corresponding SMILES) It should be straightforward to implement SELFIES using MMA term replacement (or just import the python library). Back when the paper was first posted, to understand it better I sketched out a rough demo from the appendix wolframcloud.com/obj/jschrier0/Published/… $\endgroup$ Mar 1, 2022 at 13:40
  • $\begingroup$ Thanks a lot! Do you think you could post this as an answer? $\endgroup$
    – bhopshang
    Mar 2, 2022 at 22:27
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    $\begingroup$ There is this example, Generating Molecules With SELFIES. It doesn't use machine learning explicitly, but rather shows the raw tools you would use in a ML application. $\endgroup$
    – Jason B.
    Feb 7 at 22:31

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A great paper that covers this topic can be found here:

Machine Learning Methods in Chemistry

The Author uses a Markovian text generator to generate SMILES strings that are variations on a theme. The invalid SMILES are culled with a Mathematica function. The code requires Mathematica 10 or later.

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    $\begingroup$ While this link may answer the question, it is better to include the essential parts of the answer here and provide the link for reference. Link-only answers can become invalid if the linked page changes. - From Review $\endgroup$
    – corey979
    Sep 10, 2023 at 22:46

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