
Modeling Molecules with Recurrent Neural Networks - csvoss
http://csvoss.github.io/projects/2015/10/08/rnns-and-chemistry.html
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gene-h
That is a very strange way to generate molecules. It would be interesting to
see if this is any better than other approaches used to generate molecules
like those used in drug design. It would be particularly interesting to see
how this compares with the approach that was used to generate GDB-17[1] a
database of randomly generated molecules or at least see if generated
molecules pass through the filters used to make GDB-17. Grammatically correct
does not necessarily mean physically reasonable, recall Chomsky's "colorless
green ideas sleep furiously."

While it would be interesting to model reactions with RNN, I'm not so sure
this would offer any advantage over simply searching a database of reactions
like the Crossfire Beilstein database[2][3]. I am also curious if you
investigated reaction MQL in work with the carbonate project.

This work is interesting though. Essentially you are using a neural network to
generate graphs. There are a lot of things that can be represented with
graphs, IE electric circuits and such. Maybe you could make a RNN for
generating neural networks!

[1][http://www.gdb.unibe.ch/gdb/home.html](http://www.gdb.unibe.ch/gdb/home.html)
[2][https://en.wikipedia.org/wiki/Beilstein_database](https://en.wikipedia.org/wiki/Beilstein_database)
[3][http://www.ncbi.nlm.nih.gov/pubmed/21378798](http://www.ncbi.nlm.nih.gov/pubmed/21378798)

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Xcelerate
Haha, interesting, but I thought this was going in a different direction.
There's a lot of work going on lately to try to model molecular potentials
(for molecular dynamics / quantum chemistry) using neural networks. Accurate
potentials are extremely expensive to calculate.

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sxyuan
Not the direction I was expecting either, but interesting nonetheless.
Regarding modelling molecular potentials with neural nets, do you have any
recommendations in terms of recent papers on the topic?

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tfgg
The list of speakers at the "Machine Learning Methods in Materials Modeling"
stream at this recent conference [1] are a few people in the area, though some
of those are more predicting properties than making atomic potentials.

I chatted to Gabor Csanyi (Cambridge [2]) during the conference, who I think
is probably one of the furthest ahead in the area, and they've recently moved
away from their gaussian process based methods to kernel methods. With regard
to NNs, he seemed of the opinion that CNNs (the more obvious NN model) were
too expensive and ultimately unnecessary compared to carefully chosen,
physically motivated kernels. I have to admit I didn't quite understand
everything he presented, and I can't seem to find a recent publication, but
I'm sure there's one out there.

Despite enthusiastic presentations with lovely results, I suspect from the
slow progress in this area that transferability is the main problem plaguing
these methods. You want a local atomic potential which doesn't depend on its
environment beyond a certain radius, sort of like a convolutional kernel, but
a lot of this sort of materials modelling/quantum chemistry is pretty
inherently delocalised. Machine learning isn't magic and ultimately has to
reflect and represent the underlying physics.

[1] [http://nano-bio.ehu.es/psik2015/programme.html](http://nano-
bio.ehu.es/psik2015/programme.html)

[2]
[https://camtools.cam.ac.uk/wiki/site/5b59f819-0806-4a4d-0046...](https://camtools.cam.ac.uk/wiki/site/5b59f819-0806-4a4d-0046-bcad6b9ac70f/publications.html)

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jamessb
One of Gabor's grad students, Alan Nichols, gave a half-hour talk ( _Learning
Quantum Mechanics: Machines versus Humans_ ) that was previously posted to HN:
[https://news.ycombinator.com/item?id=8912703](https://news.ycombinator.com/item?id=8912703)

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bloaf
Where did your data set come from? It contains at least one error:

WOF2, tungsten(VI) oxytetrafluoride

that correct formula is WOF4

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csvoss
Nice catch! That one is from Wikipedia:
[http://en.wikipedia.org/wiki/Dictionary_of_chemical_formulas](http://en.wikipedia.org/wiki/Dictionary_of_chemical_formulas)

I've updated the offending page.

