Chainer Chemistry: A Library for Deep Learning in Biology and Chemistry | Hacker News Reader

Chainer Chemistry: A Library for Deep Learning in Biology and Chemistry

preferredresearch.jp

59 pointswei_jok7 comments

Really cool stuff here, a lot along the same lines of what we have been trying to do with DeepChem and MoleculeNet.

We seem to be a little further along and stable than this repo. We are also based on Tensorflow instead of raw cuda which means users can play around with the networks more easily.

This is based on Chainer, not raw cuda, meaning its also very flexible for the user

Excellent. I'd been wanting to implement something like this but these guys beat me to the punch.

Most existing research on NNs in chemistry uses the SMILES string representation and feeds it into a recurrent neural network. The problem with SMILES in my opinion, is that SMILES is not unique, and there are a gazillion ways to represent the same molecule. Thus, the RNN is probably overfitting to the quirks of the SMILES serialization algorithm used by the US Patent Office and/or ChemDraw and/or whatever program was used to generate the library of molecules.

Convolutional graph networks are the obviously correct way to handle molecules.

they use canonical SMILES. Problem: there's more than one way to make canonical SMILES :(

This seems like the development of an artificial chemical intuition[0][1] except since its a computer it can intuit concrete numbers much more comfortably than humans can. I do wonder how its accuracy compares to just running the DFT calculations.

[0]wavefunction.fieldofscience.com/2016/09/what-is-chemical-intuition.html

[1]https://news.ycombinator.com/item?id=12624036

There is a lot of research on attempting to approximate DFT level energy calculations with simple Neural Networks.

https://arxiv.org/abs/1610.08935 https://github.com/deepchem/deepchem/blob/master/deepchem/mo...

http://aip.scitation.org/doi/pdf/10.1063/1.4986081

It is a pretty straight-forward application of ML to the space that is starting to have solid results in practice.

Links of Chainer Chemistry

- blog: https://preferredresearch.jp/2017/12/18/chainer-chemistry-be...

- github: https://github.com/pfnet-research/chainer-chemistry

- document: http://chainer-chemistry.readthedocs.io/en/latest/index.html

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