Automatic molecular designer

Recently, there are many articles and news about deep learning in web, journal etc.

“AI” is hot word.  You know, one of the very unique example is a system named “deep dream” which is a computer vision program created by google. The system generate new images from trained network. Neural network app also can generate songs, documents, poems and so on.

I am interested in making molecular designer using AI like deepdream. It’s mean MedChem AI!

Yesterday I found amazing article. The title was “Automatic chemical design using a data-driven continuous representation of molecules”.

One of the author is belonging to twitter inc. It’s interesting too. Is Twitter inc. interested in drug discovery ?? Hmm…

I felt the strategy of the article like a text mining because they used Smiles strings as input layer.

They used auto encoder and decoder  to generate molecules as smiles string. And RDKit is used for descriptor calculation and validate smiles. ;-)

After training and optimizing hyper parameters, the NN could generate similar but different molecules. It was amazing for me.

I think the work is nice, but there are some problems.

1st, this system used smiles strings as input and convert it to fixed length vector. Is the vector represents primitive of molecules?

2nd, the vector depends on 2D descriptors I think. For the protein, molecules are 3D object. So, we need to think the molecules as 3D.

Do data scientists produce artificial medicinal chemist, molecular designer  ?

I started to think about the  role of medicinal chemist again.








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