UPDATE: Be sure to check out the follow-up to this post if you want to improve the model: Learn how to improve SMILES based molecular autoencoders with
SMILES enumeration and vectorization for Keras
The SMILES enumeration code at GitHub has been revamped and revised into an object for easier use. It can work in conjunction with a SMILES iterator object
Learn how to teach your computer to "See" Chemistry: Free Chemception models with RDKit and Keras
The film Inception with Leonardo Di Caprio is about dreams in dreams, and gave rise to the meme “We need to go deeper”. The title has also
Cheminformatics in Excel: linking RDKit with Xlwings
Excel is widely used in businesses all over the world and can be used for many diverse tasks due to the flexibility of the program. I’ve been
Programming a simple molecular GUI browser with model-view architecture (MVC) using Python with PySide or PyQt and RDKit
One of the more popular blog post based on monthly visitors is the old Create a Simple Object Oriented GUIDE GUI in MatLAB, but since I don’t
Better Deep Learning Neural Networks with SMILES Enumeration of Molecular Data
The process of expanding an otherwise limited dataset in order to more efficiently train a neural network is known as Data Augmentation For images there have been
A deep Tox21 neural network with RDKit and Keras
I found some interesting toxicology datasets from the Tox21 challenge, and wanted to see if it was possible to build a toxicology predictor using a deep neural
A deeper look into chemical space with neural autoencoders
In the last blogpost the battle tested principal components analysis (PCA) was used as a dimensionality reduction tool. This time we’ll take a deeper look into chemical
Peeking into the chemical space using free tools
As covered before, chemical space is huge. So it could be nice if this multidimensional molecular space could be reduced and visualized to get an idea about
Molecular neural network models with RDKit and Keras in Python
Neural networks are interesting models underlying much of the newest AI applications and algorithms. Recent advances in training algorithms and GPU enabled code together with publicly available