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    • Esben Jannik Bjerrum
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    • About Cheminformania
    • Esben Jannik Bjerrum

Learn how to improve SMILES based molecular autoencoders with heteroencoders

Esben Jannik Bjerrum/ October 4, 2018

Earlier I wrote a blog post about how to build SMILES based autoencoders in Keras. It has since been a much visited page, so the topic seems

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Deep Chemometrics: Deep Learning for Spectroscopy

Esben Jannik Bjerrum/ May 26, 2018

During my postdoc project at the Chemometrics and Analytical Technology section at Copenhagen University I worked with modeling of spectroscopical data with PLS models. Chemometrics is “the

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Master your molecule generator: Seq2seq RNN models with SMILES in Keras

Esben Jannik Bjerrum/ December 14, 2017

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

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SMILES enumeration and vectorization for Keras

Esben Jannik Bjerrum/ December 1, 2017

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

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Learn how to teach your computer to "See" Chemistry: Free Chemception models with RDKit and Keras

Esben Jannik Bjerrum/ November 28, 2017

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

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Cheminformatics in Excel part 2: RDKit4Excel

Esben Jannik Bjerrum/ November 21, 2017

Previously I wrote about how to use the xlwings project to get RDKit functionality directly in Excel. Well, it wasn’t that directly as there were some intermediate

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Cheminformatics in Excel: linking RDKit with Xlwings

Esben Jannik Bjerrum/ August 11, 2017

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

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Can children fold proteins?

Esben Jannik Bjerrum/ July 31, 2017

Can children fold proteins? During the summer holidays I volunteered to hold a workshop about protein folding at the summer camp for Gifted Children Denmark. The idea

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Programming a simple molecular GUI browser with model-view architecture (MVC) using Python with PySide or PyQt and RDKit

Esben Jannik Bjerrum/ June 2, 2017

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

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Better Deep Learning Neural Networks with SMILES Enumeration of Molecular Data

Esben Jannik Bjerrum/ March 23, 2017

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

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