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Cheminformania

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    • Esben Jannik Bjerrum
  • Blog
  • About
    • About Cheminformania
    • Esben Jannik Bjerrum

Using GraphINVENT to generate novel DRD2 actives

Esbenbjerrum/ November 2, 2020

I have been writing a lot about how to use SMILES together with deep learning architectures such as RNNs and LSTM networks to perform various cheminformatic and

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Building a simple SMILES based QSAR model with LSTM cells in PyTorch

Esbenbjerrum/ June 6, 2020

Last blog-post I showed how to use PyTorch to build a feed forward neural network model for molecular property prediction (QSAR: Quantitative structure-activity relationship). RDKit was used

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Building a simple QSAR model using a feed forward neural network in PyTorch

Esbenbjerrum/ May 1, 2020

In my previous blogposts I’ve entirely been using Keras for my neural networks. Keras as a stand-alone is now no longer active developed, but are instead now

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Master your molecule generator 2. Direct steering of conditional recurrent neural networks (cRNNs)

Esbenbjerrum/ November 12, 2019

Long time ago in a GPU far-far away, the deep learning rebels are happy. They have created new ways of working with chemistry using deep learning technology

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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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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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