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

Deep Learning Reaction Prediction with PyTorch

Esbenbjerrum/ March 29, 2021

In this blogpost I’ll show how to predict chemical reactions with a sequence to sequence network based on LSTM cells. It’s the same principle as IBM’s RXN

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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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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 make a jupyter notebook widget for annotation of atom properties

Esbenbjerrum/ September 28, 2019

  Not so long ago Greg Landrum published a blog post with an example of how the SVG rendering from RDKit in a jupyter notebook can be

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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: 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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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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