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    • Esben Jannik Bjerrum
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    • About Cheminformania
    • Esben Jannik Bjerrum

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 Keras as a stand-alone is now no longer active developed, but are instead now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 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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rdEditor: An open-source molecular editor based using Python, PySide2 and RDKit

Esben Jannik Bjerrum/ March 30, 2019

At the RDKit UGM 2018 in Cambridge I made a lightning talk where I show cased rdEditor.  I’ve wanted to write a bit about it for some

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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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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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