Blog

Nov

Yesterday I moved the 300 km from Copenhagen in Denmark to Göteborg in Sweden. And today I started my new job as a Scientist at AstraZeneca. Sometimes a chapter of life must be closed to open a new and my new role is not compatible with continuing working as CEO and consultant in Wildcard Pharmaceutical Consulting. All projects with customers ...

Oct

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 interesting for a lot of people, thank you for reading. One thing that I worried about was how nearby molecules seem more related when comparing the SMILES strings rather than the molecules. ...

Jun

Troels Schwarz-Linnet

The 1st of June Troels Schwarz-Linnet started as an Intern at Wildcard Pharmaceutical Consulting. Troels recently defended his Ph.D degree in protein NMR from SBiNLab at  Copenhagen university.  We are glad that he now have chosen to use some time at Wildcard Pharmaceutical Consulting to try out new challenges and get experience with a machine ...

May

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 science of extracting information from chemical systems by data-driven means" according to Wikipedia, but I have mostly encountered the term when modeling spectroscopical data ...

Dec

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 heteroencoders I've previously written about molecular generators based on long short-term memory recurrent neural networks (LSTM-RNNs). The networks learn rules about how SMILES strings ...

Dec

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 that give on-the-fly enumeration and vectorization for training of SMILES based Recurrent Neural Network (RNN) models of molecules for ...

Nov

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 given name to the Inception networks used by Google in their Inception network. I recently stumbled across two interesting ...

Nov

Cheminformatics in Excel part 2: RDKit4Excel

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 VBA code that XLwings automatically added. It later turned out that there could be troubles with sharing workbooks and the continuous update of internal ...

Nov

Yesterday I was the external examiner at Khanhvi Tran's Master thesis defense. She had been working on upgrading the SmartCYP program from version 2.4 to 3.0, together with her supervisors Associate Professor Lars Olsen, Ph.D student Marco Montefiori  and Professor Flemming Steen Jørgensen. The program predicts site of metabolism (SOM) on ...

Aug

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 doing a fair deal of Excel templates over the years to solve an array of very different tasks. I’ve also ...