Blog

The Blog is a collection of News, Blog posts, technical tips and tricks and other writings from my sphere of interest.
- Esben Jannik Bjerrum

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 ...

Jul

Can children fold proteins?

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 was to let interested children and teenagers try the foldit game. The foldit game is a prime example of

Jul

Mads Glahder

Today Mads Glahder starts as an Intern at Wildcard Pharmaceutical Consulting. Mads is very enthusiastic about machine learning and will work with a deep learning project utilizing chemical information. He has experience with chemometrics, multivariate statistics, MATLAB and Python programming from the masters thesis he did at the Chemometrics and Analytical Technology section at Copenhagen university. Mads ...

Jun

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 program MATLAB at the moment, I thought it could be nice by making an update about how this could be done ...

May

A few weeks ago I completed the 16 week "Neural Networks for Machine Learning" on-line course from University of Montreal to deepen my understanding of Artificial Neural Networks and their fascinating properties. The course is taught by Professor, Geoffrey Hinton, which is one of the grand old men in ...

May

I was recently contacted by Gaurav Chaudhary, who is the CEO of Roots Analysis,  a firm that provide market research and consulting for the pharmaceutical industry. It turns out that Wildcard Pharmaceutical Consulting was mentioned in their report: Deep Learning in Drug Discovery and Diagnostics, 2017 ...

Mar

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 used a variety of techniques, such as flipping, rotation, sub-segmenting and cropping, zooming. The mirror image of a cat is ...

Mar

Deep Neural Networks and Spectroscopic Data - a chemometric study A Masters project is available in a collaboration between Wildcard Pharmaceutical Consulting and Department of Food, Spectroscopy and Chemometrics, KU. We are looking for a motivated student with interest in spectroscopy and computer programming to take on a project involving ...

Mar

Medico Bazar 2017

Yesterday, Wildcard had a stand at the Medico Bazar 2017 at the Danish Technical University (DTU) in Lyngby. Medico Bazar brings together researchers, startups, investors and businesses in the medical device field. Although Wildcard is more focused on chemical and biological data, there seem to be a lot of interest in machine learning technologies, which led to a ...

Mar

Congratulations to Nadia Lund

Yesterday I had the pleasure to be external examiner at Nadia Lunds Master thesis defense. She delivered a brilliant and clear presentation of her project entitled "GPCR Structural Switches Stabilizing Specific States and Signals", where she had developed and used a sequence signature method to identify potential amino acid residues which are most likely involved in the GPCR G-Protein ...

Feb

In another blog post I demonstrated how to build a deep neural network with Keras in Python to model some toxicity dataset from the Tox21 challenge. The network was however not systematically optimized, but merely put together with a few manually selected hyper parameters. Hyper parameters are understood as the parameters which are not tuned by the data ...

Feb

New option to follow comments

A new Wordpress plugin has been installed, which enables commenters to get notified when additional comments or replys are added to the blog posts. This did only work before for registered users of the Wordpress, such as writers and admins. This was rather unfortunate. But now it is not necessary to ...

Jan

I found some interesting toxicology datasets from the Tox21 challenge, and wanted to see if it was possible to build a toxicology predictor using a deep neural network. I don't know how many layers a neural network actually has to have to be called "deep", but its a buzz word, so ...

Jan

In the last blogpost the battle tested principal components analysis (PCA) was used as a dimensionality reduction tool. This time we'll take a deeper look into chemical space by using a deep learning neural autoencoder, by testing some of the newer tools based on neural networks which has shown promising results. ...

Dec

As covered before, chemical space is huge. So it could be nice if this multidimensional molecular space could be reduced and visualized to get an idea about where how query molecules relate to one another. This small tutorial show a simple example of how this could be done with the PCA decomposition from scikit-learn and molecular fingerprints calculated with ...

Dec

Neural networks are interesting models underlying much of the newest AI applications and algorithms. Recent advances in training algorithms and GPU enabled code together with publicly available highly efficient libraries such as Google's Tensorflow or Theano makes them highly interesting for modelling molecular data. Here I explore the high level Neural Network ...

Nov

I had the pleasure and opportunity to pitch for 5 minutes at the first Meet and Greet meeting at COBIS. Its an new, regular internal event for all the companies there, where we meet and network over a cup of coffee and a croissant. I was lucky to be one of the three that got the permission to pitch and ...

Nov

Neural Networks are interesting algorithms, but sometimes also a bit spooky. In this blog post I explore the possibilities for teaching the neural networks to generate completely novel drug like molecules. I have experimented for some time with recurrent neural networks with the LSTM architecture. In short, recurrent neural networks differ from more traditional feed forward neural networks because they do ...

Nov

Pay it forward

I have volunteered as a Mentor in the Mentor-Mentee network arranged by PharmaDanmark. The idea is to match up young professionals with more experienced seniors for professional sparring and discussion focusing on promoting the Mentees career. Pharmadanmark provided an extensive guide for a successful meetings and  including many suggestions and practical tools ...

Nov

BioAgora 2016

Wildcard Pharmaceutical Consulting was represented at the Bioagora2016 at Frederiksberg Campus centered about biomarkers. Read more about the event at bioagora.dk