Holger's Notes

Projects, articles and posts


My name in Holger Hoefling and I am a Statistician, Machine Learner and Bioinformatician. For the last 10 years I have worked for Novartis in various roles, currently as the Lead of the machine learning group in Data Science, NX, NIBR.

In my career I have worked on a wide range of data science problems in the healthcare field. This experience spans from working on clinical study protocols, the development of predictive algorithms for kidney disease to the statistical analysis of experiments in early non-clinical research with microarray, NGS and other biomarker data.

More recently I have been the leader of a team of machine learners working on applications in cheminformatics as well deep learning on histopathology images.


In December 2019, we published the article A deep learning model of normal histology on biorxiv.

In this article we introduce deep learning models characterizing the diversity of normal histology. We show that the models can recognize a wide array of tissue types in rat with high accuracy and the embeddings learned by the models also showed sub-clusters of structures within tissues that the model did not explicitly learn. These embeddings can also be used to classify tissues in species other than rat with minimal retraining.

Please also have a look at my other publications.


An R package for reading and writing HDF5 data, implementing most of the functionality of the C-API in R. It also has a convenient high-level interface that allows users to interact with it similar to regular arrays in R.

Potential places of interest are:

Other interests

When I don’t program for fun, I enjoy hiking, cycling as well as archery.

Latest Posts

Configuring bash in Docker

This is the first of a series of posts dealing with questions around using docker containers in data science.

hdf5r version 1.3.3 released

Another maintenance release of hdf5r. An update to the bit64 had caused a test to fail. The error was actually in the test itself, not the code it tested and was failing due to another bug that had been fixed in bit64. All fixed again.