Structural Bioinformatics

• Bio.PDB: the strutural bioinformatics module of Bioypython. Bio.PDB is a standard way to extract data from a PDB file that describes macromolecular structures and represent the data as an easy-to-use Python object. Bio.PDB is widely used in both industry and academia. An article describing Bio.PDB appeared in Bioinformatics, 2003.

Deep probabilistic programming

My group contributes to the deep probabilistic programming languages Pyro and NumPyro. The work below is by postdoc Ola Rønning.

• Energy conserved subsampling MCMC in NumPyro.
• Stein variational inference with Stein mixtures (EinSteinVI) in NumPyro.
• Skewed bivariate von Mises Sine distribution on the 2D-torus in Pyro and NumPyro.
  • An article on this appeared in the IEEE International Conference on Multisensor Fusion and Integration for Intelligent Systems 2021 (MFI)