I only skimmed the notebook, but the code looks fairly inadequate. The pandas portion, for instance, treats the data frame as a dumb array and critically ignores grouping functionality which should offer a tremendous speedup. Moreover, for the exact same task pandas should never be slower than NumPy.
Benchmarks are hard to get right but this one falls way short of saying anything at all about performance penalties incurred by various libraries and abstractions.
Benchmarks are hard to get right but this one falls way short of saying anything at all about performance penalties incurred by various libraries and abstractions.