#4 Dirichlet Processes and Neurodegenerative Diseases, with Karin Knudson

What do neurodegenerative diseases, gerrymandering and ecological inference all have in common? Well, they can all be studied with Bayesian methods — and that’s exactly what Karin Knudson is doing.

In this episode, Karin will share with us the vital and essential work she does to understand aspects of neurodegenerative diseases. She’ll also tell us more about computational neuroscience and Dirichlet processes — what they are, what they do, and when you should use them.

Karin did her doctorate in mathematics, with a focus on compressive sensing and computational neuroscience at the University of Texas at Austin. Her doctoral work included applying hierarchical Dirichlet processes in the setting of neural data and focused on one-bit compressive sensing and spike-sorting.

Formerly the chair of the math and computer science department of Phillips Academy Andover, she started a postdoc at Mass General Hospital and Harvard Medical in Fall 2019. Most importantly, rock climbing and hiking have no secrets for her!

Our theme music is « Good Bayesian », by Baba Brinkman (feat MC Lars and Mega Ran). Check out his awesome work at https://bababrinkman.com/ !  

Links from the show, personally curated by Karin Knudson:

• Karin on Twitter: https://twitter.com/karinknudson
• Spike train entropy-rate estimation using hierarchical Dirichlet process priors (Knudson and Pillow): https://pillowlab.princeton.edu/pubs/abs_Knudson_HDPentropy_NIPS13.html
• Fighting Gerrymandering with PyMC3, PyCon 2018, Colin Carroll and Karin Knudson: https://www.youtube.com/watch?v=G9I5ZnkWR0A
• Expository resources on Dirichlet Processes: Chapter 23 of Bayesian Data Analysis (Gelman et al.) and http://www.gatsby.ucl.ac.uk/~ywteh/research/npbayes/dp.pdf
• Hierarchical Dirichlet Processes (introduced the HDP and included applications in topic modeling and for working with time-series data and Hidden Markov Models): https://www.stat.berkeley.edu/~aldous/206-Exch/Papers/hierarchical_dirichlet.pdf
• A Sticky HDP-HMM with applications to speaker diarization (a nice example of how the HDP can be used with HMM, in this case cleverly adapted so that states have more persistence): https://arxiv.org/abs/0905.2592
• If you want to get deeper into the weeds and also get a sense of the history: Dirichlet Processes with Applications to Bayesian Nonparametric Problems (https://projecteuclid.org/euclid.aos/1176342871) and A Bayesian Analysis of Some Nonparametric Problems (https://projecteuclid.org/euclid.aos/1176342360)