David Knowles

	Department of Engineering Computational and Biological Learning Lab

University of Cambridge > Department of Engineering > Information Engineering > Computational and Biological Learning Lab > David Knowles

David Knowles

I'm a PhD student with Zoubin Ghahramani in the Machine Learning group of the Cambridge University Engineering Department. My undergraduate degree compromised two years of Physics before switching to Engineering to complete an MEng with Zoubin. I took the MSc Bioinformatics and Systems Biology at Imperial College in 2007/8.
My research involves applying machine learning methods to data analysis problems in biology.
You can download (an out of date version of) my CV here.

Publications

Finale Doshi, David Knowles, Shakir Mohamed and Zoubin Ghahramani (2009)
Large Scale Non-parametric Inference: Data Parallelisation in the Indian Buffet Process. pdf
In NIPS 2009, 7-12 December 2009, Vancouver, BC, Canada.
Knowles, D. and Ghahramani, Z. (2007)
Infinite Sparse Factor Analysis and Infinite Independent Components Analysis. pdf
In 7th International Conference on Independent Component Analysis and Signal Separation (ICA 2007).
Lecture Notes in Computer Science Series (LNCS). Springer.

Reports

Statistical tools for ulta-deep pyrosequencing of fast evolving viruses (2008) pdf
MSc Bioinformatics and Systems Biology, Imperial College London, Individual Project
Supervisor: Professor Susan Holmes, Stanford University
SBML-ABC: a package for data simulation, parameter inference and model selection, Group Report (2008) pdf
MSc Bioinformatics and Systems Biology, Imperial College London, Group Project
Supervisor: Professor Michael Stumpf
Infinite Independent Components Analysis (2007) pdf
MEng Information Engineering, Cambridge University, 4th year project
Supervisor: Professor Zoubin Ghahramani
Real Time Continuous Curvature Path Planner for an Autonomous Vehicle in an Urban Environment (2006) pdf
Summer Undergraduate Research Fellowship, Caltech. I was a member of Team Caltech, an entry into the DARPA Urban Challenge
Supervisor: Professor Richard Murray

Presentations

I gave a brief presentation at Microsoft Research summarising some recent attempts to improve inference in nonparametric Bayesian models. The slides are here.

Misc

Binomial p-values

Regarding my work on 454 pyrosequencing error rates with Professor Holmes this summer, I was recently asked about how to calculate a p-value for comparing two draws from a Binomial distribution to test the hypothesis that the number of substitutions seen in the sample is significantly greater than the number of substitutions seen in the control. There is actually no need to use the Poisson approximation, and the Binomial distribution very naturally takes care of varying coverage. I explain my approach here.

Emacs for Dummies

A few notes on using Emacs for Unix non-gurus.

Blog

I got jealous that Jurgen has a blog, so I've started one too, here. We have a plan to start a MLG blog as well, the "Junction Tree", but I think that's going to wait until January. The latest posts are...

Contact details

Tel. 07728441989
E-mail: dak33 at cam dot ac dot uk
Mail: Wolfson College, Cambridge, CB3 9BB

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