Gaussian processes

• Great methods tutorial/overview with Steve. Now getting up to speed on background reading in both Gaussian processes and embedding dimensions.
  
• Will also want to look into basis approximations for SDP acceleration.

Gaussian Processes

• New project, New tag: nonparametric-bayes, and associated github repostitory

Reading

• Rasmussen & Williams (2006) 2nd ed, full text avialable online. read Ch 1 & 2.

Can be thought of as a Bayesian version of Support Vector Machines

Who knew? Working through basic regression scenarios.

Also reading:

• Deisenroth, M. P., Rasmussen, C. E., & Peters, J. (2009). Gaussian process dynamic programming. Neurocomputing, 72(7-9), 1508-1524. doi:10.1016/j.neucom.2008.12.019
• Kocijan, J., & Girard, A. (2005). Dynamic systems identification with Gaussian processes. … of Dynamical Systems. doi:10.1080/13873950500068567
• Turner, R. (2010). State-space inference and learning with Gaussian processes. Proceedings of 13th …, 868-875.

R support:

• gausspr, see also the package vignette (From the core team, probably a reasonable starting point).
• gptk (crude choice, poor software development practices)
• mlegp
• manually (e.g. for learning rather than performance)

Embedding dimensions

• Taken’s Theorem But how about the stochastic case?
• Convergent cross-mapping paper, Sugihara et al. 2012, recently in Science.
  
• Stochastic Takens: perhaps see Stark et al 2003, doi:10.1007/s00332-003-0534-4

rOpenSci

• Checked ritis, Scott submitted to CRAN
• More requests for increased functionality on rfishbase
• Contact with Roy about developing an API for FishBase. Contacted Deng
• httr 0.2 is on CRAN! Updated rfigshare dependency, plan to release soon.

Notebook

• Contacted Ben about documentation and use of EML.
  
• Posted updated semantic notebook
• Hmm, FOAF person types don’t seem to contain enough data to be valid Person objects according to Google Rich Snippets. Unfortunately this cannot be easily solved by mixing “Person” types. Note that Dublin Core and FOAF agree on what a person/agent is, but it seems data-vocabulary.org rdf does not?
• Tools for discovery and navigating ontologies? https://www.ebi.ac.uk/ontology-lookup/