Last updated: 2020-08-07

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Rmd 8971c77 Jason Willwerscheid 2020-08-07 workflowr::wflow_publish(“analysis/tree_literature.Rmd”)

This note serves to collect papers and ideas that we’ve discussed as a group.

Ways to do FA:

  • Drift
  • Straight-up flash on a covariance matrix
  • Flash as a penalized approach, constraining L = F (cf. Youngseok’s work on mr.ash)
  • A “greedy” version of drift: update \(q(f_k | f_{-k})\) and \(q(l_k)\) iteratively, keeping \(q(f_{-k})\) and \(q(l_{-k})\) fixed

To get trees:

  • Flash with three-pointmass priors
  • Spectral clustering
  • Peter’s “minimax” projection
  • MILP techniques

Papers:

Yan, Patterson, and Narasimhan, “miqoGraph: Fitting admixture graphs using mixed-integer quadratic optimization”

Rohe and Zeng, “Vintage Factor Analysis with Varimax Performs Statistical Inference” (2020)

  • Reconsiders PCA with varimax rotations.

Cabreros and Story, “A Likelihood-Free Estimator of Population Structure Bridging Admixture Models and Principal Components Analysis” (2019)

  • The ALStructure paper.

Lawson, van Dorp, and Falush, “A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots” (2018)

  • The badMIXTURE paper.

Hensman, Rattray, and Lawrence, “Fast Variational Inference in the Conjugate Exponential Family” (2012)

  • Joe used ideas from this paper for a Collapsed VI algorithm.

Nakajima and Sugiyama, “Theoretical Analysis of Bayesian Matrix Factorization” (2011)

  • Basically EBMF with normal priors.

Zhang et al, “Phylogeny Inference Based on Spectral Graph Clustering” (2011)

Bravo et al, “Estimating Tree-Structured Covariance Matrices via Mixed-Integer Programming” (2009)

Lee, Nadler, and Wasserman, “TREELETS—AN ADAPTIVE MULTI-SCALE BASIS FOR SPARSE UNORDERED DATA” (2008)

McCullagh, “Structured covariance matrices in multivariate regression models” (2006)

  • “Minimax” projections to get trees from covariance matrices.

Felsenstein, “Confidence Limits on Phylogenies: An Approach Using the Bootstrap” (1985)



sessionInfo()
R version 3.5.3 (2019-03-11)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
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loaded via a namespace (and not attached):
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[17] yaml_2.2.0      compiler_3.5.3  htmltools_0.3.6 knitr_1.22