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Visualisation of high-dimensional particle physics data



Di Cook, Ursula Laa

Monash University

bit.ly/ISCB-Cook



Aug 28, 2018

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High-dimensions

You can't see beyond 3D

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High-dimensions

You can't see beyond 3D

A universe of 10 dimensions

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High-dimensions

You can't see beyond 3D

A universe of 10 dimensions

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High-dimensions

You can't see beyond 3D

A universe of 10 dimensions

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High-dimensions

You can't see beyond 3D

A universe of 10 dimensions

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High-dimensions

You can't see beyond 3D

A universe of 10 dimensions

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High-dimensions

You can't see beyond 3D

A universe of 10 dimensions

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High-dimensions

You can't see beyond 3D

A universe of 10 dimensions

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High-dimensions

You can't see beyond 3D

A universe of 10 dimensions

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High-dimensions

You can't see beyond 3D

A universe of 10 dimensions

Its more like...

Flatland: A Romance of Many Dimensions (1884) Edwin Abbott Abbott

The story describes a two-dimensional world occupied by geometric figures, where women are simple line-segments, and men are polygons with various numbers of sides.

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How we see high-dimensions in statistics..

Increasing dimension adds an additional orthogonal axis.

If you want more high-dimensional shapes there is an R package, geozoo, which will generate cubes, spheres, simplices, mobius strips, torii, boy surface, enneper surface, dini surface, klein bottles, cones, various polytopes, ...

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High-dimensions

You can't see beyond 3D

A universe of 10 dimensions

Its more like...

And in statistics it is everywhere

  • Principal component analysis
  • Multidimensional scaling
  • Projection pursuit
  • Regression
  • Linear discriminant analysis
  • Multivariate distributions
  • Posterior distributions
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Can you tell the difference between these 5D objects?

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Can you tell the difference between these 5D objects?

Yep? You can see beyond 3D!

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Can you tell the difference between these 10D objects?

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Can you tell the difference between these 10D objects?

Yep? You really can see beyond 3D!

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Can you tell the difference between these 10D objects?

Yep? You really can see beyond 3D!

Set A are genes identified by Sarah Romanes multiDA procedure; set B are a random sample of genes. Sarah's selection are much more distinctly different than the random sample.

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Packages

  • Visualisation of high-dimensions using tours: the tourr package
    • Grand: Randomly choose target
    • Little: Basis of d of the p variables
    • Local: Randomly within a small radius
    • Guided: Define structure of interest in projection, and optimise function
    • Manual: Control the contribution of a single variable, and move along this axis (coming soon in the R package spinifex)
  • A library of high-dimensional shapes: the geozoo package, and paper Escape from Boxland
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Philosophy

  • It is common to show the data in the model space, for example, predicted vs observed plots for regression, linear discriminant plots, and principal components.
  • By displaying the model in the high-d data space, rather than low-d summaries of the data produced by the model, we expect to better understand the fit.

Wickham et al (2015) Visualizing statistical models: Removing the blindfold, SAM

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Hierarchical clustering

Dendrogram: data in the model space

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Model in the data space

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Summary

  • The tourr package is available for you to look beyond 2D
  • High-dimensional shapes, how they are defined, what they look like, how they differ is interesting
  • Think about ways to look at the model in the data space
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Multidimensional physics

You can read what we are doing with physics data here:

Dynamical projections for the visualization of PDFSense data

Dianne Cook, Ursula Laa, German Valencia

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Joint work!

  • Tours: Andreas Buja, Debby Swayne, Heike Hofmann, Hadley Wickham, Ursula Laa and Nick Spyrison
  • Library of high-d shapes: Barret Schloerke
  • Physics application: Ursula Laa, German Valencia
  • Animations made with plotly

Contact: dicook@monash.edu, visnut, dicook

Slides made with Rmarkdown, xaringan package by Yihui Xie, and lorikeet theme using the ochRe package. Available at https://github.com/dicook/ISCBASC2018

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Further reading

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High-dimensions

You can't see beyond 3D

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