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Bootstrap Confidence Intervals in Variants of Component Analysis. Marieke E. Timmerman 1 , Henk A.L. Kiers 1 , Age K. Smilde 2 & Cajo J.F. ter Braak 3

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Bootstrap confidence intervals in variants of component analysis

Bootstrap Confidence Intervals in Variants of Component Analysis

Marieke E. Timmerman1, Henk A.L. Kiers1, Age K. Smilde2 & Cajo J.F. ter Braak3

1Heymans Institute of Psychology, University of Groningen2Biosystems Data Analysis, University of Amsterdam3Biometris, Wageningen University The Netherlands


Some background of this work
Some background of this work Analysis

  • Validation (Harshman, 1984)

    • Theoretical appropriateness

    • Computational correctness

    • Explanatory validity

    • Statistical reliability


Some background of this work1
Some background of this work Analysis

  • Statistical reliability (Smilde, Bro & Geladi (2004) Multi-way analysis, p. 146) is related to ... the stability of solutions to resampling, choice of dimensionality and confidence intervals of the model parameters. The statistical reliability is often difficult to quantify in practical data analysis, e.g., because of small sample sets or poor distributional knowledge of the system.’


Statistical reliability
Statistical reliability Analysis

  • Model choice

    • choice of dimensionality

    • stability of solutions to resampling

  • Inference

    • stability of solutions to resampling

    • confidence intervals (CIs) of the model parameters

  • How to estimate CIs in component analysis? And what about the quality?


Confidence intervals of model parameters

Population Distribution Function F Analysis parameters θ

Observed random Sample x parameters = s(x)

Confidence Intervals (CI):

derived from sampling distribution of

Confidence intervals of model parameters


Bootstrap confidence intervals

Observed random Sample Analysisx parameters = s(x)

Empirical Distribution Function

Bootstrap Sample x* parameters = s(x*)

Bootstrap Confidence intervals

Population Distribution Function F  parameters θ


Example ci for population mean

θ Analysis=μ

Example: CI for population mean μ


Example ci for population mean1

θ Analysis=μ

Example: CI for population mean μ


Key questions for the bootstrap procedure
Key questions for the Bootstrap procedure Analysis

  • Sample drawn from which Population(s)?

  • What is s(x) exactly?

  • If s(x) is non-unique, how to make s(x*) comparable?

  • How to define EDF?

  • How to estimate CIs from distribution of ?


What s next
What’s next… Analysis

  • Principal Component Analysis

    • Various answers to the key questions

    • Simulation study: What’s the quality of the various resulting CIs?

  • Real multi-way/block methods

    • Tucker3/PARAFAC

    • Multilevel Component Analysis

    • Principal Response Curve Model


Principal component analysis
Principal Component Analysis Analysis

X (IJ): observed scores of I subjects on J variables

Z: standardized scores of X

F (IQ): Principal component scores

A (IQ): Principal loadings

Q: Number of selected principal components

T (QQ): Rotation matrix


1 sample drawn from which population s
1. Sample drawn from which Population(s)? Analysis

  • ‘observed scores of I subjects on J variables’


2 what is s x exactly
2. What is s( Analysisx) exactly?

  • Loadings:

    1.Principal loadings (AQ)

    2. Rotated loadings (AQT)

    a. Procrustes rotation towards external structure

    b. use one, fixed criterion (e.g., Varimax)

    c. search for ‘the optimal simple solution’

  • Oblique case: correlations between components

  • Variance accounted for


3 if s x is non unique how to make s x comparable
3. If s( Analysisx) is non-unique, how to make s(x*) comparable?

  • Loadings:

    1.Principal loadings (AQ)

    Sign of Principal loadings (AQ) is arbitrary:

    reflect columns ofAQ* to the same direction


1. AnalysisPrincipal loadings (AQ)

Sign of Principal loadings (AQ) is arbitrary:

reflect columns ofAQ* to the same direction


2 rotated loadings a q t
2. Rotated loadings Analysis(AQT)

a. Procrustes rotation towards external structure:

none (AQT* is unique)


2 rotated loadings a q t1
2. Rotated loadings Analysis(AQT)

b. use one, fixed criterion (e.g., Varimax)

Sign & order of Varimax rotated loadings is arbitrary:

reflect & reorder columns ofAQT*


2 rotated loadings a q t c search for the optimal simple solution
2. Rotated loadings Analysis(AQT)c. search for ‘the optimal simple solution’

  • How are bootstrap solutions AQT* found?

    • For each bootstrap solution: look for ‘optimal simple loadings’ (unfeasible): reflect & reorder columns ofAQT*

    • Procrustes rotation towards ‘optimally simple’ sample loadings: none (AQT* is unique)


Procrustes rotated Analysisbootstrap solutions

Varimax rotated bootstrap solutions

‘Fixed criterion’ versus ‘Procrustes towards (simple) sample loadings’

Instable varimax rotated solutions over samples?


4 how to define the edf
4. How to define the EDF? Analysis

  • non-parametric: Xb: rowwise resampling of Z

  • semi-parametric:

  • parametric:elements of Xb from particular p.d.f.



  • Based on bootstrap standard error (se*)


  • percentile method

  • BCa method (Bias Corrected and Accelerated, corrects for potential Bias and skewness of bootstrap distribution)


Quality of ci coverage
Quality of CI? Analysis Coverage

θ

  • central 1-2αCI: [CIleft;CIright)

  • P(θ<CIleft)= α P(θ>CIright)= αwith θ population parameter


  • But, what is the population parameter θ? Analysis

    • Results from PCA on population data

    • Orientation Population loadings should match Bootstrap loadings…

      1. Principal loadings (AQ*)

      2. Rotated loadings (AQT*)

      a. Procrustes rotation towards external structure

      b. use one, fixed criterion (e.g., Varimax)

      c. search for ‘the optimal simple solution’

      -B searches for optimal simple loadings-Procrustes rotation towards ‘optimally simple’ sample loadings

  • Bootstrap Varimax

  • Bootstrap Procrustes


Simulation study
Simulation study Analysis

  • CI’s for Varimax rotated Sample loadings

  • Data properties varied:

    • VAF in population (0.8,0.6,0.4)

    • number of variables (8, 16)

    • sample size (50, 100, 500)

    • distribution of component scores (normal, leptokurtic, skew)

    • simplicity of loading matrix (simple, halfsimple, complex)

  • Design completely crossed, 1000 replicates per cell


Simplicity of loading matrix Analysis

Stability of Varimax solution of samples


Quality criteria for 95 ci s p ci left p ci right
Quality criteria for 95%CI’s AnalysisP(θ<CIleft)= α P(θ>CIright)= α

  • 95%coverage(1-prop(θ<CIleft)-prop(θ>CIright))*100%

  • Exceeding Percentage (EP) ratioprop(θ<CIleft)/prop(θ>CIright)


Ep ratio symmetry of coverage
EP ratio (symmetry of coverage) Analysis

  • Bootstrap CI’s: Wald, Percentile, BCa

  • In case of skew statistic distributions (i.e., high loadings, small sample size):

    • BCa by far best

    • Wald performs poor (bootstrap & asymptotic)

  • Other conditions: hardly any differences



Key questions for the bootstrap procedure1
Key questions for the Bootstrap procedure Analysis

  • Sample drawn from which Population(s)?

  • What is s(x) exactly?

  • If s(x) is non-unique, how to make s(x*) comparable?

  • How to define EDF?

  • How to estimate CIs from distribution of ?


Real multi way methods
Real multi-way methods Analysis

  • Sample drawn from which Population(s)?

    Which mode(s) are considered fixed, which are random?

    Examples:

  • subjects, measurement occasions, variables

  • measurement occasions (of one subject), variables, situations

  • judges, food types, variables

  • Tucker3/PARAFAC


Tucker3 parafac
Tucker3/PARAFAC Analysis

2. What is s(x) exactly?

T3: Component matrices, for fixed modes only. Core matrix. Possibly after rotation…

PF: Component matrices, for fixed modes only.

3. If s(x) is non-unique, how to make s(x*) comparable?

T3: Depends on view on rotation…

PF: Reflect and reorder


Multi block methods

... Analysis

...

...

...

Multi-block methods

  • Multilevel Component Analysis, for hierarchically ordered multivariate data

  • Examples:

    • inhabitants within different countries

    • measurement occasions within different subjects


National Analysis

character

Weighted PCA

  • (Dis)similarities

  • between inhabitants

  • within each country

Simultaneous

Component Analysis


  • Sample drawn from which population(s)? Analysis

    Which mode(s) are considered fixed,

    which are random?

  • inhabitants within different countries

  • measurement occasions within different subjects

  • pupils within classes


Another multi block method
Another multi-block method Analysis

  • Principal response curve model for longitudinal multivariate data, obtained from objects within experimental conditions

  • ‘How is the development over time influenced by the experimental conditions?’




  • Results from a simulation experiment: Analysis

    • BCa confidence bands quality improves

      • with decreasing replicate variation, and simpler error structures

      • with increasing sample size

      • ...but even sample size of 20 replicates per condition generally yields satisfactory results


To conclude
To conclude Analysis

  • How to estimate CIs in component analysis?

    • Use the bootstrap!

    • 5 Key questions for the Bootstrap procedure

      • uniqueness of sample solution?

      • which modes are random/fixed?

      • ...

  • And what is the quality?

    • Generally reasonable


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