1. Object Orie’d Data Analysis, Last Time PCA Redistribution of Energy - ANOVA PCA Data Representation PCA Simulation Alternate PCA Computation Primal – Dual PCA vs. SVD (centering by means is key)

2. Primal - Dual PCA Toy Example 1: Random Curves, all in Primal Space: * Constant Shift * Linear * Quadratic Cubic (chosen to be orthonormal) Plus (small) i.i.d. Gaussian noise d = 40, n = 20

3. Primal - Dual PCA Toy Example 1: Raw Data

4. Primal - Dual PCA Toy Example 1: Raw Data Primal (Col.) curves similar to before Data mat ’ x asymmetric (but same curves) Dual (Row) curves much rougher (showing Gaussian randomness) How data were generated Color map useful? (same as mesh view) See richer structure than before Is it useful?

5. Primal - Dual PCA Toy Example 1: Primal PCA Column Curves as Data

6. Primal - Dual PCA Toy Example 1: Primal PCA Expected to recover increasing poly ’ s But didn ’ t happen Although can see the poly ’ s (order???) Mean has quad ’ ic (since only n = 20???) Scores (proj ’ ns) very random Power Spectrum shows 4 components (not affected by subtracting Primal Mean)

7. Primal - Dual PCA Toy Example 1: Dual PCA Row Curves as Data

8. Primal - Dual PCA Toy Example 1: Dual PCA Curves all very wiggly (random noise) Mean much bigger, 54% of Total Var! Scores have strong smooth structure (reflecting ordered primal e.v. ’ s) (recall primal e.v.  dual scores) Power Spectrum shows 3 components (Driven by subtraction Dual Mean) Primal – Dual mean difference is critical

9. Primal - Dual PCA Toy Example 1: Dual PCA – Scatterplot

10. Primal - Dual PCA Toy Example 1: Dual PCA - Scatterplot Smooth Curve Structure But not usual curves (Since 1-d curves not quite poly ’ s) And only in 1 st 3 components –Recall only 3 non-noise components –Since constant curve went into mean (dual) Remainder is pure noise Suggests wrong rotation of axes???

11. Primal - Dual PCA A 3 rd Type of Analysis: Called “ SVD decomposition ” Main point: subtract neither mean Viewed as a serious competitor Advantage: gives best Mean Square Approximation of Data Matrix Vs. Primal PCA: best about col. Mean Vs. Dual PCA: best about row Mean Difference in means is critical!

12. Primal - Dual PCA Toy Example 1: SVD – Curves view

13. Primal - Dual PCA Toy Example 1: SVD Curves View Col. Curves view similar to Primal PCA Row Curves quite different (from dual): –Former mean, now SV1 –Former PC1, now SV2 –i.e. very similar shapes with shifted indices Again mean centering is crucial Main difference between PCAs and SVD

14. Primal - Dual PCA Toy Example 1: SVD – Mesh-Image View

15. Primal - Dual PCA Toy Example 1: SVD Mesh-Image View Think about decomposition into modes of variation –Constant x Gaussian –Linear x Gaussian –Cubic by Gaussian –Quadratic Shows up best in image view? Why is ordering “ wrong ” ???

16. Primal - Dual PCA Toy Example 1: All Primal Why is SVD mode ordering “ wrong ” ??? Well, not expected … Key is need orthogonality Present in space of column curves But only approximate in row Gaussians The implicit orthogonalization of SVD (both rows and columns) gave mixture of the poly ’ s.

17. Primal - Dual PCA Toy Example 2: All Primal, GS Noise Started with same column space Generated i.i.d. Gaussians for row cols Then did Graham-Schmidt Ortho- normalization (in row space) Visual impression: Amazingly similar to original data (used same seeds of random # generators)

18. Primal - Dual PCA Toy Example 2: Raw Data

19. Primal - Dual PCA Compare with Earlier Toy Example 1

20. Primal - Dual PCA Toy Example 2: Primal PCA Column Curves as Data Shows Explanation (of wrong components) was correct

21. Primal - Dual PCA Toy Example 2: Dual PCA Row Curves as Data Still have big mean But Scores look much better

22. Primal - Dual PCA Toy Example 2: Dual PCA – Scatterplot

23. Primal - Dual PCA Toy Example 2: Dual PCA - Scatterplot Now poly ’ s look beautifully symmetric Much like chemo spectrum examples But still only 3 –Same reason, dual mean ~ primal constants Last one is pure noise

24. Primal - Dual PCA Toy Example 2: SVD – Matrix-Image

25. Primal - Dual PCA Toy Example 2: SVD - Matrix-Image Similar Good Effects Again have all 4 components So “ better ” to not subtract mean???

26. Primal - Dual PCA Toy Example 3: Random Curves, all in Dual Space: 1 * Constant Shift 2 * Linear 4 * Quadratic 8 * Cubic (chosen to be orthonormal) Plus (small) i.i.d. Gaussian noise d = 40, n = 20

27. Primal - Dual PCA Toy Example 3: Raw Data

28. Primal - Dual PCA Toy Example 3: Raw Data Similar Structure to e.g. 1 But Rows and Columns trade places And now cubics visually dominant (as expected)

29. Primal - Dual PCA Toy Example 3: Primal PCA Column Curves as Data Gaussian Noise Only 3 components Poly Scores (as expected)

30. Primal - Dual PCA Toy Example 3: Dual PCA Row Curves as Data Components as expected No Gram-Schmidt (since stronger signal)

31. Primal - Dual PCA Toy Example 3: SVD – Matrix-Image

32. Primal - Dual PCA Toy Example 4: Mystery #1

33. Primal - Dual PCA Toy Example 4: SVD – Curves View

34. Primal - Dual PCA Toy Example 4: SVD – Matrix-Image

35. Primal - Dual PCA Toy Example 4: Mystery #1 Structure: Primal - Dual Constant Gaussian Gaussian Linear Parabola Gaussian Gaussian Cubic Nicely revealed by Full Matrix decomposition and views

36. Primal - Dual PCA Toy Example 5: Mystery #2

37. Primal - Dual PCA Toy Example 5: SVD – Curves View

38. Primal - Dual PCA Toy Example 5: SVD – Matrix-Image

39. Primal - Dual PCA Toy Example 5: Mystery #2 Structure: Primal - Dual Constant Linear Parabola Cubic Gaussian Gaussian Visible via either curves, or matrices …

40. Primal - Dual PCA Is SVD (i.e. no mean centering) always “ better ” ? What does “ better ” mean??? A definition: Provides most useful insights into data Others???

41. Primal - Dual PCA Toy Example where SVD is less informative: Simple Two dimensional Key is subtraction of mean is bad I.e. Mean dir ’ n different from PC dir ’ ns And Mean Less Informative

42. Primal - Dual PCA Toy Example where SVD is less informative: Raw Data

43. Primal - Dual PCA PC1 mode of variation (centered at mean): Yields useful major mode of variation

44. Primal - Dual PCA PC2 mode of variation (centered at mean): Informative second mode of variation

45. Primal - Dual PCA SV1 mode of variation (centered at 0): Unintuitive major mode of variation

46. Primal - Dual PCA SV2 mode of variation (centered at 0): Unintuitive second mode of variation

47. Primal - Dual PCA Summary of SVD: Does give a decomposition I.e. sum of two pieces is data But not good insights about data structure Since center point of analysis is far from center point of data So mean strongly influences the impression of variation Maybe better to keep these separate???

48. Primal - Dual PCA Bottom line on: Primal PCA vs. SVD vs. Dual PCA These are not comparable: Each has situations where it is “ best ” And where it is “ worst ” Generally should consider all And choose on basis of insights See work of Lingsong Zhang on this …

49. Real Data: Primal - Dual PCA Analysis by: Lingsong Zhang Zhang, L., (2006), "SVD movies and plots for Singular Value Decomposition and its Visualization", University of North Carolina at Chapel Hill, available at http://www.unc.edu/~lszhang/research/net work/SVDmovie

50. Real Data: Primal - Dual PCA Use slides from a talk: LingsongZhangFunctionalSVD.pdf Main Points: Different approaches all can be “best” Show different aspects of data Generalized SCREE ploy “outliers” are interesting

51. Real Data: Primal - Dual PCA Visual Point: Rotations can show useful aspects Movies: LingsongZhangSVDcurvemovie4int30m.avi LingsongZhangSVDMOVIEbyCOMPofSV1.avi LingsongZhangSVDMOVIEbyCOMPofSV2.avi LingsongZhangSVDMOVIEbyCOMPofSV3.avi

52. Vectors vs. Functions Recall overall structure: Object Space Feature Space Curves (functions) Vectors Connection 1: Digitization Parallel Coordinates Connection 2: Basis Representation

53. Vectors vs. Functions Connection 1: Digitization: Given a function, define vector Where is a suitable grid, e.g. equally spaced:

54. Vectors vs. Functions Connection 1: Parallel Coordinates: Given a vector, define a function where And linearly interpolate to “ connect the dots ” Proposed as High Dimensional Visualization Method by Inselberg (1985)

55. Vectors vs. Functions Parallel Coordinates: Given, define Now can “ rescale argument ” To get function on [0,1], evaluated at equally spaced grid

56. Vectors vs. Functions Bridge between vectors & functions: Vectors  Functions Isometry follows from convergence of: Inner Products By Reimann Summation

57. Vectors vs. Functions Main lesson: -OK to think about functions -But actually work with vectors For me, there is little difference But there is a statistical theory, and mathematical statistical literature on this Start with Ramsay & Silverman (2005)

58. Vectors vs. Functions Recall overall structure: Object Space Feature Space Curves (functions) Vectors Connection 1: Digitization Parallel Coordinates Connection 2: Basis Representation

59. Vectors vs. Functions Connection 2: Basis Representations: Given an orthonormal basis (in function space) E.g. –Fourier –B-spline –Wavelet Represent functions as:

60. Vectors vs. Functions Connection 2: Basis Representations: Represent functions as: Bridge between discrete and continuous:

61. Vectors vs. Functions Connection 2: Basis Representations: Represent functions as: Finite dimensional approximation: Again there is mathematical statistical theory, based on (same ref.)

62. Vectors vs. Functions Repeat Main lesson: -OK to think about functions -But actually work with vectors For me, there is little difference (but only personal taste)