2. 1 Peter Fox Data Analytics – 4600/6600 Week 9a, March 29, 2016 Dimension reduction and MD scaling, Support Vector Machines

3. Paid opportunity… 2pm Fri A small medical practice in Troy is considering opening a branch office in the Capital Region. They would like some GIS analysis to assist them in evaluating options for the location of the 2nd office. Considerations would include demographics (with weighting by age), location of competitors (approximately 6), and drive-time analysis. They are open to considering other layers that might be suggested by the person(s) setting up the model. 2

4. Dimension reduction.. Principle component analysis (PCA) and metaPCA (in R) Singular Value Decomposition Feature selection, reduction Built into a lot of clustering Why? –Curse of dimensionality – or – some subset of the data should not be used as it adds noise What is it? –Various methods to reach an optimal subset 3

5. Simple example 4

6. More dimensions 5

7. Feature selection The goodness of a feature/feature subset is dependent on measures Various measures –Information measures –Distance measures –Dependence measures –Consistency measures –Accuracy measures 6

8. On your own… library(EDR) # effective dimension reduction library(dr) library(clustrd) install.packages("edrGraphicalTools") library(edrGraphicalTools) demo(edr_ex1) demo(edr_ex2) demo(edr_ex3) demo(edr_ex4) 7

9. Some examples Lab8b_dr1_2016.R Lab8b_dr2_2016.R Lab8b_dr3_2016.R Lab8b_dr4_2016.R 8

10. Multidimensional Scaling Visual representation ~ 2-D plot - patterns of proximity in a lower dimensional space "Similar" to PCA/DR but uses dissimilarity as input - > dissimilarity matrix –An MDS algorithm aims to place each object in N- dimensional space such that the between-object distances are preserved as well as possible. –Each object is then assigned coordinates in each of the N dimensions. –The number of dimensions of an MDS plot N can exceed 2 and is specified a priori. –Choosing N=2 optimizes the object locations for a two- dimensional scatterplot 9

11. Four types of MDS Classical multidimensional scaling –Also known as Principal Coordinates Analysis, Torgerson Scaling or Torgerson–Gower scaling. Takes an input matrix giving dissimilarities between pairs of items and outputs a coordinate matrix whose configuration minimizes a loss function called strain. Metric multidimensional scaling –A superset of classical MDS that generalizes the optimization procedure to a variety of loss functions and input matrices of known distances with weights and so on. A useful loss function in this context is called stress, which is often minimized using a procedure called stress majorization. 10

12. Four types of MDS ctd Non-metric multidimensional scaling –In contrast to metric MDS, non-metric MDS finds both a non-parametric monotonic relationship between the dissimilarities in the item-item matrix and the Euclidean distances between items, and the location of each item in the low-dimensional space. The relationship is typically found using isotonic regression. Generalized multidimensional scaling –An extension of metric multidimensional scaling, in which the target space is an arbitrary smooth non-Euclidean space. In cases where the dissimilarities are distances on a surface and the target space is another surface, GMDS allows finding the minimum-distortion embedding of one surface into another. 11

13. In R function (library) cmdscale() (stats) smacofSym() (smacof) wcmdscale() (vegan) pco() (ecodist) pco() (labdsv) pcoa() (ape) Only stats is loaded by default, and the rest are not installed by default 12

14. cmdscale() cmdscale(d, k = 2, eig = FALSE, add = FALSE, x.ret = FALSE) d - a distance structure such as that returned by dist or a full symmetric matrix containing the dissimilarities. k - the maximum dimension of the space which the data are to be represented in; must be in {1, 2, …, n-1}. eig - indicates whether eigenvalues should be returned. add - logical indicating if an additive constant c* should be computed, and added to the non-diagonal dissimilarities such that the modified dissimilarities are Euclidean. x.ret - indicates whether the doubly centred symmetric distance matrix should be returned. 13

15. Distances between Australian cities row.names(dist.au) <- dist.au[, 1] dist.au <- dist.au[, -1] dist.au ## A AS B D H M P S ## A 0 1328 1600 2616 1161 653 2130 1161 ## AS 1328 0 1962 1289 2463 1889 1991 2026 ## B 1600 1962 0 2846 1788 1374 3604 732 ## D 2616 1289 2846 0 3734 3146 2652 3146 ## H 1161 2463 1788 3734 0 598 3008 1057 ## M 653 1889 1374 3146 598 0 2720 713 ## P 2130 1991 3604 2652 3008 2720 0 3288 ## S 1161 2026 732 3146 1057 713 3288 0 14

16. Distances between Australian cities fit <- cmdscale(dist.au, eig = TRUE, k = 2) x <- fit$points[, 1] y <- fit$points[, 2] plot(x, y, pch = 19, xlim = range(x) + c(0, 600)) city.names <- c("Adelaide", "Alice Springs", "Brisbane", "Darwin", "Hobart", "Melbourne", "Perth", "Sydney") text(x, y, pos = 4, labels = city.names) 15

17. 16

18. R – many ways (of course) library(igraph) g <- graph.full(nrow(dist.au)) V(g)$label <- city.names layout <- layout.mds(g, dist = as.matrix(dist.au)) plot(g, layout = layout, vertex.size = 3) 17

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20. On your own (Friday) Lab8b_mds1_2016.R Lab8b_mds2_2016.R Lab8b_mds3_2016.R http://www.statmethods.net/advstats/mds.htm lhttp://www.statmethods.net/advstats/mds.htm l http://gastonsanchez.com/blog/how- to/2013/01/23/MDS-in-R.htmlhttp://gastonsanchez.com/blog/how- to/2013/01/23/MDS-in-R.html 19

21. Support Vector Machine Conceptual theory, formulae… SVM - general (nonlinear) classification, regression and outlier detection with an intuitive model representation Hyperplanes separate the classification spaces (can be multi-dimensional) Kernel functions can play a key role 20

22. Schematically 21 http://en.wikipedia.org/wiki/File:Svm_separating_hyperplanes_(SVG).svg

23. Schematically 22 http://en.wikipedia.org/wiki/File:Svm_max_sep_hyperplane_with_margin.png b=bias term, b=0 (unbiased) Support Vectors

24. Construction Construct an optimization objective function that is inherently subject to some constraints –Like minimizing least square error (quadratic) Most important: the classifier gets the points right by “at least” the margin Support Vectors can then be defined as those points in the dataset that have "non zero” Lagrange multipliers*. –make a classification on a new point by using only the support vectors – why? 23

25. Support vectors Support the “plane” 24

26. What about the “machine” part Ignore it – somewhat leftover from the “machine learning” era –It is trained and then –Classifies 25

27. No clear separation = no hyperplane? 26 Soft-margins…Non-linearity or transformation

28. Feature space 27 Mapping (transformation) using a function, i.e. a kernel  goal is – linear separability

29. Kernels or “non-linearity”… 28 the kernel function, represents a dot product of input data points mapped into the higher dimensional feature space by transformation phi + note presence of “gamma” parameter http://www.statsoft.com/Textbook/Support-Vector-Machines

30. Best Linear Separator: Supporting Plane Method Maximize distance Between two parallel supporting planes Distance = “Margin” =

31. Soft Margin SVM Just add non-negative error vector z.

32. Method 2: Find Closest Points in Convex Hulls c d

33. Plane Bisects Closest Points d c

34. Find using quadratic program Many existing and new QP solvers.

35. Dual of Closest Points Method is Support Plane Method Solution only depends on support vectors:

36. One bad example? Convex Hulls Intersect! Same argument won’t work.

37. Don’t trust a single point! Each point must depend on at least two actual data points.

38. Depend on >= two points Each point must depend on at least two actual data points.

39. Depend on >= two points Each point must depend on at least two actual data points.

40. Depend on >= two points Each point must depend on at least two actual data points.

41. Depend on >= two points Each point must depend on at least two actual data points.

42. Final Reduced/Robust Set Each point must depend on at least two actual data points. Called Reduced Convex Hull

43. Reduced Convex Hulls Don’t Intersect Reduce by adding upper bound D

44. Find Closest Points Then Bisect No change except for D. D determines number of Support Vectors.

45. Dual of Closest Points Method is Soft Margin Method Solution only depends on support vectors:

46. What will linear SVM do?

47. Linear SVM Fails

48. High Dimensional Mapping trick http://www.slideshare.net/ankitksh arma/svm-37753690

50. Nonlinear Classification: Map to higher dimensional space IDEA: Map each point to higher dimensional feature space and construct linear discriminant in the higher dimensional space. Dual SVM becomes:

51. Kernel Calculates Inner Product

52. Final Classification via Kernels The Dual SVM becomes:

53. Generalized Inner Product By Hilbert-Schmidt Kernels (Courant and Hilbert 1953) for certain  and K, e.g. Also kernels for nonvector data like strings, histograms, dna,…

54. Solve Dual SVM QP Recover primal variable b Classify new x Final SVM Algorithm Solution only depends on support vectors :

55. SVM AMPL DUAL MODEL

57. S5: Recal linear solution

58. RBF results on Sample Data

59. Have to pick parameters Effect of C

60. Effect of RBF parameter

61. General Kernel methodology Pick a learning task Start with linear function and data Define loss function Define regularization Formulate optimization problem in dual space/inner product space Construct an appropriate kernel Solve problem in dual space

62. kernlab, svmpath and klaR http://escience.rpi.edu/data/DA/v15i09.pdfhttp://escience.rpi.edu/data/DA/v15i09.pdf Work through the examples –Familiar datasets and samples procedures from 4 libraries (these are the most used) –kernlab –e1071 –svmpath –klaR 61 Karatzoglou et al. 2006

63. Application of SVM Classification, outlier, regression… Can produce labels or probabilities (and when used with tree partitioning can produce decision values) Different minimizations functions subject to different constraints (Lagrange multipliers) Observe the effect of changing the C parameter and the kernel 62 See Karatzoglou et al. 2006

64. Types of SVM (names) Classification SVM Type 1 (also known as C- SVM classification) Classification SVM Type 2 (also known as nu-SVM classification) Regression SVM Type 1 (also known as epsilon-SVM regression) Regression SVM Type 2 (also known as nu- SVM regression) 63

65. More kernels 64 Karatzoglou et al. 2006

66. Timing 65 Karatzoglou et al. 2006

67. Library capabilities 66 Karatzoglou et al. 2006

68. Extensions Many Inference Tasks –Regression –One-class Classification, novelty detection –Ranking –Clustering –Multi-Task Learning –Learning Kernels –Cannonical Correlation Analysis –Principal Component Analysis

69. Algorithms Algorithms Types: General Purpose solvers –CPLEX by ILOG –Matlab optimization toolkit Special purpose solvers exploit structure of the problem –Best linear SVM take time linear in the number of training data points. –Best kernel SVM solvers take time quadratic in the number of training data points. Good news since convex, algorithm doesn’t really matter as long as solvable.

70. Hallelujah! Generalization theory and practice meet General methodology for many types of inference problems Same Program + New Kernel = New method No problems with local minima Few model parameters. Avoids overfitting Robust optimization methods. Applicable to non-vector problems. Easy to use and tune Successful Applications BUT…

71. Catches Will SVMs beat my best hand-tuned method Z on problem X? Do SVMs scale to massive datasets? How to chose C and Kernel? How to transform data? How to incorporate domain knowledge? How to interpret results? Are linear methods enough?