# Test Dimension Reduction (DR) and Multi-Dimensional Scaling (MDS), Support Vector Machines (SVM) Peter Fox Data Analytics ITWS-4600/6600/MATP-4450 Group 3 Module 8, February 26, 2018 1 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 2 Simple example 3

More dimensions 4 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 5

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 Ndimensional 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 twodimensional scatterplot 6

Four types of MDS Classical multidimensional scaling Also known as Principal Coordinates Analysis, Torgerson Scaling or TorgersonGower 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. 7 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. 8 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 9 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. 10 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 11 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) 12 13 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) 14 15 Support Vector Machine Conceptual theory, formulae see Reading! 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 16 Schematically 17 http://en.wikipedia.org/wiki/File:Svm_separating_hyperplanes_(SVG).svg Schematically Support Vectors

18 b=bias term, b=0 (unbiased) http://en.wikipedia.org/wiki/File:Svm_max_sep_hyperplane_with_margin.png 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? 19 Support vectors Support the plane 20 What about the machine part Ignore it somewhat leftover from the

machine learning era It is trained and then Classifies 21 No clear separation = no hyperplane? Soft-margins Non-linearity or transformation 22

Feature space Mapping (transformation) using a function, i.e. a kernel goal is linear separability 23 Kernels or non-linearity http://www.statsoft.com/Textbook/Support-Vector-Machines 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

24 Best Linear Separator: Supporting Plane Method Maximize distance Between two parall supporting planes x w b 1 x w b 1 Distance

= 2 Margin = || w || Soft Margin SVM Just add non-negative error vector z. min w ,b , z s.t

1 2 2 || w || C zi i 1 zi 1 yi xi w b zi 0 i 1,.., N Method 2: Find Closest Points in

Convex Hulls d c Plane Bisects Closest Points x w b w d c d c Find using quadratic program 1 2

min ,c , d c i xi i 1 s.t. i 1 i1

i 0 d c 2 d i xi i1 1 i i 1

i 1,..., N Many existing and new QP solvers. Dual of Closest Points Method is Support Plane Method min s.t. 2 1

yi i xi || || 2 i 1 i 1 i 1 i1 min w ,b s.t. i 1

0 i 1,.., olution only depends on support vectors: w yi i xi i 1 2 1 w|| ||

2 yi xi w b 1 i 0 1 i Class 1 yi : 1 i Class 1 One bad example? Convex Hulls Intersect! Same argument wont work.

Dont trust a single point! Each point must depend on at least two actual data points. Depend on >= two points Each point must depend on at least two actual data points. Depend on >= two points Each point must depend on at least two actual data points. Depend on >= two points

Each point must depend on at least two actual data points. Depend on >= two points Each point must depend on at least two actual data points. Final Reduced/Robust Set Each point must depend on at least two actual data points. Called Reduced Convex Hull Reduced Convex Hulls Dont Intersect

d i xi iClass1 i 1 iClass1

0 i D D 1 2 Reduce by adding upper bound D Find Closest Points Then Bisect min s.t.

1 2 || i xi i1 i 1 i1

2 x || i i i 1 i 1 0 i D

No change except for D. D determines number of Support Vectors. i 1 Dual of Closest Points Method is Soft Margin Method min s.t.

2 1 yi i xi || || 2 i 1 i 1 i 1 i1 min w ,b s.t.

2 1 w|| C zi || 2 i 1 zi 1 yi xi w b i 1 D i 0

zi 0 olution only depends on support vectors: N w yi i xi i 1 i 1,.., N i 0 What will linear SVM do?

Linear SVM Fails High Dimensional Mapping trick http://www.slideshare.net/ankitksh arma/svm-37753690 Nonlinear Classification: Map to higher dimensional space Map each point to higher dimensional feature space and uct linear discriminant in the higher dimensional space.

Define : ( x) : R p R p ' p ' p Dual SVM becomes: min s.t. 1 2

N N y y ( x ) ( x i i 1 j i j

i j 1 y i i 0

i 1 C i 0 i 1, .., j ) N i i

Kernel Calculates Inner Product u [u1 , u2 ] (u) ( v ) u12 , u22 , 2u1u2 v12 , v22 , u12 v12 u22 v22 2u1u2 v1v2 u1v1 u2 v2 u v Thus: 2

2 K (u, v ) u v 2 2v1v2 Final Classification via Kernels The Dual SVM becomes: min

s.t. 1 2 N N y y i

j i j K ( xi , x j ) i 1 j 1 y i

i 0 i 1 C i 0 i 1,.., N i

i Generalized Inner Product Hilbert-Schmidt Kernels (Courant and Hilbert 1953) (u ) (v) K (u, v) for certain and K, e.g. (u ) Degree d polynomial Radial Basis Function Machine Two Layer Neural Network K (u , v)

(u v 1) d || u v ||2 exp 2 sigmoid ( (u v) c) o kernels for nonvector data like strings, histograms, dna, Final SVM Algorithm Solve Dual SVM QP

Recover primal variable b Classify new x N f ( x) sign i yi K ( x, xi ) i 1 b lution only depends on support vectors:

i 0 S5: Recall linear solution Inseparable Case: SVM Results C=10 4 A point (x,y) is misclassified If 3 x = 2

Class 1 Class -1 Hyp+ Hyp Hypw 1 0 x = 1 -1

-2 -2 x =+1 -1 0 1 2 3

4 RBF results on Sample Data Have to pick parameters Effect of C Effect of RBF parameter 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 kernlab, svmpath and klaR http://aquarius.tw.rpi.edu/html/DA/v15i09.pdf Karatzoglou et al. 2006

Work through the examples (lab) Familiar datasets and samples procedures from 4 libraries (these are the most used) kernlab e1071 svmpath klaR 55 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) See Karatzoglou et al. 2006 Observe the effect of changing the C parameter and the kernel 56 Types of SVM (names) Classification SVM Type 1 (also known as CSVM classification) Classification SVM Type 2 (also known as nuSVM classification) Regression SVM Type 1 (also known as epsilon-SVM regression)

Regression SVM Type 2 (also known as nuSVM regression) 57 More kernels 58 Karatzoglou et al. 2006 Timing 59 Karatzoglou et al. 2006

Library capabilities Karatzoglou et al. 2006 60 Extensions Many Inference Tasks

Regression One-class Classification, novelty detection Ranking Clustering Multi-Task Learning Learning Kernels Canonical Correlation Analysis Principal Component Analysis 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 doesnt really matter as long as

solvable. 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 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?