Support Vector Machine ClassificationComputation & Informatics in Biology & Medicine

Madison Retreat, November 15, 2002

Olvi L. Mangasarian

with

G. M. Fung, Y.-J. Lee, J.W. Shavlik, W. H. Wolberg

& Collaborators at ExonHit – Paris

Data Mining Institute

University of Wisconsin - Madison

What is a Support Vector Machine?

An optimally defined surface Linear or nonlinear in the input space Linear in a higher dimensional feature space Implicitly defined by a kernel function K(A,B) C

What are Support Vector Machines Used For?

Classification Regression & Data Fitting Supervised & Unsupervised Learning

Principal TopicsProximal support vector machine classification

Classify by proximity to planes instead of halfspacesMassive incremental classification

Classify by retiring old data & adding new dataKnowledge-based classification

Incorporate expert knowledge into a classifierFast Newton method classifier

Finitely terminating fast algorithm for classificationBreast cancer prognosis & chemotherapy

Classify patients on basis of distinct survival curves Isolate a class of patients that may benefit from chemotherapy

Principal Topics

Proximal support vector machine classification

Support Vector MachinesMaximize the Margin between Bounding Planes

x0w = í + 1

x0w = í à 1

A+

A-

jjwjj22

w

Proximal Support Vector Machines Maximize the Margin between Proximal Planes

x0w = í + 1

x0w = í à 1

A+

A-

jjwjj22

w

Standard Support Vector MachineAlgebra of 2-Category Linearly Separable Case

Given m points in n dimensional space Represented by an m-by-n matrix A Membership of each in class +1 or –1 specified by:A i

An m-by-m diagonal matrix D with +1 & -1 entries

D(Awà eí )=e;

More succinctly:

where e is a vector of ones.

x0w = í æ1: Separate by two bounding planes,

A iw=í + 1; for D i i = + 1;A iw5í à 1; for D i i = à 1:

Standard Support Vector Machine Formulation

Margin is maximized by minimizing21kw;í k2

2

÷> 0 Solve the quadratic program for some :

2÷kyk2

2 + 21kw;í k2

2

D(Awà eí ) + y > ey;w;ímin

s. t.(QP)

,

, denoteswhere D ii = æ1 A+ Aàor membership.

Proximal SVM Formulation (PSVM)

Standard SVM formulation:

w;í (QP)2÷kyk2

2 + 21kw;í k2

2

D(Awà eí ) + y

min

s. t. = e=

This simple, but critical modification, changes the nature of the optimization problem tremendously!!(Regularized Least Squares or Ridge Regression)

Solving for in terms of and gives:

minw;í 2

÷keà D(Awà eí )k22 + 2

1kw; í k22

y w í

Advantages of New Formulation

Objective function remains strongly convex.

An explicit exact solution can be written in terms of the problem data.

PSVM classifier is obtained by solving a single system of linear equations in the usually small dimensional input space.

Exact leave-one-out-correctness can be obtained in terms of problem data.

Linear PSVM

We want to solve:

w;ímin

2÷keà D(Awà eí )k2

2 + 21kw; í k2

2

Setting the gradient equal to zero, gives a nonsingular system of linear equations.

Solution of the system gives the desired PSVM classifier.

Linear PSVM Solution

H = [A à e]Here,

íw

h i= (÷

I + H 0H)à 1H 0De

The linear system to solve depends on:

H 0H(n + 1) â (n + 1)which is of size

is usually much smaller than n m

Linear & Nonlinear PSVM MATLAB Code

function [w, gamma] = psvm(A,d,nu)% PSVM: linear and nonlinear classification% INPUT: A, d=diag(D), nu. OUTPUT: w, gamma% [w, gamma] = psvm(A,d,nu); [m,n]=size(A);e=ones(m,1);H=[A -e]; v=(d’*H)’ %v=H’*D*e; r=(speye(n+1)/nu+H’*H)\v % solve (I/nu+H’*H)r=v w=r(1:n);gamma=r(n+1); % getting w,gamma from r

Numerical experimentsOne-Billion Two-Class Dataset

Synthetic dataset consisting of 1 billion points in 10- dimensional input space Generated by NDC (Normally Distributed Clustered) dataset generatorDataset divided into 500 blocks of 2 million points each.Solution obtained in less than 2 hours and 26 minutes on a 400Mhz About 30% of the time was spent reading data from disk.Testing set Correctness 90.79%

Principal Topics

Knowledge-based classification (NIPS*2002)

Conventional Data-Based SVM

Knowledge-Based SVM via Polyhedral Knowledge Sets

Incoporating Knowledge Sets Into an SVM Classifier

This implication is equivalent to a set of constraints that can be imposed on the classification problem.

Suppose that the knowledge set: belongs to the class A+. Hence it must lie in the halfspace :

èx??Bx 6 b

é

èxjx0w>í + 1

é

Bx6b ) x0w>í + 1

We therefore have the implication:

Numerical TestingThe Promoter Recognition Dataset

Promoter: Short DNA sequence that precedes a gene sequence.

A promoter consists of 57 consecutive DNA nucleotides belonging to {A,G,C,T} .

Important to distinguish between promoters and nonpromoters

This distinction identifies starting locations of genes in long uncharacterized DNA sequences.

The Promoter Recognition DatasetNumerical Representation

Simple “1 of N” mapping scheme for converting nominal attributes into a real valued representation:

Not most economical representation, but commonly used.

The Promoter Recognition DatasetNumerical Representation

Feature space mapped from 57-dimensional nominal space to a real valued 57 x 4=228 dimensional space.

57 nominal values

57 x 4 =228binary values

Promoter Recognition Dataset Prior Knowledge Rules

Prior knowledge consist of the following 64 rules:

R1orR2orR3orR4

2

66666664

3

77777775

V

R5orR6orR7orR8

2

66666664

3

77777775

V

R9or

R10or

R11or

R12

2

66666664

3

77777775

=) PROMOTER

Promoter Recognition Dataset Sample Rules

R8 : (pà 12 = T) ^(pà 11 = A) ^(pà 07 = T);

R4 : (pà 36 = T) ^(pà 35 = T) ^(pà 34 = G)^(pà 33 = A) ^(pà 32 = C);

R10 : (pà 45 = A) ^(pà 44 = A) ^(pà 41 = A);where denotes position of a nucleotide, with respect to a meaningful reference point starting at position and ending at positionpà 50

pj

p7:Then:

R4^R8^R10=) PROMOTER

The Promoter Recognition DatasetComparative Algorithms

KBANN Knowledge-based artificial neural network [Shavlik et al] BP: Standard back propagation for neural networks [Rumelhart et al] O’Neill’s Method Empirical method suggested by biologist O’Neill [O’Neill] NN: Nearest neighbor with k=3 [Cost et al] ID3: Quinlan’s decision tree builder[Quinlan] SVM1: Standard 1-norm SVM [Bradley et al]

The Promoter Recognition DatasetComparative Test Results

Wisconsin Breast Cancer Prognosis Dataset Description of the data

110 instances corresponding to 41 patients whose cancer had recurred and 69 patients whose cancer had not recurred

32 numerical features The domain theory: two simple rules used by doctors:

Wisconsin Breast Cancer Prognosis Dataset Numerical Testing Results

Doctor’s rules applicable to only 32 out of 110 patients.

Only 22 of 32 patients are classified correctly by this rule (20% Correctness).

KSVM linear classifier applicable to all patients with correctness of 66.4%.

Correctness comparable to best available results using conventional SVMs.

KSVM can get classifiers based on knowledge without using any data.

Principal Topics

Fast Newton method classifier

Fast Newton Algorithm for Classification

Standard quadratic programming (QP) formulation of SVM:

Newton Algorithm

f (z) = 21íí (eà D(Awà ew))+

ww2

+ 21íí w; í

íí 2

zi+1 = zi à @2f (zi)à 1r f (zi)Newton algorithm terminates in a finite number of steps

Termination at global minimum

Error rate decreases linearlyCan generate complex nonlinear classifiers

By using nonlinear kernels: K(x,y)

Nonlinear Spiral Dataset94 Red Dots & 94 White Dots

Principal Topics

Breast cancer prognosis & chemotherapy

Kaplan-Meier Curves for Overall Patients:With & Without Chemotherapy

Breast Cancer Prognosis & ChemotherapyGood, Intermediate & Poor Patient Groupings

(6 Input Features : 5 Cytological, 1 Histological)(Grouping: Utilizes 2 Histological Features &Chemotherapy)

Kaplan-Meier Survival Curvesfor Good, Intermediate & Poor Patients

82.7% Classifier Correctness via 3 SVMs

Kaplan-Meier Survival Curves for Intermediate Group Note Reversed Role of Chemotherapy

ConclusionNew methods for classification All based on rigorous mathematical foundationFast computational algorithms capable of classifying massive datasetsClassifiers based on both abstract prior knowledge as well as conventional datasetsIdentification of breast cancer patients that can benefit from chemotherapy

Future WorkExtend proposed methods to broader optimization problems

Linear & quadratic programming Preliminary results beat state-of-the-art software

Incorporate abstract concepts into optimization problems as constraintsDevelop fast online algorithms for intrusion and fraud detection Classify the effectiveness of new drug cocktails in combating various forms of cancer

Encouraging preliminary results for breast cancer

Breast Cancer Treatment ResponseJoint with ExonHit ( French BioTech)

35 patients treated by a drug cocktail 9 partial responders; 26 nonresponders25 gene expression measurements made on each patient1-Norm SVM classifier selected: 12 out of 25 genesCombinatorially selected 6 genes out of 12Separating plane obtained:

2.7915 T11 + 0.13436 S24 -1.0269 U23 -2.8108 Z23 -1.8668 A19 -1.5177 X05 +2899.1 = 0.

Leave-one-out-error: 1 out of 35 (97.1% correctness)

E1 I1 E2 I2 E3 E4 E5I3 I4DNA

3'5'E1 E2 E3I1 I2 E4 E5I3 I4 pre-mRNA

(m=messenger)

Transcription

Alternative RNA splicing

E1 E2 E4 E5E1 E2 E4 E5E3

(A)n(A)nmRNA

Chemo-Sensitive

NH2 COOH

Chemo-Resistant

NH2 COOHProteins

Translation

Detection of Alternative RNA Isoforms via DATAS(Levels of mRNA that Correlate with Senitivity to Chemotherapy)

DATAS

E3

DATAS: Differential Analysis of Transcripts with Alternative Splicing

Talk Available

www.cs.wisc.edu/~olvi