Classifying Lymphoma Dataset Using SVM: Advanced Data Mining Techniques

1. Classifying Lymphoma Dataset Using Multi-class Support Vector Machines INFS-795 Advanced Data Mining Prof. Domeniconi Presented by Hong Chai

2. Agenda (1) Lymphoma Dataset Description (2) Data Preprocessing - Formatting -Dealing with Missing Values - Gene Selections (3) Multi-class SVM Classification -1-against-all - 1-against-1 (4) Tools (5) References

3. Lymphoma Dataset • Alizadeh et al.(2000), Distinct Types of Diffuse Large B-cell Lymphoma Identified by Gene Expression Profiling • Publicly available at http://llmpp.nih.gov/lymphoma/ • In microarray data, Expression profiling of genes are measured in rows Samples are columns

4. Lymphoma Dataset • 96 samples of lymphocytes (instances) • 4026 human genes (features) • 9 classes of lymphoma: DLBCL, GCB, NIL, ABB, RAT, TCL, FL, RBB, CLL • Glimpse of data

5. Lymphoma Dataset

6. Goal Task: classification • Assign each patient sample to one of 9 categories, e.g. Diffuse Large B-cell Lymphoma (DLBCL) or Chronic Lymphocytic Leukemia (CLL). • Microarray data classification: an alternative to current malignancies classification that relies on morphological or clinical variables Medical implications • Precise categorization of cancers; more relevant diagnosis • More accurate assignment of cases to high risk or low risk categories • more targetedtherapies • Improved predictability of outcome.

7. Data Preprocessing Missing ValuesImputation • 3% of gene expression profiles data are missing • 1980 of the 4026 genes have missing values • 49.1% of genes (features) involved • Some of these genes may be highly informative for classification • Need to deal with missing values before applying to SVM

8. Missing Value Approaches • Instance or feature deletion - if dataset large enough & does not distort distribution • Replace with a randomly drawn observed value - proved to work well (http://globain/cse/psu.edu/courses/spring2003/3-norm-val.pdf) • EM algorithm • Global mode or mean substitution - will distort distribution • Local mode or mean substitution with KNN algorithm (Prof. Domeniconi)

9. Local Mean Imputation (KNN) • Partition the data set D into two sets. • Let the first set, Dm, contain instances with missing value(s). • The other set, Dc, contains instances with complete values. 2. For each instance vector x  Dm • Divide the vector into observed and missing parts as x = [xo; xm]. • Calculate the distance between xo and every instance y  Dc, using only those features that are observed in x. • From the K closest y’s (instances in Dc), calculate the mean of the feature for which x has missing value(s). Make substitution with this local mean. (Note: for nominal features use mode. n/a in microarray data)

10. Data Preprocessing Feature Selection: Motivations - Number of features large, instances small - Reduce dimensionality to overcome overfitting - A small number of discriminant “marker” genes may characterize different cancer classes Example:Guyon et al. identified 2 genes that yield zero leave- one-out error in the leukemia dataset, 4 genes in the colon cancer dataset that give 98% accuracy. (Guyon et al. Gene Selection for Cancer Classification using SVM, 2002)

11. Feature Selection Discriminant Score Ranking • Which gene is more informative in the 2-class case: + - + - Gene 1 Gene 2

12. Separation Score • Gene 1 more discriminant. Criteria: - Large difference of μ+ and μ- - Small variance within each class • Score function F(gj) = | (μj+ - μj-) / (σj+ + σj-) |

13. Separation Score • In multi-class cases, rank genes that are discriminant among multiple classes C1C2ΔC3 • A gene may functionally relates to several cancer classes such as C1 and C2

14. Separation Score • Proposing an adapted score function For each gene j Calculate μi in each classCi Sort μi in descending order Find a cutoff point with largest diff(μi, μj) μ+μexp-cutoff-left σ+σexp-cutoff-left μ-μexp-cutoff-right σ-σexp-cutoff-right F(gj) = |(μj+ - μj-) / (σj+ + σj-) | Rank genes by F(gj) Select top genes via threshold

15. Separation Score Disadvantage: • Does not yield more compact gene sets; still abundant • Does not consider mutual information between genes

16. Feature Selection Recursive Feature Elimination/SVM • In the linear SVM model on the full feature set Sign (w•x + b) w is a vector of weights for each feature, x is an input instance, and b a threshold. If wi = 0, feature Xi does not influence classification and can be eliminated from the set of features.

17. RFE/SVM 2. When w is computed for the full feature set, sort features according in descending order of weights. The lower half is eliminated. 3. A new linear SVM is built using the new set of features. Repeat the process until the set of predictors is non-divisible by two. 4. The best feature subset is chosen.

18. Feature Selection • PCA comment: not common in microarray data. • Disadvantage: none of original inputs can be discarded • We want to retain a minimum subset of informative genes to achieve best classification performance.

19. Multi-class SVM

20. Multi-class SVM Approaches 1-against-all • Each of the SVMs separates a single class from all remaining classes (Cortes and Vapnik, 1995) 1-against-1 • Pair-wise. k(k-1)/2, k Y SVMs are trained. Each SVM separates a pair of classes (Fridman, 1996) Performance similarin some experiments(Nakajima, 2000) Time complexity similar:k evaluation in 1-all, k-1 in 1-1

21. 1 -against- All • Or “one-against-rest”, a tree algorithm • Decomposed to a collection of binary classifications • k decision functions, one for each class (wk)T• x+bk,k Y • The kth classifier constructs a hyperplane between class n and the k-1 other classes Class of x = argmaxi{(wi)T •(x)+bi}

22. 1 -against- 1 • k(k-1)/2 classifiers where each one is trained on data from two classes • For training data fromithandjthclasses, run binary classification • Voting strategy: If Sign(wij)T• x+bij) says x is in class i, then add 1 to class i. Else to class j. • Assign x to class with largest vote (Max wins)

23. Kernels to Experiment • Polynomial kernels K(Xi, Xj)=(XiXj+1)^d • Gaussian Kernels K(Xi, Xj)=e^(-|| Xi -Xj ||/σ^2)

24. SVM Tools - Weka Data Preprocessing • To ARFF format • Import file

25. SVM Tools - Weka Feature Selection using SVM • Select Attribute • SVMAttributeEval

26. SVM Tools - Weka Multi-class classifier • Classify • Meta • MultiClassClassifier (Handles multi-class datasets with 2-class classifiers)

27. SVM Tools - Weka • Multi-class SVM • Classify • Functions • SMO (Weka’s SVM)

28. SVM Tools - Weka • Multi-class SVM Options • Method 1-against-1 1-against-all • Kernel options not found

29. Multi-class SVM Tools Other Tools include • SVMTorch (1-against-all) • LibSVM (1-against-1) • LightSVM

30. References • Alizadeh et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling, 1999 • Cristianini, An Introduction to Support Vector Machines, 2000 • Dor et al, Scoring Genes for Relevance, 2000 • Franc and Hlavac, Multi-class Support Vector Machines • Furey et al. Support vector machine classification and validation of cancer tissue samples using microarray expression data, 2000 • Guyon et al. Gene Selection for Cancer Classification using Support Vector Machines, 2002 • Selikoff, The SVM-Tree Algorithm, A New Method for Handling Multi-class SVM, 2003 • Shipp et al. Diffuse Large B-cell lymphoma outcome prediction by gene expression profiling and supervised machine learning, 2002 • Weston, Multi-class Support Vector Machines, Technical Report, 1998