feature (gene) selection methodssample classification methods gene filtering: variance (sd/mean)...

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Feature (Gene) Selection Methods Sample Classification Methods Gene filtering: • Variance (SD/Mean) • Principal Component Analysis Regression using variable selection: •LASSO •Ridge regression •Elastic net shrinkage •Greedy algorithm Support Vector Machines (Vapnik V, et al.) Nearest Shrunken Centroids (Tibshirani R, et al) Other methods: • Decision Tree: Random Forest, CART • k-Nearest-Neighbor • Discriminant Analysis: LDA, DLDA • Naive Bayesian classifiers: BART, Markov Chain Monte Carlo • Artificial Neural Networks •Ensemble learning: Bootstrap Aggregating, Boosting 1 Supplemental File 1, Table 1s

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Page 1: Feature (Gene) Selection MethodsSample Classification Methods Gene filtering: Variance (SD/Mean) Principal Component Analysis Regression using variable

Feature (Gene) Selection Methods Sample Classification Methods

Gene filtering:

• Variance (SD/Mean)• Principal Component Analysis

Regression using variable selection:

•LASSO•Ridge regression•Elastic net shrinkage•Greedy algorithm

Support Vector Machines (Vapnik V, et al.)

Nearest Shrunken Centroids (Tibshirani R, et al)

Other methods:

• Decision Tree: Random Forest, CART

• k-Nearest-Neighbor• Discriminant Analysis: LDA,

DLDA• Naive Bayesian classifiers:

BART, Markov Chain Monte Carlo

• Artificial Neural Networks

•Ensemble learning: Bootstrap Aggregating, Boosting

1Supplemental File 1, Table 1s

Page 2: Feature (Gene) Selection MethodsSample Classification Methods Gene filtering: Variance (SD/Mean) Principal Component Analysis Regression using variable

Supplemental File 2, Figure 2s

0 100

A

B

Page 3: Feature (Gene) Selection MethodsSample Classification Methods Gene filtering: Variance (SD/Mean) Principal Component Analysis Regression using variable

Supplemental File 3, Table 2s

Type

Patients in each class CR modeling performance

CR No CR Sensitivity Specificity

Sustained CR. 36 58 53% 81%

CR3: At the end of 3rd cycle (early-onset

or flash-point CR)12 270 ~0% ~100%

CR8: At the end of 8th cycle 36 246 30% 77%

CR20: At the end of protocol 76 206 22% 81%

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