Support Vector Machine with Polynomial Kernel using Package kernlab

Data Mining

Description for Support Vector Machine with Polynomial Kernel using Package kernlab

Yeongeun Jeon , Jung In Seo
2023-04-25

Support Vector Machine의 장점


Support Vector Machine의 단점


실습 자료 : 유니버셜 은행의 고객 2,500명에 대한 자료(출처 : Data Mining for Business Intelligence, Shmueli et al. 2010)이며, 총 13개의 변수를 포함하고 있다. 이 자료에서 TargetPersonal Loan이다.




1. 데이터 불러오기

pacman::p_load("data.table", "dplyr",
               "caret",
               "ggplot2", "GGally",
               "kernlab")


UB <- fread("../Universal Bank_Main.csv")                               # 데이터 불러오기

UB %>%
  as_tibble
# A tibble: 2,500 × 14
      ID   Age Experience Income `ZIP Code` Family CCAvg Education
   <int> <int>      <int>  <int>      <int>  <int> <dbl>     <int>
 1     1    25          1     49      91107      4   1.6         1
 2     2    45         19     34      90089      3   1.5         1
 3     3    39         15     11      94720      1   1           1
 4     4    35          9    100      94112      1   2.7         2
 5     5    35          8     45      91330      4   1           2
 6     6    37         13     29      92121      4   0.4         2
 7     7    53         27     72      91711      2   1.5         2
 8     8    50         24     22      93943      1   0.3         3
 9     9    35         10     81      90089      3   0.6         2
10    10    34          9    180      93023      1   8.9         3
# ℹ 2,490 more rows
# ℹ 6 more variables: Mortgage <int>, `Personal Loan` <int>,
#   `Securities Account` <int>, `CD Account` <int>, Online <int>,
#   CreditCard <int>

2. 데이터 전처리 I

UB %<>%
  data.frame() %>%                                                      # Data Frame 형태로 변환 
  mutate(Personal.Loan = ifelse(Personal.Loan == 1, "yes", "no")) %>%   # Target을 문자형 변수로 변환
  select(-1)                                                            # ID 변수 제거

# 1. Convert to Factor
fac.col <- c("Family", "Education", "Securities.Account", 
             "CD.Account", "Online", "CreditCard",
             # Target
             "Personal.Loan")

UB <- UB %>% 
  mutate_at(fac.col, as.factor)                                         # 범주형으로 변환

glimpse(UB)                                                             # 데이터 구조 확인
Rows: 2,500
Columns: 13
$ Age                <int> 25, 45, 39, 35, 35, 37, 53, 50, 35, 34, 6…
$ Experience         <int> 1, 19, 15, 9, 8, 13, 27, 24, 10, 9, 39, 5…
$ Income             <int> 49, 34, 11, 100, 45, 29, 72, 22, 81, 180,…
$ ZIP.Code           <int> 91107, 90089, 94720, 94112, 91330, 92121,…
$ Family             <fct> 4, 3, 1, 1, 4, 4, 2, 1, 3, 1, 4, 3, 2, 4,…
$ CCAvg              <dbl> 1.6, 1.5, 1.0, 2.7, 1.0, 0.4, 1.5, 0.3, 0…
$ Education          <fct> 1, 1, 1, 2, 2, 2, 2, 3, 2, 3, 3, 2, 3, 2,…
$ Mortgage           <int> 0, 0, 0, 0, 0, 155, 0, 0, 104, 0, 0, 0, 0…
$ Personal.Loan      <fct> no, no, no, no, no, no, no, no, no, yes, …
$ Securities.Account <fct> 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0,…
$ CD.Account         <fct> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ Online             <fct> 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 1, 0, 1,…
$ CreditCard         <fct> 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0,…
# 2. Convert One-hot Encoding for 범주형 예측 변수
dummies <- dummyVars(formula = ~ .,                                     # formula : ~ 예측 변수 / "." : data에 포함된 모든 변수를 의미
                     data = UB[,-9],                                    # Dataset including Only 예측 변수 -> Target 제외
                     fullRank = FALSE)                                  # fullRank = TRUE : Dummy Variable, fullRank = FALSE : One-hot Encoding

UB.Var   <- predict(dummies, newdata = UB) %>%                          # 범주형 예측 변수에 대한 One-hot Encoding 변환
  data.frame()                                                          # Data Frame 형태로 변환 

glimpse(UB.Var)                                                         # 데이터 구조 확인
Rows: 2,500
Columns: 21
$ Age                  <dbl> 25, 45, 39, 35, 35, 37, 53, 50, 35, 34,…
$ Experience           <dbl> 1, 19, 15, 9, 8, 13, 27, 24, 10, 9, 39,…
$ Income               <dbl> 49, 34, 11, 100, 45, 29, 72, 22, 81, 18…
$ ZIP.Code             <dbl> 91107, 90089, 94720, 94112, 91330, 9212…
$ Family.1             <dbl> 0, 0, 1, 1, 0, 0, 0, 1, 0, 1, 0, 0, 0, …
$ Family.2             <dbl> 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, …
$ Family.3             <dbl> 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, …
$ Family.4             <dbl> 1, 0, 0, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0, …
$ CCAvg                <dbl> 1.6, 1.5, 1.0, 2.7, 1.0, 0.4, 1.5, 0.3,…
$ Education.1          <dbl> 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
$ Education.2          <dbl> 0, 0, 0, 1, 1, 1, 1, 0, 1, 0, 0, 1, 0, …
$ Education.3          <dbl> 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 0, 1, …
$ Mortgage             <dbl> 0, 0, 0, 0, 0, 155, 0, 0, 104, 0, 0, 0,…
$ Securities.Account.0 <dbl> 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, …
$ Securities.Account.1 <dbl> 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, …
$ CD.Account.0         <dbl> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, …
$ CD.Account.1         <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
$ Online.0             <dbl> 1, 1, 1, 1, 1, 0, 0, 1, 0, 1, 1, 0, 1, …
$ Online.1             <dbl> 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 1, 0, …
$ CreditCard.0         <dbl> 1, 1, 1, 1, 0, 1, 1, 0, 1, 1, 1, 1, 1, …
$ CreditCard.1         <dbl> 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, …
# 3. Combine Target with 변환된 예측 변수
UB.df <- data.frame(Personal.Loan = UB$Personal.Loan, 
                    UB.Var)

UB.df %>%
  as_tibble
# A tibble: 2,500 × 22
   Personal.Loan   Age Experience Income ZIP.Code Family.1 Family.2
   <fct>         <dbl>      <dbl>  <dbl>    <dbl>    <dbl>    <dbl>
 1 no               25          1     49    91107        0        0
 2 no               45         19     34    90089        0        0
 3 no               39         15     11    94720        1        0
 4 no               35          9    100    94112        1        0
 5 no               35          8     45    91330        0        0
 6 no               37         13     29    92121        0        0
 7 no               53         27     72    91711        0        1
 8 no               50         24     22    93943        1        0
 9 no               35         10     81    90089        0        0
10 yes              34          9    180    93023        1        0
# ℹ 2,490 more rows
# ℹ 15 more variables: Family.3 <dbl>, Family.4 <dbl>, CCAvg <dbl>,
#   Education.1 <dbl>, Education.2 <dbl>, Education.3 <dbl>,
#   Mortgage <dbl>, Securities.Account.0 <dbl>,
#   Securities.Account.1 <dbl>, CD.Account.0 <dbl>,
#   CD.Account.1 <dbl>, Online.0 <dbl>, Online.1 <dbl>,
#   CreditCard.0 <dbl>, CreditCard.1 <dbl>
glimpse(UB.df)                                                          # 데이터 구조 확인
Rows: 2,500
Columns: 22
$ Personal.Loan        <fct> no, no, no, no, no, no, no, no, no, yes…
$ Age                  <dbl> 25, 45, 39, 35, 35, 37, 53, 50, 35, 34,…
$ Experience           <dbl> 1, 19, 15, 9, 8, 13, 27, 24, 10, 9, 39,…
$ Income               <dbl> 49, 34, 11, 100, 45, 29, 72, 22, 81, 18…
$ ZIP.Code             <dbl> 91107, 90089, 94720, 94112, 91330, 9212…
$ Family.1             <dbl> 0, 0, 1, 1, 0, 0, 0, 1, 0, 1, 0, 0, 0, …
$ Family.2             <dbl> 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, …
$ Family.3             <dbl> 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, …
$ Family.4             <dbl> 1, 0, 0, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0, …
$ CCAvg                <dbl> 1.6, 1.5, 1.0, 2.7, 1.0, 0.4, 1.5, 0.3,…
$ Education.1          <dbl> 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
$ Education.2          <dbl> 0, 0, 0, 1, 1, 1, 1, 0, 1, 0, 0, 1, 0, …
$ Education.3          <dbl> 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 0, 1, …
$ Mortgage             <dbl> 0, 0, 0, 0, 0, 155, 0, 0, 104, 0, 0, 0,…
$ Securities.Account.0 <dbl> 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, …
$ Securities.Account.1 <dbl> 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, …
$ CD.Account.0         <dbl> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, …
$ CD.Account.1         <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
$ Online.0             <dbl> 1, 1, 1, 1, 1, 0, 0, 1, 0, 1, 1, 0, 1, …
$ Online.1             <dbl> 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 1, 0, …
$ CreditCard.0         <dbl> 1, 1, 1, 1, 0, 1, 1, 0, 1, 1, 1, 1, 1, …
$ CreditCard.1         <dbl> 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, …

3. 데이터 탐색

ggpairs(UB,                                               # In 2-1
        columns = c("Age", "Experience", "Income",        # 수치형 예측 변수
                    "ZIP.Code", "CCAvg", "Mortgage"),                            
        aes(colour = Personal.Loan)) +                    # Target의 범주에 따라 색깔을 다르게 표현
  theme_bw()  
ggpairs(UB,                                               # In 2-1
        columns = c("Age", "Experience", "Income",        # 수치형 예측 변수
                    "ZIP.Code", "CCAvg", "Mortgage"), 
        aes(colour = Personal.Loan)) +                    # Target의 범주에 따라 색깔을 다르게 표현
  scale_colour_manual(values = c("#00798c", "#d1495b")) + # 특정 색깔 지정
  scale_fill_manual(values = c("#00798c", "#d1495b")) +   # 특정 색깔 지정
  theme_bw()
ggpairs(UB,                                               # In 2-1
        columns = c("Age", "Income",                      # 수치형 예측 변수
                    "Family", "Education"),               # 범주형 예측 변수
        aes(colour = Personal.Loan, alpha = 0.8)) +       # Target의 범주에 따라 색깔을 다르게 표현
  scale_colour_manual(values = c("#E69F00", "#56B4E9")) + # 특정 색깔 지정
  scale_fill_manual(values = c("#E69F00", "#56B4E9")) +   # 특정 색깔 지정
  theme_bw()


4. 데이터 분할

# Partition (Training Dataset : Test Dataset = 7:3)
y      <- UB.df$Personal.Loan                            # Target
 
set.seed(200)
ind    <- createDataPartition(y, p = 0.7, list = T)      # Index를 이용하여 7:3으로 분할
UB.trd <- UB.df[ind$Resample1,]                          # Training Dataset
UB.ted <- UB.df[-ind$Resample1,]                         # Test Dataset

5. 데이터 전처리 II

# Standardization
preProcValues <- preProcess(UB.trd, 
                            method = c("center", "scale"))  # Standardization 정의 -> Training Dataset에 대한 평균과 표준편차 계산 

UB.trd <- predict(preProcValues, UB.trd)                    # Standardization for Training Dataset
UB.ted <- predict(preProcValues, UB.ted)                    # Standardization for Test Dataset

glimpse(UB.trd)                                             # 데이터 구조 확인
Rows: 1,751
Columns: 22
$ Personal.Loan        <fct> no, no, no, no, no, no, no, yes, no, no…
$ Age                  <dbl> -0.05431273, -0.57446728, -0.92123699, …
$ Experience           <dbl> -0.12175295, -0.46882565, -0.98943471, …
$ Income               <dbl> -0.85867297, -1.35649686, 0.56986515, -…
$ ZIP.Code             <dbl> -1.75250883, 0.88354520, 0.53745994, -1…
$ Family.1             <dbl> -0.6355621, 1.5725118, 1.5725118, -0.63…
$ Family.2             <dbl> -0.5774051, -0.5774051, -0.5774051, -0.…
$ Family.3             <dbl> 2.0037210, -0.4987865, -0.4987865, -0.4…
$ Family.4             <dbl> -0.5967491, -0.5967491, -0.5967491, 1.6…
$ CCAvg                <dbl> -0.25119120, -0.53150921, 0.42157204, -…
$ Education.1          <dbl> 1.1482386, 1.1482386, -0.8704018, -0.87…
$ Education.2          <dbl> -0.6196534, -0.6196534, 1.6128838, 1.61…
$ Education.3          <dbl> -0.6408777, -0.6408777, -0.6408777, -0.…
$ Mortgage             <dbl> -0.5664192, -0.5664192, -0.5664192, -0.…
$ Securities.Account.0 <dbl> -2.7998134, 0.3569627, 0.3569627, 0.356…
$ Securities.Account.1 <dbl> 2.7998134, -0.3569627, -0.3569627, -0.3…
$ CD.Account.0         <dbl> 0.2613337, 0.2613337, 0.2613337, 0.2613…
$ CD.Account.1         <dbl> -0.2613337, -0.2613337, -0.2613337, -0.…
$ Online.0             <dbl> 1.2486195, 1.2486195, 1.2486195, 1.2486…
$ Online.1             <dbl> -1.2486195, -1.2486195, -1.2486195, -1.…
$ CreditCard.0         <dbl> 0.6408777, 0.6408777, 0.6408777, -1.559…
$ CreditCard.1         <dbl> -0.6408777, -0.6408777, -0.6408777, 1.5…
glimpse(UB.ted)                                             # 데이터 구조 확인
Rows: 749
Columns: 22
$ Personal.Loan        <fct> no, no, no, no, no, no, no, no, no, no,…
$ Age                  <dbl> -1.7881612, -0.7478521, 1.2460737, 0.81…
$ Experience           <dbl> -1.68358012, -0.64236200, 0.83269699, 0…
$ Income               <dbl> -0.53400522, -0.96689556, -1.11840718, …
$ ZIP.Code             <dbl> -1.17304370, -0.59585545, 1.07366441, 0…
$ Family.1             <dbl> -0.6355621, -0.6355621, 1.5725118, 1.57…
$ Family.2             <dbl> -0.5774051, -0.5774051, -0.5774051, -0.…
$ Family.3             <dbl> -0.4987865, -0.4987865, -0.4987865, -0.…
$ Family.4             <dbl> 1.6747892, 1.6747892, -0.5967491, -0.59…
$ CCAvg                <dbl> -0.19512759, -0.86789083, -0.25119120, …
$ Education.1          <dbl> 1.1482386, -0.8704018, -0.8704018, -0.8…
$ Education.2          <dbl> -0.6196534, 1.6128838, -0.6196534, 1.61…
$ Education.3          <dbl> -0.6408777, -0.6408777, 1.5594690, -0.6…
$ Mortgage             <dbl> -0.5664192, 0.9609885, -0.5664192, -0.5…
$ Securities.Account.0 <dbl> -2.7998134, 0.3569627, 0.3569627, -2.79…
$ Securities.Account.1 <dbl> 2.7998134, -0.3569627, -0.3569627, 2.79…
$ CD.Account.0         <dbl> 0.2613337, 0.2613337, 0.2613337, 0.2613…
$ CD.Account.1         <dbl> -0.2613337, -0.2613337, -0.2613337, -0.…
$ Online.0             <dbl> 1.2486195, -0.8004271, -0.8004271, 1.24…
$ Online.1             <dbl> -1.2486195, 0.8004271, 0.8004271, -1.24…
$ CreditCard.0         <dbl> 0.6408777, 0.6408777, -1.5594690, -1.55…
$ CreditCard.1         <dbl> -0.6408777, -0.6408777, 1.5594690, 1.55…

6. 모형 훈련

Package "kernlab"는 커널 기반의 기계 학습 알고리듬을 R에서 구현한 Package이며, 해당 Package를 이용하여 Support Vector Machine를 수행하면 Kernel 함수가 Radial Basis일 때, 최적의 sigma (gamma) 값을 자동으로 찾아준다는 장점이 있다. 함수 ksvm()을 이용하여 Support Vector Machine을 수행하며, 함수에서 사용할 수 있는 자세한 옵션은 여기를 참고한다.

ksvm(formula, data, kernel, C, kpar, prob.model, ...) 
svm.model.po <- ksvm(Personal.Loan ~.,     
                     data = UB.trd,  
                     kernel = "polydot", 
                     C = 1,         
                     kpar = list(degree = 2,
                                 scale = 2,
                                 offset = 1),
                     prob.model = TRUE)   

svm.model.po
Support Vector Machine object of class "ksvm" 

SV type: C-svc  (classification) 
 parameter : cost C = 1 

Polynomial kernel function. 
 Hyperparameters : degree =  2  scale =  2  offset =  1 

Number of Support Vectors : 115 

Objective Function Value : -26.9889 
Training error : 0.00514 
Probability model included. 

7. 모형 평가

Caution! 모형 평가를 위해 Test Dataset에 대한 예측 class/확률 이 필요하며, 함수 predict()를 이용하여 생성한다.

# 예측 class 생성 
svm.po.pred <- predict(svm.model.po,
                       newdata = UB.ted[,-1],         # Test Dataset including Only 예측 변수   
                       type = "response")             # 예측 class 생성       

svm.po.pred %>%
  as_tibble
# A tibble: 749 × 1
   value
   <fct>
 1 no   
 2 no   
 3 no   
 4 no   
 5 no   
 6 no   
 7 no   
 8 no   
 9 no   
10 no   
# ℹ 739 more rows


7-1. ConfusionMatrix

CM   <- caret::confusionMatrix(svm.po.pred, UB.ted$Personal.Loan, 
                               positive = "yes")      # confusionMatrix(예측 class, 실제 class, positive="관심 class")
CM
Confusion Matrix and Statistics

          Reference
Prediction  no yes
       no  656  12
       yes  17  64
                                          
               Accuracy : 0.9613          
                 95% CI : (0.9449, 0.9739)
    No Information Rate : 0.8985          
    P-Value [Acc > NIR] : 1.228e-10       
                                          
                  Kappa : 0.7937          
                                          
 Mcnemar's Test P-Value : 0.4576          
                                          
            Sensitivity : 0.84211         
            Specificity : 0.97474         
         Pos Pred Value : 0.79012         
         Neg Pred Value : 0.98204         
             Prevalence : 0.10147         
         Detection Rate : 0.08545         
   Detection Prevalence : 0.10814         
      Balanced Accuracy : 0.90842         
                                          
       'Positive' Class : yes             
                                          


7-2. ROC 곡선

# 예측 확률 생성
test.svm.prob <- predict(svm.model.po, 
                         newdata = UB.ted[,-1],       # Test Dataset including Only 예측 변수  
                         type = "probabilities")      # 예측 확률 생성     

test.svm.prob %>%
  as_tibble
# A tibble: 749 × 2
      no       yes
   <dbl>     <dbl>
 1 0.963 0.0369   
 2 1.00  0.000179 
 3 0.999 0.000856 
 4 1.00  0.0000446
 5 1.00  0.0000743
 6 0.998 0.00241  
 7 0.999 0.000863 
 8 0.976 0.0237   
 9 0.920 0.0802   
10 0.998 0.00240  
# ℹ 739 more rows
test.svm.prob <- test.svm.prob[,2]                    # "Personal.Loan = yes"에 대한 예측 확률

ac  <- UB.ted$Personal.Loan                           # Test Dataset의 실제 class 
pp  <- as.numeric(test.svm.prob)                      # 예측 확률을 수치형으로 변환

1) Package “pROC”

pacman::p_load("pROC")

svm.roc  <- roc(ac, pp, plot = T, col = "gray")       # roc(실제 class, 예측 확률)
auc      <- round(auc(svm.roc), 3)
legend("bottomright", legend = auc, bty = "n")

Caution! Package "pROC"를 통해 출력한 ROC 곡선은 다양한 함수를 이용해서 그래프를 수정할 수 있다.

# 함수 plot.roc() 이용
plot.roc(svm.roc,   
         col="gray",                                  # Line Color
         print.auc = TRUE,                            # AUC 출력 여부
         print.auc.col = "red",                       # AUC 글씨 색깔
         print.thres = TRUE,                          # Cutoff Value 출력 여부
         print.thres.pch = 19,                        # Cutoff Value를 표시하는 도형 모양
         print.thres.col = "red",                     # Cutoff Value를 표시하는 도형의 색깔
         auc.polygon = TRUE,                          # 곡선 아래 면적에 대한 여부
         auc.polygon.col = "gray90")                  # 곡선 아래 면적의 색깔

# 함수 ggroc() 이용
ggroc(svm.roc) +
annotate(geom = "text", x = 0.9, y = 1.0,
label = paste("AUC = ", auc),
size = 5,
color="red") +
theme_bw()

2) Package “Epi”

pacman::p_load("Epi")       
# install_version("etm", version = "1.1", repos = "http://cran.us.r-project.org")

ROC(pp, ac, plot = "ROC")                             # ROC(예측 확률, 실제 class)  

3) Package “ROCR”

pacman::p_load("ROCR")

svm.pred <- prediction(pp, ac)                        # prediction(예측 확률, 실제 class)    

svm.perf <- performance(svm.pred, "tpr", "fpr")       # performance(, "민감도", "1-특이도")                      
plot(svm.perf, col = "gray")                          # ROC Curve

perf.auc   <- performance(svm.pred, "auc")            # AUC
auc        <- attributes(perf.auc)$y.values 
legend("bottomright", legend = auc, bty = "n")


7-3. 향상 차트

1) Package “ROCR”

svm.perf <- performance(svm.pred, "lift", "rpp")      # Lift Chart
plot(svm.perf, main = "lift curve", 
     colorize = T,                                    # Coloring according to cutoff
     lwd = 2)  

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