Redes Neuronales

Teoría

Una Red Neuronal Artificial (ANN) modela la relación entre un conjunto de entradas y una salida, resolviendo un problema de aprendizaje.

Ejemplo prácticos de aplicación de Redes Neuronales son:

La recomendación de contenido de Netflix. El feed de Instagram o Tiktok. *Determinar el número o letra escrito a mano.

Instalar paquetes y llamar librerías

#install.packages("neuralnet")
library(neuralnet)
#install.packages("rpart")
library(rpart)
#install.packages("rpart.plot")
library(rpart.plot)
#install.packages("ggplot2") #Graficos
library(ggplot2)
#install.packages("lattice") #Graficos
library(lattice)
#install.packages("caret") #Algoritmos de aprendizaje automático
library(caret)
#install.packages("datasets") #Usar bases de datos, en caso Iris
library(datasets)
#install.packages("DataExplorer") #Análisis exploratorio
library(DataExplorer)

Alimentar ejemplos

examen <- c(20,10,30,20,80,30)
proyecto <- c(90,20,40,50,50,80)
estatus <- c(1,0,0,0,0,1)
df <- data.frame(examen, proyecto, estatus)

Generar la Red Neuronal

#Grafica la mejor red, con menor error
red_neuronal <- neuralnet(estatus~., data=df)
plot(red_neuronal, rep= "best")

Generar la Red Neuronal

#
set.seed(123)
prueba_examen <- c(30,40,85)
prueba_proyecto <- c(85,50,40)
prueba <- data.frame(prueba_examen,prueba_proyecto)
prediccion <- compute(red_neuronal, prueba)
prediccion$net.result

##             [,1]
## [1,]  1.01018489
## [2,]  0.01817863
## [3,] -0.01744580

probabilidad <- prediccion$net.result
resultado <- ifelse(probabilidad>0.5,1,0)
resultado

##      [,1]
## [1,]    1
## [2,]    0
## [3,]    0

Ejercicio: Cáncer de mama

Importar la base de datos de Cáncer de mama

Cancer_mama <- read.csv("C:\\Users\\atene\\Downloads\\R_Concentracion\\cancer_de_mama.csv")

Entender la base de datos

summary(Cancer_mama)

##   diagnosis          radius_mean      texture_mean   perimeter_mean  
##  Length:569         Min.   : 6.981   Min.   : 9.71   Min.   : 43.79  
##  Class :character   1st Qu.:11.700   1st Qu.:16.17   1st Qu.: 75.17  
##  Mode  :character   Median :13.370   Median :18.84   Median : 86.24  
##                     Mean   :14.127   Mean   :19.29   Mean   : 91.97  
##                     3rd Qu.:15.780   3rd Qu.:21.80   3rd Qu.:104.10  
##                     Max.   :28.110   Max.   :39.28   Max.   :188.50  
##    area_mean      smoothness_mean   compactness_mean  concavity_mean   
##  Min.   : 143.5   Min.   :0.05263   Min.   :0.01938   Min.   :0.00000  
##  1st Qu.: 420.3   1st Qu.:0.08637   1st Qu.:0.06492   1st Qu.:0.02956  
##  Median : 551.1   Median :0.09587   Median :0.09263   Median :0.06154  
##  Mean   : 654.9   Mean   :0.09636   Mean   :0.10434   Mean   :0.08880  
##  3rd Qu.: 782.7   3rd Qu.:0.10530   3rd Qu.:0.13040   3rd Qu.:0.13070  
##  Max.   :2501.0   Max.   :0.16340   Max.   :0.34540   Max.   :0.42680  
##  concave_points_mean symmetry_mean    fractal_dimension_mean   radius_se     
##  Min.   :0.00000     Min.   :0.1060   Min.   :0.04996        Min.   :0.1115  
##  1st Qu.:0.02031     1st Qu.:0.1619   1st Qu.:0.05770        1st Qu.:0.2324  
##  Median :0.03350     Median :0.1792   Median :0.06154        Median :0.3242  
##  Mean   :0.04892     Mean   :0.1812   Mean   :0.06280        Mean   :0.4052  
##  3rd Qu.:0.07400     3rd Qu.:0.1957   3rd Qu.:0.06612        3rd Qu.:0.4789  
##  Max.   :0.20120     Max.   :0.3040   Max.   :0.09744        Max.   :2.8730  
##    texture_se      perimeter_se       area_se        smoothness_se     
##  Min.   :0.3602   Min.   : 0.757   Min.   :  6.802   Min.   :0.001713  
##  1st Qu.:0.8339   1st Qu.: 1.606   1st Qu.: 17.850   1st Qu.:0.005169  
##  Median :1.1080   Median : 2.287   Median : 24.530   Median :0.006380  
##  Mean   :1.2169   Mean   : 2.866   Mean   : 40.337   Mean   :0.007041  
##  3rd Qu.:1.4740   3rd Qu.: 3.357   3rd Qu.: 45.190   3rd Qu.:0.008146  
##  Max.   :4.8850   Max.   :21.980   Max.   :542.200   Max.   :0.031130  
##  compactness_se      concavity_se     concave_points_se   symmetry_se      
##  Min.   :0.002252   Min.   :0.00000   Min.   :0.000000   Min.   :0.007882  
##  1st Qu.:0.013080   1st Qu.:0.01509   1st Qu.:0.007638   1st Qu.:0.015160  
##  Median :0.020450   Median :0.02589   Median :0.010930   Median :0.018730  
##  Mean   :0.025478   Mean   :0.03189   Mean   :0.011796   Mean   :0.020542  
##  3rd Qu.:0.032450   3rd Qu.:0.04205   3rd Qu.:0.014710   3rd Qu.:0.023480  
##  Max.   :0.135400   Max.   :0.39600   Max.   :0.052790   Max.   :0.078950  
##  fractal_dimension_se  radius_worst   texture_worst   perimeter_worst 
##  Min.   :0.0008948    Min.   : 7.93   Min.   :12.02   Min.   : 50.41  
##  1st Qu.:0.0022480    1st Qu.:13.01   1st Qu.:21.08   1st Qu.: 84.11  
##  Median :0.0031870    Median :14.97   Median :25.41   Median : 97.66  
##  Mean   :0.0037949    Mean   :16.27   Mean   :25.68   Mean   :107.26  
##  3rd Qu.:0.0045580    3rd Qu.:18.79   3rd Qu.:29.72   3rd Qu.:125.40  
##  Max.   :0.0298400    Max.   :36.04   Max.   :49.54   Max.   :251.20  
##    area_worst     smoothness_worst  compactness_worst concavity_worst 
##  Min.   : 185.2   Min.   :0.07117   Min.   :0.02729   Min.   :0.0000  
##  1st Qu.: 515.3   1st Qu.:0.11660   1st Qu.:0.14720   1st Qu.:0.1145  
##  Median : 686.5   Median :0.13130   Median :0.21190   Median :0.2267  
##  Mean   : 880.6   Mean   :0.13237   Mean   :0.25427   Mean   :0.2722  
##  3rd Qu.:1084.0   3rd Qu.:0.14600   3rd Qu.:0.33910   3rd Qu.:0.3829  
##  Max.   :4254.0   Max.   :0.22260   Max.   :1.05800   Max.   :1.2520  
##  concave_points_worst symmetry_worst   fractal_dimension_worst
##  Min.   :0.00000      Min.   :0.1565   Min.   :0.05504        
##  1st Qu.:0.06493      1st Qu.:0.2504   1st Qu.:0.07146        
##  Median :0.09993      Median :0.2822   Median :0.08004        
##  Mean   :0.11461      Mean   :0.2901   Mean   :0.08395        
##  3rd Qu.:0.16140      3rd Qu.:0.3179   3rd Qu.:0.09208        
##  Max.   :0.29100      Max.   :0.6638   Max.   :0.20750

str(Cancer_mama)

## 'data.frame':    569 obs. of  31 variables:
##  $ diagnosis              : chr  "M" "M" "M" "M" ...
##  $ radius_mean            : num  18 20.6 19.7 11.4 20.3 ...
##  $ texture_mean           : num  10.4 17.8 21.2 20.4 14.3 ...
##  $ perimeter_mean         : num  122.8 132.9 130 77.6 135.1 ...
##  $ area_mean              : num  1001 1326 1203 386 1297 ...
##  $ smoothness_mean        : num  0.1184 0.0847 0.1096 0.1425 0.1003 ...
##  $ compactness_mean       : num  0.2776 0.0786 0.1599 0.2839 0.1328 ...
##  $ concavity_mean         : num  0.3001 0.0869 0.1974 0.2414 0.198 ...
##  $ concave_points_mean    : num  0.1471 0.0702 0.1279 0.1052 0.1043 ...
##  $ symmetry_mean          : num  0.242 0.181 0.207 0.26 0.181 ...
##  $ fractal_dimension_mean : num  0.0787 0.0567 0.06 0.0974 0.0588 ...
##  $ radius_se              : num  1.095 0.543 0.746 0.496 0.757 ...
##  $ texture_se             : num  0.905 0.734 0.787 1.156 0.781 ...
##  $ perimeter_se           : num  8.59 3.4 4.58 3.44 5.44 ...
##  $ area_se                : num  153.4 74.1 94 27.2 94.4 ...
##  $ smoothness_se          : num  0.0064 0.00522 0.00615 0.00911 0.01149 ...
##  $ compactness_se         : num  0.049 0.0131 0.0401 0.0746 0.0246 ...
##  $ concavity_se           : num  0.0537 0.0186 0.0383 0.0566 0.0569 ...
##  $ concave_points_se      : num  0.0159 0.0134 0.0206 0.0187 0.0188 ...
##  $ symmetry_se            : num  0.03 0.0139 0.0225 0.0596 0.0176 ...
##  $ fractal_dimension_se   : num  0.00619 0.00353 0.00457 0.00921 0.00511 ...
##  $ radius_worst           : num  25.4 25 23.6 14.9 22.5 ...
##  $ texture_worst          : num  17.3 23.4 25.5 26.5 16.7 ...
##  $ perimeter_worst        : num  184.6 158.8 152.5 98.9 152.2 ...
##  $ area_worst             : num  2019 1956 1709 568 1575 ...
##  $ smoothness_worst       : num  0.162 0.124 0.144 0.21 0.137 ...
##  $ compactness_worst      : num  0.666 0.187 0.424 0.866 0.205 ...
##  $ concavity_worst        : num  0.712 0.242 0.45 0.687 0.4 ...
##  $ concave_points_worst   : num  0.265 0.186 0.243 0.258 0.163 ...
##  $ symmetry_worst         : num  0.46 0.275 0.361 0.664 0.236 ...
##  $ fractal_dimension_worst: num  0.1189 0.089 0.0876 0.173 0.0768 ...

head(Cancer_mama)

##   diagnosis radius_mean texture_mean perimeter_mean area_mean smoothness_mean
## 1         M       17.99        10.38         122.80    1001.0         0.11840
## 2         M       20.57        17.77         132.90    1326.0         0.08474
## 3         M       19.69        21.25         130.00    1203.0         0.10960
## 4         M       11.42        20.38          77.58     386.1         0.14250
## 5         M       20.29        14.34         135.10    1297.0         0.10030
## 6         M       12.45        15.70          82.57     477.1         0.12780
##   compactness_mean concavity_mean concave_points_mean symmetry_mean
## 1          0.27760         0.3001             0.14710        0.2419
## 2          0.07864         0.0869             0.07017        0.1812
## 3          0.15990         0.1974             0.12790        0.2069
## 4          0.28390         0.2414             0.10520        0.2597
## 5          0.13280         0.1980             0.10430        0.1809
## 6          0.17000         0.1578             0.08089        0.2087
##   fractal_dimension_mean radius_se texture_se perimeter_se area_se
## 1                0.07871    1.0950     0.9053        8.589  153.40
## 2                0.05667    0.5435     0.7339        3.398   74.08
## 3                0.05999    0.7456     0.7869        4.585   94.03
## 4                0.09744    0.4956     1.1560        3.445   27.23
## 5                0.05883    0.7572     0.7813        5.438   94.44
## 6                0.07613    0.3345     0.8902        2.217   27.19
##   smoothness_se compactness_se concavity_se concave_points_se symmetry_se
## 1      0.006399        0.04904      0.05373           0.01587     0.03003
## 2      0.005225        0.01308      0.01860           0.01340     0.01389
## 3      0.006150        0.04006      0.03832           0.02058     0.02250
## 4      0.009110        0.07458      0.05661           0.01867     0.05963
## 5      0.011490        0.02461      0.05688           0.01885     0.01756
## 6      0.007510        0.03345      0.03672           0.01137     0.02165
##   fractal_dimension_se radius_worst texture_worst perimeter_worst area_worst
## 1             0.006193        25.38         17.33          184.60     2019.0
## 2             0.003532        24.99         23.41          158.80     1956.0
## 3             0.004571        23.57         25.53          152.50     1709.0
## 4             0.009208        14.91         26.50           98.87      567.7
## 5             0.005115        22.54         16.67          152.20     1575.0
## 6             0.005082        15.47         23.75          103.40      741.6
##   smoothness_worst compactness_worst concavity_worst concave_points_worst
## 1           0.1622            0.6656          0.7119               0.2654
## 2           0.1238            0.1866          0.2416               0.1860
## 3           0.1444            0.4245          0.4504               0.2430
## 4           0.2098            0.8663          0.6869               0.2575
## 5           0.1374            0.2050          0.4000               0.1625
## 6           0.1791            0.5249          0.5355               0.1741
##   symmetry_worst fractal_dimension_worst
## 1         0.4601                 0.11890
## 2         0.2750                 0.08902
## 3         0.3613                 0.08758
## 4         0.6638                 0.17300
## 5         0.2364                 0.07678
## 6         0.3985                 0.12440

#create_report(Cancer_mama)
plot_missing(Cancer_mama) #graficar cuantos NA´s hay por variable

plot_histogram(Cancer_mama)

plot_correlation(Cancer_mama)

Crear árbol de desiciones

#Creo una copia de dataframe original
Cancer_mama_facto <- Cancer_mama
Cancer_mama_facto$diagnosis <- as.factor(Cancer_mama$diagnosis)

str(Cancer_mama_facto)

## 'data.frame':    569 obs. of  31 variables:
##  $ diagnosis              : Factor w/ 2 levels "B","M": 2 2 2 2 2 2 2 2 2 2 ...
##  $ radius_mean            : num  18 20.6 19.7 11.4 20.3 ...
##  $ texture_mean           : num  10.4 17.8 21.2 20.4 14.3 ...
##  $ perimeter_mean         : num  122.8 132.9 130 77.6 135.1 ...
##  $ area_mean              : num  1001 1326 1203 386 1297 ...
##  $ smoothness_mean        : num  0.1184 0.0847 0.1096 0.1425 0.1003 ...
##  $ compactness_mean       : num  0.2776 0.0786 0.1599 0.2839 0.1328 ...
##  $ concavity_mean         : num  0.3001 0.0869 0.1974 0.2414 0.198 ...
##  $ concave_points_mean    : num  0.1471 0.0702 0.1279 0.1052 0.1043 ...
##  $ symmetry_mean          : num  0.242 0.181 0.207 0.26 0.181 ...
##  $ fractal_dimension_mean : num  0.0787 0.0567 0.06 0.0974 0.0588 ...
##  $ radius_se              : num  1.095 0.543 0.746 0.496 0.757 ...
##  $ texture_se             : num  0.905 0.734 0.787 1.156 0.781 ...
##  $ perimeter_se           : num  8.59 3.4 4.58 3.44 5.44 ...
##  $ area_se                : num  153.4 74.1 94 27.2 94.4 ...
##  $ smoothness_se          : num  0.0064 0.00522 0.00615 0.00911 0.01149 ...
##  $ compactness_se         : num  0.049 0.0131 0.0401 0.0746 0.0246 ...
##  $ concavity_se           : num  0.0537 0.0186 0.0383 0.0566 0.0569 ...
##  $ concave_points_se      : num  0.0159 0.0134 0.0206 0.0187 0.0188 ...
##  $ symmetry_se            : num  0.03 0.0139 0.0225 0.0596 0.0176 ...
##  $ fractal_dimension_se   : num  0.00619 0.00353 0.00457 0.00921 0.00511 ...
##  $ radius_worst           : num  25.4 25 23.6 14.9 22.5 ...
##  $ texture_worst          : num  17.3 23.4 25.5 26.5 16.7 ...
##  $ perimeter_worst        : num  184.6 158.8 152.5 98.9 152.2 ...
##  $ area_worst             : num  2019 1956 1709 568 1575 ...
##  $ smoothness_worst       : num  0.162 0.124 0.144 0.21 0.137 ...
##  $ compactness_worst      : num  0.666 0.187 0.424 0.866 0.205 ...
##  $ concavity_worst        : num  0.712 0.242 0.45 0.687 0.4 ...
##  $ concave_points_worst   : num  0.265 0.186 0.243 0.258 0.163 ...
##  $ symmetry_worst         : num  0.46 0.275 0.361 0.664 0.236 ...
##  $ fractal_dimension_worst: num  0.1189 0.089 0.0876 0.173 0.0768 ...

arbol_cancer <-rpart(diagnosis ~., data=Cancer_mama_facto)
rpart.plot(arbol_cancer)

prp(arbol_cancer, extra=2, prefix= "fracción\n")

Conclusión

Entre el 33% de casos, el 94% presenta un cancer de mama maligno mientras que el 9% representa un diagnostico benigno.

Generar la Red Neuronal

#Copia para convertir a numericos 
Cancer_num <- Cancer_mama

# diagnosis como numérica (M=1, B=0)
Cancer_num$diagnosis <- factor(Cancer_num$diagnosis, levels = c("B","M"))

Generar la mejor Red Neuronal

#Grafica la mejor red, con menor error
red_neuronal <- neuralnet(diagnosis~., data=Cancer_num)
plot(red_neuronal, rep= "best")

Dividir la información en entrenamiento y test

#Split repartido en 20 y 80
set.seed(123)
idx <- createDataPartition(Cancer_num$diagnosis, p = 0.8, list = FALSE)
entrenamiento <- Cancer_num[idx, ]
prueba        <- Cancer_num[-idx, ]

Generar la Red Neuronal

#Creación de red neuronal
set.seed(123)
ctrl <- trainControl(method = "cv", number = 10)
Red_mama <- train(
  diagnosis ~ ., data = entrenamiento,
  method = "nnet",
  preProcess = c("center","scale"),
  trControl = ctrl,
  tuneLength = 5,
  trace = FALSE,
  MaxNWts = 20000
)

Predicciones

# 4) Predicciones (factores con mismos niveles)
pred_train <- predict(Red_mama, entrenamiento, type = "raw")
pred_test  <- predict(Red_mama, prueba,        type = "raw")
pred_train <- factor(pred_train, levels = levels(entrenamiento$diagnosis))
pred_test  <- factor(pred_test,  levels = levels(prueba$diagnosis))

#Matriz de Confusión del Resultado de prueba
#mcrp_cancer_mama <- confusionMatrix(resultado_prueba_red_mama, prueba$diagnosis)
#mcrp_cancer_mama

Matriz de Confusión de la Red Neuronal

# 5) Matrices de confusión
mcre_cancer_mama <- confusionMatrix(pred_train, entrenamiento$diagnosis)
mcrp_cancer_mama <- confusionMatrix(pred_test,  prueba$diagnosis)

mcre_cancer_mama

## Confusion Matrix and Statistics
## 
##           Reference
## Prediction   B   M
##          B 286   0
##          M   0 170
##                                      
##                Accuracy : 1          
##                  95% CI : (0.9919, 1)
##     No Information Rate : 0.6272     
##     P-Value [Acc > NIR] : < 2.2e-16  
##                                      
##                   Kappa : 1          
##                                      
##  Mcnemar's Test P-Value : NA         
##                                      
##             Sensitivity : 1.0000     
##             Specificity : 1.0000     
##          Pos Pred Value : 1.0000     
##          Neg Pred Value : 1.0000     
##              Prevalence : 0.6272     
##          Detection Rate : 0.6272     
##    Detection Prevalence : 0.6272     
##       Balanced Accuracy : 1.0000     
##                                      
##        'Positive' Class : B          
## 

mcrp_cancer_mama

## Confusion Matrix and Statistics
## 
##           Reference
## Prediction  B  M
##          B 70  1
##          M  1 41
##                                           
##                Accuracy : 0.9823          
##                  95% CI : (0.9375, 0.9978)
##     No Information Rate : 0.6283          
##     P-Value [Acc > NIR] : <2e-16          
##                                           
##                   Kappa : 0.9621          
##                                           
##  Mcnemar's Test P-Value : 1               
##                                           
##             Sensitivity : 0.9859          
##             Specificity : 0.9762          
##          Pos Pred Value : 0.9859          
##          Neg Pred Value : 0.9762          
##              Prevalence : 0.6283          
##          Detection Rate : 0.6195          
##    Detection Prevalence : 0.6283          
##       Balanced Accuracy : 0.9811          
##                                           
##        'Positive' Class : B               
##