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kjetil b halvorsen
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There is a simple geometric explanation. Try the following example in R and recall that the first principal component maximizes variance.

library(ggplot2)

n <- 400
z <- matrix(rnorm(n * 2), nrow = n, ncol = 2)
y <- sample(c(-1,1), size = n, replace = TRUE)

# PCA helps
df.good <- data.frame(
    y = as.factor(y), 
    x = z + tcrossprod(y, c(10, 0))
)
qplot(x.1, x.2, data = df.good, color = y) + coord_equal()

# PCA hurts
df.bad <- data.frame(
    y = as.factor(y), 
    x = z %*% diag(c(10, 1), 2, 2) + tcrossprod(y, c(0, 8))
)
qplot(x.1, x.2, data = df.bad, color = y) + coord_equal()
library(ggplot2)

n <- 400
z <- matrix(rnorm(n * 2), nrow = n, ncol = 2)
y <- sample(c(-1,1), size = n, replace = TRUE)

# PCA helps
df.good <- data.frame(
    y = as.factor(y), 
    x = z + tcrossprod(y, c(10, 0))
)
qplot(x.1, x.2, data = df.good, color = y) + coord_equal()

# PCA hurts
df.bad <- data.frame(
    y = as.factor(y), 
    x = z %*% diag(c(10, 1), 2, 2) + tcrossprod(y, c(0, 8))
)
qplot(x.1, x.2, data = df.bad, color = y) + coord_equal()

PCA Helps   

PCA helps

The direction of maximal variance is horizontal, and the classes are separated horizontally.

PCA Hurts   

PCA hurts

The direction of maximal variance is horizontal, but the classes are separated vertically

There is a simple geometric explanation. Try the following example in R and recall that the first principal component maximizes variance.

library(ggplot2)

n <- 400
z <- matrix(rnorm(n * 2), nrow = n, ncol = 2)
y <- sample(c(-1,1), size = n, replace = TRUE)

# PCA helps
df.good <- data.frame(
    y = as.factor(y), 
    x = z + tcrossprod(y, c(10, 0))
)
qplot(x.1, x.2, data = df.good, color = y) + coord_equal()

# PCA hurts
df.bad <- data.frame(
    y = as.factor(y), 
    x = z %*% diag(c(10, 1), 2, 2) + tcrossprod(y, c(0, 8))
)
qplot(x.1, x.2, data = df.bad, color = y) + coord_equal()

PCA Helps  PCA helps

The direction of maximal variance is horizontal, and the classes are separated horizontally.

PCA Hurts  PCA hurts

The direction of maximal variance is horizontal, but the classes are separated vertically

There is a simple geometric explanation. Try the following example in R and recall that the first principal component maximizes variance.

library(ggplot2)

n <- 400
z <- matrix(rnorm(n * 2), nrow = n, ncol = 2)
y <- sample(c(-1,1), size = n, replace = TRUE)

# PCA helps
df.good <- data.frame(
    y = as.factor(y), 
    x = z + tcrossprod(y, c(10, 0))
)
qplot(x.1, x.2, data = df.good, color = y) + coord_equal()

# PCA hurts
df.bad <- data.frame(
    y = as.factor(y), 
    x = z %*% diag(c(10, 1), 2, 2) + tcrossprod(y, c(0, 8))
)
qplot(x.1, x.2, data = df.bad, color = y) + coord_equal()

PCA Helps 

PCA helps

The direction of maximal variance is horizontal, and the classes are separated horizontally.

PCA Hurts 

PCA hurts

The direction of maximal variance is horizontal, but the classes are separated vertically

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vqv
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There is a simple geometric explanation. Try the following example in R and recall that the first principal component maximizes variance.

library(ggplot2)

n <- 400
z <- matrix(rnorm(n * 2), nrow = n, ncol = 2)
y <- sample(c(-1,1), size = n, replace = TRUE)

# PCA helps
df.good <- data.frame(
    y = as.factor(y), 
    x = z + tcrossprod(y, c(10, 0))
)
qplot(x.1, x.2, data = df.good, color = y) + coord_equal()

# PCA hurts
df.bad <- data.frame(
    y = as.factor(y), 
    x = z %*% diag(c(10, 1), 2, 2) + tcrossprod(y, c(0, 8))
)
qplot(x.1, x.2, data = df.bad, color = y) + coord_equal()

PCA Helps PCA helps

The direction of maximal variance is horizontal, and the classes are separated horizontally.

PCA Hurts PCA hurts

The direction of maximal variance is horizontal, but the classes are separated vertically