From 650621542afba098a54699c5ff24f9c30d934ec6 Mon Sep 17 00:00:00 2001
From: JOlths <71876557+JOlths@users.noreply.github.com>
Date: Wed, 1 Mar 2023 11:55:22 +0100
Subject: [PATCH 1/3] Described tutorial part 4 in different steps.

---
 R/p004.R | 124 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 124 insertions(+)
 create mode 100644 R/p004.R

diff --git a/R/p004.R b/R/p004.R
new file mode 100644
index 0000000..85baa4f
--- /dev/null
+++ b/R/p004.R
@@ -0,0 +1,124 @@
+#part 1 introduction ####
+##create inputs
+inputs <- c(1,2,3,2.5)
+inputs <- matrix(inputs, ncol = 4) 
+inputs
+
+##create weights
+weights <- c(
+  c(0.2, 0.8, -0.5, 1.0),
+  c(0.5, -0.91, 0.26, -0.5),
+  c(-0.26, -0.27, 0.17, 0.87)
+)
+
+weights <- matrix(weights, ncol = 4, byrow = T) #change into matrix for easier dot product, use byrow = TRUE to get the familiar shape in the tutorial
+weights <- t(weights) # transpose the weights (this can also be obtained by removing byrow = TRUE in the previous line)
+weights
+
+##create biases
+biases <- c(2,3,0.5)
+biases <- matrix(biases, ncol = 3, byrow = T)
+biases
+
+#create output
+outputs <- (inputs %*% weights) + biases
+outputs <- inputs %*% weights
+outputs
+
+## part 2: multiple inputs ####
+#create more inputs
+multiple_inputs <- c(
+  c(1,2,3,2.5),
+  c(2.0,5.0,-1.0,2.0),
+  c(-1.5,2.7,3.3,-0.8)
+)
+multiple_inputs <- matrix(multiple_inputs, ncol = 4, byrow = T)
+multiple_inputs
+
+# we still use the same weights as defined in part 1, but for the new layer (layer 2) we will define new weights
+weights # weights layer 1 as previously defined
+
+weights2 <- c(
+  c(0.1,-0.14,0.5),
+  c(-0.5, 0.12, -0.33),
+  c(-0.44, 0.73, -0.13)
+) #notice how the weights changed in dimension (3,3) relative to the first set of weights (3,4). This is because of the three outputs of the first layer
+weights2 <- matrix(weights2, ncol = 3, byrow = T)
+weights2 <- t(weights2)
+weights2
+
+#adjust biases of the first layer, because of the greater output and because R doesn't do well summing with one-array matrices. So we got to duplicate the biases for every array of outcomes
+biases1 <- c(2,3,0.5)
+biases1 <- matrix(rep(biases1,3), ncol = 3, byrow = T)
+biases1
+
+#create new set of biases for the second layer
+biases2 <- c(-1, 2, -0.5)
+biases2 <- matrix(rep(biases2, 3), ncol = 3, byrow = T)
+biases2
+
+#define new output line: layer1_outputs
+layer1_outputs <- multiple_inputs %*% weights + biases1
+layer1_outputs
+
+#give output of layer 1 as input into layer 2 and give the respective weights and biases
+layer2_outputs <- layer1_outputs %*% weights2 + biases2
+
+#show output of layer 2
+layer2_outputs
+
+## Part 3 create object class ####
+#create more inputs
+set.seed(115)
+X <- matrix(
+  c(1,2,3,2.5,
+    2.0,5.0,-1.0,2.0,
+    -1.5,2.7,3.3,-0.8),
+  nrow = 3, ncol = 4, byrow = T)
+X
+
+#define class
+setClass("DenseLayer", slots = c(n_inputs = 'numeric', n_neurons = 'numeric'))
+
+#set init (constructor)
+setGeneric('init', function(layer) standardGeneric('init'))
+
+#set method for init
+setMethod('init', 'DenseLayer',
+          function(layer) {
+            n_weights <- layer@n_inputs * layer@n_neurons
+            weights <- matrix(rnorm(n_weights),
+                              nrow = layer@n_inputs,
+                              ncol = layer@n_neurons
+            )
+            attr(layer, 'weights') <- 0.10 * weights
+            attr(layer, 'biases') <- rep(0, layer@n_neurons)
+            layer
+          })
+
+#set method for forward function
+setGeneric('forward', function(layer, inputs) standardGeneric('forward'))
+setMethod('forward', 'DenseLayer',
+          function(layer, inputs){
+            attr(layer, 'outputs') <- inputs %*% layer@weights + layer@biases
+            layer
+          })
+
+#create wrapper for initializing layer object
+LayerDense <- function(n_inputs, n_neurons){
+  init(new('DenseLayer', n_inputs=n_inputs, n_neurons=n_neurons))
+}
+
+#create first layer
+layer1 <- LayerDense(n_inputs = 4, n_neurons = 5)
+
+layer1 <- forward(layer1, X)
+
+layer1@outputs
+
+#create second layer
+layer2 <- LayerDense(n_inputs = 5, n_neurons = 10)
+
+layer2 <- forward(layer2, layer1@outputs)
+
+layer2@outputs
\ No newline at end of file

From 96b924e7e5567b94dffe34dc5e147bcc47a90085 Mon Sep 17 00:00:00 2001
From: JOlths <71876557+JOlths@users.noreply.github.com>
Date: Thu, 2 Mar 2023 10:48:32 +0100
Subject: [PATCH 2/3] Created R code for episode 5 in two different parts.

---
 R/p005.R | 79 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 79 insertions(+)
 create mode 100644 R/p005.R

diff --git a/R/p005.R b/R/p005.R
new file mode 100644
index 0000000..603eaab
--- /dev/null
+++ b/R/p005.R
@@ -0,0 +1,79 @@
+## Neural Network from p4 ####
+#create more inputs
+set.seed(0)
+X <- matrix(
+  c(1,2,3,2.5,
+    2.0,5.0,-1.0,2.0,
+    -1.5,2.7,3.3,-0.8),
+  nrow = 3, ncol = 4, byrow = T)
+X
+
+## part 1: simple activation ####
+inputs = c(0,2,-1,3.3,-2.7,1.1,2.2,-100)
+outputs = c()
+
+# first method
+for (i in inputs){
+  if (i>0){
+    outputs <- append(outputs, i)
+  } else {
+    outputs <- append(outputs, 0)
+  }
+}
+
+# second method
+for (i in inputs){
+  outputs <- append(outputs, max(0,i))
+}
+
+outputs
+
+
+## part 2: neural network with activation ####
+#activation function.
+Activation_ReLU <- function(inputs){
+  return(pmax(inputs,0))
+}
+
+#define class
+setClass("DenseLayer", slots = c(n_inputs = 'numeric', n_neurons = 'numeric'))
+
+#set init (constructor)
+setGeneric('init', function(layer) standardGeneric('init'))
+
+#set method for init
+setMethod('init', 'DenseLayer',
+          function(layer) {
+            n_weights <- layer@n_inputs * layer@n_neurons
+            weights <- matrix(rnorm(n_weights),
+                              nrow = layer@n_inputs,
+                              ncol = layer@n_neurons
+            )
+            attr(layer, 'weights') <- 0.10 * weights
+            attr(layer, 'biases') <- rep(0, layer@n_neurons)
+            layer
+          })
+
+#set method for forward function
+setGeneric('forward', function(layer, inputs) standardGeneric('forward'))
+setMethod('forward', 'DenseLayer',
+          function(layer, inputs){
+            attr(layer, 'outputs') <- inputs %*% layer@weights + layer@biases
+            layer
+          })
+
+#create wrapper for initializing layer object
+LayerDense <- function(n_inputs, n_neurons){
+  init(new('DenseLayer', n_inputs=n_inputs, n_neurons=n_neurons))
+}
+
+
+
+#create first layer
+layer1 <- LayerDense(n_inputs = 4, n_neurons = 5)
+
+layer1 <- forward(layer1, X)
+
+layer1@outputs
+
+Activation_ReLU(layer1@outputs)

From 531eb1c0422243e42c4c5c02f85422e6697a607f Mon Sep 17 00:00:00 2001
From: JOlths <71876557+JOlths@users.noreply.github.com>
Date: Tue, 21 Mar 2023 00:01:53 +0100
Subject: [PATCH 3/3] Wrote code for part 006 of the tutorial in R studio (with
 custom spiral dataset function).

---
 R/p006.R | 154 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 154 insertions(+)
 create mode 100644 R/p006.R

diff --git a/R/p006.R b/R/p006.R
new file mode 100644
index 0000000..4f85d60
--- /dev/null
+++ b/R/p006.R
@@ -0,0 +1,154 @@
+##part 1 ####
+#example outputs
+layer_outputs <- c(4.8, 1.21, 2.385)
+
+#exponentiated list of outputs
+exp_values <- c()
+
+#exponentiation of the layer outputs to prevent for example negative values
+#without losing meaning of difference in outputs
+for (output in layer_outputs) {
+  exp_values = c(exp_values, exp(output))
+}
+
+#show values(expected: 121.510418   3.353485  10.859063)
+exp_values
+
+##part 2: normalization####
+#get sum of exp. values
+norm_base <- sum(exp_values)
+norm_base
+
+#insert normalized values of exponential outputs
+norm_values <- c()
+
+for (value in exp_values) {
+  norm_values <- c(norm_values, value/norm_base)
+}
+
+#show normalized output
+norm_values
+
+#show that total is 100%
+sum(norm_values)
+
+##part 3: functional code####
+layer_outputs <- matrix(c(4.8, 1.21, 2.385), ncol=3)
+exp_values <- exp(layer_outputs)
+norm_values <- exp_values / sum(exp_values)
+norm_values
+
+##part 4: ####
+layer_outputs <- matrix(c(4.8, 1.21, 2.385,
+                          8.9, -1.81, 0.2, 
+                          1.41, 1.051, 0.026), ncol = 3,
+                        byrow = T)
+
+layer_outputs
+matrix(apply(layer_outputs, 1, max))
+matrix(mapply("-", layer_outputs, apply(layer_outputs, 1, max)), nrow = ncol(layer_outputs))
+
+exp_values <- exp(layer_outputs)
+exp_values
+
+sums_exp <- rowSums(exp_values)
+sums_exp
+
+#norm_values <- exp_values / sums_exp
+
+matrix(mapply("/", exp_values, sums_exp), nrow = ncol(exp_values))
+
+##part 5: implement in existing neural network from p005####
+#activation function.
+Activation_ReLU <- function(inputs){
+  return(pmax(inputs,0))
+}
+
+Activation_Softmax <- function(inputs){
+  exp_values <- exp(matrix(mapply("-", inputs, apply(inputs, 1, max)), ncol = ncol(inputs)))
+  probabilities <- matrix(mapply("/", exp_values, rowSums(exp_values)), ncol = ncol(exp_values)) 
+  return(probabilities)
+}
+
+Activation_Softmax(matrix(c(4,0,3,1,2,3), ncol = 2, byrow = T))
+
+#define class
+setClass("DenseLayer", slots = c(n_inputs = 'numeric', n_neurons = 'numeric'))
+
+#set init (constructor)
+setGeneric('init', function(layer) standardGeneric('init'))
+
+#set method for init
+setMethod('init', 'DenseLayer',
+          function(layer) {
+            n_weights <- layer@n_inputs * layer@n_neurons
+            weights <- matrix(rnorm(n_weights),
+                              nrow = layer@n_inputs,
+                              ncol = layer@n_neurons
+            )
+            attr(layer, 'weights') <- 0.10 * weights
+            attr(layer, 'biases') <- rep(0, layer@n_neurons)
+            layer
+          })
+
+#set method for forward function
+setGeneric('forward', function(layer, inputs) standardGeneric('forward'))
+setMethod('forward', 'DenseLayer',
+          function(layer, inputs){
+            attr(layer, 'outputs') <- inputs %*% layer@weights + layer@biases
+            layer
+          })
+
+#create wrapper for initializing layer object
+LayerDense <- function(n_inputs, n_neurons){
+  init(new('DenseLayer', n_inputs=n_inputs, n_neurons=n_neurons))
+}
+
+#spiral dataset
+##define spiral dataset with 4 classes and 200 examples each ####
+N <- 100 #number of points per class
+D <- 2 #number of dimensions
+K <- 3 #number of classes
+X <- data.frame() #data matrix
+y <- data.frame() #class labels
+
+set.seed(308) #set random seed for testing purposes
+
+##creating dataset ####
+for (j in (1:K)){
+  r <- seq(0.05, 1, length.out=N) #radius
+  t <- seq((j-1)*4.7,j*4.7, length.out=N) + rnorm(N,sd=0.3) #theta ??
+  Xtemp <- data.frame(x = r*sin(t), y= r*cos(t))
+  ytemp <- data.frame(matrix(j,N,1))
+  X <- rbind(X, Xtemp)
+  y <- rbind(y, ytemp)
+}
+
+data <- cbind(X, y)
+colnames(data) <- c(colnames(X), 'label')
+data
+
+library(ggplot2)
+ggplot() +
+  geom_point(data = data, aes(x=x, y=y, color=as.character(label)), size=2) +
+  scale_color_discrete(name = 'Label') + coord_fixed(ratio = 0.6) +
+  theme(axis.ticks=element_blank(), panel.grid.major = element_blank(), panel.grid.minor = element_blank(), 
+        axis.text=element_blank(),legend.position = 'none')
+
+#make 'prediction' (no feedback yet, just testing softmax function)
+#create first layer
+#input is 2, since we have 2 variables (x,y)
+layer1 <- LayerDense(n_inputs = 2, n_neurons = 3)
+layer1 <- forward(layer1, as.matrix(X))
+layer1@outputs
+
+#input is 3, since output of layer 1 is 3 neurons. n_neurons is 3 since we have three classes.
+#ReLU activation is initialized here
+layer2 <- LayerDense(n_inputs = 3, n_neurons = 3)
+layer2 <- forward(layer2, Activation_ReLU(layer1@outputs))
+
+#view first 5 output with softmax activation
+head(Activation_Softmax(layer2@outputs))
+
+
+