Help me with my backprop implementation in Python

Question

EDIT2:

New training set...

Inputs:

[
 [0.0, 0.0], 
 [0.0, 1.0], 
 [0.0, 2.0], 
 [0.0, 3.0], 
 [0.0, 4.0], 
 [1.0, 0.0], 
 [1.0, 1.0], 
 [1.0, 2.0], 
 [1.0, 3.0], 
 [1.0, 4.0], 
 [2.0, 0.0], 
 [2.0, 1.0], 
 [2.0, 2.0], 
 [2.0, 3.0], 
 [2.0, 4.0], 
 [3.0, 0.0], 
 [3.0, 1.0], 
 [3.0, 2.0], 
 [3.0, 3.0], 
 [3.0, 4.0],
 [4.0, 0.0], 
 [4.0, 1.0], 
 [4.0, 2.0], 
 [4.0, 3.0], 
 [4.0, 4.0]
]

Outputs:

[
 [0.0], 
 [0.0], 
 [0.0], 
 [0.0], 
 [0.0], 
 [0.0], 
 [0.0], 
 [0.0], 
 [0.0], 
 [0.0], 
 [0.0], 
 [0.0], 
 [0.0], 
 [0.0], 
 [0.0], 
 [0.0], 
 [0.0], 
 [0.0], 
 [1.0], 
 [1.0], 
 [0.0], 
 [0.0], 
 [0.0], 
 [1.0], 
 [1.0]
]

EDIT1:

I have updated the question with my latest code. I fixed few minor issues but I am still getting the same output for all input combinations after the network has learned.

Here is the backprop algorithm explained: Backprop algorithm

---

Yes, this is a homework, to make this clear right at the beginning.

I am supposed to implement a simple backpropagation algorithm on a simple neural network.

I have chosen Python as a language of choice for this task and I have chosen a neural network like this:

3 layers: 1 input, 1 hidden, 1 output layer:

O         O

                    O

O         O

There is an integer on both inptut neurons and 1 or 0 on an output neuron.

Here is my entire implementation (a bit long). Bellow it I will choose just shorter relevant snippets where I think an error could be located at:

import os
import math
import Image
import random
from random import sample

#------------------------------ class definitions

class Weight:
    def __init__(self, fromNeuron, toNeuron):
        self.value = random.uniform(-0.5, 0.5)
        self.fromNeuron = fromNeuron
        self.toNeuron = toNeuron
        fromNeuron.outputWeights.append(self)
        toNeuron.inputWeights.append(self)
        self.delta = 0.0 # delta value, this will accumulate and after each training cycle used to adjust the weight value

    def calculateDelta(self, network):
        self.delta += self.fromNeuron.value * self.toNeuron.error

class Neuron:
    def __init__(self):
        self.value = 0.0        # the output
        self.idealValue = 0.0   # the ideal output
        self.error = 0.0        # error between output and ideal output
        self.inputWeights = []
        self.outputWeights = []

    def activate(self, network):
        x = 0.0;
        for weight in self.inputWeights:
            x += weight.value * weight.fromNeuron.value
        # sigmoid function
        if x < -320:
            self.value = 0
        elif x > 320:
            self.value = 1
        else:
            self.value = 1 / (1 + math.exp(-x))

class Layer:
    def __init__(self, neurons):
        self.neurons = neurons

    def activate(self, network):
        for neuron in self.neurons:
            neuron.activate(network)

class Network:
    def __init__(self, layers, learningRate):
        self.layers = layers
        self.learningRate = learningRate # the rate at which the network learns
        self.weights = []
        for hiddenNeuron in self.layers[1].neurons:
            for inputNeuron in self.layers[0].neurons:
                self.weights.append(Weight(inputNeuron, hiddenNeuron))
            for outputNeuron in self.layers[2].neurons:
                self.weights.append(Weight(hiddenNeuron, outputNeuron))

    def setInputs(self, inputs):
        self.layers[0].neurons[0].value = float(inputs[0])
        self.layers[0].neurons[1].value = float(inputs[1])

    def setExpectedOutputs(self, expectedOutputs):
        self.layers[2].neurons[0].idealValue = expectedOutputs[0]

    def calculateOutputs(self, expectedOutputs):
        self.setExpectedOutputs(expectedOutputs)
        self.layers[1].activate(self) # activation function for hidden layer
        self.layers[2].activate(self) # activation function for output layer        

    def calculateOutputErrors(self):
        for neuron in self.layers[2].neurons:
            neuron.error = (neuron.idealValue - neuron.value) * neuron.value * (1 - neuron.value)

    def calculateHiddenErrors(self):
        for neuron in self.layers[1].neurons:
            error = 0.0
            for weight in neuron.outputWeights:
                error += weight.toNeuron.error * weight.value
            neuron.error = error * neuron.value * (1 - neuron.value)

    def calculateDeltas(self):
        for weight in self.weights:
            weight.calculateDelta(self)

    def train(self, inputs, expectedOutputs):
        self.setInputs(inputs)
        self.calculateOutputs(expectedOutputs)
        self.calculateOutputErrors()
        self.calculateHiddenErrors()
        self.calculateDeltas()

    def learn(self):
        for weight in self.weights:
            weight.value += self.learningRate * weight.delta

    def calculateSingleOutput(self, inputs):
        self.setInputs(inputs)
        self.layers[1].activate(self)
        self.layers[2].activate(self)
        #return round(self.layers[2].neurons[0].value, 0)
        return self.layers[2].neurons[0].value


#------------------------------ initialize objects etc


inputLayer = Layer([Neuron() for n in range(2)])
hiddenLayer = Layer([Neuron() for n in range(100)])
outputLayer = Layer([Neuron() for n in range(1)])

learningRate = 0.5

network = Network([inputLayer, hiddenLayer, outputLayer], learningRate)

# just for debugging, the real training set is much larger
trainingInputs = [
    [0.0, 0.0],
    [1.0, 0.0],
    [2.0, 0.0],
    [0.0, 1.0],
    [1.0, 1.0],
    [2.0, 1.0],
    [0.0, 2.0],
    [1.0, 2.0],
    [2.0, 2.0]
]
trainingOutputs = [
    [0.0],
    [1.0],
    [1.0],
    [0.0],
    [1.0],
    [0.0],
    [0.0],
    [0.0],
    [1.0]
]

#------------------------------ let's train

for i in range(500):
    for j in range(len(trainingOutputs)):
        network.train(trainingInputs[j], trainingOutputs[j])
        network.learn()

#------------------------------ let's check


for pattern in trainingInputs:
    print network.calculateSingleOutput(pattern)

Now, the problem is that after learning the network seems to be returning a float number very close to 0.0 for all input combinations, even those that should be close to 1.0.

I train the network in 100 cycles, in each cycle I do:

For every set of inputs in the training set:

• Set network inputs
• Calculate outputs by using a sigmoid function
• Calculate errors in the output layer
• Calculate errors in the hidden layer
• Calculate weights' deltas

Then I adjust the weights based on the learning rate and the accumulated deltas.

Here is my activation function for neurons:

def activationFunction(self, network):
    """
    Calculate an activation function of a neuron which is a sum of all input weights * neurons where those weights start
    """
    x = 0.0;
    for weight in self.inputWeights:
        x += weight.value * weight.getFromNeuron(network).value
    # sigmoid function
    self.value = 1 / (1 + math.exp(-x))

This how I calculate the deltas:

def calculateDelta(self, network):
    self.delta += self.getFromNeuron(network).value * self.getToNeuron(network).error

This is a general flow of my algorithm:

for i in range(numberOfIterations):
    for k,expectedOutput in trainingSet.iteritems():
        coordinates = k.split(",")
        network.setInputs((float(coordinates[0]), float(coordinates[1])))
        network.calculateOutputs([float(expectedOutput)])
        network.calculateOutputErrors()
        network.calculateHiddenErrors()
        network.calculateDeltas()
    oldWeights = network.weights
    network.adjustWeights()
    network.resetDeltas()
    print "Iteration ", i
    j = 0
    for weight in network.weights:
        print "Weight W", weight.i, weight.j, ": ", oldWeights[j].value, " ............ Adjusted value : ", weight.value
        j += j

The last two lines of the output are:

0.552785449458 # this should be close to 1
0.552785449458 # this should be close to 0

It actually returns the output number for all input combinations.

Am I missing something?

Answer 1

Looks like what you get is nearly the initial state of Neuron (nearly self.idealValue). Maybe you should not initialize this Neuron before having actual data to provide ?

EDIT: OK, I looked a bit deeper in the code and simplified it a bit (will post simplified version below). Basically your code has two minor errors (looks like things you just overlooked), but that leads to a network that definitely won't work.

• you forgot to set value of expectedOutput in output layer while in learning phase. Without that the network definitely can't learn anything and will always be stuck with initial idealValue. (That is the bahavior that I spotted at first reading). This one could even have been spotted in your description of the training steps (and probably would have if you hadn't posted the code, this is one of the rare case I know where actually posting the code was hiding the error instead of making it obvious). You fixed this one after your EDIT1.
• when activating network in calculateSingleOutputs, you forgot to activate the hidden layer.

Obviously any of these two problems will lead to a disfonctional network.

Once corrected, it works (well, it does in my simplified version of your code).

The errors were not easy to spot because the initial code was much too complicated. You should think twice before introducing new classes or new methods. Not creating enough methods or classes will make code hard to read and to maintain, but creating too many may make it even harder to read and maintain. You have to find the right balance. My personal method to find this balance is to follow code smells and refactoring techniques wherever they lead me. Sometimes adding methods or creating classes, sometimes removing them. It's certainly not perfect but that's what works for me.

Below is my version of code after some refactoring applied. I spent about one hour changing your code but always keeping it functionaly equivalent. I took that as a good refactoring exercise, as the initial code was really horrible to read. After refactoring it just took 5 minutes to spot the problems.

import os
import math

"""
A simple backprop neural network. It has 3 layers:
    Input layer: 2 neurons
    Hidden layer: 2 neurons
    Output layer: 1 neuron
"""

class Weight:
    """
    Class representing a weight between two neurons
    """
    def __init__(self, value, from_neuron, to_neuron):
        self.value = value
        self.from_neuron = from_neuron
        from_neuron.outputWeights.append(self)
        self.to_neuron = to_neuron
        to_neuron.inputWeights.append(self)

        # delta value, this will accumulate and after each training cycle
        # will be used to adjust the weight value
        self.delta = 0.0

class Neuron:
    """
    Class representing a neuron.
    """
    def __init__(self):
        self.value = 0.0        # the output
        self.idealValue = 0.0   # the ideal output
        self.error = 0.0        # error between output and ideal output
        self.inputWeights = []    # weights that end in the neuron
        self.outputWeights = []  # weights that starts in the neuron

    def activate(self):
        """
        Calculate an activation function of a neuron which is 
        a sum of all input weights * neurons where those weights start
        """
        x = 0.0;
        for weight in self.inputWeights:
            x += weight.value * weight.from_neuron.value
        # sigmoid function
        self.value = 1 / (1 + math.exp(-x))

class Network:
    """
    Class representing a whole neural network. Contains layers.
    """
    def __init__(self, layers, learningRate, weights):
        self.layers = layers
        self.learningRate = learningRate    # the rate at which the network learns
        self.weights = weights

    def training(self, entries, expectedOutput):
        for i in range(len(entries)):
            self.layers[0][i].value = entries[i]
        for i in range(len(expectedOutput)):
            self.layers[2][i].idealValue = expectedOutput[i]
        for layer in self.layers[1:]:
            for n in layer:
                n.activate()
        for n in self.layers[2]:
            error = (n.idealValue - n.value) * n.value * (1 - n.value)
            n.error = error
        for n in self.layers[1]:
            error = 0.0
            for w in n.outputWeights:
                error += w.to_neuron.error * w.value
            n.error = error
        for w in self.weights:
            w.delta += w.from_neuron.value * w.to_neuron.error

    def updateWeights(self):
        for w in self.weights:
            w.value += self.learningRate * w.delta

    def calculateSingleOutput(self, entries):
        """
        Calculate a single output for input values.
        This will be used to debug the already learned network after training.
        """
        for i in range(len(entries)):
            self.layers[0][i].value = entries[i]
        # activation function for output layer
        for layer in self.layers[1:]:
            for n in layer:
                n.activate()
        print self.layers[2][0].value


#------------------------------ initialize objects etc

neurons = [Neuron() for n in range(5)]

w1 = Weight(-0.79, neurons[0], neurons[2])
w2 = Weight( 0.51, neurons[0], neurons[3])
w3 = Weight( 0.27, neurons[1], neurons[2])
w4 = Weight(-0.48, neurons[1], neurons[3])
w5 = Weight(-0.33, neurons[2], neurons[4])
w6 = Weight( 0.09, neurons[3], neurons[4])

weights = [w1, w2, w3, w4, w5, w6]
inputLayer  = [neurons[0], neurons[1]]
hiddenLayer = [neurons[2], neurons[3]]
outputLayer = [neurons[4]]
learningRate = 0.3
network = Network([inputLayer, hiddenLayer, outputLayer], learningRate, weights)

# just for debugging, the real training set is much larger
trainingSet = [([0.0,0.0],[0.0]),
               ([1.0,0.0],[1.0]),
               ([2.0,0.0],[1.0]),
               ([0.0,1.0],[0.0]),
               ([1.0,1.0],[1.0]),
               ([2.0,1.0],[0.0]),
               ([0.0,2.0],[0.0]),
               ([1.0,2.0],[0.0]),
               ([2.0,2.0],[1.0])]

#------------------------------ let's train
for i in range(100): # training iterations
    for entries, expectedOutput in trainingSet:
        network.training(entries, expectedOutput)
    network.updateWeights()

#network has learned, let's check
network.calculateSingleOutput((1, 0)) # this should be close to 1
network.calculateSingleOutput((0, 0)) # this should be close to 0

By the way there is still a third problem I didn't corrected (but easy to correct). If x is too big or too small (> 320 or < -320) math.exp() will raise an exception. This will occur if you apply for training iterations, say a few thousands. The most simple way to correct that I see is to check for value of x and if it's too big or too small set Neuron's value to 0 or 1 depending on the case, which is the limit value.