func TestNeuronAddOutlinkNonRecurrent(t *testing.T) {
ng.SeedRandom()
madeNonRecurrentLink := false
madeRecurrentLink := false
for i := 0; i < 100; i++ {
xnorCortex := BasicCortex()
neuron := xnorCortex.NeuronUUIDMap()["hidden-neuron1"]
ok, mutateResult := NeuronAddOutlinkNonRecurrent(neuron)
if !ok {
continue
}
outboundConnection := mutateResult.(*ng.OutboundConnection)
if neuron.IsConnectionRecurrent(outboundConnection) {
madeRecurrentLink = true
} else {
madeNonRecurrentLink = true
}
}
assert.True(t, madeNonRecurrentLink)
assert.False(t, madeRecurrentLink)
}
func init() {
logg.LogKeys["MAIN"] = true
logg.LogKeys["DEBUG"] = false
logg.LogKeys["NEURVOLVE"] = true
logg.LogKeys["NODE_STATE"] = false
ng.SeedRandom()
}
func TestNeuronAddOutlinkRecurrent(t *testing.T) {
ng.SeedRandom()
madeNonRecurrentLink := false
madeRecurrentLink := false
for i := 0; i < 100; i++ {
xnorCortex := BasicCortex()
neuron := xnorCortex.NeuronUUIDMap()["hidden-neuron1"]
numOutlinksBefore := len(neuron.Outbound)
ok, mutateResult := NeuronAddOutlinkRecurrent(neuron)
if !ok {
continue
}
outboundConnection := mutateResult.(*ng.OutboundConnection)
numOutlinksAfter := len(neuron.Outbound)
assert.Equals(t, numOutlinksBefore+1, numOutlinksAfter)
if neuron.IsConnectionRecurrent(outboundConnection) {
// the first time we make a nonRecurrentInlink,
// test the network out
if madeRecurrentLink == false {
// make sure the network actually works
examples := ng.XnorTrainingSamples()
fitness := xnorCortex.Fitness(examples)
assert.True(t, fitness >= 0)
}
madeRecurrentLink = true
} else {
// the first time we make a nonRecurrentInlink,
// test the network out
if madeNonRecurrentLink == false {
// make sure the network doesn't totally break
examples := ng.XnorTrainingSamples()
fitness := xnorCortex.Fitness(examples)
assert.True(t, fitness >= 0)
}
madeNonRecurrentLink = true
}
}
assert.True(t, madeNonRecurrentLink)
assert.True(t, madeRecurrentLink)
}
func TestNeuronMutateActivation(t *testing.T) {
ng.SeedRandom()
neuron := &ng.Neuron{
ActivationFunction: ng.EncodableSigmoid(),
NodeId: ng.NewNeuronId("neuron", 0.25),
Bias: 10,
}
NeuronMutateActivation(neuron)
assert.True(t, neuron.ActivationFunction != nil)
assert.True(t, neuron.ActivationFunction.Name != ng.EncodableSigmoid().Name)
}
func TestOutspliceNonRecurrent(t *testing.T) {
ng.SeedRandom()
numOutspliced := 0
numIterations := 100
for i := 0; i < numIterations; i++ {
cortex := BasicCortex()
numNeuronsBefore := len(cortex.Neurons)
neuronLayerMapBefore := cortex.NeuronLayerMap()
ok, mutateResult := OutspliceNonRecurrent(cortex)
neuron := mutateResult.(*ng.Neuron)
if !ok {
continue
} else {
numOutspliced += 1
}
assert.True(t, neuron.ActivationFunction != nil)
numNeuronsAfter := len(cortex.Neurons)
assert.Equals(t, numNeuronsAfter, numNeuronsBefore+1)
// should have 1 outbound and inbound
assert.Equals(t, len(neuron.Inbound), 1)
assert.Equals(t, len(neuron.Outbound), 1)
// should be no recurrent connections
assert.Equals(t, len(neuron.RecurrentInboundConnections()), 0)
assert.Equals(t, len(neuron.RecurrentOutboundConnections()), 0)
// should have one more layer (this makes an assumption
// about the BasicCortex architecture)
numLayersBefore := len(neuronLayerMapBefore)
numLayersAfter := len(cortex.NeuronLayerMap())
assert.Equals(t, numLayersAfter, numLayersBefore+1)
// run network make sure it runs
examples := ng.XnorTrainingSamples()
fitness := cortex.Fitness(examples)
assert.True(t, fitness >= 0)
}
assert.True(t, numOutspliced > 0)
}
func RunTopologyMutatingTrainer() bool {
ng.SeedRandom()
// training set
examples := ng.XnorTrainingSamples()
// create netwwork with topology capable of solving XNOR
cortex := ng.BasicCortex()
// verify it can not yet solve the training set (since training would be useless in that case)
verified := cortex.Verify(examples)
if verified {
panic("neural net already trained, nothing to do")
}
shc := &nv.StochasticHillClimber{
FitnessThreshold: ng.FITNESS_THRESHOLD,
MaxIterationsBeforeRestart: 20000,
MaxAttempts: 10,
WeightSaturationRange: []float64{-10000, 10000},
}
tmt := &nv.TopologyMutatingTrainer{
MaxAttempts: 100,
MaxIterationsBeforeRestart: 5,
StochasticHillClimber: shc,
}
cortexTrained, succeeded := tmt.TrainExamples(cortex, examples)
if succeeded {
logg.LogTo("MAIN", "Successfully trained net: %v", ng.JsonString(cortexTrained))
// verify it can now solve the training set
verified = cortexTrained.Verify(examples)
if !verified {
logg.LogTo("MAIN", "Failed to verify neural net")
succeeded = false
}
}
if !succeeded {
logg.LogTo("MAIN", "Failed to train neural net")
}
return succeeded
}
func TestAddNeuronNonRecurrent(t *testing.T) {
ng.SeedRandom()
numUnableToAdd := 0
numIterations := 100
for i := 0; i < numIterations; i++ {
cortex := BasicCortex()
numNeuronsBefore := len(cortex.Neurons)
ok, mutateResult := AddNeuronNonRecurrent(cortex)
if !ok {
numUnableToAdd += 1
continue
}
neuron := mutateResult.(*ng.Neuron)
assert.True(t, neuron.ActivationFunction != nil)
numNeuronsAfter := len(cortex.Neurons)
addedNeuron := numNeuronsAfter == numNeuronsBefore+1
assert.True(t, addedNeuron)
if !addedNeuron {
break
}
// should have 1 outbound and inbound
assert.Equals(t, len(neuron.Inbound), 1)
assert.Equals(t, len(neuron.Outbound), 1)
// should be no recurrent connections
assert.Equals(t, len(neuron.RecurrentInboundConnections()), 0)
assert.Equals(t, len(neuron.RecurrentOutboundConnections()), 0)
// run network make sure it runs
examples := ng.XnorTrainingSamples()
fitness := cortex.Fitness(examples)
assert.True(t, fitness >= 0)
}
assert.True(t, numUnableToAdd <= (numIterations/3))
}
func DisabledTestUnmarshalCortexFitness(t *testing.T) {
ng.SeedRandom()
logg.LogKeys["DEBUG"] = true
logg.LogKeys["NEURGO"] = true
// this test is disabled by default since it can take a long time
// this was a real net that was evolved by the topological mutator
// before it went through the memetic step.
// jsonString := `{"NodeId":{"UUID":"cortex","NodeType":"CORTEX","LayerIndex":0},"Sensors":[{"NodeId":{"UUID":"sensor","NodeType":"SENSOR","LayerIndex":0},"VectorLength":2,"Outbound":[{"NodeId":{"UUID":"neuron","NodeType":"NEURON","LayerIndex":0.25}},{"NodeId":{"UUID":"todo=394057419","NodeType":"NEURON","LayerIndex":0.25}}]}],"Neurons":[{"NodeId":{"UUID":"neuron","NodeType":"NEURON","LayerIndex":0.25},"Bias":0,"Inbound":[{"NodeId":{"UUID":"sensor","NodeType":"SENSOR","LayerIndex":0},"Weights":[20,20]}],"Outbound":[{"NodeId":{"UUID":"todo=3342881449","NodeType":"NEURON","LayerIndex":0.375}}],"ActivationFunction":{"Name":"sigmoid"}},{"NodeId":{"UUID":"todo=3342881449","NodeType":"NEURON","LayerIndex":0.375},"Bias":-0.36421027459743627,"Inbound":[{"NodeId":{"UUID":"neuron","NodeType":"NEURON","LayerIndex":0.25},"Weights":[1.8610633947514623]},{"NodeId":{"UUID":"todo=394057419","NodeType":"NEURON","LayerIndex":0.25},"Weights":[0.45355591271633067]}],"Outbound":[{"NodeId":{"UUID":"actuator","NodeType":"ACTUATOR","LayerIndex":0.5}}],"ActivationFunction":{"Name":"sigmoid"}},{"NodeId":{"UUID":"todo=394057419","NodeType":"NEURON","LayerIndex":0.25},"Bias":0.4665982575854781,"Inbound":[{"NodeId":{"UUID":"sensor","NodeType":"SENSOR","LayerIndex":0},"Weights":[0.6618610678776169,3.065256532332561]}],"Outbound":[{"NodeId":{"UUID":"todo=3342881449","NodeType":"NEURON","LayerIndex":0.375}}],"ActivationFunction":{"Name":"tanh"}}],"Actuators":[{"NodeId":{"UUID":"actuator","NodeType":"ACTUATOR","LayerIndex":0.5},"VectorLength":1,"Inbound":[{"NodeId":{"UUID":"todo=3342881449","NodeType":"NEURON","LayerIndex":0.375},"Weights":null}]}]}`
jsonString2 := `{"NodeId":{"UUID":"cortex","NodeType":"CORTEX","LayerIndex":0},"Sensors":[{"NodeId":{"UUID":"sensor","NodeType":"SENSOR","LayerIndex":0},"VectorLength":2,"Outbound":[{"NodeId":{"UUID":"neuron","NodeType":"NEURON","LayerIndex":0.25}},{"NodeId":{"UUID":"todo=8550407276","NodeType":"NEURON","LayerIndex":0.25}}]}],"Neurons":[{"NodeId":{"UUID":"neuron","NodeType":"NEURON","LayerIndex":0.25},"Bias":0,"Inbound":[{"NodeId":{"UUID":"sensor","NodeType":"SENSOR","LayerIndex":0},"Weights":[20,20]}],"Outbound":[{"NodeId":{"UUID":"todo=6014372025","NodeType":"NEURON","LayerIndex":0.375}}],"ActivationFunction":{"Name":"sigmoid"}},{"NodeId":{"UUID":"todo=6014372025","NodeType":"NEURON","LayerIndex":0.375},"Bias":1.216286900747618,"Inbound":[{"NodeId":{"UUID":"neuron","NodeType":"NEURON","LayerIndex":0.25},"Weights":[1.767095335462158]},{"NodeId":{"UUID":"todo=8550407276","NodeType":"NEURON","LayerIndex":0.25},"Weights":[1.0905530851150242]}],"Outbound":[{"NodeId":{"UUID":"actuator","NodeType":"ACTUATOR","LayerIndex":0.5}}],"ActivationFunction":{"Name":"sigmoid"}},{"NodeId":{"UUID":"todo=8550407276","NodeType":"NEURON","LayerIndex":0.25},"Bias":-0.23064534306604623,"Inbound":[{"NodeId":{"UUID":"sensor","NodeType":"SENSOR","LayerIndex":0},"Weights":[-2.069786342256813,-2.0791073119872916]}],"Outbound":[{"NodeId":{"UUID":"todo=6014372025","NodeType":"NEURON","LayerIndex":0.375}}],"ActivationFunction":{"Name":"sigmoid"}}],"Actuators":[{"NodeId":{"UUID":"actuator","NodeType":"ACTUATOR","LayerIndex":0.5},"VectorLength":1,"Inbound":[{"NodeId":{"UUID":"todo=6014372025","NodeType":"NEURON","LayerIndex":0.375},"Weights":null}]}]}`
jsonBytes := []byte(jsonString2)
cortex := &ng.Cortex{}
err := json.Unmarshal(jsonBytes, cortex)
if err != nil {
log.Fatal(err)
}
assert.True(t, err == nil)
shc := &StochasticHillClimber{
FitnessThreshold: ng.FITNESS_THRESHOLD,
MaxIterationsBeforeRestart: 20000,
MaxAttempts: 10,
}
examples := ng.XnorTrainingSamples()
cortexTrained, succeeded := shc.TrainExamples(cortex, examples)
assert.True(t, succeeded)
// verify it can now solve the training set
verified := cortexTrained.Verify(examples)
assert.True(t, verified)
fitness := cortexTrained.Fitness(examples)
log.Printf("Final fitness: %v", fitness)
}
func TestAddNeuronRecurrent(t *testing.T) {
ng.SeedRandom()
numAdded := 0
numIterations := 100
for i := 0; i < numIterations; i++ {
cortex := BasicCortex()
numNeuronsBefore := len(cortex.Neurons)
ok, mutateResult := AddNeuronRecurrent(cortex)
neuron := mutateResult.(*ng.Neuron)
if !ok {
continue
} else {
numAdded += 1
}
assert.True(t, neuron != nil)
assert.True(t, neuron.ActivationFunction != nil)
numNeuronsAfter := len(cortex.Neurons)
addedNeuron := numNeuronsAfter == numNeuronsBefore+1
if !addedNeuron {
logg.LogPanic("AddNeuronRecurrent %v did not add exactly one neuron. before: %v after: %v", i, numNeuronsBefore, numNeuronsAfter)
}
// run network make sure it runs
examples := ng.XnorTrainingSamples()
fitness := cortex.Fitness(examples)
assert.True(t, fitness >= 0)
}
assert.True(t, numAdded > 0)
}
func RunStochasticHillClimber() {
ng.SeedRandom()
// training set -- todo: examples := ng.XnorTrainingSamples()
examples := ng.XnorTrainingSamples()
// create netwwork with topology capable of solving XNOR
cortex := ng.XnorCortexUntrained()
// verify it can not yet solve the training set (since training would be useless in that case)
verified := cortex.Verify(examples)
if verified {
panic("neural net already trained, nothing to do")
}
shc := &nv.StochasticHillClimber{
FitnessThreshold: ng.FITNESS_THRESHOLD,
MaxIterationsBeforeRestart: 2000,
MaxAttempts: 2000,
WeightSaturationRange: []float64{-100 * math.Pi, 100 * math.Pi},
}
cortexTrained, _, succeeded := shc.TrainExamples(cortex, examples)
if !succeeded {
panic("could not train neural net")
}
// verify it can now solve the training set
verified = cortexTrained.Verify(examples)
if !verified {
panic("could not verify neural net")
}
logg.LogTo("DEBUG", "trained cortex: %v", cortexTrained)
logg.Log("done")
}
func (shc *StochasticHillClimber) Train(cortex *ng.Cortex, scape Scape) (resultNeuralNet *ng.Cortex, fitness float64, succeeded bool) {
shc.validate()
numAttempts := 0
fittestNeuralNet := cortex.Copy()
resultNeuralNet = cortex
// Apply NN to problem and save fitness
fitness = scape.Fitness(fittestNeuralNet)
logg.LogTo("MAIN", "Initial fitness: %v", fitness)
if fitness > shc.FitnessThreshold {
succeeded = true
return
}
for i := 0; ; i++ {
// Save the genotype
candidateNeuralNet := fittestNeuralNet.Copy()
// Perturb synaptic weights and biases
PerturbParameters(candidateNeuralNet, shc.WeightSaturationRange)
// Re-Apply NN to problem
candidateFitness := scape.Fitness(candidateNeuralNet)
logg.LogTo("DEBUG", "candidate fitness: %v", fitness)
// If fitness of perturbed NN is higher, discard original NN and keep new
// If fitness of original is higher, discard perturbed and keep old.
if candidateFitness > fitness {
logg.LogTo("MAIN", "i: %v candidateFitness: %v > fitness: %v", i, candidateFitness, fitness)
i = 0
fittestNeuralNet = candidateNeuralNet
resultNeuralNet = candidateNeuralNet.Copy()
fitness = candidateFitness
}
if candidateFitness > shc.FitnessThreshold {
logg.LogTo("MAIN", "candidateFitness: %v > Threshold. Success at i=%v", candidateFitness, i)
succeeded = true
break
}
if ng.IntModuloProper(i, shc.MaxIterationsBeforeRestart) {
logg.LogTo("MAIN", "** restart hill climber. fitness: %f i/max: %d/%d", fitness, numAttempts, shc.MaxAttempts)
numAttempts += 1
i = 0
shc.resetParametersToRandom(fittestNeuralNet)
ng.SeedRandom()
}
if numAttempts >= shc.MaxAttempts {
succeeded = false
break
}
}
return
}
func TestNeuronAddInlinkNonRecurrent(t *testing.T) {
ng.SeedRandom()
madeNonRecurrentInlink := false
madeRecurrentInlink := false
firstTime := true
// since it's stochastic, repeat the operation many times and make
// sure that it always produces expected behavior
for i := 0; i < 100; i++ {
xnorCortex := ng.XnorCortex()
sensor := xnorCortex.Sensors[0]
neuron := xnorCortex.NeuronUUIDMap()["output-neuron"]
hiddenNeuron1 := xnorCortex.NeuronUUIDMap()["hidden-neuron1"]
targetLayerIndex := hiddenNeuron1.NodeId.LayerIndex
// add a new neuron at the same layer index as the hidden neurons
hiddenNeuron3 := &ng.Neuron{
ActivationFunction: ng.EncodableSigmoid(),
NodeId: ng.NewNeuronId("hidden-neuron3", targetLayerIndex),
Bias: -30,
}
hiddenNeuron3.Init()
xnorCortex.Neurons = append(xnorCortex.Neurons, hiddenNeuron3)
weights := randomWeights(sensor.VectorLength)
sensor.ConnectOutbound(hiddenNeuron3)
hiddenNeuron3.ConnectInboundWeighted(sensor, weights)
ok, mutateResult := NeuronAddInlinkNonRecurrent(neuron)
if !ok {
continue
}
inboundConnection := mutateResult.(*ng.InboundConnection)
if neuron.IsInboundConnectionRecurrent(inboundConnection) {
madeRecurrentInlink = true
} else {
madeNonRecurrentInlink = true
}
if firstTime == true {
// only two possibilities - the hiddenNeuron3 or the
// sensor. if it was the sensor, then the hiddenNeuron3
// is "dangliing" and so lets connect it
if inboundConnection.NodeId.UUID == "sensor" {
weights2 := randomWeights(1)
hiddenNeuron3.ConnectOutbound(neuron)
neuron.ConnectInboundWeighted(hiddenNeuron3, weights2)
}
// run network make sure it runs
examples := ng.XnorTrainingSamples()
fitness := xnorCortex.Fitness(examples)
assert.True(t, fitness >= 0)
firstTime = false
}
}
assert.True(t, madeNonRecurrentInlink)
assert.False(t, madeRecurrentInlink)
}
func TestOutspliceRecurrent(t *testing.T) {
logg.LogKeys["TEST"] = true
logg.LogKeys["NEURVOLVE"] = true
ng.SeedRandom()
numOutspliced := 0
numOutsplicedWithNewLayer := 0
numOutsplicedWithExistingLayer := 0
numIterations := 100
for i := 0; i < numIterations; i++ {
cortex := BasicCortexRecurrent()
// run network make sure it runs
examplesBefore := ng.XnorTrainingSamples()
fitnessBefore := cortex.Fitness(examplesBefore)
assert.True(t, fitnessBefore >= 0)
// recreate network
cortex = BasicCortexRecurrent()
numNeuronsBefore := len(cortex.Neurons)
neuronLayerMapBefore := cortex.NeuronLayerMap()
ok, mutateResult := OutspliceRecurrent(cortex)
neuron := mutateResult.(*ng.Neuron)
if !ok {
continue
} else {
numOutspliced += 1
}
assert.True(t, neuron.ActivationFunction != nil)
numNeuronsAfter := len(cortex.Neurons)
assert.Equals(t, numNeuronsAfter, numNeuronsBefore+1)
// should have 1 outbound and inbound
assert.Equals(t, len(neuron.Inbound), 1)
assert.Equals(t, len(neuron.Outbound), 1)
// increment counter if layer added
numLayersBefore := len(neuronLayerMapBefore)
numLayersAfter := len(cortex.NeuronLayerMap())
if numLayersAfter == numLayersBefore+1 {
numOutsplicedWithNewLayer += 1
} else {
numOutsplicedWithExistingLayer += 1
}
// run network make sure it runs
examples := ng.XnorTrainingSamples()
fitness := cortex.Fitness(examples)
assert.True(t, fitness >= 0)
}
assert.True(t, numOutspliced > 0)
assert.True(t, numOutsplicedWithNewLayer > 0)
assert.True(t, numOutsplicedWithExistingLayer > 0)
}
func (tmt *TopologyMutatingTrainer) Train(cortex *ng.Cortex, scape Scape) (fittestCortex *ng.Cortex, succeeded bool) {
ng.SeedRandom()
shc := tmt.StochasticHillClimber
includeNonTopological := false
mutators := CortexMutatorsNonRecurrent(includeNonTopological)
originalCortex := cortex.Copy()
currentCortex := cortex
// Apply NN to problem and save fitness
logg.LogTo("MAIN", "Get initial fitness")
fitness := scape.Fitness(currentCortex)
logg.LogTo("MAIN", "Initial fitness: %v", fitness)
if fitness > shc.FitnessThreshold {
succeeded = true
return
}
for i := 0; ; i++ {
logg.LogTo("MAIN", "Before mutate. i/max: %d/%d", i, tmt.MaxAttempts)
// before we mutate the cortex, we need to init it,
// otherwise things like Outsplice will fail because
// there are no DataChan's.
currentCortex.Init()
// mutate the network
randInt := RandomIntInRange(0, len(mutators))
mutator := mutators[randInt]
ok, _ := mutator(currentCortex)
if !ok {
logg.LogTo("MAIN", "Mutate didn't work, retrying...")
continue
}
isValid := currentCortex.Validate()
if !isValid {
logg.LogPanic("Cortex did not validate")
}
filenameJson := fmt.Sprintf("cortex-%v.json", i)
currentCortex.MarshalJSONToFile(filenameJson)
filenameSvg := fmt.Sprintf("cortex-%v.svg", i)
currentCortex.RenderSVGFile(filenameSvg)
logg.LogTo("MAIN", "Post mutate cortex svg: %v json: %v", filenameSvg, filenameJson)
logg.LogTo("MAIN", "Run stochastic hill climber..")
// memetic step: call stochastic hill climber and see if it can solve it
fittestCortex, _, succeeded = shc.Train(currentCortex, scape)
logg.LogTo("MAIN", "stochastic hill climber finished. succeeded: %v", succeeded)
if succeeded {
succeeded = true
break
}
if i >= tmt.MaxAttempts {
succeeded = false
break
}
if ng.IntModuloProper(i, tmt.MaxIterationsBeforeRestart) {
logg.LogTo("MAIN", "** Restart . i/max: %d/%d", i, tmt.MaxAttempts)
currentCortex = originalCortex.Copy()
isValid := currentCortex.Validate()
if !isValid {
currentCortex.Repair() // TODO: remove workaround
isValid = currentCortex.Validate()
if !isValid {
logg.LogPanic("Cortex could not be repaired")
}
}
}
}
return
}