Merge pull request #59 from yaricom/performance-optimizations

Performance optimizations and refactoring

README.md

@@ -5,7 +5,7 @@
 
 [![version](https://img.shields.io/github/v/tag/yaricom/goNEAT.svg?sort=semver)](https://github.com/yaricom/goNEAT/releases/latest)
 [![Build Status](https://travis-ci.org/yaricom/goNEAT.svg?branch=master)](https://travis-ci.org/yaricom/goNEAT) [![GoDoc](https://godoc.org/github.com/yaricom/goNEAT/neat?status.svg)](https://godoc.org/github.com/yaricom/goNEAT/neat)
-[![Go version](https://img.shields.io/badge/go-1.17-blue.svg)](https://github.com/moovweb/gvm)
+[![Go version](https://img.shields.io/badge/go-1.18-blue.svg)](https://github.com/moovweb/gvm)
 [![license](https://img.shields.io/github/license/yaricom/goNEAT.svg)](https://github.com/yaricom/goNEAT/blob/master/LICENSE)
 [![yaricom/goNEAT](https://tokei.rs/b1/github/yaricom/goNEAT?category=lines)](https://github.com/yaricom/goNEAT)
 [![Sourcegraph](https://sourcegraph.com/github.com/yaricom/goNEAT/-/badge.svg)](https://sourcegraph.com/github.com/yaricom/goNEAT?badge)
@@ -26,7 +26,7 @@ and their interconnections).
 ## Minimum requirements
 | Requirement | Notes            |
 |-------------|------------------|
-| Go version  | Go1.17 or higher |
+| Go version  | Go1.18 or higher |
 
 ## Releases
 

examples/performance/performance_test.go

@@ -0,0 +1,155 @@
+package performance
+
+import (
+	"bytes"
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+	"github.com/yaricom/goNEAT/v4/neat/genetics"
+	"github.com/yaricom/goNEAT/v4/neat/network"
+	"testing"
+)
+
+const genomeStr = `genomestart 0
+trait 1 0.1 0 0 0 0 0 0 0
+trait 2 0.2 0 0 0 0 0 0 0
+trait 3 0.3 0 0 0 0 0 0 0
+node 1 1 1 1 SigmoidSteepenedActivation
+node 2 2 1 1 SigmoidSteepenedActivation
+node 3 1 1 1 SigmoidSteepenedActivation
+node 4 1 1 1 SigmoidSteepenedActivation
+node 5 1 1 1 SigmoidSteepenedActivation
+node 6 3 1 1 SigmoidSteepenedActivation
+node 7 1 1 3 SigmoidSteepenedActivation
+node 8 1 0 2 SigmoidSteepenedActivation
+node 30 3 0 0 SigmoidSteepenedActivation
+node 71 1 0 0 SigmoidSteepenedActivation
+node 266 1 0 0 SigmoidSteepenedActivation
+node 1685 1 0 0 SigmoidSteepenedActivation
+node 1811 1 0 0 SigmoidSteepenedActivation
+node 3436 1 0 0 SigmoidSteepenedActivation
+node 3627 1 0 0 SigmoidSteepenedActivation
+node 4077 1 0 0 SigmoidSteepenedActivation
+node 6640 2 0 0 SigmoidSteepenedActivation
+gene 1 1 8 -4.08386891981225 false 1 -4.08386891981225 true
+gene 2 2 8 -2.1690052056140163 false 2 -2.1690052056140163 true
+gene 3 3 8 -10.699778103607123 false 3 -10.699778103607123 true
+gene 1 4 8 -9.342647981011918 false 4 -9.342647981011918 true
+gene 2 5 8 6.996472488106343 false 5 6.996472488106343 true
+gene 2 6 8 2.2286271196270824 false 6 2.2286271196270824 true
+gene 2 7 8 5.305934250174099 false 7 5.305934250174099 true
+gene 1 1 30 5.327875888469306 false 121 5.327875888469306 true
+gene 1 30 8 5.684209149585454 false 122 5.684209149585454 true
+gene 3 3 30 0.9475646340769113 false 271 0.9475646340769113 true
+gene 3 5 30 1.2529446872848236 false 439 1.2529446872848236 true
+gene 1 1 71 2.0097007140389365 false 583 2.0097007140389365 true
+gene 1 71 8 -2.6692540269378506 false 584 -2.6692540269378506 true
+gene 1 3 71 -4.073066558696308 false 834 -4.073066558696308 true
+gene 3 2 71 2.0095928118285507 false 1223 2.0095928118285507 true
+gene 3 2 266 3.4187907757610367 false 1627 3.4187907757610367 true
+gene 3 266 71 -3.2830938391621856 false 1628 -3.2830938391621856 true
+gene 1 6 71 -3.463234141766563 false 2528 -3.463234141766563 true
+gene 3 3 266 -2.281968137235494 false 3056 -2.281968137235494 true
+gene 2 4 266 3.497559408686352 false 4212 3.497559408686352 true
+gene 3 30 71 -2.8430156534468214 false 4678 -2.8430156534468214 true
+gene 1 7 71 -3.45518023982917 false 6526 -3.45518023982917 true
+gene 1 71 1685 2.338576667094656 false 7008 2.338576667094656 true
+gene 1 1685 8 -0.2433441365216774 false 7009 -0.2433441365216774 true
+gene 1 30 1811 -1.1814519616174946 false 7485 -1.1814519616174946 true
+gene 1 1811 8 -0.9537417818325291 false 7486 -0.9537417818325291 true
+gene 2 7 266 2.748821688559035 false 9914 2.748821688559035 true
+gene 2 1811 266 3.908454872776794 false 10435 3.908454872776794 true
+gene 3 6 266 7.145812334508661 false 12872 7.145812334508661 true
+gene 1 71 3436 -0.09282935033826101 false 13446 -0.09282935033826101 true
+gene 1 3436 1685 2.021217174697969 false 13447 2.021217174697969 true
+gene 2 1811 3627 -3.0538854223916507 false 14092 -3.0538854223916507 true
+gene 2 3627 266 -3.0405574668478694 false 14093 -3.0405574668478694 true
+gene 1 71 4077 6.692035802696705 false 15777 6.692035802696705 true
+gene 1 4077 1685 -3.413636512977078 false 15778 -3.413636512977078 true
+gene 1 3627 30 1.11052014349801 true 16364 1.11052014349801 true
+gene 2 1811 4077 5.8503253679873435 false 17006 5.8503253679873435 true
+gene 2 2 30 1.6963498266122063 false 17650 1.6963498266122063 true
+gene 1 2 3627 -6.386739930810184 false 18335 -6.386739930810184 true
+gene 1 266 4077 -3.4520706013634195 false 22326 -3.4520706013634195 true
+gene 1 4077 3436 4.013733453814073 false 24107 4.013733453814073 true
+gene 1 3 6640 -0.4098657935148693 false 24713 -0.4098657935148693 true
+gene 1 6640 71 -1.753803731332276 false 24714 -1.753803731332276 true
+gene 2 3627 4077 -0.28877942085982367 false 25611 -0.28877942085982367 true
+genomeend 0`
+
+const genomeStrSimple = `genomestart 131
+trait 1 0.1 0 0 0 0 0 0 0
+trait 2 0.2 0 0 0 0 0 0 0
+trait 3 0.3 0 0 0 0 0 0 0
+node 1 1 1 3 SigmoidSteepenedActivation
+node 2 1 1 1 SigmoidSteepenedActivation
+node 3 1 1 1 SigmoidSteepenedActivation
+node 4 1 1 1 SigmoidSteepenedActivation
+node 5 1 1 1 SigmoidSteepenedActivation
+node 6 3 0 2 SigmoidSteepenedActivation
+node 7 1 0 2 SigmoidSteepenedActivation
+node 9 1 0 0 SigmoidSteepenedActivation
+gene 1 1 6 2.2319059895867506 false 1 2.2319059895867506 true
+gene 2 2 6 -1.2321454922952315 false 2 -1.2321454922952315 true
+gene 3 3 6 -0.49043752407567043 false 3 -0.49043752407567043 true
+gene 1 4 6 0.46891774508325124 false 4 0.46891774508325124 true
+gene 2 5 6 -2.4300089957414337 false 5 -2.4300089957414337 true
+gene 3 1 7 -1.6431550383146705 false 6 -1.6431550383146705 true
+gene 1 2 7 0.5398285078832726 false 7 0.5398285078832726 true
+gene 1 3 7 0.13384471791198438 false 8 0.13384471791198438 true
+gene 3 4 7 2.6321796987645034 false 9 2.6321796987645034 true
+gene 1 5 7 -0.09060533978387858 false 10 -0.09060533978387858 true
+gene 3 3 9 -3.089340847206661 false 13 -3.089340847206661 true
+gene 3 9 6 0.5616266601637229 false 14 0.5616266601637229 true
+genomeend 131`
+
+func buildNetworkFromGenome(str string) (*network.Network, error) {
+	buf := bytes.NewBufferString(str)
+	reader, err := genetics.NewGenomeReader(buf, genetics.PlainGenomeEncoding)
+	if err != nil {
+		return nil, err
+	}
+	if genome, err := reader.Read(); err != nil {
+		return nil, err
+	} else {
+		return genome.Genesis(0)
+	}
+}
+
+func TestNetwork_MaxActivationDepth_FromGenome(t *testing.T) {
+	net, err := buildNetworkFromGenome(genomeStr)
+	require.NoError(t, err)
+
+	str := logNetworkActivationPath(net, t)
+	t.Log(str)
+
+	depth, err := net.MaxActivationDepth()
+	assert.NoError(t, err, "failed to calculate max depth")
+	assert.Equal(t, 9, depth)
+}
+
+func TestNetwork_MaxActivationDepthCap_FromGenome(t *testing.T) {
+	net, err := buildNetworkFromGenome(genomeStr)
+	require.NoError(t, err)
+
+	limit := 5
+	depth, err := net.MaxActivationDepthWithCap(limit)
+	require.EqualError(t, err, network.ErrMaximalNetDepthExceeded.Error())
+	assert.Equal(t, limit, depth)
+}
+
+func Test_PrintAllActivationDepthPaths_simple(t *testing.T) {
+	net, err := buildNetworkFromGenome(genomeStrSimple)
+	require.NoError(t, err)
+
+	str := logNetworkActivationPath(net, t)
+	t.Log(str)
+	expected := "1 -> 6\n2 -> 6\n3 -> 6\n4 -> 6\n5 -> 6\n3 -> 9 -> 6\n1 -> 7\n2 -> 7\n3 -> 7\n4 -> 7\n5 -> 7\n"
+	assert.Equal(t, expected, str)
+}
+
+func logNetworkActivationPath(net *network.Network, t *testing.T) string {
+	buf := bytes.NewBufferString("")
+	err := network.PrintAllActivationDepthPaths(net, buf)
+	require.NoError(t, err)
+	return buf.String()
+}

examples/pole/cart2pole.go

@@ -3,11 +3,11 @@ package pole
 import (
 	"context"
 	"fmt"
-	"github.com/yaricom/goNEAT/v3/experiment"
-	"github.com/yaricom/goNEAT/v3/experiment/utils"
-	"github.com/yaricom/goNEAT/v3/neat"
-	"github.com/yaricom/goNEAT/v3/neat/genetics"
-	"github.com/yaricom/goNEAT/v3/neat/network"
+	"github.com/yaricom/goNEAT/v4/experiment"
+	"github.com/yaricom/goNEAT/v4/experiment/utils"
+	"github.com/yaricom/goNEAT/v4/neat"
+	"github.com/yaricom/goNEAT/v4/neat/genetics"
+	"github.com/yaricom/goNEAT/v4/neat/network"
 	"math"
 	"sort"
 )
@@ -140,6 +140,10 @@ func (e *cartDoublePoleGenerationEvaluator) GenerationEvaluate(ctx context.Conte
 		// the organism champion
 		champion := currSpecies.FindChampion()
 		championFitness := champion.Fitness
+		championPhenotype, err := champion.Phenotype()
+		if err != nil {
+			return err
+		}
 
 		// Now check to make sure the champion can do 100'000 evaluations
 		cartPole.nonMarkovLong = true
@@ -174,7 +178,7 @@ func (e *cartDoublePoleGenerationEvaluator) GenerationEvaluate(ctx context.Conte
 							// The champion needs to be flushed here because it may have
 							// leftover activation from its last test run that could affect
 							// its recurrent memory
-							if _, err = champion.Phenotype.Flush(); err != nil {
+							if _, err = championPhenotype.Flush(); err != nil {
 								return err
 							}
 
@@ -231,12 +235,9 @@ func (e *cartDoublePoleGenerationEvaluator) GenerationEvaluate(ctx context.Conte
 	}
 
 	if epoch.Solved {
-		// print winner organism
+		// print winner organism's statistics
 		org := epoch.Champion
-		// The max depth of the network to be activated
-		if depth, err := org.Phenotype.MaxActivationDepthFast(0); err == nil {
-			neat.InfoLog(fmt.Sprintf("Activation depth of the winner: %d\n", depth))
-		}
+		utils.PrintActivationDepth(org, true)
 
 		genomeFile := "pole2_winner_genome"
 		// Prints the winner organism to file!
@@ -246,7 +247,7 @@ func (e *cartDoublePoleGenerationEvaluator) GenerationEvaluate(ctx context.Conte
 			neat.InfoLog(fmt.Sprintf("Generation #%d winner's genome dumped to: %s\n", epoch.Id, orgPath))
 		}
 
-		// Prints the winner organism's Phenotype to the Cytoscape JSON file!
+		// Prints the winner organism's phenotype to the Cytoscape JSON file!
 		if orgPath, err := utils.WriteGenomeCytoscapeJSON(genomeFile, e.OutputPath, org, epoch); err != nil {
 			neat.ErrorLog(fmt.Sprintf("Failed to dump winner organism's phenome Cytoscape JSON graph, reason: %s\n", err))
 		} else {
@@ -261,7 +262,11 @@ func (e *cartDoublePoleGenerationEvaluator) GenerationEvaluate(ctx context.Conte
 // orgEvaluate method evaluates fitness of the organism for cart double pole-balancing task
 func (e *cartDoublePoleGenerationEvaluator) orgEvaluate(organism *genetics.Organism, cartPole *CartPole) (winner bool, err error) {
 	// Try to balance a pole now
-	organism.Fitness, err = cartPole.evalNet(organism.Phenotype, e.ActionType)
+	phenotype, err := organism.Phenotype()
+	if err != nil {
+		return false, err
+	}
+	organism.Fitness, err = cartPole.evalNet(phenotype, e.ActionType)
 	if err != nil {
 		return false, err
 	}
@@ -316,7 +321,7 @@ func (p *CartPole) evalNet(net *network.Network, actionType ActionType) (steps f
 
 	p.resetState()
 
-	netDepth, err := net.MaxActivationDepthFast(0) // The max depth of the network to be activated
+	netDepth, err := net.MaxActivationDepthWithCap(0) // The max depth of the network to be activated
 	if err != nil {
 		neat.WarnLog(fmt.Sprintf(
 			"Failed to estimate activation depth of the network, skipping evaluation: %s", err))

examples/pole/cart2pole_test.go

@@ -4,9 +4,9 @@ import (
 	"fmt"
 	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/require"
-	"github.com/yaricom/goNEAT/v3/examples/utils"
-	experiment2 "github.com/yaricom/goNEAT/v3/experiment"
-	"github.com/yaricom/goNEAT/v3/neat"
+	"github.com/yaricom/goNEAT/v4/examples/utils"
+	experiment2 "github.com/yaricom/goNEAT/v4/experiment"
+	"github.com/yaricom/goNEAT/v4/neat"
 	"math/rand"
 	"testing"
 )

examples/pole/cartpole.go

@@ -3,11 +3,11 @@ package pole
 import (
 	"context"
 	"fmt"
-	"github.com/yaricom/goNEAT/v3/experiment"
-	"github.com/yaricom/goNEAT/v3/experiment/utils"
-	"github.com/yaricom/goNEAT/v3/neat"
-	"github.com/yaricom/goNEAT/v3/neat/genetics"
-	"github.com/yaricom/goNEAT/v3/neat/network"
+	"github.com/yaricom/goNEAT/v4/experiment"
+	"github.com/yaricom/goNEAT/v4/experiment/utils"
+	"github.com/yaricom/goNEAT/v4/neat"
+	"github.com/yaricom/goNEAT/v4/neat/genetics"
+	"github.com/yaricom/goNEAT/v4/neat/network"
 	"math"
 	"math/rand"
 )
@@ -75,11 +75,9 @@ func (e *cartPoleGenerationEvaluator) GenerationEvaluate(ctx context.Context, po
 	}
 
 	if epoch.Solved {
-		// print winner organism
+		// print winner organism's statistics
 		org := epoch.Champion
-		if depth, err := org.Phenotype.MaxActivationDepthFast(0); err == nil {
-			neat.InfoLog(fmt.Sprintf("Activation depth of the winner: %d\n", depth))
-		}
+		utils.PrintActivationDepth(org, true)
 
 		genomeFile := "pole1_winner_genome"
 		// Prints the winner organism to file!
@@ -89,7 +87,7 @@ func (e *cartPoleGenerationEvaluator) GenerationEvaluate(ctx context.Context, po
 			neat.InfoLog(fmt.Sprintf("Generation #%d winner's genome dumped to: %s\n", epoch.Id, orgPath))
 		}
 
-		// Prints the winner organism's Phenotype to the Cytoscape JSON file!
+		// Prints the winner organism's phenotype to the Cytoscape JSON file!
 		if orgPath, err := utils.WriteGenomeCytoscapeJSON(genomeFile, e.OutputPath, org, epoch); err != nil {
 			neat.ErrorLog(fmt.Sprintf("Failed to dump winner organism's phenome Cytoscape JSON graph, reason: %s\n", err))
 		} else {
@@ -103,8 +101,13 @@ func (e *cartPoleGenerationEvaluator) GenerationEvaluate(ctx context.Context, po
 
 // orgEvaluate evaluates provided organism for cart pole balancing task
 func (e *cartPoleGenerationEvaluator) orgEvaluate(organism *genetics.Organism) (bool, error) {
+	phenotype, err := organism.Phenotype()
+	if err != nil {
+		return false, err
+	}
+
 	// Try to balance a pole now
-	if fitness, err := e.runCart(organism.Phenotype); err != nil {
+	if fitness, err := e.runCart(phenotype); err != nil {
 		return false, nil
 	} else {
 		organism.Fitness = float64(fitness)
@@ -150,7 +153,7 @@ func (e *cartPoleGenerationEvaluator) runCart(net *network.Network) (steps int,
 		thetaDot = float64(rand.Int31()%3000)/1000.0 - 1.5
 	}
 
-	netDepth, err := net.MaxActivationDepthFast(0) // The max depth of the network to be activated
+	netDepth, err := net.MaxActivationDepthWithCap(0) // The max depth of the network to be activated
 	if err != nil {
 		neat.WarnLog(fmt.Sprintf(
 			"Failed to estimate maximal depth of the network with loop.\nUsing default depth: %d", netDepth))

examples/pole/cartpole_test.go

@@ -4,9 +4,9 @@ import (
 	"fmt"
 	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/require"
-	"github.com/yaricom/goNEAT/v3/examples/utils"
-	experiment2 "github.com/yaricom/goNEAT/v3/experiment"
-	"github.com/yaricom/goNEAT/v3/neat"
+	"github.com/yaricom/goNEAT/v4/examples/utils"
+	experiment2 "github.com/yaricom/goNEAT/v4/experiment"
+	"github.com/yaricom/goNEAT/v4/neat"
 	"math/rand"
 	"testing"
 	"time"

examples/utils/utils.go

@@ -2,8 +2,8 @@ package utils
 
 import (
 	"github.com/pkg/errors"
-	"github.com/yaricom/goNEAT/v3/neat"
-	"github.com/yaricom/goNEAT/v3/neat/genetics"
+	"github.com/yaricom/goNEAT/v4/neat"
+	"github.com/yaricom/goNEAT/v4/neat/genetics"
 	"os"
 )