seekia/internal/genetics/geneticPrediction/geneticPrediction.go

// geneticPrediction provides functions to train and query neural network models
// These models are used to predict attributes such as eye color and autism from user genome files

package geneticPrediction

// I am a novice in the ways of neural networks.
// Machine learning experts should chime in and offer improvements.
// We have to make sure that model inference remains very fast
// 		Sorting matches by offspring total polygenic disease score will require inference on dozens of models for each match
// We could create slower models that provide more accurate predictions

import "seekia/resources/geneticReferences/polygenicDiseases"
import "seekia/resources/geneticReferences/traits"
import "seekia/resources/geneticPredictionModels"

import "seekia/internal/genetics/locusValue"
import "seekia/internal/genetics/readBiobankData"
import "seekia/internal/helpers"

import "gorgonia.org/gorgonia"
import "gorgonia.org/tensor"

import mathRand "math/rand/v2"
import "math"
import "bytes"
import "encoding/gob"
import "slices"
import "errors"


type NeuralNetwork struct{

	// ExprGraph is a data structure for a directed acyclic graph (of expressions).
	graph *gorgonia.ExprGraph

	// These are the weights for each layer of neurons
	weights1 *gorgonia.Node
	weights2 *gorgonia.Node
	weights3 *gorgonia.Node

	// This is the computed prediction
	prediction *gorgonia.Node
}

// This struct stores a user's training data
// Each TrainingData represents a single data example
// For example, the InputLayer is a column of neurons representing a user's genetics,
//		and the OutputLayer is a column representing their phenotype, such as eye color
type TrainingData struct{

	// InputLayer stores relevant rsID values for each attribute from the user's genomes
	// It also stores if each rsID is phased and if each rsID exists
	InputLayer []float32

	// OutputLayer stores user phenotype data as neurons
	// Each neuron represents an outcome
	// For example, for Eye Color, each neuron represents an eye color
	OutputLayer []float32
}


func EncodeTrainingDataObjectToBytes(inputTrainingData TrainingData)([]byte, error){

	buffer := new(bytes.Buffer)

	encoder := gob.NewEncoder(buffer)

	err := encoder.Encode(inputTrainingData)
	if (err != nil) { return nil, err }

	trainingDataBytes := buffer.Bytes()

	return trainingDataBytes, nil
}

func DecodeBytesToTrainingDataObject(inputTrainingData []byte)(TrainingData, error){

	if (inputTrainingData == nil){
		return TrainingData{}, errors.New("DecodeBytesToTrainingDataObject called with nil inputTrainingData.")
	}

	buffer := bytes.NewBuffer(inputTrainingData)

	decoder := gob.NewDecoder(buffer)

	var newTrainingData TrainingData

	err := decoder.Decode(&newTrainingData)
	if (err != nil){ return TrainingData{}, err }

	return newTrainingData, nil
}

// We use this to store a neural network's weights as a .gob file
type neuralNetworkForEncoding struct{

	// These are the weights for each layer of neurons
	Weights1 []float32
	Weights2 []float32
	Weights3 []float32

	Weights1Rows int
	Weights1Columns int
	Weights2Rows int
	Weights2Columns int
	Weights3Rows int
	Weights3Columns int
}

func EncodeNeuralNetworkObjectToBytes(inputNeuralNetwork NeuralNetwork)([]byte, error){

	weights1 := inputNeuralNetwork.weights1
	weights2 := inputNeuralNetwork.weights2
	weights3 := inputNeuralNetwork.weights3

	weights1Slice := weights1.Value().Data().([]float32)
	weights2Slice := weights2.Value().Data().([]float32)
	weights3Slice := weights3.Value().Data().([]float32)

	weights1Rows := weights1.Shape()[0]
	weights1Columns := weights1.Shape()[1]
	weights2Rows := weights2.Shape()[0]
	weights2Columns := weights2.Shape()[1]
	weights3Rows := weights3.Shape()[0]
	weights3Columns := weights3.Shape()[1]

	newNeuralNetworkForEncoding := neuralNetworkForEncoding{
		Weights1: weights1Slice,
		Weights2: weights2Slice,
		Weights3: weights3Slice,

		Weights1Rows: weights1Rows,
		Weights1Columns: weights1Columns,
		Weights2Rows: weights2Rows,
		Weights2Columns: weights2Columns,
		Weights3Rows: weights3Rows,
		Weights3Columns: weights3Columns,
	}

	buffer := new(bytes.Buffer)

	encoder := gob.NewEncoder(buffer)

	err := encoder.Encode(newNeuralNetworkForEncoding)
	if (err != nil) { return nil, err }

	neuralNetworkBytes := buffer.Bytes()

	return neuralNetworkBytes, nil
}

func DecodeBytesToNeuralNetworkObject(inputNeuralNetwork []byte)(NeuralNetwork, error){

	if (inputNeuralNetwork == nil){
		return NeuralNetwork{}, errors.New("DecodeBytesToNeuralNetworkObject called with nil inputNeuralNetwork.")
	}

	buffer := bytes.NewBuffer(inputNeuralNetwork)

	decoder := gob.NewDecoder(buffer)

	var newNeuralNetworkForEncoding neuralNetworkForEncoding

	err := decoder.Decode(&newNeuralNetworkForEncoding)
	if (err != nil){ return NeuralNetwork{}, err }

	weights1 := newNeuralNetworkForEncoding.Weights1
	weights2 := newNeuralNetworkForEncoding.Weights2
	weights3 := newNeuralNetworkForEncoding.Weights3

	weights1Rows := newNeuralNetworkForEncoding.Weights1Rows
	weights1Columns := newNeuralNetworkForEncoding.Weights1Columns
	weights2Rows := newNeuralNetworkForEncoding.Weights2Rows
	weights2Columns := newNeuralNetworkForEncoding.Weights2Columns
	weights3Rows := newNeuralNetworkForEncoding.Weights3Rows
	weights3Columns := newNeuralNetworkForEncoding.Weights3Columns

	// This is the graph object we add each layer to
	newGraph := gorgonia.NewGraph()

	// A layer is a column of neurons
	// Each neuron has an initial value between 0 and 1
	getNewNeuralNetworkLayerWeights := func(layerName string, layerNeuronRows int, layerNeuronColumns int, layerWeightsList []float32)*gorgonia.Node{

		layerNameObject := gorgonia.WithName(layerName)

		layerBacking := tensor.WithBacking(layerWeightsList)
		layerShape := tensor.WithShape(layerNeuronRows, layerNeuronColumns)
		layerTensor := tensor.New(layerBacking, layerShape)

		layerValueObject := gorgonia.WithValue(layerTensor)

		layerObject := gorgonia.NewMatrix(newGraph, tensor.Float32, layerNameObject, layerValueObject)

		return layerObject
	}

	layer1 := getNewNeuralNetworkLayerWeights("Weights1", weights1Rows, weights1Columns, weights1)
	layer2 := getNewNeuralNetworkLayerWeights("Weights2", weights2Rows, weights2Columns, weights2)
	layer3 := getNewNeuralNetworkLayerWeights("Weights3", weights3Rows, weights3Columns, weights3)

	newNeuralNetworkObject := NeuralNetwork{

		graph: newGraph,

		weights1: layer1,
		weights2: layer2,
		weights3: layer3,
	}

	return newNeuralNetworkObject, nil
}

// This map is used to store information about how accurate genetic prediction models are for discrete traits
// Map Structure: Discrete Trait Outcome Info -> Discrete Trait Prediction Accuracy Info
type DiscreteTraitPredictionAccuracyInfoMap map[DiscreteTraitOutcomeInfo]DiscreteTraitPredictionAccuracyInfo

type DiscreteTraitOutcomeInfo struct{

	// This is the outcome which was predicted
	// Example: "Blue"
	OutcomeName string

	// This is a value between 0-100 which describes the percentage of the loci which were tested for the input for the prediction
	PercentageOfLociTested int

	// This is a value between 0-100 which describes the percentage of the tested loci which were phased for the input for the prediction
	PercentageOfPhasedLoci int
}

type DiscreteTraitPredictionAccuracyInfo struct{

	// This contains the quantity of examples for the outcome with the specified percentageOfLociTested and percentageOfPhasedLoci
	QuantityOfExamples int

	// This contains the quantity of predictions for the outcome with the specified percentageOfLociTested and percentageOfPhasedLoci
	// Prediction = our model predicted this outcome
	QuantityOfPredictions int

	// This stores the probability (0-100) that our model will accurately predict this outcome for a genome which has
	//		the specified percentageOfLociTested and percentageOfPhasedLoci
	// In other words: What is the probability that if you give Seekia a blue-eyed genome, it will give you a correct Blue prediction?
	// This value is only accurate is QuantityOfExamples > 0
	ProbabilityOfCorrectGenomePrediction int

	// This stores the probability (0-100) that our model is correct if our model predicts that a genome
	//		with the specified percentageOfLociTested and percentageOfPhasedLoci has this outcome
	// In other words: What is the probability that if Seekia says a genome will have blue eyes, it is correct?
	// This value is only accurate is QuantityOfPredictions > 0
	ProbabilityOfCorrectOutcomePrediction int
}

func EncodeDiscreteTraitPredictionAccuracyInfoMapToBytes(inputMap DiscreteTraitPredictionAccuracyInfoMap)([]byte, error){

	buffer := new(bytes.Buffer)

	encoder := gob.NewEncoder(buffer)

	err := encoder.Encode(inputMap)
	if (err != nil) { return nil, err }

	inputMapBytes := buffer.Bytes()

	return inputMapBytes, nil
}

func DecodeBytesToDiscreteTraitPredictionAccuracyInfoMap(inputBytes []byte)(DiscreteTraitPredictionAccuracyInfoMap, error){

	if (inputBytes == nil){
		return nil, errors.New("DecodeBytesToDiscreteTraitPredictionAccuracyInfoMap called with nil inputBytes.")
	}

	buffer := bytes.NewBuffer(inputBytes)

	decoder := gob.NewDecoder(buffer)

	var newDiscreteTraitPredictionAccuracyInfoMap DiscreteTraitPredictionAccuracyInfoMap

	err := decoder.Decode(&newDiscreteTraitPredictionAccuracyInfoMap)
	if (err != nil){ return nil, err }

	return newDiscreteTraitPredictionAccuracyInfoMap, nil
}

type NumericAttributePredictionAccuracyInfoMap map[NumericAttributePredictionInfo]NumericAttributePredictionAccuracyRangesMap

type NumericAttributePredictionInfo struct{

	// This is a value between 0-100 which describes the percentage of the loci which were tested for the input for the prediction
	PercentageOfLociTested int

	// This is a value between 0-100 which describes the percentage of the tested loci which were phased for the input for the prediction
	PercentageOfPhasedLoci int
}

// Map Structure: Accuracy Percentage (AP) -> Amount needed to deviate from prediction for the value to be accurate (AP)% of the time
// For example, if the model predicted that someone was 150 centimeters tall, how many centimeters would we have to deviate in both directions
//		in order for the true outcome to fall into the range 10% of the time, 20% of the time, 30% of the time, etc...
// Example:
//		-90%+: 50 centimeters
//			If you travel 50 centimeters in both directions from the prediction,
//				the true height value will fall into this range 90% of the time.
//		-50%+: 20 centimeters
//		-10%+: 10 centimeters
type NumericAttributePredictionAccuracyRangesMap map[int]float64


func EncodeNumericAttributePredictionAccuracyInfoMapToBytes(inputMap NumericAttributePredictionAccuracyInfoMap)([]byte, error){

	buffer := new(bytes.Buffer)

	encoder := gob.NewEncoder(buffer)

	err := encoder.Encode(inputMap)
	if (err != nil) { return nil, err }

	inputMapBytes := buffer.Bytes()

	return inputMapBytes, nil
}

func DecodeBytesToNumericAttributePredictionAccuracyInfoMap(inputBytes []byte)(NumericAttributePredictionAccuracyInfoMap, error){

	if (inputBytes == nil){
		return nil, errors.New("DecodeBytesToNumericAttributePredictionAccuracyInfoMap called with nil inputBytes.")
	}

	buffer := bytes.NewBuffer(inputBytes)

	decoder := gob.NewDecoder(buffer)

	var newNumericAttributePredictionAccuracyInfoMap NumericAttributePredictionAccuracyInfoMap

	err := decoder.Decode(&newNumericAttributePredictionAccuracyInfoMap)
	if (err != nil){ return nil, err }

	return newNumericAttributePredictionAccuracyInfoMap, nil
}

//Outputs:
//	-bool: Neural network model exists for this trait (trait prediction is possible for this trait)
//	-bool: Trait prediction is possible for this user (User has at least 1 known trait locus value)
//	-string: Predicted trait outcome (Example: "Blue")
//	-int: Confidence: Probability (0-100) that the prediction is accurate
//	-int: Quantity of loci known
//	-int: Quantity of phased loci
//	-error
func GetNeuralNetworkDiscreteTraitPredictionFromGenomeMap(traitName string, genomeMap map[int64]locusValue.LocusValue)(bool, bool, string, int, int, int, error){

	traitObject, err := traits.GetTraitObject(traitName)
	if (err != nil) { return false, false, "", 0, 0, 0, err }

	traitIsDiscreteOrNumeric := traitObject.DiscreteOrNumeric
	if (traitIsDiscreteOrNumeric != "Discrete"){
		return false, false, "", 0, 0, 0, errors.New("GetNeuralNetworkDiscreteTraitPredictionFromGenomeMap called with non-discrete trait: " + traitName)
	}

	// This is a map of rsIDs which influence this trait
	traitRSIDsList := traitObject.LociList

	if (len(traitRSIDsList) == 0){
		// Neural network trait prediction is not possible for this trait
		return false, false, "", 0, 0, 0, nil
	}

	predictionModelExists, predictionModelBytes := geneticPredictionModels.GetGeneticPredictionModelBytes(traitName)
	if (predictionModelExists == false){
		// Neural network trait prediction is not possible for this trait
		return false, false, "", 0, 0, 0, nil
	}

	traitRSIDsListCopy := slices.Clone(traitRSIDsList)
	slices.Sort(traitRSIDsListCopy)

	neuralNetworkInput, quantityOfLociKnown, quantityOfPhasedLoci, err := createInputNeuralNetworkLayerFromGenomeMap(traitRSIDsListCopy, genomeMap)
	if (err != nil) { return false, false, "", 0, 0, 0, err }

	if (quantityOfLociKnown == 0){
		// We can't predict anything about this trait for this genome
		return true, false, "", 0, 0, 0, nil
	}

	neuralNetworkObject, err := DecodeBytesToNeuralNetworkObject(predictionModelBytes)
	if (err != nil) { return false, false, "", 0, 0, 0, err }

	outputLayer, err := GetNeuralNetworkRawPrediction(&neuralNetworkObject, false, neuralNetworkInput)
	if (err != nil) { return false, false, "", 0, 0, 0, err }

	predictedOutcomeName, err := GetDiscreteOutcomeNameFromOutputLayer(traitName, false, outputLayer)
	if (err != nil) { return false, false, "", 0, 0, 0, err }

	modelTraitAccuracyInfoFile, err := geneticPredictionModels.GetPredictionModelDiscreteTraitAccuracyInfoBytes(traitName)
	if (err != nil) { return false, false, "", 0, 0, 0, err }

	modelTraitAccuracyInfoMap, err := DecodeBytesToDiscreteTraitPredictionAccuracyInfoMap(modelTraitAccuracyInfoFile)
	if (err != nil) { return false, false, "", 0, 0, 0, err }

	// We find the model trait accuracy info object that is the most similar to our predicted outcome

	getPredictionAccuracy := func()int{

		totalNumberOfTraitLoci := len(traitRSIDsList)

		proportionOfLociTested := float64(quantityOfLociKnown)/float64(totalNumberOfTraitLoci)
		percentageOfLociTested := int(proportionOfLociTested * 100)

		proportionOfPhasedLoci := float64(quantityOfPhasedLoci)/float64(totalNumberOfTraitLoci)
		percentageOfPhasedLoci := int(proportionOfPhasedLoci * 100)

		// This is a value between 0 and 100 that represents the most likely accuracy probability for this prediction
		closestPredictionAccuracy := 0

		// This is a value that represents the distance our closest prediction accuracy has from the current prediction
		// Consider each prediction accuracy value on an (X,Y) coordinate plane
		// X = Number of loci tested
		// Y = Number of phased loci
		closestPredictionAccuracyDistance := float64(0)

		anyOutcomeAccuracyFound := false

		for traitOutcomeInfo, traitPredictionAccuracyInfo := range modelTraitAccuracyInfoMap{

			outcomeName := traitOutcomeInfo.OutcomeName
			if (outcomeName != predictedOutcomeName){
				continue
			}

			probabilityOfCorrectOutcomePrediction := traitPredictionAccuracyInfo.ProbabilityOfCorrectOutcomePrediction

			currentPercentageOfLociTested := traitOutcomeInfo.PercentageOfLociTested
			currentPercentageOfPhasedLoci := traitOutcomeInfo.PercentageOfPhasedLoci

			// Distance Formula for 2 coordinates (x1, y1) and (x2, y2):
			//	distance = √((x2 - x1)^2 + (y2 - y1)^2)

			differenceInX := float64(currentPercentageOfLociTested - percentageOfLociTested)
			differenceInY := float64(currentPercentageOfPhasedLoci - percentageOfPhasedLoci)

			distance := math.Sqrt(math.Pow(differenceInX, 2) + math.Pow(differenceInY, 2))

			if (distance == 0){
				// We found the exact prediction accuracy
				return probabilityOfCorrectOutcomePrediction
			}

			if (anyOutcomeAccuracyFound == false){
				closestPredictionAccuracyDistance = distance
				closestPredictionAccuracy = probabilityOfCorrectOutcomePrediction
				anyOutcomeAccuracyFound = true
				continue
			} else {
				if (distance < closestPredictionAccuracyDistance){
					closestPredictionAccuracyDistance = distance
					closestPredictionAccuracy = probabilityOfCorrectOutcomePrediction
				}
			}
		}

		if (anyOutcomeAccuracyFound == false){
			// This means that our model has never actually predicted this outcome
			// This shouldn't happen unless our model is really bad, or our training set has very few people with this outcome.
			// We return a 0% accuracy rating
			return 0
		}

		return closestPredictionAccuracy
	}

	predictionAccuracy := getPredictionAccuracy()

	return true, true, predictedOutcomeName, predictionAccuracy, quantityOfLociKnown, quantityOfPhasedLoci, nil
}

// This function is used to predict numeric traits and polygenic disease risk scores
//Outputs:
//	-bool: Neural network model exists for this attribute (neural network prediction is possible for this attribute)
//	-bool: Attribute prediction is possible for this user (User has at least 1 known attribute locus value)
//	-float64: Predicted attribute outcome (Example: Height in centimeters)
//	-map[int]float64: Accuracy ranges map
//		-Map Structure: Probability prediction is accurate (X) -> Distance from prediction that must be travelled in both directions to
//			create a range in which the true value will fall into, X% of the time
//	-int: Quantity of loci known
//	-int: Quantity of phased loci
//	-error
func GetNeuralNetworkNumericAttributePredictionFromGenomeMap(attributeName string, attributeLociList []int64, genomeMap map[int64]locusValue.LocusValue)(bool, bool, float64, map[int]float64, int, int, error){

	predictionModelExists, predictionModelBytes := geneticPredictionModels.GetGeneticPredictionModelBytes(attributeName)
	if (predictionModelExists == false){
		// Prediction is not possible for this attribute
		return false, false, 0, nil, 0, 0, nil
	}

	if (len(attributeLociList) == 0){
		return false, false, 0, nil, 0, 0, errors.New("GetNeuralNetworkNumericAttributePredictionFromGenomeMap called with empty attributeLociList for attribute with an existing neural network.")
	}

	attributeLociListCopy := slices.Clone(attributeLociList)
	slices.Sort(attributeLociListCopy)

	neuralNetworkInput, quantityOfLociKnown, quantityOfPhasedLoci, err := createInputNeuralNetworkLayerFromGenomeMap(attributeLociListCopy, genomeMap)
	if (err != nil) { return false, false, 0, nil, 0, 0, err }

	if (quantityOfLociKnown == 0){
		// We can't predict anything about this attribute for this genome
		return true, false, 0, nil, 0, 0, nil
	}

	neuralNetworkObject, err := DecodeBytesToNeuralNetworkObject(predictionModelBytes)
	if (err != nil) { return false, false, 0, nil, 0, 0, err }

	outputLayer, err := GetNeuralNetworkRawPrediction(&neuralNetworkObject, true, neuralNetworkInput)
	if (err != nil) { return false, false, 0, nil, 0, 0, err }

	predictedOutcomeValue, err := GetNumericOutcomeValueFromOutputLayer(attributeName, outputLayer)
	if (err != nil) { return false, false, 0, nil, 0, 0, err }

	modelAccuracyInfoFile, err := geneticPredictionModels.GetPredictionModelNumericAttributeAccuracyInfoBytes(attributeName)
	if (err != nil) { return false, false, 0, nil, 0, 0, err }

	modelAccuracyInfoMap, err := DecodeBytesToNumericAttributePredictionAccuracyInfoMap(modelAccuracyInfoFile)
	if (err != nil) { return false, false, 0, nil, 0, 0, err }

	// We create a prediction confidence ranges map for our prediction

	getPredictionConfidenceRangesMap := func()map[int]float64{

		totalNumberOfAttributeLoci := len(attributeLociListCopy)

		proportionOfLociTested := float64(quantityOfLociKnown)/float64(totalNumberOfAttributeLoci)
		percentageOfLociTested := int(proportionOfLociTested * 100)

		proportionOfPhasedLoci := float64(quantityOfPhasedLoci)/float64(totalNumberOfAttributeLoci)
		percentageOfPhasedLoci := int(proportionOfPhasedLoci * 100)

		// This is a value between 0 and 100 that represents the most similar confidence ranges map for this prediction
		var closestPredictionConfidenceRangesMap map[int]float64

		// This is a value that represents the distance our closest prediction confidence ranges map has from the current prediction
		// Consider each prediction accuracy value on an (X,Y) coordinate plane
		// X = Number of loci tested
		// Y = Number of phased loci
		closestPredictionConfidenceRangesMapDistance := float64(0)

		for attributeOutcomeInfo, attributePredictionConfidenceRangesMap := range modelAccuracyInfoMap{

			currentPercentageOfLociTested := attributeOutcomeInfo.PercentageOfLociTested
			currentPercentageOfPhasedLoci := attributeOutcomeInfo.PercentageOfPhasedLoci

			// Distance Formula for 2 coordinates (x1, y1) and (x2, y2):
			//	distance = √((x2 - x1)^2 + (y2 - y1)^2)

			differenceInX := float64(currentPercentageOfLociTested - percentageOfLociTested)
			differenceInY := float64(currentPercentageOfPhasedLoci - percentageOfPhasedLoci)

			distance := math.Sqrt(math.Pow(differenceInX, 2) + math.Pow(differenceInY, 2))

			if (distance == 0){
				// We found the exact prediction confidence ranges map
				return attributePredictionConfidenceRangesMap
			}

			if (closestPredictionConfidenceRangesMap == nil || distance < closestPredictionConfidenceRangesMapDistance){
				closestPredictionConfidenceRangesMapDistance = distance
				closestPredictionConfidenceRangesMap = attributePredictionConfidenceRangesMap
			}
		}

		return closestPredictionConfidenceRangesMap
	}

	predictionConfidenceRangesMap := getPredictionConfidenceRangesMap()

	return true, true, predictedOutcomeValue, predictionConfidenceRangesMap, quantityOfLociKnown, quantityOfPhasedLoci, nil
}


//Outputs:
//	-[]float32: Input layer for neural network
//	-int: Quantity of known loci
//	-int: Quantity of phased loci
//	-error
func createInputNeuralNetworkLayerFromGenomeMap(rsidsList []int64, genomeMap map[int64]locusValue.LocusValue)([]float32, int, int, error){

	// In the inputLayer, each locus value is represented by 3 neurons:
	//	1. LocusExists/LocusIsPhased
	//		-0 = Locus value is unknown
	//		-0.5 = Locus Is known, phase is unknown
	//		-1 = Locus Is Known, phase is known
	//	2. Allele1 Locus Value (Value between 0-1)
	//		-0 = Value is unknown
	//	3. Allele2 Locus Value (Value between 0-1)
	//		-0 = Value is unknown
	// 
	neuralNetworkInput := make([]float32, 0)

	quantityOfLociKnown := 0
	quantityOfPhasedLoci := 0

	for _, rsID := range rsidsList{

		userLocusValue, exists := genomeMap[rsID]
		if (exists == false){
			neuralNetworkInput = append(neuralNetworkInput, 0, 0, 0)
			continue
		}

		quantityOfLociKnown += 1

		locusAllele1 := userLocusValue.Base1Value
		locusAllele2 := userLocusValue.Base2Value
		locusIsPhased := userLocusValue.LocusIsPhased

		getNeuron1 := func()float32{
			if (locusIsPhased == false){
				return 0.5
			}

			quantityOfPhasedLoci += 1
			return 1
		}

		neuron1 := getNeuron1()

		neuron2, err := convertAlleleToNeuron(locusAllele1)
		if (err != nil) { return nil, 0, 0, err }

		neuron3, err := convertAlleleToNeuron(locusAllele2)
		if (err != nil) { return nil, 0, 0, err }

		neuralNetworkInput = append(neuralNetworkInput, neuron1, neuron2, neuron3)
	}

	return neuralNetworkInput, quantityOfLociKnown, quantityOfLociKnown, nil
}

//Outputs:
//	-int: Number of loci values that are known
//	-int: Number of loci values that are known and phased
//	-int: Number of loci
//	-error
func GetLociInfoFromNetworkInputLayer(inputLayer []float32)(int, int, int, error){

	// Each input layer has 3 neurons for each locus
	// Each rsID (locus) is represented by 3 neurons: LocusExists/LocusIsPhased, Allele1 Value, Allele2 Value
	// The LocusExists/LocusIsPhased neuron stores information like so:
	//		-0 = Locus value is unknown
	//		-0.5 = Locus Is known, phase is unknown
	//		-1 = Locus Is Known, phase is known 
	// Each rsID's neurons are concatenated together to form the inputLayer

	inputLayerLength := len(inputLayer)

	if (inputLayerLength%3 != 0){
		return 0, 0, 0, errors.New("GetLociInfoFromNetworkInputLayer called with invalid length input layer: Not evenly divisible by 4.")
	}

	numberOfLoci := len(inputLayer)/3

	numberOfLociValuesThatAreKnown := 0
	numberOfLociValuesThatAreKnownAndPhased := 0

	for index, neuronValue := range inputLayer{

		indexRemainder := index%3

		if (indexRemainder == 0){

			if (neuronValue == 0){
				continue
			}

			numberOfLociValuesThatAreKnown += 1

			/// We use an inequality instead of ==1 because floats are imprecise 
			if (neuronValue > 0.99){
				numberOfLociValuesThatAreKnown += 1
				numberOfLociValuesThatAreKnownAndPhased += 1
			}
		}
	}

	if (numberOfLociValuesThatAreKnown == 0){
		return 0, 0, 0, errors.New("GetLociInfoFromNetworkInputLayer called with input layer with no known loci values.")
	}

	return numberOfLociValuesThatAreKnown, numberOfLociValuesThatAreKnownAndPhased, numberOfLoci, nil
}

// This function returns which outcome is being described from a neural network's final output layer
// This is only used for discrete traits
// Outputs:
//	-string: Output Name (Example: "Blue")
//	-error
func GetDiscreteOutcomeNameFromOutputLayer(traitName string, verifyOutputLayer bool, outputLayer []float32)(string, error){

	if (verifyOutputLayer == true){

		// We make sure all neurons sum to 1

		summedNeurons := float32(0)

		for _, neuronValue := range outputLayer{
			summedNeurons += neuronValue
		}

		// We allow a small amount of inaccuracy due to the imprecise nature of floats.
		if (summedNeurons > 1.01 || summedNeurons < .99){
			summedNeuronsString := helpers.ConvertFloat32ToString(summedNeurons)
			return "", errors.New("GetOutcomeNameFromOutputLayer called with layer containing neuron values which don't sum to 1: " + summedNeuronsString)
		}
	}

	getBiggestNeuronIndex := func()int{

		biggestNeuronValue := float32(0)
		biggestNeuronIndex := 0

		for index, neuronValue := range outputLayer{

			if (index == 0){
				biggestNeuronValue = neuronValue
			} else {

				if (neuronValue > biggestNeuronValue){
					biggestNeuronValue = neuronValue
					biggestNeuronIndex = index
				}
			}
		}

		return biggestNeuronIndex
	}

	biggestNeuronIndex := getBiggestNeuronIndex()

	switch traitName{

		case "Eye Color":{

			if (len(outputLayer) != 4){
				return "", errors.New("GetOutcomeNameFromOutputLayer called with invalid length output layer.")
			}

			switch biggestNeuronIndex{
				case 0:{
					return "Blue", nil
				}
				case 1:{
					return "Green", nil
				}
				case 2:{
					return "Hazel", nil
				}
				case 3:{
					return "Brown", nil
				}
			}
		}
		case "Lactose Tolerance":{

			if (len(outputLayer) != 2){
				return "", errors.New("GetOutcomeNameFromOutputLayer called with invalid length output layer.")
			}

			switch biggestNeuronIndex{
				case 0:{
					return "Tolerant", nil
				}
				case 1:{
					return "Intolerant", nil
				}
			}
		}
	}

	return "", errors.New("GetOutcomeNameFromOutputLayer called with unknown traitName: " + traitName)
}


// This function returns which outcome is being described from a neural network's final output layer
// This is only used for numeric traits and polygenic diseases
// Outputs:
//	-float64: Output Value (example: 150 centimeters)
//	-error
func GetNumericOutcomeValueFromOutputLayer(attributeName string, outputLayer []float32)(float64, error){

	if (len(outputLayer) != 1){
		return 0, errors.New("GetNumericOutcomeValueFromOutputLayer called with output layer which is not length of 1")
	}

	outputNeuron := outputLayer[0]

	if (outputNeuron < 0 || outputNeuron > 1){
		return 0, errors.New("GetNumericOutcomeValueFromOutputLayer called with output layer contains out-of-bounds neuron")
	}

	getOutcomeMinAndMax := func()(float64, float64, error){

		switch attributeName{
			case "Height":{
				// Shortest person of all time: 54 cm
				// Tallest person of all time: 272 cm
				return 54, 272, nil
			}
			case "Autism",
				"Homosexualness",
				"Obesity":{
				return 0, 10, nil
			}
		}

		return 0, 0, errors.New("GetNumericOutcomeValueFromOutputLayer called with unknown attributeName: " + attributeName)
	}

	outcomeMin, outcomeMax, err := getOutcomeMinAndMax()
	if (err != nil) { return 0, err }

	outcomeValue, err := helpers.ScaleFloat64Proportionally(true, float64(outputNeuron), 0, 1, outcomeMin, outcomeMax)
	if (err != nil) { return 0, err }

	return outcomeValue, nil
}

//Outputs:
//	-int: Layer 1 neuron count (input layer)
//	-int: Layer 2 neuron count
//	-int: Layer 3 neuron count
//	-int: Layer 4 neuron count (output layer)
//	-error
func getNeuralNetworkLayerSizes(attributeName string)(int, int, int, int, error){

	switch attributeName{

		case "Eye Color":{

			// There are 282 input neurons
			// There are 4 output neurons, each representing a color
			// There are 4 colors: Blue, Green, Brown, Hazel

			return 282, 100, 50, 4, nil
		}
		case "Lactose Tolerance":{

			// There are 6 input neurons
			// There are 2 output neurons, each representing a tolerance: Tolerant, Intolerant
			return 6, 4, 3, 2, nil
		}
		case "Height":{
			// There are 3000 input neurons
			// There is 1 output neuron, representing a height value
			return 3000, 3, 2, 1, nil
		}
		case "Autism":{
			// There are 1428 input neurons
			// There is 1 output neuron, representing an autism value
			return 1428, 3, 2, 1, nil
		}
		case "Homosexualness":{
			// There are 12 input neurons
			// There is 1 output neuron, representing a homosexualness value
			return 12, 10, 5, 1, nil
		}
		case "Obesity":{
			// There are 3000 input neurons
			// There is 1 output neuron, representing an obesity value
			return 3000, 3, 2, 1, nil
		}
	}

	return 0, 0, 0, 0, errors.New("getNeuralNetworkLayerSizes called with unknown attributeName: " + attributeName)
}

//This function converts a genome allele to a neuron to use in a tensor
// A value of 0 means that the allele is unknown
func convertAlleleToNeuron(allele string)(float32, error){

	switch allele{

		case "C":{

			return 0.16, nil
		}
		case "A":{

			return 0.32, nil
		}
		case "T":{

			return 0.48, nil
		}
		case "G":{

			return 0.64, nil
		}
		case "I":{

			return 0.8, nil
		}
		case "D":{

			return 1, nil
		}
	}

	return 0, errors.New("convertAlleleToNeuron called with invalid allele: " + allele)
}


// This function returns training data to use to train each neural network prediction model
// Outputs:
//	-bool: User has phenotype data and enough loci to train model
//	-[]TrainingData: List of TrainingData for the user which we will use to train the model
//	-error
func CreateGeneticPredictionTrainingData_OpenSNP(
		attributeName string,
		userPhenotypeDataObject readBiobankData.PhenotypeData_OpenSNP,
		userLocusValuesMap map[int64]locusValue.LocusValue)(bool, []TrainingData, error){

	//Outputs:
	//	-[]int64: Attribute rsIDs list
	//	-error
	getAttributeLociList := func()([]int64, error){

		switch attributeName{

			case "Eye Color",
				"Lactose Tolerance",
				"Height",
				"Homosexualness":{

				traitObject, err := traits.GetTraitObject(attributeName)
				if (err != nil) { return nil, err }

				// This is a list of rsIDs which influence this trait
				traitLociList := traitObject.LociList

				return traitLociList, nil
			}
			case "Autism",
				"Obesity":{

				diseaseObject, err := polygenicDiseases.GetPolygenicDiseaseObject(attributeName)
				if (err != nil) { return nil, err }

				// This is a list of rsIDs which influence this disease
				diseaseLociList := diseaseObject.LociList

				return diseaseLociList, nil
			}
		}

		return nil, errors.New("CreateGeneticPredictionTrainingData_OpenSNP called with unknown attributeName: " + attributeName)
	}

	attributeLociList, err := getAttributeLociList()
	if (err != nil) { return false, nil, err }

	if (len(attributeLociList) == 0){
		return false, nil, errors.New("getAttributeLociList returning empty attributeLociList.")
	}

	// Each layer is represented as a []float32
	// Each float is a value between 0 and 1
	//
	// Each TrainingData holds a variation of the user's genome rsID values
	// We add many rows with withheld data to improve training data

	numberOfInputLayerRows, _, _, numberOfOutputLayerRows, err := getNeuralNetworkLayerSizes(attributeName)
	if (err != nil) { return false, nil, err }

	// Each rsID is represented by 3 neurons: LocusExists/LocusIsPhased, Allele1 Value, Allele2 Value
	// The LocusExists/LocusIsPhased neuron stores information like so:
	//		-0 = Locus value is unknown
	//		-0.5 = Locus Is known, phase is unknown
	//		-1 = Locus Is Known, phase is known 
	expectedNumberOfInputLayerRows := len(attributeLociList) * 3

	if (numberOfInputLayerRows != expectedNumberOfInputLayerRows){

		expectedNumberOfInputLayerRowsString := helpers.ConvertIntToString(expectedNumberOfInputLayerRows)

		return false, nil, errors.New("numberOfInputLayerRows is not expected: " + expectedNumberOfInputLayerRowsString)
	}

	checkIfAnyAttributeLocusValuesExist := func()bool{

		for _, rsID := range attributeLociList{

			_, exists := userLocusValuesMap[rsID]
			if (exists == true){
				return true
			}
		}

		return false
	}

	anyAttributeLocusValuesExist := checkIfAnyAttributeLocusValuesExist()
	if (anyAttributeLocusValuesExist == false){
		// The user's genome does not contain any of this attribute's locus values
		// We will not train on their data
		return false, nil, nil
	}

	// We sort rsIDs in ascending order

	attributeLociListCopy := slices.Clone(attributeLociList)
	slices.Sort(attributeLociListCopy)

	// This function returns the outputLayer for all trainingDatas for this user
	// Each outputLayer represents the user's attribute value (Example: "Blue" for Eye Color)
	// Each outputLayer is identical, because each TrainingData example belongs to the same user
	//
	// Outputs:
	//	-bool: User attribute value is known
	//	-[]float32: Neuron values for layer
	//	-error
	getUserAttributeValueNeurons := func()(bool, []float32, error){

		switch attributeName{

			case "Eye Color":{

				userEyeColorIsKnown := userPhenotypeDataObject.EyeColorIsKnown
				if (userEyeColorIsKnown == false){
					return false, nil, nil
				}

				userEyeColor := userPhenotypeDataObject.EyeColor

				if (userEyeColor == "Blue"){

					return true, []float32{1, 0, 0, 0}, nil

				} else if (userEyeColor == "Green"){

					return true, []float32{0, 1, 0, 0}, nil

				} else if (userEyeColor == "Hazel"){

					return true, []float32{0, 0, 1, 0}, nil

				} else if (userEyeColor == "Brown"){

					return true, []float32{0, 0, 0, 1}, nil
				}

				return false, nil, errors.New("Malformed userPhenotypeDataObject: Invalid eyeColor: " + userEyeColor)
			}
			case "Lactose Tolerance":{

				userLactoseToleranceIsKnown := userPhenotypeDataObject.LactoseToleranceIsKnown
				if (userLactoseToleranceIsKnown == false){
					return false, nil, nil
				}

				userLactoseTolerance := userPhenotypeDataObject.LactoseTolerance

				if (userLactoseTolerance == true){

					return true, []float32{1, 0}, nil
				}

				return true, []float32{0, 1}, nil
			}
			case "Height":{

				userHeightIsKnown := userPhenotypeDataObject.HeightIsKnown
				if (userHeightIsKnown == false){
					return false, nil, nil
				}

				userHeight := userPhenotypeDataObject.Height

				// Shortest person of all time: 54 cm
				// Tallest person of all time: 272 cm

				outputValue, err := helpers.ScaleFloat64Proportionally(true, userHeight, 54, 272, 0, 1)
				if (err != nil) { return false, nil, err }

				outputValueFloat32 := float32(outputValue)

				outputLayer := []float32{outputValueFloat32}

				return true, outputLayer, nil
			}
			case "Autism":{

				userAutismIsKnown := userPhenotypeDataObject.AutismIsKnown
				if (userAutismIsKnown == false){
					return false, nil, nil
				}

				userAutism := userPhenotypeDataObject.Autism

				outputValueFloat32 := float32(userAutism)

				outputLayer := []float32{outputValueFloat32}

				return true, outputLayer, nil
			}
			case "Homosexualness":{

				userHomosexualnessIsKnown := userPhenotypeDataObject.HomosexualnessIsKnown
				if (userHomosexualnessIsKnown == false){
					return false, nil, nil
				}

				userHomosexualness := userPhenotypeDataObject.Homosexualness

				outputValueFloat32 := float32(userHomosexualness)

				outputLayer := []float32{outputValueFloat32}

				return true, outputLayer, nil
			}
			case "Obesity":{

				userObesityIsKnown := userPhenotypeDataObject.ObesityIsKnown
				if (userObesityIsKnown == false){
					return false, nil, nil
				}

				userObesity := userPhenotypeDataObject.Obesity

				outputValueFloat32 := float32(userObesity)

				outputLayer := []float32{outputValueFloat32}

				return true, outputLayer, nil
			}
		}

		return false, nil, errors.New("Unknown attributeName: " + attributeName)
	}

	userAttributeValueExists, userAttributeValueNeurons, err := getUserAttributeValueNeurons()
	if (err != nil) { return false, nil, err }
	if (userAttributeValueExists == false){
		// User cannot be used to train the model.
		// They do not have a value for this attribute.
		return false, nil, nil
	}

	if (len(userAttributeValueNeurons) != numberOfOutputLayerRows){
		return false, nil, errors.New("getUserAttributeValueNeurons returning invalid length layer slice.")
	}

	// We want the initial training data to be the same for each call of this function that has the same input parameters
	// This is a necessary step so our neural network models will be reproducable
	// Reproducable means that other people can run the code and produce the same models, byte-for-byte

	pseudorandomNumberGenerator := mathRand.New(mathRand.NewPCG(1, 2))

	// We create 110 examples per user.
	// We randomize allele order whenever phase for the locus is unknown
	// 50% of the time we randomize allele order even when phase is known to train the model on unphased data
	// Unphased data is data where the order each allele (Example: G;A) has no meaning, because phase data was not captured
	// We randomize allele order to simulate unphased data
	// For example, if a user's genome is phased, we will randomize the base pair order and set the LocusIsPhased neuron to false
	// 
	// Examples 0-10: 100% of the user's loci are used
	// Examples 11-30: 90% of the user's loci are used
	// Examples 31-50: 70% of the user's loci are used
	// Examples 51-70: 50% of the user's loci are used
	// Examples 71-90: 30% of the user's loci are used
	// Examples 91-110: 10% of the user's loci are used

	// We now add this user's data to the trainingDataList

	trainingDataList := make([]TrainingData, 0, 110)

	for i:=0; i < 110; i++{

		getRandomizePhaseBool := func()bool{

			if (i%2 == 0){
				return true
			}
			return false
		}

		randomizePhaseBool := getRandomizePhaseBool()

		getProbabilityOfUsingLoci := func()float64{

			if (i <= 10){
				return 1

			} else if (i <= 30){
				return 0.9

			} else if (i <= 50){
				return 0.7

			} else if (i <= 70){
				return 0.5

			} else if (i <= 90){
				return 0.3
			}

			return 0.1
		}

		probabilityOfUsingLoci := getProbabilityOfUsingLoci()

		// In the inputLayer, each locus value is represented by 3 neurons:
		//	1. LocusExists/LocusIsPhased
		//		-0 = Locus value is unknown
		//		-0.5 = Locus Is known, phase is unknown
		//		-1 = Locus Is Known, phase is known
		//	2. Allele1 Locus Value (Value between 0-1)
		//		-0 = Value is unknown
		//	3. Allele2 Locus Value (Value between 0-1)
		//		-0 = Value is unknown

		anyLocusExists := false

		inputLayerLength := len(attributeLociListCopy) * 3

		inputLayer := make([]float32, 0, inputLayerLength)

		for _, rsID := range attributeLociListCopy{

			randomFloat := pseudorandomNumberGenerator.Float64()
			if (randomFloat > probabilityOfUsingLoci){
				// This if statement has a !probabilityOfUsingLoci chance of being true.
				// We are skipping this locus
				inputLayer = append(inputLayer, 0, 0, 0)
				continue
			}

			userLocusValue, exists := userLocusValuesMap[rsID]
			if (exists == false){
				// This user's locus value is unknown
				inputLayer = append(inputLayer, 0, 0, 0)
				continue
			}

			anyLocusExists = true

			//Outputs:
			//	-float32: Final neuron value
			//		-0 == Value is unknown
			//		-0.5 == Value is known, phase is unknown
			//		-1 == Value is known, phase is known
			//	-string: Allele 1 value
			//	-string: Allele 2 value
			getFirstNeuronAndLocusAlleles := func()(float32, string, string){

				locusAllele1 := userLocusValue.Base1Value
				locusAllele2 := userLocusValue.Base2Value

				if (locusAllele1 == locusAllele2){
					// Locus phase is unimportant
					return 1, locusAllele1, locusAllele2
				}

				locusIsPhased := userLocusValue.LocusIsPhased

				if (randomizePhaseBool == false && locusIsPhased == true){
					return 1, locusAllele1, locusAllele2
				}

				// We randomize the phase of the locus
				// We always do this if the locus is not phased, because the genome data might actually be partially/fully phased,
				//		even if it is not advertised as being phased

				randomNumber := pseudorandomNumberGenerator.IntN(2)
				if (randomNumber == 1){
					// This has a 50% chance of being true.
					return 0.5, locusAllele1, locusAllele2
				}

				return 0.5, locusAllele2, locusAllele1
			}

			locusIsKnownAndPhasedNeuronValue, locusAllele1, locusAllele2 := getFirstNeuronAndLocusAlleles()

			locusAllele1NeuronValue, err := convertAlleleToNeuron(locusAllele1)
			if (err != nil){ return false, nil, err }
			locusAllele2NeuronValue, err := convertAlleleToNeuron(locusAllele2)
			if (err != nil) { return false, nil, err }

			inputLayer = append(inputLayer, locusIsKnownAndPhasedNeuronValue, locusAllele1NeuronValue, locusAllele2NeuronValue)
		}

		if (anyLocusExists == false){
			// We have 0 known loci for this training example.
			// We won't add it to the training data.
			continue
		}

		userAttributeValueNeuronsCopy := slices.Clone(userAttributeValueNeurons)

		newTrainingData := TrainingData{
			InputLayer: inputLayer,
			OutputLayer: userAttributeValueNeuronsCopy,
		}

		trainingDataList = append(trainingDataList, newTrainingData)
	}

	return true, trainingDataList, nil
}

func GetNewUntrainedNeuralNetworkObject(attributeName string)(*NeuralNetwork, error){

	layer1NeuronCount, layer2NeuronCount, layer3NeuronCount, layer4NeuronCount, err := getNeuralNetworkLayerSizes(attributeName)
	if (err != nil) { return nil, err }

	// This is the graph object we add each layer to
	newGraph := gorgonia.NewGraph()

	// We want the initial weights to be the same for each call of this function that has the same input parameters
	// This is a necessary step so our neural network models will be reproducable
	// Reproducable means that other people can run the code and produce the same models, byte-for-byte

	pseudorandomNumberGenerator := mathRand.New(mathRand.NewPCG(1, 2))

	// A layer is a column of neurons
	// Each neuron has an initial value between 0 and 1
	getNewNeuralNetworkLayerWeights := func(layerName string, layerNeuronRows int, layerNeuronColumns int)*gorgonia.Node{

		layerNameObject := gorgonia.WithName(layerName)

		totalNumberOfNeurons := layerNeuronRows * layerNeuronColumns

		layerInitialWeightsList := make([]float32, 0, totalNumberOfNeurons)

		for i:=0; i < totalNumberOfNeurons; i++{

			// We initialize the weights with He initialization
			// He initialization = (0 +/- sqrt(2/n) where n is the number of nodes in the prior layer)

			// pseudorandomNumberGenerator.Float32() returns a pseudo-random number between 0 and 1

			newWeight := ((pseudorandomNumberGenerator.Float32()-0.5)*2) * float32(math.Sqrt(float64(2)/float64(layerNeuronRows)))

			layerInitialWeightsList = append(layerInitialWeightsList, newWeight)
		}

		layerBacking := tensor.WithBacking(layerInitialWeightsList)

		layerShape := tensor.WithShape(layerNeuronRows, layerNeuronColumns)

		layerTensor := tensor.New(layerBacking, layerShape)

		layerValueObject := gorgonia.WithValue(layerTensor)

		layerObject := gorgonia.NewMatrix(newGraph, tensor.Float32, layerNameObject, layerValueObject)

		return layerObject
	}

	layer1 := getNewNeuralNetworkLayerWeights("Weights1", layer1NeuronCount, layer2NeuronCount)
	layer2 := getNewNeuralNetworkLayerWeights("Weights2", layer2NeuronCount, layer3NeuronCount)
	layer3 := getNewNeuralNetworkLayerWeights("Weights3", layer3NeuronCount, layer4NeuronCount)

	newNeuralNetworkObject := NeuralNetwork{

		graph: newGraph,

		weights1: layer1,
		weights2: layer2,
		weights3: layer3,
	}

	return &newNeuralNetworkObject, nil
}

// This function returns the weights of the neural network
// We need this for training
func (inputNetwork *NeuralNetwork)getLearnables()gorgonia.Nodes{

	weights1 := inputNetwork.weights1
	weights2 := inputNetwork.weights2
	weights3 := inputNetwork.weights3

	result := gorgonia.Nodes{weights1, weights2, weights3}

	return result
}


// This function will train the neural network
// The function is passed a batch of TrainingData examples to train on
// Inputs:
//	-string: Attribute Name
//	-bool: Attribute is Numeric
//		-An example of a numeric attribute is Height
//		-An example of a discrete attribute is Eye Color, which has discrete outcomes (colors)
//	-*NeuralNetwork
//	-func()(bool, bool, TrainingData, error): Function to get the next training data.
//		-Outputs:
//		-bool: User stopped the training run
//		-bool: Another training data exists
//		-TrainingData: The next training data example
//		-error
// Outputs:
//	-bool: Process completed (was not stopped mid-way)
//	-error
func TrainNeuralNetwork(attributeName string, attributeIsNumeric bool, neuralNetworkObject *NeuralNetwork, getNextTrainingData func()(bool, bool, TrainingData, error))(bool, error){

	layer1NeuronCount, _, _, layer4NeuronCount, err := getNeuralNetworkLayerSizes(attributeName)
	if (err != nil) { return false, err }

	neuralNetworkGraph := neuralNetworkObject.graph

	// We first create the input and output nodes
	// They don't have any values yet.

	trainingDataInputNode := gorgonia.NewMatrix(neuralNetworkGraph,
		tensor.Float32,
		gorgonia.WithName("Input"),
		gorgonia.WithShape(1, layer1NeuronCount),
	)

	trainingDataExpectedOutputNode := gorgonia.NewMatrix(neuralNetworkGraph,
		tensor.Float32,
		gorgonia.WithName("ExpectedOutput"),
		gorgonia.WithShape(1, layer4NeuronCount),
	)

	err = neuralNetworkObject.buildNeuralNetwork(trainingDataInputNode, attributeIsNumeric)
	if (err != nil) { return false, err }

	// This computes the loss (how accurate was our prediction)
	losses, err := gorgonia.Sub(trainingDataExpectedOutputNode, neuralNetworkObject.prediction)
	if (err != nil) { return false, err }

	squareOfLosses, err := gorgonia.Square(losses)
	if (err != nil) { return false, err }

	// Cost is an average of the square of losses
	cost, err := gorgonia.Mean(squareOfLosses)
	if (err != nil) { return false, err }

	neuralNetworkLearnables := neuralNetworkObject.getLearnables()

	// Grad takes a scalar cost node and a list of with-regards-to, and returns the gradient
	_, err = gorgonia.Grad(cost, neuralNetworkLearnables...)
	if (err != nil) { return false, err }

	bindDualValues := gorgonia.BindDualValues(neuralNetworkLearnables...)

	// NewTapeMachine creates a Virtual Machine that compiles a graph into a prog.
	virtualMachine := gorgonia.NewTapeMachine(neuralNetworkGraph, bindDualValues)

	// This is the learn rate or step size for the solver.
	learningRate := gorgonia.WithLearnRate(.01)

	// This clips the gradient if it gets too crazy
//	gradientClip := gorgonia.WithClip(.05)

	solver := gorgonia.NewVanillaSolver(learningRate)
//	solver := gorgonia.NewVanillaSolver(learningRate, gradientClip)
	defer virtualMachine.Close()

	for {

		userStoppedTraining, nextDataExists, trainingDataObject, err := getNextTrainingData()
		if (err != nil) { return false, err }
		if (userStoppedTraining == true){
			// User manually stopped the training run
			return false, nil
		}
		if (nextDataExists == false){
			// We are done training
			break
		}

		// We convert our input training data slices to the type *Dense and assign them to our nodes

		// This inputLayer contains the allele values for this training example
		trainingDataInputLayer := trainingDataObject.InputLayer

		// This outputLayer contains the phenotype for this training example (example: Eye color of Blue)
		trainingDataOutputLayer := trainingDataObject.OutputLayer

		inputTensorShapeObject := tensor.WithShape(1, layer1NeuronCount)
		outputTensorShapeObject := tensor.WithShape(1, layer4NeuronCount)

		inputTensorBacking := tensor.WithBacking(trainingDataInputLayer)
		outputTensorBacking := tensor.WithBacking(trainingDataOutputLayer)

		inputTensor := tensor.New(inputTensorShapeObject, inputTensorBacking)
		outputTensor := tensor.New(outputTensorShapeObject, outputTensorBacking)

		err = gorgonia.Let(trainingDataInputNode, inputTensor)
		if (err != nil) { return false, err }

		err = gorgonia.Let(trainingDataExpectedOutputNode, outputTensor)
		if (err != nil) { return false, err }

		err = virtualMachine.RunAll()
		if (err != nil) { return false, err }

		// NodesToValueGrads is a utility function that converts a Nodes to a slice of ValueGrad for the solver
		valueGrads := gorgonia.NodesToValueGrads(neuralNetworkLearnables)

		err = solver.Step(valueGrads)
		if (err != nil) { return false, err }

		virtualMachine.Reset()
	}

	return true, nil
}


// This function computes a raw prediction from the neural network
// Outputs:
//	-[]float32: Output neurons
//	-error
func GetNeuralNetworkRawPrediction(inputNeuralNetwork *NeuralNetwork, attributeIsNumeric bool, inputLayer []float32)([]float32, error){

	neuralNetworkGraph := inputNeuralNetwork.graph

	numberOfInputNeurons := len(inputLayer)

	inputNode := gorgonia.NewMatrix(neuralNetworkGraph,
		tensor.Float32,
		gorgonia.WithName("Input"),
		gorgonia.WithShape(1, numberOfInputNeurons),
	)

	// We convert the inputLayer []float32 to a tensor *Dense object

	inputTensorShapeObject := tensor.WithShape(1, numberOfInputNeurons)

	inputTensorBacking := tensor.WithBacking(inputLayer)

	inputTensor := tensor.New(inputTensorShapeObject, inputTensorBacking)

	err := gorgonia.Let(inputNode, inputTensor)
	if (err != nil) { return nil, err }


	err = inputNeuralNetwork.buildNeuralNetwork(inputNode, attributeIsNumeric)
	if (err != nil){ return nil, err }

	// Now we create a virtual machine to compute the prediction

	neuralNetworkLearnables := inputNeuralNetwork.getLearnables()

	bindDualValues := gorgonia.BindDualValues(neuralNetworkLearnables...)

	virtualMachine := gorgonia.NewTapeMachine(neuralNetworkGraph, bindDualValues)

	err = virtualMachine.RunAll()
	if (err != nil) { return nil, err }

	prediction := inputNeuralNetwork.prediction

	predictionValues := prediction.Value().Data().([]float32)

	return predictionValues, nil
}


// This function will take a neural network and input layer and build the network to be able to compute a prediction
// We need to run a virtual machine after calling this function in order for the prediction to be generated
func (inputNetwork *NeuralNetwork)buildNeuralNetwork(inputLayer *gorgonia.Node, predictionIsNumeric bool)error{

	// We copy node pointer (says to do this in a resource i'm reading)

	inputLayerCopy := inputLayer

	// We multiply weights at each layer and perform ReLU (Rectification) after each multiplication

	weights1 := inputNetwork.weights1

	layer1Product, err := gorgonia.Mul(inputLayerCopy, weights1)
	if (err != nil) {
		return errors.New("Layer 1 multiplication failed: " + err.Error())
	}

	layer1ProductRectified, err := gorgonia.Rectify(layer1Product)
	if (err != nil){
		return errors.New("Layer 1 Rectify failed: " + err.Error())
	}

	weights2 := inputNetwork.weights2

	layer2Product, err := gorgonia.Mul(layer1ProductRectified, weights2)
	if (err != nil) {
		return errors.New("Layer 2 multiplication failed: " + err.Error())
	}

	layer2ProductRectified, err := gorgonia.Rectify(layer2Product)
	if (err != nil){
		return errors.New("Layer 2 Rectify failed: " + err.Error())
	}

	weights3 := inputNetwork.weights3

	layer3Product, err := gorgonia.Mul(layer2ProductRectified, weights3)
	if (err != nil) {
		return errors.New("Layer 3 multiplication failed: " + err.Error())
	}

	if (predictionIsNumeric == false){

		// We SoftMax the output to get the prediction

		prediction, err := gorgonia.SoftMax(layer3Product)
		if (err != nil) {
			return errors.New("SoftMax failed: " + err.Error())
		}

		inputNetwork.prediction = prediction

	} else {

		// We Sigmoid the output to get the prediction

		prediction, err := gorgonia.Sigmoid(layer3Product)
		if (err != nil) {
			return errors.New("Sigmoid failed: " + err.Error())
		}

		inputNetwork.prediction = prediction
	}

	return nil
}