/// <summary>
/// Constructs with the provided input/output node count, activation function library,
/// node and connection lists.
/// </summary>
public NetworkDefinition(int inputNodeCount, int outputNodeCount,
IActivationFunctionLibrary activationFnLib,
INodeList nodeList, IConnectionList connectionList)
{
_inputNodeCount = inputNodeCount;
_outputNodeCount = outputNodeCount;
_activationFnLib = activationFnLib;
_nodeList = nodeList;
_connectionList = connectionList;
_isAcyclic = !CyclicNetworkTest.IsNetworkCyclic(this);
}
private static void InternalDecode(INetworkDefinition networkDef,
out List <Neuron> neuronList,
out List <Connection> connectionList)
{
// Build a list of neurons.
INodeList nodeDefList = networkDef.NodeList;
int nodeCount = nodeDefList.Count;
neuronList = new List <Neuron>(nodeCount);
// A dictionary of neurons keyed on their innovation ID.
var neuronDictionary = new Dictionary <uint, Neuron>(nodeCount);
// Loop neuron genes.
IActivationFunctionLibrary activationFnLib = networkDef.ActivationFnLibrary;
for (int i = 0; i < nodeCount; i++)
{ // Create a Neuron, add it to the neuron list and add an entry into neuronDictionary -
// required for next loop.
INetworkNode nodeDef = nodeDefList[i];
// Note that we explicitly translate between the two NeuronType enums even though
// they define the same types and could therefore be cast from one to the other.
// We do this to keep genome and phenome classes completely separated and also to
// prevent bugs - e.g. if one of the enums is changed then TranslateNeuronType() will
// need to be modified to prevent exceptions at runtime. Otherwise a silent bug may
// be introduced.
Neuron neuron = new Neuron(nodeDef.Id,
nodeDef.NodeType,
activationFnLib.GetFunction(nodeDef.ActivationFnId),
nodeDef.AuxState);
neuronList.Add(neuron);
neuronDictionary.Add(nodeDef.Id, neuron);
}
// Build a list of connections.
IConnectionList connectionDefList = networkDef.ConnectionList;
int connectionCount = connectionDefList.Count;
connectionList = new List <Connection>(connectionCount);
// Loop connection genes.
for (int i = 0; i < connectionCount; i++)
{
INetworkConnection connDef = connectionDefList[i];
connectionList.Add(
new Connection(neuronDictionary[connDef.SourceNodeId],
neuronDictionary[connDef.TargetNodeId],
connDef.Weight));
}
}
/// <summary>
/// Create an IOGraph that represents the structure described by the provided INetworkDefinition.
/// </summary>
public IOGraph CreateGraph(INetworkDefinition networkDef)
{
// Perform depth analysis of network.
NetworkDepthInfo depthInfo;
if (networkDef.IsAcyclic)
{
AcyclicNetworkDepthAnalysis depthAnalysis = new AcyclicNetworkDepthAnalysis();
depthInfo = depthAnalysis.CalculateNodeDepths(networkDef);
}
else
{
CyclicNetworkDepthAnalysis depthAnalysis = new CyclicNetworkDepthAnalysis();
depthInfo = depthAnalysis.CalculateNodeDepths(networkDef);
}
// Create an IOGraph, allocating storage for the node lists.
INodeList nodeList = networkDef.NodeList;
int nodeCount = nodeList.Count;
int inputCount = networkDef.InputNodeCount + 1; // + to count bias as an input layer node.
int outputCount = networkDef.OutputNodeCount;
int hiddenCount = nodeCount - (inputCount + outputCount);
IOGraph ioGraph = new IOGraph(inputCount, outputCount, hiddenCount, 0f, depthInfo._networkDepth);
// We also build a dictionary of nodes keyed by innovation ID. This is used later
// to assign connections to nodes.
Dictionary <uint, GraphNode> nodeDict = new Dictionary <uint, GraphNode>(nodeCount);
// Loop input nodes.
int idx = 0;
for (int i = 0; i < inputCount; i++, idx++)
{ // Create node, assign it a tag and add it to the node dictionary and the
// input node list of the IOGraph.
uint innovationId = nodeList[idx].Id;
GraphNode node = new GraphNode(innovationId.ToString());
node.AuxData = CreateGraphNodeAuxData(nodeList[idx]);
node.Depth = depthInfo._nodeDepthArr[idx];
nodeDict.Add(innovationId, node);
ioGraph.InputNodeList.Add(node);
}
// Loop output nodes.
for (int i = 0; i < outputCount; i++, idx++)
{ // Create node, assign it a tag and add it to the node dictionary and the
// output node list of the IOGraph.
uint innovationId = nodeList[idx].Id;
GraphNode node = new GraphNode(innovationId.ToString());
node.AuxData = CreateGraphNodeAuxData(nodeList[idx]);
node.Depth = depthInfo._nodeDepthArr[idx];
nodeDict.Add(innovationId, node);
ioGraph.OutputNodeList.Add(node);
}
// Loop hidden nodes.
for (; idx < nodeCount; idx++)
{ // Create node, assign it a tag and add it to the node dictionary and the
// hidden node list of the IOGraph.
uint innovationId = nodeList[idx].Id;
GraphNode node = new GraphNode(innovationId.ToString());
node.AuxData = CreateGraphNodeAuxData(nodeList[idx]);
node.Depth = depthInfo._nodeDepthArr[idx];
nodeDict.Add(innovationId, node);
ioGraph.HiddenNodeList.Add(node);
}
// Loop connections. Build GraphConnection objects and connect them to their source
// and target nodes.
double maxAbsWeight = 0.1; // Start at a non-zero value to prevent possibility of a divide by zero occuring.
IConnectionList connectionList = networkDef.ConnectionList;
int connCount = connectionList.Count;
for (int i = 0; i < connCount; i++)
{
// Create connection object and assign its source and target nodes.
INetworkConnection connection = connectionList[i];
GraphNode sourceNode = nodeDict[connection.SourceNodeId];
GraphNode targetNode = nodeDict[connection.TargetNodeId];
GraphConnection conn = new GraphConnection(sourceNode, targetNode, (float)connection.Weight);
// Add the connection to the connection lists on the source and target nodes.
sourceNode.OutConnectionList.Add(conn);
targetNode.InConnectionList.Add(conn);
// Track weight range oevr all connections.
double absWeight = Math.Abs(connection.Weight);
if (absWeight > maxAbsWeight)
{
maxAbsWeight = absWeight;
}
}
ioGraph.ConnectionWeightRange = (float)maxAbsWeight;
return(ioGraph);
}
/// <summary>
/// Creates a AcyclicNetwork from an INetworkDefinition.
/// </summary>
public static FastAcyclicNetwork CreateFastAcyclicNetwork(INetworkDefinition networkDef)
{
Debug.Assert(!CyclicNetworkTest.IsNetworkCyclic(networkDef), "Attempt to decode a cyclic network into a FastAcyclicNetwork.");
// Determine the depth of each node in the network.
// Node depths are used to separate the nodes into depth based layers, these layers can then be
// used to determine the order in which signals are propagated through the network.
AcyclicNetworkDepthAnalysis depthAnalysis = new AcyclicNetworkDepthAnalysis();
NetworkDepthInfo netDepthInfo = depthAnalysis.CalculateNodeDepths(networkDef);
// Construct an array of NodeInfo, ordered by node depth.
// Create/populate NodeInfo array.
int[] nodeDepthArr = netDepthInfo._nodeDepthArr;
INodeList nodeList = networkDef.NodeList;
int nodeCount = nodeList.Count;
NodeInfo[] nodeInfoByDepth = new NodeInfo[nodeCount];
for (int i = 0; i < nodeCount; i++)
{
nodeInfoByDepth[i]._nodeId = nodeList[i].Id;
nodeInfoByDepth[i]._definitionIdx = i;
nodeInfoByDepth[i]._nodeDepth = nodeDepthArr[i];
}
// Sort NodeInfo array.
// We use an IComparer here because an anonymous method is not accepted on the method overload that accepts
// a sort range, which we use to avoid sorting the input and bias nodes. Sort() performs an unstable sort therefore
// we must restrict the range of the sort to ensure the input and bias node indexes are unchanged. Restricting the
// sort to the required range is also more efficient (less items to sort).
int inputAndBiasCount = networkDef.InputNodeCount + 1;
Array.Sort(nodeInfoByDepth, inputAndBiasCount, nodeCount - inputAndBiasCount, NodeDepthComparer.__NodeDepthComparer);
// Array of live node indexes indexed by their index in the original network definition. This allows us to
// locate the position of input and output nodes in their new positions in the live network data structures.
int[] newIdxByDefinitionIdx = new int[nodeCount];
// Dictionary of live node indexes keyed by node ID. This allows us to convert the network definition connection
// endpoints from node IDs to indexes into the live/runtime network data structures.
Dictionary <uint, int> newIdxById = new Dictionary <uint, int>(nodeCount);
// Populate both the lookup array and dictionary.
for (int i = 0; i < nodeCount; i++)
{
NodeInfo nodeInfo = nodeInfoByDepth[i];
newIdxByDefinitionIdx[nodeInfo._definitionIdx] = i;
newIdxById.Add(nodeInfo._nodeId, i);
}
// Make a copy of the sub-range of newIdxByDefinitionIdx that represents the output nodes.
int outputCount = networkDef.OutputNodeCount;
int[] outputNeuronIdxArr = new int[outputCount];
// Note. 'inputAndBiasCount' holds the index of the first output node.
Array.Copy(newIdxByDefinitionIdx, inputAndBiasCount, outputNeuronIdxArr, 0, outputCount);
// Construct arrays with additional 'per node' data/refs (activation functions, activation fn auxiliary data).
IActivationFunctionLibrary activationFnLibrary = networkDef.ActivationFnLibrary;
IActivationFunction[] nodeActivationFnArr = new IActivationFunction[nodeCount];
double[][] nodeAuxArgsArray = new double[nodeCount][];
for (int i = 0; i < nodeCount; i++)
{
int definitionIdx = nodeInfoByDepth[i]._definitionIdx;
nodeActivationFnArr[i] = activationFnLibrary.GetFunction(nodeList[definitionIdx].ActivationFnId);
nodeAuxArgsArray[i] = nodeList[definitionIdx].AuxState;
}
//=== Create array of FastConnection(s).
// Loop the connections and lookup the node IDs for each connection's end points using newIdxById.
IConnectionList connectionList = networkDef.ConnectionList;
int connectionCount = connectionList.Count;
FastConnection[] fastConnectionArray = new FastConnection[connectionCount];
for (int i = 0; i < connectionCount; i++)
{
INetworkConnection conn = connectionList[i];
fastConnectionArray[i]._srcNeuronIdx = newIdxById[conn.SourceNodeId];
fastConnectionArray[i]._tgtNeuronIdx = newIdxById[conn.TargetNodeId];
fastConnectionArray[i]._weight = conn.Weight;
}
// Sort fastConnectionArray by source node index. This allows us to activate the connections in the
// order they are present within the network (by depth). We also secondary sort by target index to
// improve CPU cache coherency of the data (in order accesses that are as close to each other as possible).
Array.Sort(fastConnectionArray, delegate(FastConnection x, FastConnection y)
{
if (x._srcNeuronIdx < y._srcNeuronIdx)
{
return(-1);
}
if (x._srcNeuronIdx > y._srcNeuronIdx)
{
return(1);
}
// Secondary sort on target index.
if (x._tgtNeuronIdx < y._tgtNeuronIdx)
{
return(-1);
}
if (x._tgtNeuronIdx > y._tgtNeuronIdx)
{
return(1);
}
// Connections are equal (this should not actually happen).
return(0);
});
// Create an array of LayerInfo(s). Each LayerInfo contains the index + 1 of both the last node and last
// connection in that layer.
// The array is in order of depth, from layer zero (bias and inputs nodes) to the last layer
// (usually output nodes, but not necessarily if there is a dead end pathway with a high number of hops).
// Note. There is guaranteed to be at least one connection with a source at a given depth level, this is
// because for there to be a layer N there must necessarily be a connection from a node in layer N-1
// to a node in layer N.
int netDepth = netDepthInfo._networkDepth;
LayerInfo[] layerInfoArr = new LayerInfo[netDepth];
// Scanning over nodes can start at inputAndBiasCount instead of zero,
// because we know that all nodes prior to that index are at depth zero.
int nodeIdx = inputAndBiasCount;
int connIdx = 0;
for (int currDepth = 0; currDepth < netDepth; currDepth++)
{
// Scan for last node at the current depth.
for (; nodeIdx < nodeCount && nodeInfoByDepth[nodeIdx]._nodeDepth == currDepth; nodeIdx++)
{
;
}
// Scan for last connection at the current depth.
for (; connIdx < fastConnectionArray.Length && nodeInfoByDepth[fastConnectionArray[connIdx]._srcNeuronIdx]._nodeDepth == currDepth; connIdx++)
{
;
}
// Store node and connection end indexes for the layer.
layerInfoArr[currDepth]._endNodeIdx = nodeIdx;
layerInfoArr[currDepth]._endConnectionIdx = connIdx;
}
return(new FastAcyclicNetwork(nodeActivationFnArr, nodeAuxArgsArray, fastConnectionArray, layerInfoArr, outputNeuronIdxArr,
nodeCount, networkDef.InputNodeCount, networkDef.OutputNodeCount));
}
/// <summary>
/// Create an array of FastConnection(s) representing the connectivity of the provided INetworkDefinition.
/// </summary>
private static FastConnection[] CreateFastConnectionArray(INetworkDefinition networkDef)
{
// We vary the decode logic depending on the size of the genome. The most CPU intensive aspect of
// decoding is the conversion of the neuron IDs at connection endpoints into neuron indexes. For small
// genomes we simply use the BinarySearch() method on NeuronGeneList for each lookup; Each lookup is
// an operation with O(log n) time complexity. Thus for C connections and N neurons the number of operations
// to perform all lookups is approximately = 2*C*Log(N)
//
// For larger genomes we invest time in building a Dictionary that maps neuron IDs to their indexes, this on the
// basis that the time invested will be more than recovered in time saved performing lookups; The time complexity
// of a dictionary lookup is near constant O(1). Thus number of operations is approximately = O(2*C*1) + the time
// required to build the dictionary which is approximately O(N).
//
// Therefore the choice of lookup type is based on which of these two expressions gives the lowest value.
//
// Binary search. LookupOps = 2 * C * Log2(N) * x
// Dictionary Search. LookupOps = (N * y) + (2 * C * z)
//
// Where x, y and z are constants that adjust for the relative speeds of the lookup and dictionary building operations.
// Note that the actual time required to perform these separate algorithms is actually a far more complex problem, and
// for modern CPUs exact times cannot be calculated because of large memory caches and superscalar architecture that
// makes execution times in a real environment effectively non-deterministic. Thus these calculations are a rough
// guide/heuristic that estimate which algorithm will perform best. The constants can be found experimentally but will
// tend to vary depending on factors such as CPU and memory architecture, .Net framework version and what other tasks the
// CPU is currently doing which may affect our utilisation of memory caches.
// TODO: Experimentally determine reasonably good values for constants x,y and z in some common real world runtime platform.
IConnectionList connectionList = networkDef.ConnectionList;
INodeList nodeList = networkDef.NodeList;
int connectionCount = connectionList.Count;
int nodeCount = nodeList.Count;
FastConnection[] fastConnectionArray = new FastConnection[connectionCount];
if ((2.0 * connectionCount * Math.Log(nodeCount, 2.0)) < ((2.0 * connectionCount) + nodeCount))
{
// Binary search requires items to be sorted.
Debug.Assert(nodeList.IsSorted());
// Loop the connections and lookup the neuron IDs for each connection's end points using a binary search
// on nGeneList. This is probably the quickest approach for small numbers of lookups.
for (int i = 0; i < connectionCount; i++)
{
INetworkConnection conn = connectionList[i];
fastConnectionArray[i]._srcNeuronIdx = nodeList.BinarySearch(conn.SourceNodeId);
fastConnectionArray[i]._tgtNeuronIdx = nodeList.BinarySearch(conn.TargetNodeId);
fastConnectionArray[i]._weight = conn.Weight;
// Check that the correct neuron indexes were found.
Debug.Assert(
nodeList[fastConnectionArray[i]._srcNeuronIdx].Id == conn.SourceNodeId &&
nodeList[fastConnectionArray[i]._tgtNeuronIdx].Id == conn.TargetNodeId);
}
}
else
{
// Build dictionary of neuron indexes keyed on neuron innovation ID.
Dictionary <uint, int> neuronIndexDictionary = new Dictionary <uint, int>(nodeCount);
for (int i = 0; i < nodeCount; i++)
{
// ENHANCEMENT: Check if neuron innovation ID requires further manipulation to make a good hash code.
neuronIndexDictionary.Add(nodeList[i].Id, i);
}
// Loop the connections and lookup the neuron IDs for each connection's end points using neuronIndexDictionary.
// This is probably the quickest approach for large numbers of lookups.
for (int i = 0; i < connectionCount; i++)
{
INetworkConnection conn = connectionList[i];
fastConnectionArray[i]._srcNeuronIdx = neuronIndexDictionary[conn.SourceNodeId];
fastConnectionArray[i]._tgtNeuronIdx = neuronIndexDictionary[conn.TargetNodeId];
fastConnectionArray[i]._weight = conn.Weight;
// Check that the correct neuron indexes were found.
Debug.Assert(
nodeList[fastConnectionArray[i]._srcNeuronIdx].Id == conn.SourceNodeId &&
nodeList[fastConnectionArray[i]._tgtNeuronIdx].Id == conn.TargetNodeId);
}
}
return(fastConnectionArray);
}
