public GWNeuralNetwork(List <NeuralNetworkInputNode <InputData> > inputNodes, int[] innerLayers)
{
Graph = new GWGraph <NeuralNetworkNodeData, NeuralNetworkEdgeData, GWNeuralNetwork <InputData> >();
Graph.GraphStyle = GraphStyle.Directed;
InputNodes = inputNodes.ToList();
// init layers
Layers = new List <GWNode <NeuralNetworkNodeData, NeuralNetworkEdgeData, GWNeuralNetwork <InputData> > > [innerLayers.Length + 2];
for (int layer = 0; layer < Layers.Length; layer++)
{
Layers[layer] = new List <GWNode <NeuralNetworkNodeData, NeuralNetworkEdgeData, GWNeuralNetwork <InputData> > >();
}
//inputLayer:
for (int i = 0; i < InputNodes.Count; i++)
{
var node = Graph.CreateNode();
node.Data = InputNodes[i];
Layers[0].Add(node);
}
//create inner layers
var random = new Random();
int defConnects = 4;
for (int layer = 1; layer <= innerLayers.Length; layer++)
{
Layers[layer] = new List <GWNode <NeuralNetworkNodeData, NeuralNetworkEdgeData, GWNeuralNetwork <InputData> > >();
for (int i = 0; i < innerLayers[layer - 1]; i++)
{
var node = Graph.CreateNode();
node.Data = new NeuralNetworkNodeData();
//connect with former layer
for (int k = 0; k < defConnects; k++)
{
var otherNode = Layers[layer - 1].RandomElement(random);
var edge = Graph.CreateEdge(otherNode, node);
edge.Data = new NeuralNetworkEdgeData();
edge.Data.Weight = random.NextDouble();
}
Layers[layer].Add(node);
}
}
//create endingPoint
var endnode = Graph.CreateNode();
endnode.Data = new NeuralNetworkNodeData();
for (int i = 0; i < Layers[Layers.Length - 2].Count; i++)
{
var edge = Graph.CreateEdge(Layers[Layers.Length - 2][i], endnode);
edge.Data = new NeuralNetworkEdgeData();
edge.Data.Weight = random.NextDouble();
}
Layers[Layers.Length - 1].Add(endnode);
}
public static GWGraph <SGLNodeData, SGLEdgeData, SGLGraphData> ParseFile_CRF_Class(string file)
{
var graph = new GWGraph <SGLNodeData, SGLEdgeData, SGLGraphData>();
graph.Data = new SGLGraphData();
using (var reader = new StreamReader(file))
{
//if (reader.ReadLine() != "reflabels:")
// throw new IOException("unbekanntes FileFormat - File sollte mit 'numlabels:' beginnen");
//int refLabels = int.Parse(reader.ReadLine());
//if (reader.ReadLine() != "observations:")
// throw new IOException("unbekanntes FileFormat - File sollte mit 'numlabels:' beginnen");
//int observations = int.Parse(reader.ReadLine());
if (reader.ReadLine() != "nodes:")
{
throw new IOException("unbekanntes FileFormat - File sollte 'nodes:' in Zeile 3 enthalten");
}
string line = string.Empty;
while ((line = reader.ReadLine()) != "edges:" && line.NotNullOrEmpty())
{
string[] words = Regex.Split(line, "\\s");
var node = graph.CreateNode();
var scores = new List <double>();
node.Data = new SGLNodeData();
node.Data.ReferenceLabel = int.Parse(words[1]);
node.Data.Observation = int.Parse(words[2]);
if (words.Length > 3)
{
node.Data.AssignedLabel = int.Parse(words[3]);
}
node.Data.Id = words[0];
}
while ((line = reader.ReadLine()).NotNullOrEmpty())
{
string[] words = Regex.Split(line, "\\s");
string name = words[0] + "_" + words[1];
string check = words[1] + "_" + words[0];
var edge = graph.CreateEdge(graph.Nodes.First((n) => n.Data.Id.Equals(words[0])), graph.Nodes.First((n) => n.Data.Id.Equals(words[1])));
edge.Data = new SGLEdgeData();
}
}
return(graph);
}
//Davids files
public static GWGraph <ICRFNodeData, ICRFEdgeData, ICRFGraphData> ParseFileFormatThree(string file)
{
var graph = new GWGraph <ICRFNodeData, ICRFEdgeData, ICRFGraphData>();
var edgeMode = false;
int CountAdd = 0;
using (var reader = new StreamReader(file))
{
string line = string.Empty;
while ((line = reader.ReadLine()) != null)
{
if (line.Equals("NODES"))
{
reader.ReadLine();
edgeMode = false;
}
else if (line.Equals("EDGES"))
{
reader.ReadLine();
edgeMode = true;
}
else if (!edgeMode)
{
string[] words = Regex.Split(line, ";");
var node = graph.CreateNode();
var scoreI = int.Parse(words[1]);
var scoreN = int.Parse(words[2]);
var scores = new List <double>();
scores.AddRange(scoreN + CountAdd, scoreI + CountAdd);
graph.Nodes.Add(node);
node.Data.Scores = scores.ToArray();
node.Data.Id = words[0];
node.Data.ReferenceLabel = (words[3].Equals("N")) ? 0 : 1;
}
else
{
string[] words = Regex.Split(line, ";");
var headId = words[0];
var footId = words[1];
var head = graph.Nodes.First(n => n.Data.Id.Equals(headId));
var foot = graph.Nodes.First(n => n.Data.Id.Equals(footId));
var edge = new GWEdge <ICRFNodeData, ICRFEdgeData, ICRFGraphData>(head, foot);
graph.Edges.Add(edge);
}
}
}
return(graph);
}
public static GWGraph <ICRFNodeData, ICRFEdgeData, ICRFGraphData> CreateGraph(this ProteinGraph graph, IDictionary <ResidueNodeData, double[]> nodescores, IDictionary <SimpleEdgeData, double[, ]> edgescores)
{
var clonegraph = new GWGraph <ICRFNodeData, ICRFEdgeData, ICRFGraphData>();
foreach (var node in graph.Nodes)
{
var clone = clonegraph.CreateNode();
clone.Data = new CRFNodeData()
{
Id = node.Data.Residue.Id, Scores = nodescores[node.Data]
};
clonegraph.Nodes.Add(clone);
}
foreach (var edge in graph.Edges)
{
var newEdge = new GWEdge <ICRFNodeData, ICRFEdgeData, ICRFGraphData>(clonegraph.Nodes.First(n => n.Data.Id.Equals(edge.Head.Data.Residue.Id)),
clonegraph.Nodes.First(n => n.Data.Id.Equals(edge.Foot.Data.Residue.Id)));
newEdge.Data = new CRFEdgeData();
newEdge.Data.Scores = edgescores[edge.Data];
clonegraph.Edges.Add(newEdge);
}
return(clonegraph);
}
public static IGWGraph <ICRFNodeData, ICRFEdgeData, ICRFGraphData> ParseFileFormatTwo(string file)
{
var graph = new GWGraph <ICRFNodeData, ICRFEdgeData, ICRFGraphData>();
using (var reader = new StreamReader(file))
{
string line = string.Empty;
while ((line = reader.ReadLine()) != null)
{
if (line.StartsWith("#"))
{
continue;
}
else if (line.StartsWith("NODE"))
{
string[] words = Regex.Split(line, "\\s").Where(s => !string.IsNullOrWhiteSpace(s)).ToArray();
var node = graph.CreateNode();
var scores = new List <double>();
for (int counter = 0; counter < 2; counter++)
{
try
{
scores.Add(double.Parse(words[counter + 5], CultureInfo.InvariantCulture));
}
catch (FormatException ex)
{
if (words[counter + 5].Equals("N_INF"))
{
scores.Add(double.NegativeInfinity);
}
else
{
throw ex;
}
}
}
graph.Nodes.Add(node);
node.Data = new CRFNodeData();
node.Data.Scores = scores.ToArray();
node.Data.Id = words[1];
node.Data.ReferenceLabel = int.Parse(words[7]);
}
else if (line.StartsWith("NEIGH"))
{
string[] words = Regex.Split(line, "\\s").Where(s => !string.IsNullOrWhiteSpace(s)).ToArray();
var stringNode = words[1].Substring(0, words[1].Length - 1);
for (int nb = 2; nb < words.Length; nb++)
{
//Don't use the double occurence edges
if (stringNode.CompareTo(words[nb]) > 0)
{
continue;
}
var edge = new GWEdge <ICRFNodeData, ICRFEdgeData, ICRFGraphData>(graph.Nodes.First((n) => n.Data.Id.Equals(stringNode)), graph.Nodes.First((n) => n.Data.Id.Equals(words[nb])));
edge.Data = new CRFEdgeData();
graph.Edges.Add(edge);
}
}
}
}
return(graph);
}
public static IGWGraph <ICRFNodeData, ICRFEdgeData, ICRFGraphData> ParseFile(string file)
{
var graph = new GWGraph <ICRFNodeData, ICRFEdgeData, ICRFGraphData>();
using (var reader = new StreamReader(file))
{
if (reader.ReadLine() != "numlabels:")
{
throw new IOException("unbekanntes FileFormat - File sollte mit 'numlabels:' beginnen");
}
int numberLabels = int.Parse(reader.ReadLine());
if (reader.ReadLine() != "nodes:")
{
throw new IOException("unbekanntes FileFormat - File sollte 'nodes:' in Zeile 3 enthalten");
}
string line = string.Empty;
while ((line = reader.ReadLine()) != "edges:")
{
string[] words = Regex.Split(line, "\\s");
var node = graph.CreateNode();
var scores = new List <double>();
for (int counter = 1; counter < numberLabels + 1; counter++)
{
try
{
scores.Add(double.Parse(words[counter], CultureInfo.InvariantCulture));
}
catch (FormatException ex)
{
if (words[counter].Equals("N_INF"))
{
scores.Add(double.NegativeInfinity);
}
else
{
throw ex;
}
}
}
graph.Nodes.Add(node);
node.Data.Scores = scores.ToArray();
node.Data.Id = words[0];
}
while ((line = reader.ReadLine()) != null)
{
string[] words = Regex.Split(line, "\\s");
string name = words[0] + "_" + words[1];
string check = words[1] + "_" + words[0];
//Don't use the double occurence edges
if (words[0].CompareTo(words[1]) > 0)
{
continue;
}
var edge = new GWEdge <ICRFNodeData, ICRFEdgeData, ICRFGraphData>(graph.Nodes.First((n) => n.Data.Id.Equals(words[0])), graph.Nodes.First((n) => n.Data.Id.Equals(words[1])));
graph.Edges.Add(edge);
edge.Data.Scores = new double[numberLabels, numberLabels];
int word = 2;
for (int dounter = 0; dounter < numberLabels; dounter++)
{
for (int counter = 0; counter < numberLabels; counter++)
{
edge.Data.Scores[dounter, counter] = (double.Parse(words[word], CultureInfo.InvariantCulture));
word++;
}
}
}
}
return(graph);
}
