public static IGWGraph <ITrainingInputNodeData, ITrainingInputEdgeData, ITrainingInputGraphData> ParseTrainingData(string file)
{
var graph = JSONX.LoadFromJSON <GWGraph <TrainingInputNodeData, TrainingInputEdgeData, TrainingInputGraphData> >(file);
return(graph);
}
protected override void OnRequest(LoadCRFGraph request)
{
var graph = default(IGWGraph <SGLNodeData, SGLEdgeData, SGLGraphData>);
{
OpenFileDialog openFileDialog1 = new OpenFileDialog();
openFileDialog1.Filter = "Graph Files|*.crf";
openFileDialog1.Title = "Select a CRF graph File";
if (openFileDialog1.ShowDialog() == System.Windows.Forms.DialogResult.OK)
{
graph = JSONX.LoadFromJSON <GWGraph <SGLNodeData, SGLEdgeData, SGLGraphData> >(openFileDialog1.FileName);
}
}
if (graph != null)
{
int nodeCounter = 0;
foreach (var node in graph.Nodes)
{
node.Data.Ordinate = nodeCounter;
nodeCounter++;
}
}
request.Graph = graph;
}
private void LoadParametersetB_Click(object sender, RoutedEventArgs e)
{
OpenFileDialog openFileDialog1 = new OpenFileDialog();
openFileDialog1.Filter = "Parameter Files|*.par";
openFileDialog1.Title = "Select a Parameter File";
if (openFileDialog1.ShowDialog() == System.Windows.Forms.DialogResult.OK)
{
CRFToolData.IsingData = JSONX.LoadFromJSON <IsingData>(openFileDialog1.FileName);
}
}
public List <GWGraph <CRFNodeData, CRFEdgeData, CRFGraphData> > LoadCRFGraphs()
{
var list = new List <GWGraph <CRFNodeData, CRFEdgeData, CRFGraphData> >();
OpenFileDialog openFileDialog1 = new OpenFileDialog();
openFileDialog1.Filter = "Graph Files|*.crfs";
openFileDialog1.Title = "Select a CRF graph list File";
if (openFileDialog1.ShowDialog() == System.Windows.Forms.DialogResult.OK)
{
var graphsList = JSONX.LoadFromJSON <List <string> >(openFileDialog1.FileName);
foreach (var item in graphsList)
{
var graph = JSONX.LoadFromJSON <GWGraph <CRFNodeData, CRFEdgeData, CRFGraphData> >(item);
list.Add(graph);
}
}
return(list);
}
private void MainWindow_KeyDown(object sender, KeyEventArgs e)
{
switch (e.Key)
{
case Key.Space:
if (EmbeddingControl == null)
{
Embed();
}
else
{
EmbeddingControl.Stop();
EmbeddingControl = null;
}
break;
case Key.Tab:
ViewModel.ViewType = ViewModel.ViewType.Next();
break;
case Key.S:
viewModel.EvalResult.SaveAsJSON("testFile.txt");
break;
case Key.L:
ViewModel.EvalResults.Add(JSONX.LoadFromJSON <OLMEvaluationResult>("testFile.txt"));
break;
case Key.N:
ViewModel.EvalResPointer++;
break;
case Key.P:
ViewModel.EvalResPointer--;
break;
default:
break;
}
}
public GWGraph <CRFNodeData, CRFEdgeData, CRFGraphData> LoadCRFGraph()
{
var graph = default(GWGraph <CRFNodeData, CRFEdgeData, CRFGraphData>);
var thread = new Thread(
() =>
{
OpenFileDialog openFileDialog1 = new OpenFileDialog();
openFileDialog1.Filter = "Graph Files|*.crf";
openFileDialog1.Title = "Select a CRF graph File";
if (openFileDialog1.ShowDialog() == System.Windows.Forms.DialogResult.OK)
{
graph = JSONX.LoadFromJSON <GWGraph <CRFNodeData, CRFEdgeData, CRFGraphData> >(openFileDialog1.FileName);
}
});
thread.SetApartmentState(ApartmentState.STA);
thread.Start();
thread.Join();
Data.SelectedGraph = graph;
return(graph);
}
public void Execute()
{
// - Prerequisites:
// - Graphstructure
// - Training Data
// - 2 Node Classifications
TrainingData = new List <GWGraph <CRFNodeData, CRFEdgeData, CRFGraphData> >();
EvaluationData = new List <GWGraph <CRFNodeData, CRFEdgeData, CRFGraphData> >();
// decision wether user wants to train or load pre-trained data
var requestTraining = new UserDecision("Use Training.", "Load Training Result.");
requestTraining.Request();
if (requestTraining.Decision == 0) // use training
{
// -n characteristics for each node
{
var request = new UserInput(UserInputLookFor.Folder);
request.DefaultPath = "..\\..\\CRFToolApp\\bin\\Graphs";
request.TextForUser = "******";
request.Request();
GraphDataFolder = request.UserText;
foreach (var file in Directory.EnumerateFiles(GraphDataFolder))
{
var graph = JSONX.LoadFromJSON <GWGraph <CRFNodeData, CRFEdgeData, CRFGraphData> >(file);
TrainingData.Add(graph);
}
}
// - Step 1:
// - discretize characteristics
#region Use Training Pede
{
// create features
CreateFeatures(Dataset, TrainingData);
InitCRFScores(TrainingData);
var request = new OLMRequest(OLMVariant.Ising, TrainingData);
request.BasisMerkmale.AddRange(Dataset.NodeFeatures);
request.BasisMerkmale.AddRange(Dataset.EdgeFeatures);
request.LossFunctionValidation = OLM.LossRatio;
request.Request();
// zugehörige Scores erzeugen für jeden Graphen (auch Evaluation)
CreateCRFScores(TrainingData, Dataset.NodeFeatures, request.Result.ResultingWeights);
// store trained Weights
Dataset.NumberIntervals = NumberIntervals;
Dataset.Characteristics = TrainingData.First().Data.Characteristics.ToArray();
Dataset.EdgeCharacteristic = "IsingEdgeCharacteristic";
Dataset.Weights = request.Result.ResultingWeights;
Dataset.SaveAsJSON("results.json");
}
#endregion
}
else
{ // load pre-trained data
var request = new UserInput();
request.TextForUser = "******";
request.Request();
var file = request.UserText;
var trainingResult = JSONX.LoadFromJSON <WorkflowOneDataset>(file);
Dataset = trainingResult;
}
//- Step2:
// User Choice here
{
var request = new UserInput(UserInputLookFor.Folder);
request.TextForUser = "******";
request.Request();
GraphDataFolder = request.UserText;
foreach (var file in Directory.EnumerateFiles(GraphDataFolder))
{
var graph = JSONX.LoadFromJSON <GWGraph <CRFNodeData, CRFEdgeData, CRFGraphData> >(file);
EvaluationData.Add(graph);
}
}
// remove double edges
{
var edgesToRemove = new LinkedList <GWEdge <CRFNodeData, CRFEdgeData, CRFGraphData> >();
foreach (var graph in EvaluationData)
{
foreach (var edge in graph.Edges.ToList())
{
if (graph.Edges.Any(e => (e != edge) && ((e.Foot == edge.Head && e.Head == edge.Foot && e.GWId.CompareTo(edge.GWId) < 0) || (e.Foot == edge.Foot && e.Head == edge.Head && e.GWId.CompareTo(edge.GWId) < 0))))
{
edgesToRemove.Add(edge);
graph.Edges.Remove(edge);
}
}
}
foreach (var edge in edgesToRemove)
{
edge.Foot.Edges.Remove(edge);
edge.Head.Edges.Remove(edge);
}
}
//scores erzeugen
CreateCRFScores(EvaluationData, Dataset.NodeFeatures, Dataset.Weights);
// - Create ROC Curve
{
}
// - Give Maximum with Viterbi
{
foreach (var graph in EvaluationData)
{
var request = new SolveInference(graph, null, 2);
request.Request();
graph.Data.AssginedLabeling = request.Solution.Labeling;
}
//show results in 3D Viewer
{
//var request = new ShowGraphs();
//request.Graphs = EvaluationData;
//request.Request();
}
}
// - Give Sample with MCMC
{
foreach (var graph in EvaluationData)
{
SoftwareGraphLearningParameters parameters = new SoftwareGraphLearningParameters();
parameters.NumberOfGraphs = 60;
parameters.NumberNodes = 50;
parameters.NumberLabels = 2;
parameters.NumberCategories = 4;
parameters.IntraConnectivityDegree = 0.15;
parameters.InterConnectivityDegree = 0.01;
//sample parameters
var samplerParameters = new MHSamplerParameters();
var sglGraph = graph.Convert((nodeData) => new SGLNodeData()
{
}, (edgeData) => new SGLEdgeData(), (graphData) => new SGLGraphData());
samplerParameters.Graph = sglGraph;
samplerParameters.NumberChains = 1;
//sampler starten
var gibbsSampler = new MHSampler();
gibbsSampler.Do(samplerParameters);
}
}
}
private static double[] calculateTerminationConditionForSeeding()
{
double[] averageRatioItoS = new double[3];
if (ComputeTerminationCondition)
{
List <double> ratios = new List <double>();
// Getting the ratio of all surface nodes to the interface nodes
// to get a reality near parameter when to stop the seeding
foreach (var file in Directory.GetFiles(fileFolder))
{
var pdbFile = PDBExt.Parse(file);
pdbFile.Name = file.Substring(fileFolder.Length + 1, 4);
var nameWithChain = file.Substring(fileFolder.Length + 1, 6);
// counting all the nodes
var rasaRequest = new RequestRasa(pdbFile);
rasaRequest.RequestInDefaultContext();
// counting all the surface nodes
int SurfaceCounter = 0;
foreach (var rasa in rasaRequest.Rasavalues)
{
SurfaceCounter += rasa.Value > 0.15 ? 1 : 0;
rasa.Key.IsCore = rasa.Value <= 0.15;
}
// counting the interface nodes for each file
int InterfaceCounter = 0;
using (var reader = new StreamReader(InterfaceDefLocation))
{
var line = "";
while ((line = reader.ReadLine()) != null)
{
var nuss = nameWithChain;
InterfaceCounter += line.StartsWith(nameWithChain) ? 1 : 0;
}
}
double ratio = 1.0 * InterfaceCounter / SurfaceCounter;
ratios.Add(ratio);
}
// calculation of the average ratio between surface and interface nodes
double ratioSum = 0.0;
for (int i = 0; i < ratios.Count; i++)
{
ratioSum += ratios[i];
}
double max = ratios.Max();
double min = ratios.Min();
averageRatioItoS[0] = ratioSum / ratios.Count;
averageRatioItoS[1] = min;
averageRatioItoS[2] = max;
averageRatioItoS.SaveAsJSON("terminationCondition.txt");
}
else
{
averageRatioItoS = JSONX.LoadFromJSON <double[]>("terminationCondition.txt");
}
return(averageRatioItoS);
}