public static void Main()
{
var sequenceLength = 250;
var chromosomeNr = 7;
var chromosomeDataSource = new ChromosomeDataSource($@"G:\Projects\HumanGenome\chromosomes\Homo_sapiens.GRCh38.dna.primary_assembly.chromosome_{chromosomeNr}.fa", sequenceLength);
var rbmSettings = new RestrictedBoltzmannMachineSettings
{
HiddenNodes = (int)(0.2 * sequenceLength),
InputNodes = 2 * sequenceLength,
LearningRate = 0.1,
TrainingIterations = 10 * 1000 * 1000
};
var rbm = new RestrictedBoltzmannMachine(rbmSettings);
rbm.Train(chromosomeDataSource);
//rbm.OutputModel($@"G:\Projects\HumanGenome\chromosomes\chromosome{chromosomeNr}_rbm_model.txt");
OutputNucleotideSequences(rbm, rbmSettings, $@"G:\Projects\HumanGenome\chromosomes\chromosome{chromosomeNr}_nucelotides.txt");
}
private static void OutputNucleotideSequences(RestrictedBoltzmannMachine rbm, RestrictedBoltzmannMachineSettings rbmSettings, string outputFile)
{
var output = new List <string>();
for (var hiddenIdx = 0; hiddenIdx < rbmSettings.HiddenNodes; hiddenIdx++)
{
var unitVector = Enumerable.Range(0, rbmSettings.HiddenNodes).Select(x => x == hiddenIdx ? 1.0 : 0.0).ToArray();
var response = rbm.ToInputLayer(unitVector);
var thresholdedResponse = response.Select(x => x > 0.5).ToArray();
var nucleotides = NucleotidesFromBoolArray(thresholdedResponse);
output.Add(new string(nucleotides.ToArray()));
}
File.WriteAllLines(outputFile, output);
}
