private double CalcSimOnDAG_Max(string rna1, string rna2, GOSimHelper goSimHelper)
{
double sim = 0;
var goSet1 = _miRNAs[rna1].GOs;
var goSet2 = _miRNAs[rna2].GOs;
var filteredGOSet1 = goSimHelper.FilterGOs(goSet1);
var filteredGOSet2 = goSimHelper.FilterGOs(goSet2);
if (filteredGOSet1.Count == 0 || filteredGOSet2.Count == 0)
{
return(0.0);
}
foreach (var go in filteredGOSet1)
{
foreach (var go2 in filteredGOSet2)
{
var sim2 = _useGSESAME ? goSimHelper.CalcGOSim_GSESAME(go, go2) : goSimHelper.CalcGOSim(go, go2);
if (sim < sim2)
{
sim = (float)sim2;
}
}
}
return(sim);
}
private float CalcGoGeneSim(int go, List <int> geneGOSet, GOSimHelper goSimHelper)
{
var maxSim = float.MinValue;
foreach (var geneGO in geneGOSet)
{
var sim = _useGSESAME ? goSimHelper.CalcGOSim_GSESAME(go, geneGO) : goSimHelper.CalcGOSim(go, geneGO); //6355,8150 = Infinity?
if (maxSim < sim)
{
maxSim = (float)sim;
}
}
return(maxSim);
}
private double GetOrSetWeightCache(string rna, int go, GOSimHelper goSimHelper)
{
double wx = 0;
if (_miRNAs[rna].WeightCache.ContainsKey(go))
{
wx = _miRNAs[rna].WeightCache[go];
}
else
{
wx = HyperWeight.CalculateWeight(goSimHelper.TotalGenes, goSimHelper.Dag[go].P_an, _miRNAs[rna].nTargetGeneCount, _miRNAs[rna].kGOAnnotatedCount[go]);
_miRNAs[rna].WeightCache[go] = wx;
}
return(wx);
}
private double CalcSimOnDAG_Euclidean(string rna1, string rna2, GOSimHelper goSimHelper)
{
double sim = 0;
var goSet1 = _miRNAs[rna1].GOs;
var goSet2 = _miRNAs[rna2].GOs;
var filteredGOSet1 = goSimHelper.FilterGOs(goSet1);
var filteredGOSet2 = goSimHelper.FilterGOs(goSet2);
foreach (var go in filteredGOSet1)
{
double wx = GetOrSetWeightCache(rna1, go, goSimHelper);
double cSim = CalcGoGeneSim(go, filteredGOSet2, goSimHelper);
sim += (wx * cSim * wx * cSim);
}
return(Math.Sqrt(sim));
}
public static void RunAllRNA(bool useGSESAME, MicroRNASimHelper.Mode mode, int start = 0, int end = 10000)
{
string simFileName = string.Format("sim_{0}_{1}", useGSESAME ? "GSESAME" : "Ours", mode.ToString());
Config.DAGPathPattern = @"DAG_new{0}.txt";
Config.MiRNAPath = "miranda";
Config.GeneralTablePath = "Go_annotated_times.txt";
Config.RNASimCacheFile = simFileName + "Cache.json";
RNASimCache.Read(Config.RNASimCacheFile);
var stateTimer = new Timer(obj => RNASimCache.Save(Config.RNASimCacheFile), null, 600000, 60000);
int maxConcurrency = Math.Min(20, Environment.ProcessorCount);
Console.WriteLine("Using {0} threads.", maxConcurrency);
var miRNAs = DAGLoader.LoadMicroRNA2(Config.MiRNAPath);
GOSimHelper.InitGOSimCache(miRNAs.SelectMany(m => m.Value.GOs).Distinct().ToArray());
List <MicroRNASimHelper> helpers = new List <MicroRNASimHelper>();
for (int i = 0; i < maxConcurrency; i++)
{
helpers.Add(new MicroRNASimHelper(miRNAs, useGSESAME, mode));
Console.WriteLine("Helper {0} initialized.", i);
}
var allRNAs = helpers.First().AllRNAs;
end = Math.Min(end, allRNAs.Length);
for (int i = start; i < end; i++)
{
for (int j = mode == MicroRNASimHelper.Mode.Euclidean ? start : i; j < allRNAs.Length; j++)
{
helpers[i % maxConcurrency].AddJob(allRNAs[i], allRNAs[j]);
}
}
var tasks = helpers.Select(h => h.CalcAllJobsAsync()).ToArray();
Task.WaitAll(tasks);
var sims = tasks.SelectMany(t => t.Result).ToList();
stateTimer.Dispose();
File.WriteAllText(simFileName + ".json", JsonConvert.SerializeObject(sims));
}
public static void TestSingle()
{
Config.DAGPathPattern = @"DAG_new{0}.txt";
Config.MiRNAPath = "miranda";
var miRNAs = DAGLoader.LoadMicroRNA2(Config.MiRNAPath);
GOSimHelper.InitGOSimCache(miRNAs.SelectMany(m => m.Value.GOs).Distinct().ToArray());
MicroRNASimHelper rnaSim = new MicroRNASimHelper(miRNAs, false, MicroRNASimHelper.Mode.Euclidean);
Stopwatch watch = new Stopwatch();
watch.Start();
//hsa-let-7c,hsa-let-7d-star
Console.WriteLine(string.Join(", ", rnaSim.CalcSim("hsa-let-7c", "hsa-let-7d-star")));
Console.WriteLine("used seconds: " + watch.ElapsedMilliseconds / 1000.0);
Console.ReadKey();
}
private double CalcSimOnDAG_HyperOrCount(string rna1, string rna2, GOSimHelper goSimHelper)
{
double sim = 0;
int count = 0;
var goSet1 = _miRNAs[rna1].GOs;
var goSet2 = _miRNAs[rna2].GOs;
var filteredGOSet1 = goSimHelper.FilterGOs(goSet1);
var filteredGOSet2 = goSimHelper.FilterGOs(goSet2);
if (filteredGOSet1.Count == 0 || filteredGOSet2.Count == 0)
{
return(0.0);
}
Dictionary <int, double> maxSimReverse = new Dictionary <int, double>();
foreach (var go in filteredGOSet2)
{
maxSimReverse[go] = double.MinValue;
}
foreach (var go in filteredGOSet1)
{
double wx = 0;
if (_mode == Mode.Hyper)
{
wx = GetOrSetWeightCache(rna1, go, goSimHelper);
}
else
{
wx = _miRNAs[rna1].kGOAnnotatedCount[go];
count += _miRNAs[rna1].kGOAnnotatedCount[go];
}
var maxSim = float.MinValue;
foreach (var go2 in filteredGOSet2)
{
var sim2 = _useGSESAME ? goSimHelper.CalcGOSim_GSESAME(go, go2) : goSimHelper.CalcGOSim(go, go2);
if (maxSim < sim2)
{
maxSim = (float)sim2;
}
if (maxSimReverse[go2] < sim2)
{
maxSimReverse[go2] = sim2;
}
}
sim += wx * maxSim;
}
foreach (var go in filteredGOSet2)
{
double wx = 0;
if (_mode == Mode.Hyper)
{
wx = GetOrSetWeightCache(rna2, go, goSimHelper);
}
else
{
wx = _miRNAs[rna2].kGOAnnotatedCount[go];
count += _miRNAs[rna2].kGOAnnotatedCount[go];
}
sim += wx * maxSimReverse[go];
}
return(sim / (_mode == Mode.Hyper ? (filteredGOSet1.Count + filteredGOSet2.Count) : count));
}