TCoda Class Reference

#include <agmdirected.h>

Collaboration diagram for TCoda:

Public Member Functions
	TCoda (const PNGraph &GraphPt, const int &InitComs, const int RndSeed=0)
	TCoda ()
void	SetGraph (const PNGraph &GraphPt)
PNGraph	GetGraph ()
PNGraph	GetGraphRawNID ()
void	SetRegCoef (const double _RegCoef)
double	GetRegCoef ()
void	RandomInit (const int InitComs)
int	GetNumComs ()
void	NeighborComInit (const int InitComs)
void	NeighborComInit (TFltIntPrV &NIdPhiV, const int InitComs)
void	SetCmtyVV (const TVec< TIntV > &CmtyVVOut, const TVec< TIntV > &CmtyVVIn)
double	Likelihood (const bool DoParallel=false)
double	LikelihoodForNode (const bool IsRow, const int UID)
double	LikelihoodForNode (const bool IsRow, const int UID, const TIntFltH &FU)
void	GetNonEdgePairScores (TFltIntIntTrV &ScoreV)
void	GetNIDValH (TIntFltH &NIdValInOutH, TIntFltH &NIdValOutH, TIntFltH &NIdValInH, const int CID, const double Thres)
void	DumpMemberships (const TStr &OutFNm, const TStrHash< TInt > &NodeNameH)
void	DumpMemberships (const TStr &OutFNm, const TStrHash< TInt > &NodeNameH, const double Thres)
void	GetCmtyS (TIntSet &CmtySOut, TIntSet &CmtySIn, const int CID, const double Thres)
void	DumpMemberships (const TStr &OutFNm, const double Thres)
void	DumpMemberships (const TStr &OutFNm)
void	GetCommunity (TIntV &CmtyVIn, TIntV &CmtyVOut, const int CID)
void	GetCommunity (TIntV &CmtyVIn, TIntV &CmtyVOut, const int CID, const double Thres)
	extract community affiliation for given community ID More...
void	GetTopCIDs (TIntV &CIdV, const int TopK, const int IsAverage=1, const int MinSz=1)
void	GradientForNode (const bool IsRow, const int UID, TIntFltH &GradU, const TIntSet &CIDSet)
void	SetHoldOut (const double HOFrac)
void	GetCmtyVV (TVec< TIntV > &CmtyVVOut, TVec< TIntV > &CmtyVVIn, const int MinSz=3)
void	GetCmtyVV (TVec< TIntV > &CmtyVVOut, TVec< TIntV > &CmtyVVIn, const double ThresOut, const double ThresIn, const int MinSz=3)
void	GetCmtyVV (const bool IsOut, TVec< TIntV > &CmtyVV)
void	GetCmtyVV (const bool IsOut, TVec< TIntV > &CmtyVV, const double Thres, const int MinSz=3)
	extract community affiliation for outgoing edges from F_uc More...
void	GetCmtyVVUnSorted (const bool IsOut, TVec< TIntV > &CmtyVV, const double Thres, const int MinSz=3)
void	GetCmtyVVUnSorted (TVec< TIntV > &CmtyVVOut, TVec< TIntV > &CmtyVVIn)
int	FindComsByCV (TIntV &ComsV, const double HOFrac=0.2, const int NumThreads=20, const TStr PlotLFNm=TStr(), const int EdgesForCV=100, const double StepAlpha=0.3, const double StepBeta=0.1)
int	FindComsByCV (const int NumThreads, const int MaxComs, const int MinComs, const int DivComs, const TStr OutFNm, const int EdgesForCV=100, const double StepAlpha=0.3, const double StepBeta=0.3)
	estimate number of communities using cross validation More...
double	LikelihoodHoldOut (const bool DoParallel=false)
double	GetStepSizeByLineSearch (const bool IsRow, const int UID, const TIntFltH &DeltaV, const TIntFltH &GradV, const double &Alpha, const double &Beta, const int MaxIter=10)
int	MLEGradAscent (const double &Thres, const int &MaxIter, const TStr PlotNm, const double StepAlpha=0.3, const double StepBeta=0.1)
int	MLEGradAscentParallel (const double &Thres, const int &MaxIter, const int ChunkNum, const int ChunkSize, const TStr PlotNm, const double StepAlpha=0.3, const double StepBeta=0.1)
int	MLEGradAscentParallel (const double &Thres, const int &MaxIter, const int ChunkNum, const TStr PlotNm=TStr(), const double StepAlpha=0.3, const double StepBeta=0.1)
void	Save (TSOut &SOut)
void	Load (TSIn &SIn, const int &RndSeed=0)
TFlt &	GetSumVal (const bool IsOut, const int CID)
double	GetCom (const bool IsOut, const int &NID, const int &CID)
double	GetComOut (const int &NID, const int &CID)
double	GetComIn (const int &NID, const int &CID)
void	AddCom (const bool IsOut, const int &NID, const int &CID, const double &Val)
void	AddComOut (const int &NID, const int &CID, const double &Val)
void	AddComIn (const int &NID, const int &CID, const double &Val)
void	DelCom (const bool IsOut, const int &NID, const int &CID)
void	DelComOut (const int &NID, const int &CID)
void	DelComIn (const int &NID, const int &CID)
double	DotProduct (const TIntFltH &UV, const TIntFltH &VV)
double	DotProductUtoV (const int &UID, const int &VID)
double	Prediction (const TIntFltH &FU, const TIntFltH &HV)
double	Prediction (const int &UID, const int &VID)
double	Sum (const TIntFltH &UV)
double	Norm2 (const TIntFltH &UV)

Public Attributes
TFlt	MinVal
TFlt	MaxVal
TFlt	NegWgt
TFlt	PNoCom
TBool	DoParallel

Private Attributes
PNGraph	G
TVec< TIntFltH >	F
TVec< TIntFltH >	H
TRnd	Rnd
TIntV	NIDV
TFlt	RegCoef
TFltV	SumFV
TFltV	SumHV
TBool	NodesOk
TInt	NumComs
TVec< TIntSet >	HOVIDSV

Detailed Description

Definition at line 7 of file agmdirected.h.

Constructor & Destructor Documentation

TCoda::TCoda ( const PNGraph &  GraphPt, const int &  InitComs, const int  RndSeed = 0  )

inline

Definition at line 27 of file agmdirected.h.

References RandomInit(), and SetGraph().

                                                                           : Rnd(RndSeed), RegCoef(0), 
    NodesOk(true), MinVal(0.0), MaxVal(1000.0), NegWgt(1.0) { SetGraph(GraphPt); RandomInit(InitComs); }

Here is the call graph for this function:

TCoda::TCoda ( )

inline

Definition at line 29 of file agmdirected.h.

References TNGraph::New().

{ G = TNGraph::New(); }

Here is the call graph for this function:

Member Function Documentation

void TCoda::AddCom ( const bool  IsOut, const int &  NID, const int &  CID, const double &  Val  )

inline

Definition at line 114 of file agmdirected.h.

References AddComIn(), and AddComOut().

Referenced by MLEGradAscent().

                                                                                          {
    if (IsOut) {
      AddComOut(NID, CID, Val);
    } else {
      AddComIn(NID, CID, Val);
    }
  }

Here is the call graph for this function:

Here is the caller graph for this function:

void TCoda::AddComIn ( const int &  NID, const int &  CID, const double &  Val  )

inline

Definition at line 128 of file agmdirected.h.

References TVec< TVal, TSizeTy >::GetDat().

Referenced by AddCom(), NeighborComInit(), RandomInit(), and SetCmtyVV().

                                                                          {
    if (H[NID].IsKey(CID)) {
      SumHV[CID] -= H[NID].GetDat(CID);
    }
    H[NID].AddDat(CID) = Val;
    SumHV[CID] += Val;
  }

Here is the call graph for this function:

Here is the caller graph for this function:

void TCoda::AddComOut ( const int &  NID, const int &  CID, const double &  Val  )

inline

Definition at line 121 of file agmdirected.h.

References TVec< TVal, TSizeTy >::GetDat().

Referenced by AddCom(), NeighborComInit(), RandomInit(), and SetCmtyVV().

                                                                           {
    if (F[NID].IsKey(CID)) {
      SumFV[CID] -= F[NID].GetDat(CID);
    }
    F[NID].AddDat(CID) = Val;
    SumFV[CID] += Val;
  }

Here is the call graph for this function:

Here is the caller graph for this function:

void TCoda::DelCom ( const bool  IsOut, const int &  NID, const int &  CID  )

inline

Definition at line 135 of file agmdirected.h.

References DelComIn(), and DelComOut().

Referenced by MLEGradAscent().

                                                                       {
    if (IsOut) {
      return DelComOut(NID, CID);
    } else {
      return DelComIn(NID, CID);
    }
  }

Here is the call graph for this function:

Here is the caller graph for this function:

void TCoda::DelComIn ( const int &  NID, const int &  CID  )

inline

Definition at line 148 of file agmdirected.h.

References TVec< TVal, TSizeTy >::GetDat().

Referenced by DelCom().

                                                       {
    if (H[NID].IsKey(CID)) {
      SumHV[CID] -= H[NID].GetDat(CID);
      H[NID].DelKey(CID);
    }
  }

Here is the call graph for this function:

Here is the caller graph for this function:

void TCoda::DelComOut ( const int &  NID, const int &  CID  )

inline

Definition at line 142 of file agmdirected.h.

References TVec< TVal, TSizeTy >::GetDat().

Referenced by DelCom().

                                                        {
    if (F[NID].IsKey(CID)) {
      SumFV[CID] -= F[NID].GetDat(CID);
      F[NID].DelKey(CID);
    }
  }

Here is the call graph for this function:

Here is the caller graph for this function:

double TCoda::DotProduct ( const TIntFltH &  UV, const TIntFltH &  VV  )

inline

Definition at line 154 of file agmdirected.h.

References THash< TKey, TDat, THashFunc >::BegI(), THash< TKey, TDat, THashFunc >::EndI(), THash< TKey, TDat, THashFunc >::GetDat(), THash< TKey, TDat, THashFunc >::IsKey(), and THash< TKey, TDat, THashFunc >::Len().

Referenced by DotProductUtoV(), GetStepSizeByLineSearch(), LikelihoodForNode(), and Prediction().

                                                                   {
    double DP = 0;
    if (UV.Len() > VV.Len()) {
      for (TIntFltH::TIter HI = UV.BegI(); HI < UV.EndI(); HI++) {
        if (VV.IsKey(HI.GetKey())) { 
          DP += VV.GetDat(HI.GetKey()) * HI.GetDat(); 
        }
      }
    } else {
      for (TIntFltH::TIter HI = VV.BegI(); HI < VV.EndI(); HI++) {
        if (UV.IsKey(HI.GetKey())) { 
          DP += UV.GetDat(HI.GetKey()) * HI.GetDat(); 
        }
      }
    }
    return DP;
  }

Here is the call graph for this function:

Here is the caller graph for this function:

double TCoda::DotProductUtoV ( const int &  UID, const int &  VID  )

inline

Definition at line 171 of file agmdirected.h.

References DotProduct().

                                                               {
    return DotProduct(F[UID], H[VID]);
  }

Here is the call graph for this function:

void TCoda::DumpMemberships ( const TStr &  OutFNm, const TStrHash< TInt > &  NodeNameH  )

inline

Definition at line 45 of file agmdirected.h.

References DumpMemberships().

Referenced by DumpMemberships().

{ DumpMemberships(OutFNm, NodeNameH, sqrt(PNoCom)); }

Here is the call graph for this function:

Here is the caller graph for this function:

void TCoda::DumpMemberships	(	const TStr &	OutFNm,
		const TStrHash< TInt > &	NodeNameH,
		const double	Thres
	)

Definition at line 617 of file agmdirected.cpp.

References TStr::CStr(), G, THash< TKey, TDat, THashFunc >::GetKey(), TStrHash< TDat, TStringPool, THashFunc >::GetKey(), GetNIDValH(), TNGraph::GetNodes(), GetSumVal(), IAssert, THash< TKey, TDat, THashFunc >::Len(), TStrHash< TDat, TStringPool, THashFunc >::Len(), NumComs, and TFlt::Val.

                                                                                                   {
  if (NodeNameH.Len() > 0) { IAssert(NodeNameH.Len() == G->GetNodes()); }
  FILE* FId = fopen(OutFNm.CStr(), "wt");
  TIntFltH CIDSumFH(NumComs);
  for (int c = 0; c < NumComs; c++) {
    CIDSumFH.AddDat(c, GetSumVal(true, c) * GetSumVal(false, c));
  }
  CIDSumFH.SortByDat(false);
  for (int c = 0; c < NumComs; c++) {
    int CID = CIDSumFH.GetKey(c);
    TIntFltH NIDOutFH, NIDInFH, NIDInOutFH;
    GetNIDValH(NIDInOutFH, NIDOutFH, NIDInFH, CID, Thres);
    if (NIDOutFH.Len() == 0 || NIDInFH.Len() == 0) { continue; }
    
    /*
    if (GetSumVal(true, CID) < Thres && GetSumVal(false, CID) < Thres) { continue; }
    for (int u = 0; u < NIDV.Len(); u++) {
      if (GetCom(true, u, CID) >= Thres && GetCom(false, u, CID) >= Thres) { 
        NIDInOutFH.AddDat(u, GetCom(true, u, CID) + GetCom(false, u, CID)); 
      } else if (GetCom(true, u, CID) >= Thres) {
        NIDOutFH.AddDat(u, GetCom(true, u, CID));
      } else if (GetCom(false, u, CID) >= Thres) {
        NIDInFH.AddDat(u, GetCom(false, u, CID));
      }
    }
    NIDInOutFH.SortByDat(false);
    NIDInFH.SortByDat(false);
    NIDOutFH.SortByDat(false);
    */
    fprintf(FId, "%d\t%d\t%d\t%f\t%f\t%f\t", NIDInOutFH.Len(), NIDInFH.Len() - NIDInOutFH.Len(), NIDOutFH.Len() - NIDInOutFH.Len(), CIDSumFH.GetDat(CID).Val, GetSumVal(false, CID).Val, GetSumVal(true, CID).Val);
    fprintf(FId, "InOut:\t");
    for (int u = 0; u < NIDInOutFH.Len(); u++) {
      int NIdx = NIDInOutFH.GetKey(u);
      fprintf(FId, "%s (%f)\t", NodeNameH.GetKey(NIdx), NIDInOutFH[u].Val);
    }
    fprintf(FId, "In:\t");
    for (int u = 0; u < NIDInFH.Len(); u++) {
      int NIdx = NIDInFH.GetKey(u);
      fprintf(FId, "%s (%f)\t", NodeNameH.GetKey(NIdx), NIDInFH[u].Val);
    }
    fprintf(FId, "Out:\t");
    for (int u = 0; u < NIDOutFH.Len(); u++) {
      int NIdx = NIDOutFH.GetKey(u);
      fprintf(FId, "%s (%f)\t", NodeNameH.GetKey(NIdx), NIDOutFH[u].Val);
    }
    fprintf(FId, "\n");
  }
  fclose(FId);
}

Here is the call graph for this function:

void TCoda::DumpMemberships	(	const TStr &	OutFNm,
		const double	Thres
	)

Definition at line 668 of file agmdirected.cpp.

References TStrHash< TDat, TStringPool, THashFunc >::AddKey(), DumpMemberships(), TStr::Fmt(), G, TNGraph::GetNodes(), TVec< TVal, TSizeTy >::Len(), and NIDV.

                                                                  {
  TStrHash<TInt> NodeNameH(G->GetNodes(), false);
  for (int u = 0; u < NIDV.Len(); u++) { NodeNameH.AddKey(TStr::Fmt("%d", NIDV[u].Val)); }
  DumpMemberships(OutFNm, NodeNameH, Thres);
}

Here is the call graph for this function:

void TCoda::DumpMemberships ( const TStr &  OutFNm )

inline

Definition at line 49 of file agmdirected.h.

References DumpMemberships().

Referenced by DumpMemberships().

{ DumpMemberships(OutFNm, sqrt(PNoCom)); }

Here is the call graph for this function:

Here is the caller graph for this function:

int TCoda::FindComsByCV	(	TIntV &	ComsV,
		const double	HOFrac = 0.2,
		const int	NumThreads = 20,
		const TStr	PlotLFNm = TStr(),
		const int	EdgesForCV = 100,
		const double	StepAlpha = 0.3,
		const double	StepBeta = 0.1
	)

Definition at line 746 of file agmdirected.cpp.

References TVec< TVal, TSizeTy >::Add(), TStr::Empty(), G, TAGMFastUtil::GenHoldOutPairs(), TNGraph::GetNodes(), HOVIDSV, TVec< TVal, TSizeTy >::Last(), TVec< TVal, TSizeTy >::Len(), Likelihood(), LikelihoodHoldOut(), MLEGradAscent(), MLEGradAscentParallel(), TFlt::Mn, NeighborComInit(), TGnuPlot::PlotValV(), RandomInit(), and Rnd.

Referenced by FindComsByCV().

                                                                                                                                                                         {
  if (ComsV.Len() == 0) {
    int MaxComs = G->GetNodes() / 5;
    ComsV.Add(2);
    while(ComsV.Last() < MaxComs) { ComsV.Add(ComsV.Last() * 2); }
  }
  int MaxIterCV = 3;

  TVec<TVec<TIntSet> > HoldOutSets(MaxIterCV);
  TFltIntPrV NIdPhiV;
  TAGMFastUtil::GetNIdPhiV<PNGraph>(G, NIdPhiV);

  if (G->GetEdges() > EdgesForCV) { //if edges are many enough, use CV
    printf("generating hold out set\n");
    TIntV NIdV1, NIdV2;
    G->GetNIdV(NIdV1);
    G->GetNIdV(NIdV2);
    for (int IterCV = 0; IterCV < MaxIterCV; IterCV++) {
      // generate holdout sets
      TAGMFastUtil::GenHoldOutPairs(G, HoldOutSets[IterCV], HOFrac, Rnd);
      /*
      HoldOutSets[IterCV].Gen(G->GetNodes());
      const int HOTotal = int(HOFrac * G->GetNodes() * (G->GetNodes() - 1) / 2.0);
      int HOCnt = 0;
      int HOEdges = (int) TMath::Round(HOFrac * G->GetEdges());
      printf("holding out %d edges...\n", HOEdges);
      for (int he = 0; he < (int) HOEdges; he++) {
        HoldOutSets[IterCV][EdgeV[he].Val1].AddKey(EdgeV[he].Val2);
        HoldOutSets[IterCV][EdgeV[he].Val2].AddKey(EdgeV[he].Val1);
        HOCnt++;
      }
      printf("%d Edges hold out\n", HOCnt);
      while(HOCnt++ < HOTotal) {
        int SrcNID = Rnd.GetUniDevInt(G->GetNodes());
        int DstNID = Rnd.GetUniDevInt(G->GetNodes());
        HoldOutSets[IterCV][SrcNID].AddKey(DstNID);
        HoldOutSets[IterCV][DstNID].AddKey(SrcNID);
      }
      */
    }
    
    printf("hold out set generated\n");
  }

  TFltV HOLV(ComsV.Len());
  TIntFltPrV ComsLV;
  for (int c = 0; c < ComsV.Len(); c++) {
    const int Coms = ComsV[c];
    printf("Try number of Coms:%d\n", Coms);

    if (G->GetEdges() > EdgesForCV) { //if edges are many enough, use CV
      for (int IterCV = 0; IterCV < MaxIterCV; IterCV++) {
        HOVIDSV = HoldOutSets[IterCV];
        NeighborComInit(NIdPhiV, Coms);
        printf("Initialized\n");

        if (NumThreads == 1) {
          printf("MLE without parallelization begins\n");
          MLEGradAscent(0.05, 10 * G->GetNodes(), "", StepAlpha, StepBeta);
        } else {
          printf("MLE with parallelization begins\n");
          MLEGradAscentParallel(0.05, 100, NumThreads, "", StepAlpha, StepBeta);
        }
        double HOL = LikelihoodHoldOut();
        HOL = HOL < 0? HOL: TFlt::Mn;
        HOLV[c] += HOL;
      }
    }
    else {
      HOVIDSV.Gen(G->GetNodes());
      MLEGradAscent(0.0001, 100 * G->GetNodes(), "");
      double BIC = 2 * Likelihood() - (double) G->GetNodes() * Coms * 2.0 * log ( (double) G->GetNodes());
      HOLV[c] = BIC;
    }
  }
  int EstComs = 2;
  double MaxL = TFlt::Mn;
  printf("\n");
  for (int c = 0; c < ComsV.Len(); c++) {
    ComsLV.Add(TIntFltPr(ComsV[c].Val, HOLV[c].Val));
    printf("%d(%f)\t", ComsV[c].Val, HOLV[c].Val);
    if (MaxL < HOLV[c]) {
      MaxL = HOLV[c];
      EstComs = ComsV[c];
    }
  }
  printf("\n");
  RandomInit(EstComs);
  HOVIDSV.Gen(G->GetNodes());
  if (! PlotLFNm.Empty()) {
    TGnuPlot::PlotValV(ComsLV, PlotLFNm, "hold-out likelihood", "communities", "likelihood");
  }
  return EstComs;
}

Here is the call graph for this function:

Here is the caller graph for this function:

int TCoda::FindComsByCV	(	const int	NumThreads,
		const int	MaxComs,
		const int	MinComs,
		const int	DivComs,
		const TStr	OutFNm,
		const int	EdgesForCV = 100,
		const double	StepAlpha = 0.3,
		const double	StepBeta = 0.3
	)

estimate number of communities using cross validation

Definition at line 733 of file agmdirected.cpp.

References TVec< TVal, TSizeTy >::Add(), FindComsByCV(), TVec< TVal, TSizeTy >::Last(), TVec< TVal, TSizeTy >::Len(), TMath::Log(), and TInt::Val.

                                                                                                                                                                                             {
    double ComsGap = exp(TMath::Log((double) MaxComs / (double) MinComs) / (double) DivComs);
    TIntV ComsV;
    ComsV.Add(MinComs);
    while (ComsV.Len() < DivComs) {
      int NewComs = int(ComsV.Last() * ComsGap);
      if (NewComs == ComsV.Last().Val) { NewComs++; }
      ComsV.Add(NewComs);
    }
    if (ComsV.Last() < MaxComs) { ComsV.Add(MaxComs); }
    return FindComsByCV(ComsV, 0.1, NumThreads, OutFNm, EdgesForCV, StepAlpha, StepBeta);
}

Here is the call graph for this function:

void TCoda::GetCmtyS	(	TIntSet &	CmtySOut,
		TIntSet &	CmtySIn,
		const int	CID,
		const double	Thres
	)

Definition at line 674 of file agmdirected.cpp.

References G, THashSet< TKey, THashFunc >::Gen(), GetCom(), TNGraph::GetNodes(), TVec< TVal, TSizeTy >::Len(), and NIDV.

                                                                                           {
  CmtySOut.Gen(G->GetNodes() / 10);
  CmtySIn.Gen(G->GetNodes() / 10);
  for (int u = 0; u < NIDV.Len(); u++) {
    if (GetCom(true, u, CID) > Thres) {
      //CmtySOut.AddKey(
    }
  }
}

Here is the call graph for this function:

void TCoda::GetCmtyVV	(	TVec< TIntV > &	CmtyVVOut,
		TVec< TIntV > &	CmtyVVIn,
		const int	MinSz = 3
	)

Definition at line 717 of file agmdirected.cpp.

References G, and TNGraph::GetNodes().

Referenced by GetCmtyVV().

                                                                                    {
  GetCmtyVV(false, CmtyVVIn, sqrt(1.0 / G->GetNodes()), MinSz);
  GetCmtyVV(true, CmtyVVOut, sqrt(1.0 / G->GetNodes()), MinSz);
}

Here is the call graph for this function:

Here is the caller graph for this function:

void TCoda::GetCmtyVV	(	TVec< TIntV > &	CmtyVVOut,
		TVec< TIntV > &	CmtyVVIn,
		const double	ThresOut,
		const double	ThresIn,
		const int	MinSz = 3
	)

Definition at line 727 of file agmdirected.cpp.

References GetCmtyVV().

                                                                                                                                 {
  GetCmtyVV(false, CmtyVVIn, ThresIn, MinSz);
  GetCmtyVV(true, CmtyVVOut, ThresOut, MinSz);
}

Here is the call graph for this function:

void TCoda::GetCmtyVV	(	const bool	IsOut,
		TVec< TIntV > &	CmtyVV
	)

Definition at line 501 of file agmdirected.cpp.

References G, GetCmtyVV(), and TNGraph::GetNodes().

                                                           {
  GetCmtyVV(IsOut, CmtyVV, sqrt(1.0 / G->GetNodes()), 3);
}

Here is the call graph for this function:

void TCoda::GetCmtyVV	(	const bool	IsOut,
		TVec< TIntV > &	CmtyVV,
		const double	Thres,
		const int	MinSz = 3
	)

extract community affiliation for outgoing edges from F_uc

Definition at line 539 of file agmdirected.cpp.

References TVec< TVal, TSizeTy >::Add(), THash< TKey, TDat, THashFunc >::AddDat(), TVec< TVal, TSizeTy >::Gen(), THash< TKey, TDat, THashFunc >::GetKey(), THash< TKey, TDat, THashFunc >::GetKeyV(), GetNIDValH(), GetSumVal(), TVec< TVal, TSizeTy >::Len(), NumComs, and THash< TKey, TDat, THashFunc >::SortByDat().

                                                                                                {
  CmtyVV.Gen(NumComs, 0);
  TIntFltH CIDSumFH(NumComs);
  for (int c = 0; c < NumComs; c++) {
    CIDSumFH.AddDat(c, GetSumVal(IsOut, c));
  }
  CIDSumFH.SortByDat(false);
  for (int c = 0; c < NumComs; c++) {
    int CID = CIDSumFH.GetKey(c);
    TIntFltH NIDFucH, NIDHucH, NIDInOutH;
    TIntV CmtyV;
    GetNIDValH(NIDInOutH, NIDFucH, NIDHucH, CID, Thres);
    if (IsOut) {
      NIDFucH.GetKeyV(CmtyV);
    } else {
      NIDHucH.GetKeyV(CmtyV);
    }
    if (CmtyV.Len() >= MinSz) { CmtyVV.Add(CmtyV); }
  }
  if ( NumComs != CmtyVV.Len()) {
    printf("Community vector generated. %d communities are ommitted\n", NumComs.Val - CmtyVV.Len());
  }
}

Here is the call graph for this function:

void TCoda::GetCmtyVVUnSorted	(	const bool	IsOut,
		TVec< TIntV > &	CmtyVV,
		const double	Thres,
		const int	MinSz = 3
	)

Definition at line 563 of file agmdirected.cpp.

References TVec< TVal, TSizeTy >::Add(), G, TVec< TVal, TSizeTy >::Gen(), GetCom(), TNGraph::GetNodes(), GetSumVal(), TVec< TVal, TSizeTy >::Len(), NIDV, and NumComs.

Referenced by GetCmtyVVUnSorted().

                                                                                                        {
  CmtyVV.Gen(NumComs, 0);
  for (int c = 0; c < NumComs; c++) {
    TIntV CmtyV((int) (GetSumVal(IsOut, c) * 10), 0);
    for (int u = 0; u < G->GetNodes(); u++) {
      if (GetCom(IsOut, u, c) > Thres) { CmtyV.Add(NIDV[u]); }
    }
    if (CmtyV.Len() >= MinSz) { CmtyVV.Add(CmtyV); }
  }
  if ( NumComs != CmtyVV.Len()) {
    printf("Community vector generated. %d communities are ommitted\n", NumComs.Val - CmtyVV.Len());
  }
}

Here is the call graph for this function:

Here is the caller graph for this function:

void TCoda::GetCmtyVVUnSorted	(	TVec< TIntV > &	CmtyVVOut,
		TVec< TIntV > &	CmtyVVIn
	)

Definition at line 722 of file agmdirected.cpp.

References G, GetCmtyVVUnSorted(), and TNGraph::GetNodes().

                                                                           {
  GetCmtyVVUnSorted(false, CmtyVVIn, sqrt(1.0 / G->GetNodes()));
  GetCmtyVVUnSorted(true, CmtyVVOut, sqrt(1.0 / G->GetNodes()));
}

Here is the call graph for this function:

double TCoda::GetCom ( const bool  IsOut, const int &  NID, const int &  CID  )

inline

Definition at line 93 of file agmdirected.h.

References GetComIn(), and GetComOut().

Referenced by GetCmtyS(), GetCmtyVVUnSorted(), GetCommunity(), GetNIDValH(), GetStepSizeByLineSearch(), GradientForNode(), LikelihoodForNode(), and MLEGradAscent().

                                                                         {
    if (IsOut) {
      return GetComOut(NID, CID);
    } else {
      return GetComIn(NID, CID);
    }
  }

Here is the call graph for this function:

Here is the caller graph for this function:

double TCoda::GetComIn ( const int &  NID, const int &  CID  )

inline

Definition at line 107 of file agmdirected.h.

References TVec< TVal, TSizeTy >::GetDat().

Referenced by GetCom().

                                                         {
    if (H[NID].IsKey(CID)) {
      return H[NID].GetDat(CID);
    } else {
      return 0.0;
    }
  }

Here is the call graph for this function:

Here is the caller graph for this function:

void TCoda::GetCommunity ( TIntV &  CmtyVIn, TIntV &  CmtyVOut, const int  CID  )

inline

Definition at line 50 of file agmdirected.h.

References GetCommunity().

Referenced by GetCommunity(), and GetTopCIDs().

{ GetCommunity(CmtyVIn, CmtyVOut, CID, sqrt(PNoCom)); }

Here is the call graph for this function:

Here is the caller graph for this function:

void TCoda::GetCommunity	(	TIntV &	CmtyVIn,
		TIntV &	CmtyVOut,
		const int	CID,
		const double	Thres
	)

extract community affiliation for given community ID

Definition at line 506 of file agmdirected.cpp.

References F, GetCom(), TVec< TVal, TSizeTy >::Len(), NIDV, and NodesOk.

                                                                                           {
  TIntFltH NIDFucH(F.Len() / 10), NIDHucH(F.Len() / 10);
  for (int u = 0; u < NIDV.Len(); u++) {
    int NID = u;
    if (! NodesOk) { NID = NIDV[u]; }
    if (GetCom(true, u, CID) >= Thres) { NIDFucH.AddDat(NID, GetCom(true, u, CID)); }
    if (GetCom(false, u, CID) >= Thres) { NIDHucH.AddDat(NID, GetCom(false, u, CID)); }
  }
  NIDFucH.SortByDat(false);
  NIDHucH.SortByDat(false);
  NIDFucH.GetKeyV(CmtyVOut);
  NIDHucH.GetKeyV(CmtyVIn);
}

Here is the call graph for this function:

double TCoda::GetComOut ( const int &  NID, const int &  CID  )

inline

Definition at line 100 of file agmdirected.h.

References TVec< TVal, TSizeTy >::GetDat().

Referenced by GetCom().

                                                          {
    if (F[NID].IsKey(CID)) {
      return F[NID].GetDat(CID);
    } else {
      return 0.0;
    }
  }

Here is the call graph for this function:

Here is the caller graph for this function:

PNGraph TCoda::GetGraph ( )

inline

Definition at line 31 of file agmdirected.h.

References G.

{ return G; }

PNGraph TCoda::GetGraphRawNID

(

)

Definition at line 577 of file agmdirected.cpp.

References TNGraph::AddEdge(), TNGraph::AddNode(), TNGraph::BegNI(), TNGraph::EndNI(), G, TNGraph::GetEdges(), TNGraph::GetNodes(), IAssert, TNGraph::IsNode(), TNGraph::New(), and NIDV.

Referenced by TCodaAnalyzer::TCodaAnalyzer().

                              {
  PNGraph NewG = TNGraph::New(G->GetNodes(), -1);
  for (TNGraph::TNodeI NI = G->BegNI(); NI < G->EndNI(); NI++) {
    //add node
    int NIdx = NI.GetId();
    int NID = NIDV[NIdx];
    if (! NewG->IsNode(NID)) { NewG->AddNode(NID); }
    //add edge
    for (int e = 0; e < NI.GetOutDeg(); e++) {
      int OutNID = NIDV[NI.GetOutNId(e)];
      if (! NewG->IsNode(OutNID)) { NewG->AddNode(OutNID); }
      NewG->AddEdge(NID, OutNID);
    }
  }
  IAssert(G->GetNodes() == NewG->GetNodes());
  IAssert(G->GetEdges() == NewG->GetEdges());
  return NewG;
}

Here is the call graph for this function:

Here is the caller graph for this function:

void TCoda::GetNIDValH	(	TIntFltH &	NIdValInOutH,
		TIntFltH &	NIdValOutH,
		TIntFltH &	NIdValInH,
		const int	CID,
		const double	Thres
	)

Definition at line 596 of file agmdirected.cpp.

References THash< TKey, TDat, THashFunc >::AddDat(), THash< TKey, TDat, THashFunc >::Gen(), GetCom(), GetSumVal(), TVec< TVal, TSizeTy >::Len(), NIDV, and THash< TKey, TDat, THashFunc >::SortByDat().

Referenced by DumpMemberships(), GetCmtyVV(), and TCodaAnalyzer::TCodaAnalyzer().

                                                                                                                           {
  NIdValOutH.Gen((int) GetSumVal(true, CID) + 1);
  NIdValInH.Gen((int) GetSumVal(false, CID) + 1);
  NIdValInOutH.Gen((int) GetSumVal(false, CID) + 1);
  if (GetSumVal(true, CID) < Thres && GetSumVal(false, CID) < Thres) { return; }
  for (int u = 0; u < NIDV.Len(); u++) {
    if (GetCom(true, u, CID) >= Thres && GetCom(false, u, CID) >= Thres) {
      NIdValInOutH.AddDat(NIDV[u], GetCom(true, u, CID) + GetCom(false, u, CID));
    }
    if (GetCom(true, u, CID) >= Thres) {
      NIdValOutH.AddDat(NIDV[u], GetCom(true, u, CID));
    }
    if (GetCom(false, u, CID) >= Thres) {
      NIdValInH.AddDat(NIDV[u], GetCom(false, u, CID));
    }
  }
  NIdValInH.SortByDat(false);
  NIdValOutH.SortByDat(false);
  NIdValInOutH.SortByDat(false);
}

Here is the call graph for this function:

Here is the caller graph for this function:

void TCoda::GetNonEdgePairScores

(

TFltIntIntTrV &

ScoreV

)

Definition at line 153 of file agmdirected.cpp.

References TVec< TVal, TSizeTy >::Add(), G, TVec< TVal, TSizeTy >::Gen(), TNGraph::GetNIdV(), TNGraph::GetNodes(), TNGraph::IsEdge(), TVec< TVal, TSizeTy >::Len(), NIDV, and Prediction().

                                                      {
  ScoreV.Gen(G->GetNodes() * G->GetNodes(), 0);
  TIntV NIDV;
  G->GetNIdV(NIDV);
  TIntSet Cuv;
  for (int u = 0; u < NIDV.Len(); u++) {
    int UID = NIDV[u];
    for (int v = 0; v < NIDV.Len(); v++) {
      int VID = NIDV[v];
      if (UID == VID) { continue; }
      if (! G->IsEdge(UID, VID)) {
        double Val = 1.0 - Prediction(UID, VID);
        ScoreV.Add(TFltIntIntTr(Val, UID, VID));
      }
    }
  }
}

Here is the call graph for this function:

int TCoda::GetNumComs ( )

inline

Definition at line 36 of file agmdirected.h.

References TInt::Val.

Referenced by GetTopCIDs(), and TCodaAnalyzer::TCodaAnalyzer().

{ return NumComs.Val; }

Here is the caller graph for this function:

double TCoda::GetRegCoef ( )

inline

Definition at line 34 of file agmdirected.h.

References RegCoef.

{ return RegCoef; }

double TCoda::GetStepSizeByLineSearch	(	const bool	IsRow,
		const int	UID,
		const TIntFltH &	DeltaV,
		const TIntFltH &	GradV,
		const double &	Alpha,
		const double &	Beta,
		const int	MaxIter = 10
	)

Definition at line 859 of file agmdirected.cpp.

References DotProduct(), GetCom(), THash< TKey, TDat, THashFunc >::GetDat(), THash< TKey, TDat, THashFunc >::GetKey(), THash< TKey, TDat, THashFunc >::Len(), LikelihoodForNode(), MaxVal, and MinVal.

Referenced by MLEGradAscent(), and MLEGradAscentParallel().

                                                                                                                                                                                {
  double StepSize = 1.0;
  double InitLikelihood = LikelihoodForNode(IsRow, UID);
  TIntFltH NewVarV(DeltaV.Len());
  for(int iter = 0; iter < MaxIter; iter++) {
    for (int i = 0; i < DeltaV.Len(); i++){
      int CID = DeltaV.GetKey(i);
      double NewVal;
      NewVal = GetCom(IsRow, UID, CID) + StepSize * DeltaV.GetDat(CID);
      if (NewVal < MinVal) { NewVal = MinVal; }
      if (NewVal > MaxVal) { NewVal = MaxVal; }
      NewVarV.AddDat(CID, NewVal);
    }
    if (LikelihoodForNode(IsRow, UID, NewVarV) < InitLikelihood + Alpha * StepSize * DotProduct(GradV, DeltaV)) {
      StepSize *= Beta;
    } else {
      break;
    }
    if (iter == MaxIter - 1) { 
      StepSize = 0.0;
      break;
    }
  }
  return StepSize;
}

Here is the call graph for this function:

Here is the caller graph for this function:

TFlt& TCoda::GetSumVal ( const bool  IsOut, const int  CID  )

inline

Definition at line 86 of file agmdirected.h.

Referenced by DumpMemberships(), GetCmtyVV(), GetCmtyVVUnSorted(), GetNIDValH(), GetTopCIDs(), GradientForNode(), and LikelihoodForNode().

                                                   { 
    if (IsOut) {
      return SumFV[CID];
    } else {
      return SumHV[CID];
    }
  }

Here is the caller graph for this function:

void TCoda::GetTopCIDs	(	TIntV &	CIdV,
		const int	TopK,
		const int	IsAverage = 1,
		const int	MinSz = 1
	)

Definition at line 520 of file agmdirected.cpp.

References THash< TKey, TDat, THashFunc >::AddDat(), GetCommunity(), THash< TKey, TDat, THashFunc >::GetKeyV(), GetNumComs(), GetSumVal(), THash< TKey, TDat, THashFunc >::Len(), TVec< TVal, TSizeTy >::Len(), THash< TKey, TDat, THashFunc >::SortByDat(), and TVec< TVal, TSizeTy >::Trunc().

Referenced by TCodaAnalyzer::TCodaAnalyzer().

                                                                                        {
  TIntFltH CIdFHH;
  for (int c = 0; c < GetNumComs(); c++) {
    if (IsAverage == 1) {
      TIntV CmtyVIn, CmtyVOut;
      GetCommunity(CmtyVIn, CmtyVOut, c);
      if (CmtyVIn.Len() == 0 || CmtyVOut.Len() == 0) { continue; }
      if (CmtyVIn.Len() < MinSz || CmtyVOut.Len() < MinSz) { continue; }
      CIdFHH.AddDat(c, GetSumVal(true, c) * GetSumVal(false, c) / (double) CmtyVIn.Len() / (double) CmtyVOut.Len());
    } else {
      CIdFHH.AddDat(c, GetSumVal(true, c) * GetSumVal(false, c));
    }
  }
  CIdFHH.SortByDat(false);
  CIdFHH.GetKeyV(CIdV);
  if (TopK < CIdFHH.Len()) { CIdV.Trunc(TopK); }
}

Here is the call graph for this function:

Here is the caller graph for this function:

void TCoda::GradientForNode	(	const bool	IsRow,
		const int	UID,
		TIntFltH &	GradU,
		const TIntSet &	CIDSet
	)

Definition at line 377 of file agmdirected.cpp.

References THash< TKey, TDat, THashFunc >::AddDat(), G, THash< TKey, TDat, THashFunc >::Gen(), TVec< TVal, TSizeTy >::Gen(), GetCom(), TNGraph::TNodeI::GetInDeg(), TNGraph::TNodeI::GetInNId(), THashSet< TKey, THashFunc >::GetKey(), TNGraph::GetNI(), TNGraph::TNodeI::GetOutDeg(), TNGraph::TNodeI::GetOutNId(), GetSumVal(), HOVIDSV, IAssert, THash< TKey, TDat, THashFunc >::Len(), TVec< TVal, TSizeTy >::Len(), THashSet< TKey, THashFunc >::Len(), NegWgt, NumComs, Prediction(), RegCoef, and SumHV.

Referenced by MLEGradAscent(), and MLEGradAscentParallel().

                                                                                                   {
  GradU.Gen(CIDSet.Len());

  TFltV HOSumHV; //adjust for Hv of v hold out
  if (HOVIDSV[UID].Len() > 0) {
    HOSumHV.Gen(NumComs);
    for (int e = 0; e < HOVIDSV[UID].Len(); e++) {
      for (int c = 0; c < SumHV.Len(); c++) {
        HOSumHV[c] += GetCom(! IsRow, HOVIDSV[UID][e], c);
      }
    }
  }
    
  TNGraph::TNodeI NI = G->GetNI(UID);
  int Deg = IsRow ? NI.GetOutDeg(): NI.GetInDeg();
  TFltV PredV(Deg), GradV(CIDSet.Len());
  TIntV CIDV(CIDSet.Len());
  for (int e = 0; e < Deg; e++) {
    int VID = IsRow? NI.GetOutNId(e): NI.GetInNId(e);
    if (VID == UID) { continue; }
    if (HOVIDSV[UID].IsKey(VID)) { continue; }
    PredV[e] = IsRow? Prediction(UID, VID): Prediction(VID, UID);
  }
  
  for (int c = 0; c < CIDSet.Len(); c++) {
    int CID = CIDSet.GetKey(c);
    double Val = 0.0;
    for (int e = 0; e < Deg; e++) {
      int VID = IsRow? NI.GetOutNId(e): NI.GetInNId(e);
      if (VID == UID) { continue; }
      if (HOVIDSV[UID].IsKey(VID)) { continue; }
      Val += PredV[e] * GetCom(! IsRow, VID, CID) / (1.0 - PredV[e]) + NegWgt * GetCom(! IsRow, VID, CID);
    }
    double HOSum = HOVIDSV[UID].Len() > 0?  HOSumHV[CID].Val: 0.0;//subtract Hold out pairs only if hold out pairs exist
    Val -= NegWgt * (GetSumVal(! IsRow, CID) - HOSum - GetCom(! IsRow, UID, CID));
    CIDV[c] = CID;
    GradV[c] = Val;
  }
  //add regularization
  if (RegCoef > 0.0) { //L1
    for (int c = 0; c < GradV.Len(); c++) {
      GradV[c] -= RegCoef; 
    }
  }
  if (RegCoef < 0.0) { //L2
    for (int c = 0; c < GradV.Len(); c++) {
      GradV[c] += 2 * RegCoef * GetCom(IsRow, UID, CIDV[c]); 
    }
  }
  for (int c = 0; c < GradV.Len(); c++) {
    if (GetCom(IsRow, UID, CIDV[c]) == 0.0 && GradV[c] < 0.0) { continue; }
    if (fabs(GradV[c]) < 0.0001) { continue; }
    GradU.AddDat(CIDV[c], GradV[c]);
  }
  for (int c = 0; c < GradU.Len(); c++) {
    if (GradU[c] >= 10) { GradU[c] = 10; }
    if (GradU[c] <= -10) { GradU[c] = -10; }
    IAssert(GradU[c] >= -10);
  }
}

Here is the call graph for this function:

Here is the caller graph for this function:

double TCoda::Likelihood

(

const bool

DoParallel = false

)

Definition at line 231 of file agmdirected.cpp.

References F, and LikelihoodForNode().

Referenced by FindComsByCV(), MLEGradAscent(), and MLEGradAscentParallel().

                                               { 
  TExeTm ExeTm;
  double L = 0.0;
  if (_DoParallel) {
  #pragma omp parallel for 
    for (int u = 0; u < F.Len(); u++) {
      double LU = LikelihoodForNode(true, u);
      #pragma omp atomic
        L += LU;
    }
  }
  else {
    for (int u = 0; u < F.Len(); u++) {
      double LU = LikelihoodForNode(true, u);
        L += LU;
    }
  }
  return L;
}

Here is the call graph for this function:

Here is the caller graph for this function:

double TCoda::LikelihoodForNode	(	const bool	IsRow,
		const int	UID
	)

Definition at line 251 of file agmdirected.cpp.

References F, and H.

Referenced by GetStepSizeByLineSearch(), and Likelihood().

                                                               {
  if (IsRow) {
    return LikelihoodForNode(IsRow, UID, F[UID]);
  } else {
    return LikelihoodForNode(IsRow, UID, H[UID]);
  }
}

Here is the caller graph for this function:

double TCoda::LikelihoodForNode	(	const bool	IsRow,
		const int	UID,
		const TIntFltH &	FU
	)

Definition at line 259 of file agmdirected.cpp.

References THash< TKey, TDat, THashFunc >::BegI(), DotProduct(), THash< TKey, TDat, THashFunc >::EndI(), F, G, TVec< TVal, TSizeTy >::Gen(), GetCom(), TNGraph::TNodeI::GetInDeg(), TNGraph::TNodeI::GetInNId(), TNGraph::GetNI(), TNGraph::TNodeI::GetOutDeg(), TNGraph::TNodeI::GetOutNId(), GetSumVal(), H, HOVIDSV, TVec< TVal, TSizeTy >::Len(), NegWgt, Norm2(), NumComs, Prediction(), RegCoef, Sum(), and SumHV.

                                                                                   {
  double L = 0.0;
  TFltV HOSumHV; //adjust for Hv of v hold out
  if (HOVIDSV[UID].Len() > 0) {
    HOSumHV.Gen(NumComs);
    for (int e = 0; e < HOVIDSV[UID].Len(); e++) {
      for (int c = 0; c < SumHV.Len(); c++) {
        HOSumHV[c] += GetCom(! IsRow, HOVIDSV[UID][e], c);
      }
    }
  }
  TNGraph::TNodeI NI = G->GetNI(UID);
  const int Deg = IsRow ? NI.GetOutDeg(): NI.GetInDeg();
  for (int e = 0; e < Deg; e++) {
    const int v = IsRow ? NI.GetOutNId(e): NI.GetInNId(e);
    if (v == UID) { continue; }
    if (HOVIDSV[UID].IsKey(v)) { continue; }
    if (IsRow) {
      L += log (1.0 - Prediction(FU, H[v])) + NegWgt * DotProduct(FU, H[v]);
    } else {
      L += log (1.0 - Prediction(F[v], FU)) + NegWgt * DotProduct(F[v], FU);
    }
  }
  for (TIntFltH::TIter HI = FU.BegI(); HI < FU.EndI(); HI++) {
    double HOSum = HOVIDSV[UID].Len() > 0?  HOSumHV[HI.GetKey()].Val: 0.0;//subtract Hold out pairs only if hold out pairs exist
    L -= NegWgt * (GetSumVal(! IsRow, HI.GetKey()) - HOSum - GetCom(! IsRow, UID, HI.GetKey())) * HI.GetDat();
  }
  //add regularization
  if (RegCoef > 0.0) { //L1
    L -= RegCoef * Sum(FU);
  }
  if (RegCoef < 0.0) { //L2
    L += RegCoef * Norm2(FU);
  }
  return L;
}

Here is the call graph for this function:

double TCoda::LikelihoodHoldOut

(

const bool

DoParallel = false

)

Definition at line 841 of file agmdirected.cpp.

References G, HOVIDSV, TNGraph::IsEdge(), NegWgt, and Prediction().

Referenced by FindComsByCV().

                                                     { 
  double L = 0.0;
  for (int u = 0; u < HOVIDSV.Len(); u++) {
    for (int e = 0; e < HOVIDSV[u].Len(); e++) {
      int VID = HOVIDSV[u][e];
      if (VID == u) { continue; } 
      double Pred = Prediction(u, VID);
      if (G->IsEdge(u, VID)) {
        L += log(1.0 - Pred);
      }
      else {
        L += NegWgt * log(Pred);
      }
    }
  }
  return L;
}

Here is the call graph for this function:

Here is the caller graph for this function:

void TCoda::Load	(	TSIn &	SIn,
		const int &	RndSeed = 0
	)

Definition at line 25 of file agmdirected.cpp.

References F, G, H, HOVIDSV, TNGraph::Load(), TVec< TVal, TSizeTy >::Load(), TBool::Load(), TInt::Load(), TFlt::Load(), MaxVal, MinVal, NegWgt, NIDV, NodesOk, NumComs, PNoCom, TRnd::PutSeed(), RegCoef, Rnd, SumFV, and SumHV.

                                              {
  G->Load(SIn);
  F.Load(SIn);
  H.Load(SIn);
  NIDV.Load(SIn);
  RegCoef.Load(SIn);
  SumFV.Load(SIn);
  SumHV.Load(SIn);
  NodesOk.Load(SIn);
  MinVal.Load(SIn);
  MaxVal.Load(SIn);
  NegWgt.Load(SIn);
  NumComs.Load(SIn);
  HOVIDSV.Load(SIn);
  PNoCom.Load(SIn);
  Rnd.PutSeed(RndSeed);
}

Here is the call graph for this function:

int TCoda::MLEGradAscent	(	const double &	Thres,
		const int &	MaxIter,
		const TStr	PlotNm,
		const double	StepAlpha = 0.3,
		const double	StepBeta = 0.1
	)

Definition at line 885 of file agmdirected.cpp.

References TVec< TVal, TSizeTy >::Add(), AddCom(), THashSet< TKey, THashFunc >::AddKey(), THash< TKey, TDat, THashFunc >::BegI(), DelCom(), TStr::Empty(), THashSet< TKey, THashFunc >::Empty(), THash< TKey, TDat, THashFunc >::EndI(), F, G, GetCom(), TNGraph::TNodeI::GetInDeg(), TNGraph::TNodeI::GetInNId(), TNGraph::GetNI(), TNGraph::GetNodes(), TNGraph::TNodeI::GetOutDeg(), TNGraph::TNodeI::GetOutNId(), GetStepSizeByLineSearch(), TExeTm::GetTmStr(), GradientForNode(), H, HOVIDSV, IAssert, THashSet< TKey, THashFunc >::IsKey(), Likelihood(), TFlt::Mn, Norm2(), NumComs, TGnuPlot::PlotValV(), and Rnd.

Referenced by FindComsByCV().

                                                                                                                                  {
  time_t InitTime = time(NULL);
  TExeTm ExeTm, CheckTm;
  int iter = 0, PrevIter = 0;
  TIntFltPrV IterLV;
  TNGraph::TNodeI UI;
  double PrevL = TFlt::Mn, CurL = 0.0;
  TIntV NIdxV(F.Len(), 0);
  for (int i = 0; i < F.Len(); i++) { NIdxV.Add(i); }
  IAssert(NIdxV.Len() == F.Len());
  TIntFltH GradV;
  while(iter < MaxIter) {
    NIdxV.Shuffle(Rnd);
    for (int ui = 0; ui < F.Len(); ui++, iter++) {
      const bool IsRow = (ui % 2 == 0);
      int u = NIdxV[ui]; //
      //find set of candidate c (we only need to consider c to which a neighbor of u belongs to)
      UI = G->GetNI(u);
      const int Deg = IsRow? UI.GetOutDeg(): UI.GetInDeg();
      TIntSet CIDSet(5 * Deg);
      for (int e = 0; e < Deg; e++) {
        int VID = IsRow? UI.GetOutNId(e): UI.GetInNId(e);
        if (HOVIDSV[u].IsKey(VID)) { continue; }
        TIntFltH NbhCIDH = IsRow? H[VID]: F[VID];
        for (TIntFltH::TIter CI = NbhCIDH.BegI(); CI < NbhCIDH.EndI(); CI++) {
          CIDSet.AddKey(CI.GetKey());
          //printf("CI.GetKey:%d\n", CI.GetKey());
          IAssert(CI.GetKey() <= NumComs);
        }
      }
      TIntFltH& CurMem = IsRow? F[u]: H[u];
      for (TIntFltH::TIter CI = CurMem.BegI(); CI < CurMem.EndI(); CI++) { //remove the community membership which U does not share with its neighbors
        if (! CIDSet.IsKey(CI.GetKey())) {
          DelCom(IsRow, u, CI.GetKey());
        }
      }
      if (CIDSet.Empty()) { continue; }
      GradientForNode(IsRow, u, GradV, CIDSet);
      if (Norm2(GradV) < 1e-4) { continue; }
      double LearnRate = GetStepSizeByLineSearch(IsRow, u, GradV, GradV, StepAlpha, StepBeta);
      if (LearnRate == 0.0) { continue; }
      for (int ci = 0; ci < GradV.Len(); ci++) {
        int CID = GradV.GetKey(ci);
        double Change = LearnRate * GradV.GetDat(CID);
        double NewFuc = GetCom(IsRow, u, CID) + Change;
        if (NewFuc <= 0.0) {
          DelCom(IsRow, u, CID);
        } else {
          AddCom(IsRow, u, CID, NewFuc);
        }
      }
      if (! PlotNm.Empty() && (iter + 1) % G->GetNodes() == 0) {
        IterLV.Add(TIntFltPr(iter, Likelihood(false)));
      }
    }
    printf("\r%d iterations (%f) [%lu sec]", iter, CurL, time(NULL) - InitTime);
    fflush(stdout);
    if (iter - PrevIter >= 2 * G->GetNodes() && iter > 10000) {
      PrevIter = iter;
      CurL = Likelihood();
      if (PrevL > TFlt::Mn && ! PlotNm.Empty()) {
        printf("\r%d iterations, Likelihood: %f, Diff: %f", iter, CurL,  CurL - PrevL);
      }
      fflush(stdout);
      if (CurL - PrevL <= Thres * fabs(PrevL)) { break; }
      else { PrevL = CurL; }
    }
    
  }
  printf("\n");
  printf("MLE for Lambda completed with %d iterations(%s)\n", iter, ExeTm.GetTmStr());
  if (! PlotNm.Empty()) {
    TGnuPlot::PlotValV(IterLV, PlotNm + ".likelihood_Q");
  }
  return iter;
}

Here is the call graph for this function:

Here is the caller graph for this function:

int TCoda::MLEGradAscentParallel	(	const double &	Thres,
		const int &	MaxIter,
		const int	ChunkNum,
		const int	ChunkSize,
		const TStr	PlotNm,
		const double	StepAlpha = 0.3,
		const double	StepBeta = 0.1
	)

Definition at line 962 of file agmdirected.cpp.

References TVec< TVal, TSizeTy >::Add(), THash< TKey, TDat, THashFunc >::AddDat(), THashSet< TKey, THashFunc >::AddKey(), THash< TKey, TDat, THashFunc >::BegI(), THash< TKey, TDat, THashFunc >::Clr(), THash< TKey, TDat, THashFunc >::Defrag(), THash< TKey, TDat, THashFunc >::DelIfKey(), TStr::Empty(), THashSet< TKey, THashFunc >::Empty(), THash< TKey, TDat, THashFunc >::EndI(), F, G, THash< TKey, TDat, THashFunc >::GetDat(), TVec< TVal, TSizeTy >::GetDat(), TNGraph::TNodeI::GetDeg(), TNGraph::TNodeI::GetInDeg(), TNGraph::TNodeI::GetInNId(), THash< TKey, TDat, THashFunc >::GetKey(), TNGraph::TNodeI::GetNbrNId(), TNGraph::GetNI(), TNGraph::GetNodes(), TNGraph::TNodeI::GetOutDeg(), TNGraph::TNodeI::GetOutNId(), GetStepSizeByLineSearch(), GradientForNode(), H, HOVIDSV, IAssert, THash< TKey, TDat, THashFunc >::IsKey(), THashSet< TKey, THashFunc >::IsKey(), THash< TKey, TDat, THashFunc >::Len(), TVec< TVal, TSizeTy >::Len(), Likelihood(), Norm2(), TGnuPlot::PlotValV(), TVec< TVal, TSizeTy >::PutAll(), Rnd, SumFV, and SumHV.

Referenced by FindComsByCV(), and MLEGradAscentParallel().

                                                                                                                                                                                   {
  //parallel
  time_t InitTime = time(NULL);
  //uint64 StartTm = TSecTm::GetCurTm().GetAbsSecs();
  TExeTm ExeTm, CheckTm;
  double PrevL = Likelihood(true);
  TIntFltPrV IterLV;
  int PrevIter = 0;
  int iter = 0;
  TIntV NIdxV(F.Len(), 0);
  for (int i = 0; i < F.Len(); i++) { NIdxV.Add(i); }
  TIntV NIDOPTV(F.Len()); //check if a node needs optimization or not 1: does not require optimization
  NIDOPTV.PutAll(0);
  TVec<TIntFltH> NewF(ChunkNum * ChunkSize);
  TIntV NewNIDV(ChunkNum * ChunkSize);
  TBoolV IsRowV(ChunkNum * ChunkSize);
  for (iter = 0; iter < MaxIter; iter++) {
    NIdxV.Clr(false);
    for (int i = 0; i < F.Len(); i++) { 
      //if (NIDOPTV[i] == 0) {  NIdxV.Add(i); }
      NIdxV.Add(i);
    }
    IAssert (NIdxV.Len() <= F.Len());
    NIdxV.Shuffle(Rnd);
    // compute gradient for chunk of nodes
#pragma omp parallel for schedule(static, 1)
    for (int TIdx = 0; TIdx < ChunkNum; TIdx++) {
      TIntFltH GradV;
      for (int ui = TIdx * ChunkSize; ui < (TIdx + 1) * ChunkSize; ui++) {
        const bool IsRow = (ui % 2 == 0);
        NewNIDV[ui] = -1;
        if (ui > NIdxV.Len()) { continue; }
        const int u = NIdxV[ui]; //
        //find set of candidate c (we only need to consider c to which a neighbor of u belongs to)
        TNGraph::TNodeI UI = G->GetNI(u);
        const int Deg = IsRow? UI.GetOutDeg(): UI.GetInDeg();
        TIntSet CIDSet(5 * Deg);
        TIntFltH CurFU = IsRow? F[u]: H[u];
        for (int e = 0; e < Deg; e++) {
          int VID = IsRow? UI.GetOutNId(e): UI.GetInNId(e);
          if (HOVIDSV[u].IsKey(VID)) { continue; }
          TIntFltH& NbhCIDH = IsRow? H[VID]: F[VID];
          for (TIntFltH::TIter CI = NbhCIDH.BegI(); CI < NbhCIDH.EndI(); CI++) {
            CIDSet.AddKey(CI.GetKey());
          }
        }
        if (CIDSet.Empty()) { 
          CurFU.Clr();
        }
        else {
          for (TIntFltH::TIter CI = CurFU.BegI(); CI < CurFU.EndI(); CI++) { //remove the community membership which U does not share with its neighbors
            if (! CIDSet.IsKey(CI.GetKey())) {
              CurFU.DelIfKey(CI.GetKey());
            }
          }
          GradientForNode(IsRow, u, GradV, CIDSet);
          if (Norm2(GradV) < 1e-4) { NIDOPTV[u] = 1; continue; }
          double LearnRate = GetStepSizeByLineSearch(IsRow, u, GradV, GradV, StepAlpha, StepBeta);
          if (LearnRate == 0.0) { NewNIDV[ui] = -2; continue; }
          for (int ci = 0; ci < GradV.Len(); ci++) {
            int CID = GradV.GetKey(ci);
            double Change = LearnRate * GradV.GetDat(CID);
            double NewFuc = CurFU.IsKey(CID)? CurFU.GetDat(CID) + Change : Change;
            if (NewFuc <= 0.0) {
              CurFU.DelIfKey(CID);
            } else {
              CurFU.AddDat(CID) = NewFuc;
            }
          }
          CurFU.Defrag();
        }
        //store changes
        NewF[ui] = CurFU;
        NewNIDV[ui] = u;
        IsRowV[ui] = IsRow;
      }
    }
    int NumNoChangeGrad = 0;
    int NumNoChangeStepSize = 0;
    for (int ui = 0; ui < NewNIDV.Len(); ui++) {
      int NewNID = NewNIDV[ui];
      if (NewNID == -1) { NumNoChangeGrad++; continue; }
      if (NewNID == -2) { NumNoChangeStepSize++; continue; }
      if (IsRowV[ui]) {
        for (TIntFltH::TIter CI = F[NewNID].BegI(); CI < F[NewNID].EndI(); CI++) {
          SumFV[CI.GetKey()] -= CI.GetDat();
        }
      } else {
        for (TIntFltH::TIter CI = H[NewNID].BegI(); CI < H[NewNID].EndI(); CI++) {
          SumHV[CI.GetKey()] -= CI.GetDat();
        }
      }
    }
#pragma omp parallel for
    for (int ui = 0; ui < NewNIDV.Len(); ui++) {
      int NewNID = NewNIDV[ui];
      if (NewNID < 0) { continue; }
      if (IsRowV[ui]) {
        F[NewNID] = NewF[ui];
      } else {
        H[NewNID] = NewF[ui];
      }
    }
    for (int ui = 0; ui < NewNIDV.Len(); ui++) {
      int NewNID = NewNIDV[ui];
      if (NewNID < 0) { continue; }
      if (IsRowV[ui]) {
        for (TIntFltH::TIter CI = F[NewNID].BegI(); CI < F[NewNID].EndI(); CI++) {
          SumFV[CI.GetKey()] += CI.GetDat();
        }
      } else {
        for (TIntFltH::TIter CI = H[NewNID].BegI(); CI < H[NewNID].EndI(); CI++) {
          SumHV[CI.GetKey()] += CI.GetDat();
        }
      }
    }
    // update the nodes who are optimal
    for (int ui = 0; ui < NewNIDV.Len(); ui++) {
      int NewNID = NewNIDV[ui];
      if (NewNID < 0) { continue; }
      TNGraph::TNodeI UI = G->GetNI(NewNID);
      NIDOPTV[NewNID] = 0;
      for (int e = 0; e < UI.GetDeg(); e++) {
        NIDOPTV[UI.GetNbrNId(e)] = 0;
      }
    }
    int OPTCnt = 0;
    for (int i = 0; i < NIDOPTV.Len(); i++) { if (NIDOPTV[i] == 1) { OPTCnt++; } }
    /*
    if (! PlotNm.Empty()) {
      printf("\r%d iterations [%s] %lu secs", iter * ChunkSize * ChunkNum, ExeTm.GetTmStr(), TSecTm::GetCurTm().GetAbsSecs() - StartTm);
      if (PrevL > TFlt::Mn) { printf(" (%f) %d g %d s %d OPT", PrevL, NumNoChangeGrad, NumNoChangeStepSize, OPTCnt); }
      fflush(stdout);
    }
    */
    if ((iter - PrevIter) * ChunkSize * ChunkNum >= G->GetNodes()) {
      PrevIter = iter;
      double CurL = Likelihood(true);
      IterLV.Add(TIntFltPr(iter * ChunkSize * ChunkNum, CurL));
      printf("\r%d iterations, Likelihood: %f, Diff: %f [%lu secs]", iter, CurL,  CurL - PrevL, time(NULL) - InitTime);
       fflush(stdout);
      if (CurL - PrevL <= Thres * fabs(PrevL)) { 
        break;
      }
      else {
        PrevL = CurL;
      }
    }
  }
  if (! PlotNm.Empty()) {
    printf("\nMLE completed with %d iterations(%lu secs)\n", iter, time(NULL) - InitTime);
    TGnuPlot::PlotValV(IterLV, PlotNm + ".likelihood_Q");
  } else {
    printf("\rMLE completed with %d iterations(%lu secs)\n", iter, time(NULL) - InitTime);
    fflush(stdout);
  }
  return iter;
}

Here is the call graph for this function:

Here is the caller graph for this function:

int TCoda::MLEGradAscentParallel ( const double &  Thres, const int &  MaxIter, const int  ChunkNum, const TStr  PlotNm = TStr(), const double  StepAlpha = 0.3, const double  StepBeta = 0.1  )

inline

Definition at line 74 of file agmdirected.h.

References TNGraph::GetNodes(), and MLEGradAscentParallel().

                                                                                                                                                                                {
    int ChunkSize = G->GetNodes() / 10 / ChunkNum;
    if (ChunkSize == 0) { ChunkSize = 1; }
    return MLEGradAscentParallel(Thres, MaxIter, ChunkNum, ChunkSize, PlotNm, StepAlpha, StepBeta);
  }

Here is the call graph for this function:

void TCoda::NeighborComInit

(

const int

InitComs

)

Definition at line 83 of file agmdirected.cpp.

References F, and G.

Referenced by FindComsByCV().

                                              {
  //initialize with best neighborhood communities (Gleich et.al. KDD'12)
  TExeTm RunTm;
  TFltIntPrV NIdPhiV(F.Len(), 0);
  TAGMFastUtil::GetNIdPhiV<PNGraph>(G, NIdPhiV);
  NeighborComInit(NIdPhiV, InitComs);
}

Here is the caller graph for this function:

void TCoda::NeighborComInit	(	TFltIntPrV &	NIdPhiV,
		const int	InitComs
	)

Definition at line 91 of file agmdirected.cpp.

References AddComIn(), AddComOut(), F, G, TVec< TVal, TSizeTy >::Gen(), TNGraph::TNodeI::GetDeg(), TNGraph::TNodeI::GetInDeg(), TNGraph::TNodeI::GetNbrNId(), TNGraph::GetNI(), TNGraph::GetNodes(), TNGraph::TNodeI::GetOutDeg(), TRnd::GetUniDev(), TRnd::GetUniDevInt(), H, TVec< TVal, TSizeTy >::Len(), NumComs, Rnd, TVec< TVal, TSizeTy >::Sort(), SumFV, and SumHV.

                                                                   {
  NIdPhiV.Sort(true);
  F.Gen(G->GetNodes());
  H.Gen(G->GetNodes());
  SumFV.Gen(InitComs);
  SumHV.Gen(InitComs);
  NumComs = InitComs;
  //TIntFltH NCPhiH(F.Len());
  TIntSet InvalidNIDS(F.Len());
  TIntV ChosenNIDV(InitComs, 0); //FOR DEBUG
  //choose nodes with local minimum in conductance
  int CurCID = 0;
  for (int ui = 0; ui < NIdPhiV.Len(); ui++) {
    int UID = NIdPhiV[ui].Val2;
    fflush(stdout);
    if (InvalidNIDS.IsKey(UID)) { continue; }
    ChosenNIDV.Add(UID); //FOR DEBUG
    //add the node and its neighbors to the current community
    TNGraph::TNodeI NI = G->GetNI(UID);
    if (NI.GetOutDeg() > 0) { AddComOut(UID, CurCID, 1.0); }
    if (NI.GetInDeg() > 0) { AddComIn(UID, CurCID, 1.0); }
    fflush(stdout);
    //add neighbors depending on whether they have incoming / outgoing edges from the center node (NI)
    for (int e = 0; e < NI.GetDeg(); e++) {
      int VID = NI.GetNbrNId(e);
      TNGraph::TNodeI VI = G->GetNI(VID);
      if (VI.GetOutDeg() > 0) { AddComOut(VID, CurCID, 1.0); }
      if (VI.GetInDeg() > 0) { AddComIn(VID, CurCID, 1.0); }
    }
    //exclude its neighbors from the next considerations
    for (int e = 0; e < NI.GetDeg(); e++) {
      InvalidNIDS.AddKey(NI.GetNbrNId(e));
    }
    CurCID++;
    fflush(stdout);
    if (CurCID >= NumComs) { break;  }
  }
  if (NumComs > CurCID) {
    printf("%d communities needed to fill randomly\n", NumComs - CurCID);
  }
  //assign a member to zero-member community (if any)
  for (int c = 0; c < SumFV.Len(); c++) {
    if (SumFV[c] == 0.0) {
      int ComSz = 10;
      for (int u = 0; u < ComSz; u++) {
        int UID = Rnd.GetUniDevInt(G->GetNodes());
        AddComOut(UID, c, Rnd.GetUniDev());
      }
    }
  }
  //assign a member to zero-member community (if any)
  for (int c = 0; c < SumHV.Len(); c++) {
    if (SumHV[c] == 0.0) {
      int ComSz = 10;
      for (int u = 0; u < ComSz; u++) {
        int UID = Rnd.GetUniDevInt(G->GetNodes());
        AddComIn(UID, c, Rnd.GetUniDev());
      }
    }
  }
}

Here is the call graph for this function:

double TCoda::Norm2 ( const TIntFltH &  UV )

inline

Definition at line 189 of file agmdirected.h.

References THash< TKey, TDat, THashFunc >::BegI(), and THash< TKey, TDat, THashFunc >::EndI().

Referenced by LikelihoodForNode(), MLEGradAscent(), and MLEGradAscentParallel().

                                          {
    double N = 0.0;
    for (TIntFltH::TIter HI = UV.BegI(); HI < UV.EndI(); HI++) {
      N += HI.GetDat() * HI.GetDat();
    }
    return N;
  }

Here is the call graph for this function:

Here is the caller graph for this function:

double TCoda::Prediction ( const TIntFltH &  FU, const TIntFltH &  HV  )

inline

Definition at line 174 of file agmdirected.h.

References DotProduct(), TStr::Fmt(), and IAssertR.

Referenced by GetNonEdgePairScores(), GradientForNode(), LikelihoodForNode(), LikelihoodHoldOut(), and Prediction().

                                                                   {
    double DP = log (1.0 / (1.0 - PNoCom)) + DotProduct(FU, HV);
    IAssertR(DP > 0.0, TStr::Fmt("DP: %f", DP));
    return exp(- DP);
  }

Here is the call graph for this function:

Here is the caller graph for this function:

double TCoda::Prediction ( const int &  UID, const int &  VID  )

inline

Definition at line 179 of file agmdirected.h.

References Prediction().

                                                           {
    return Prediction(F[UID], H[VID]);
  }

Here is the call graph for this function:

void TCoda::RandomInit

(

const int

InitComs

)

Definition at line 43 of file agmdirected.cpp.

References AddComIn(), AddComOut(), F, G, TVec< TVal, TSizeTy >::Gen(), TNGraph::TNodeI::GetInDeg(), TNGraph::GetNI(), TNGraph::GetNodes(), TNGraph::TNodeI::GetOutDeg(), TRnd::GetUniDev(), TRnd::GetUniDevInt(), H, TVec< TVal, TSizeTy >::Len(), NumComs, Rnd, SumFV, and SumHV.

Referenced by FindComsByCV(), and TCoda().

                                         {
  F.Gen(G->GetNodes());
  H.Gen(G->GetNodes());
  SumFV.Gen(InitComs);
  SumHV.Gen(InitComs);
  NumComs = InitComs;
  for (int u = 0; u < F.Len(); u++) {
    //assign to just one community
    int Mem = G->GetNI(u).GetOutDeg();
    if (Mem > 10) { Mem = 10; }
    for (int c = 0; c < Mem; c++) {
      int CID = Rnd.GetUniDevInt(InitComs);
      AddComOut(u, CID, Rnd.GetUniDev());
    }
  }
  for (int u = 0; u < H.Len(); u++) {
    //assign to just one community
    int Mem = G->GetNI(u).GetInDeg();
    if (Mem > 10) { Mem = 10; }
    for (int c = 0; c < Mem; c++) {
      int CID = Rnd.GetUniDevInt(InitComs);
      AddComIn(u, CID, Rnd.GetUniDev());
    }
  }
  //assign a member to zero-member community (if any)
  for (int c = 0; c < SumFV.Len(); c++) {
    if (SumFV[c] == 0.0) {
      int UID = Rnd.GetUniDevInt(G->GetNodes());
      AddComOut(UID, c, Rnd.GetUniDev());
    }
  }
  //assign a member to zero-member community (if any)
  for (int c = 0; c < SumHV.Len(); c++) {
    if (SumHV[c] == 0.0) {
      int UID = Rnd.GetUniDevInt(G->GetNodes());
      AddComIn(UID, c, Rnd.GetUniDev());
    }
  }
}

Here is the call graph for this function:

Here is the caller graph for this function:

void TCoda::Save

(

TSOut &

SOut

)

Definition at line 8 of file agmdirected.cpp.

References F, G, H, HOVIDSV, MaxVal, MinVal, NegWgt, NIDV, NodesOk, NumComs, PNoCom, RegCoef, TNGraph::Save(), TVec< TVal, TSizeTy >::Save(), TBool::Save(), TInt::Save(), TFlt::Save(), SumFV, and SumHV.

                            {
  G->Save(SOut);
  F.Save(SOut);
  H.Save(SOut);
  NIDV.Save(SOut);
  RegCoef.Save(SOut);
  SumFV.Save(SOut);
  SumHV.Save(SOut);
  NodesOk.Save(SOut);
  MinVal.Save(SOut);
  MaxVal.Save(SOut);
  NegWgt.Save(SOut);
  NumComs.Save(SOut);
  HOVIDSV.Save(SOut);
  PNoCom.Save(SOut);
}

Here is the call graph for this function:

void TCoda::SetCmtyVV	(	const TVec< TIntV > &	CmtyVVOut,
		const TVec< TIntV > &	CmtyVVIn
	)

Definition at line 171 of file agmdirected.cpp.

References AddComIn(), AddComOut(), THash< TKey, TDat, THashFunc >::AddDat(), F, G, TVec< TVal, TSizeTy >::Gen(), TVec< TVal, TSizeTy >::GetDat(), TNGraph::GetNodes(), H, IAssert, TNGraph::IsNode(), TVec< TVal, TSizeTy >::Len(), NIDV, NodesOk, NumComs, SumFV, and SumHV.

                                                                               {
  IAssert(CmtyVVOut.Len() == CmtyVVIn.Len());
  F.Gen(G->GetNodes());
  H.Gen(G->GetNodes());
  SumFV.Gen(CmtyVVOut.Len());
  SumHV.Gen(CmtyVVIn.Len());
  NumComs = CmtyVVOut.Len();
  TIntH NIDIdxH(NIDV.Len());
  if (! NodesOk) {
    for (int u = 0; u < NIDV.Len(); u++) {
      NIDIdxH.AddDat(NIDV[u], u);
    }
  }
  for (int c = 0; c < CmtyVVOut.Len(); c++) {
    for (int u = 0; u < CmtyVVOut[c].Len(); u++) {
      int UID = CmtyVVOut[c][u];
      if (! NodesOk) { UID = NIDIdxH.GetDat(UID); }
      if (G->IsNode(UID)) { 
        AddComOut(UID, c, 1.0);
      }
    }
  }
  for (int c = 0; c < CmtyVVIn.Len(); c++) {
    for (int u = 0; u < CmtyVVIn[c].Len(); u++) {
      int UID = CmtyVVIn[c][u];
      if (! NodesOk) { UID = NIDIdxH.GetDat(UID); }
      if (G->IsNode(UID)) { 
        AddComIn(UID, c, 1.0);
      }
    }
  }
}

Here is the call graph for this function:

void TCoda::SetGraph

(

const PNGraph &

GraphPt

)

Definition at line 204 of file agmdirected.cpp.

References TSnap::DelSelfEdges(), DoParallel, G, TNGraph::GetNIdV(), TNGraph::GetNodes(), TSnap::GetSubGraph(), HOVIDSV, IAssert, TNGraph::IsNode(), TFlt::Mx, NegWgt, NIDV, NodesOk, and PNoCom.

Referenced by TCoda().

                                           {
  G = GraphPt;
  HOVIDSV.Gen(G->GetNodes());  
  NodesOk = true;
  GraphPt->GetNIdV(NIDV);
  // check that nodes IDs are {0,1,..,Nodes-1}
  for (int nid = 0; nid < GraphPt->GetNodes(); nid++) {
    if (! GraphPt->IsNode(nid)) { 
      NodesOk = false; 
      break; 
    } 
  }
  if (! NodesOk) {
    printf("rearrage nodes\n");
    G = TSnap::GetSubGraph(GraphPt, NIDV, true);
    for (int nid = 0; nid < G->GetNodes(); nid++) {
      IAssert(G->IsNode(nid)); 
    }
  }
  TSnap::DelSelfEdges(G);
  
  PNoCom = 1.0 / (double) G->GetNodes();
  DoParallel = false;
  if (1.0 / PNoCom > sqrt(TFlt::Mx)) { PNoCom = 0.99 / sqrt(TFlt::Mx); } // to prevent overflow
  NegWgt = 1.0;
}

Here is the call graph for this function:

Here is the caller graph for this function:

void TCoda::SetHoldOut ( const double  HOFrac )

inline

Definition at line 54 of file agmdirected.h.

References TAGMFastUtil::GenHoldOutPairs().

{ TVec<TIntSet> HoldOut; TAGMFastUtil::GenHoldOutPairs(G, HoldOut, HOFrac, Rnd); HOVIDSV = HoldOut; }

Here is the call graph for this function:

void TCoda::SetRegCoef ( const double  _RegCoef )

inline

Definition at line 33 of file agmdirected.h.

{ RegCoef = _RegCoef; }

double TCoda::Sum ( const TIntFltH &  UV )

inline

Definition at line 182 of file agmdirected.h.

References THash< TKey, TDat, THashFunc >::BegI(), and THash< TKey, TDat, THashFunc >::EndI().

Referenced by LikelihoodForNode().

                                        {
    double N = 0.0;
    for (TIntFltH::TIter HI = UV.BegI(); HI < UV.EndI(); HI++) {
      N += HI.GetDat();
    }
    return N;
  }

Here is the call graph for this function:

Here is the caller graph for this function:

Member Data Documentation

TBool TCoda::DoParallel

Definition at line 25 of file agmdirected.h.

Referenced by SetGraph().

TVec<TIntFltH> TCoda::F

private

Definition at line 10 of file agmdirected.h.

Referenced by GetCommunity(), Likelihood(), LikelihoodForNode(), Load(), MLEGradAscent(), MLEGradAscentParallel(), NeighborComInit(), RandomInit(), Save(), and SetCmtyVV().

PNGraph TCoda::G

private

Definition at line 9 of file agmdirected.h.

Referenced by DumpMemberships(), FindComsByCV(), GetCmtyS(), GetCmtyVV(), GetCmtyVVUnSorted(), GetGraph(), GetGraphRawNID(), GetNonEdgePairScores(), GradientForNode(), LikelihoodForNode(), LikelihoodHoldOut(), Load(), MLEGradAscent(), MLEGradAscentParallel(), NeighborComInit(), RandomInit(), Save(), SetCmtyVV(), and SetGraph().

TVec<TIntFltH> TCoda::H

private

Definition at line 11 of file agmdirected.h.

Referenced by LikelihoodForNode(), Load(), MLEGradAscent(), MLEGradAscentParallel(), NeighborComInit(), RandomInit(), Save(), and SetCmtyVV().

TVec<TIntSet> TCoda::HOVIDSV

private

Definition at line 19 of file agmdirected.h.

Referenced by FindComsByCV(), GradientForNode(), LikelihoodForNode(), LikelihoodHoldOut(), Load(), MLEGradAscent(), MLEGradAscentParallel(), Save(), and SetGraph().

TFlt TCoda::MaxVal

Definition at line 22 of file agmdirected.h.

Referenced by GetStepSizeByLineSearch(), Load(), and Save().

TFlt TCoda::MinVal

Definition at line 21 of file agmdirected.h.

Referenced by GetStepSizeByLineSearch(), Load(), and Save().

TFlt TCoda::NegWgt

Definition at line 23 of file agmdirected.h.

Referenced by GradientForNode(), LikelihoodForNode(), LikelihoodHoldOut(), Load(), Save(), and SetGraph().

TIntV TCoda::NIDV

private

Definition at line 13 of file agmdirected.h.

Referenced by DumpMemberships(), GetCmtyS(), GetCmtyVVUnSorted(), GetCommunity(), GetGraphRawNID(), GetNIDValH(), GetNonEdgePairScores(), Load(), Save(), SetCmtyVV(), and SetGraph().

TBool TCoda::NodesOk

private

Definition at line 17 of file agmdirected.h.

Referenced by GetCommunity(), Load(), Save(), SetCmtyVV(), and SetGraph().

TInt TCoda::NumComs

private

Definition at line 18 of file agmdirected.h.

Referenced by DumpMemberships(), GetCmtyVV(), GetCmtyVVUnSorted(), GradientForNode(), LikelihoodForNode(), Load(), MLEGradAscent(), NeighborComInit(), RandomInit(), Save(), and SetCmtyVV().

TFlt TCoda::PNoCom

Definition at line 24 of file agmdirected.h.

Referenced by Load(), Save(), SetGraph(), and TCodaAnalyzer::TCodaAnalyzer().

TFlt TCoda::RegCoef

private

Definition at line 14 of file agmdirected.h.

Referenced by GetRegCoef(), GradientForNode(), LikelihoodForNode(), Load(), and Save().

TRnd TCoda::Rnd

private

Definition at line 12 of file agmdirected.h.

Referenced by FindComsByCV(), Load(), MLEGradAscent(), MLEGradAscentParallel(), NeighborComInit(), and RandomInit().

TFltV TCoda::SumFV

private

Definition at line 15 of file agmdirected.h.

Referenced by Load(), MLEGradAscentParallel(), NeighborComInit(), RandomInit(), Save(), and SetCmtyVV().

TFltV TCoda::SumHV

private

Definition at line 16 of file agmdirected.h.

Referenced by GradientForNode(), LikelihoodForNode(), Load(), MLEGradAscentParallel(), NeighborComInit(), RandomInit(), Save(), and SetCmtyVV().

---

The documentation for this class was generated from the following files:

• snap-adv/agmdirected.h
• snap-adv/agmdirected.cpp