SNAP Library 2.4, Developer Reference  2015-05-11 19:40:56
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TAGMFit Class Reference

Fitting the Affilialiton Graph Model (AGM). More...

#include <agmfit.h>

Collaboration diagram for TAGMFit:

Public Member Functions

 TAGMFit ()
 
 ~TAGMFit ()
 
 TAGMFit (const PUNGraph &GraphPt, const TVec< TIntV > &CmtyVVPt, const int RndSeed=0)
 COMMENT. Use to describribe parameters. More...
 
 TAGMFit (const PUNGraph &GraphPt, const int InitComs, const int RndSeed=0)
 COMMENT. Use to describribe parameters. More...
 
 TAGMFit (const PUNGraph &GraphPt, const TVec< TIntV > &CmtyVVPt, const TRnd &RndPt)
 COMMENT. Use to describribe parameters. More...
 
void Save (TSOut &SOut)
 
void Load (TSIn &SIn, const int &RndSeed=0)
 
void RandomInitCmtyVV (const int InitComs, const double ComSzAlpha=1.3, const double MemAlpha=1.8, const int MinComSz=8, const int MaxComSz=200, const int MinMem=1, const int MaxMem=10)
 Randomly initialize bipartite community affiliation graph. More...
 
void AddBaseCmty ()
 Add Epsilon community (base community which includes all nodes) into community affiliation graph. This means that we will later fit the value of epsilon. More...
 
double Likelihood ()
 COMMENT. More...
 
double Likelihood (const TFltV &NewLambdaV)
 
double Likelihood (const TFltV &NewLambdaV, double &LEdges, double &LNoEdges)
 
void SetRegCoef (const double Val)
 
void GetEdgeJointCom ()
 For each (u, v) in edges, precompute C_uv (the set of communities nodes u and v share). More...
 
void NeighborComInit (const int InitComs)
 Initialize node community memberships using best neighborhood communities (see D. Gleich et al. KDD'12). More...
 
void GradLogLForLambda (TFltV &GradV)
 
int MLEGradAscentGivenCAG (const double &Thres=0.001, const int &MaxIter=10000, const TStr PlotNm=TStr())
 Gradient descent for p_c while keeping the community affiliation graph (CAG) fixed. More...
 
void SetDefaultPNoCom ()
 Set Epsilon (the probability that two nodes sharing no communities connect) to the default value. More...
 
void SetPNoCom (const double &Epsilon)
 Set Epsilon (the probability that two nodes sharing no communities connect) to the default value. More...
 
double GetPNoCom ()
 
double CalcPNoComByCmtyVV (const int &SamplePairs=-1)
 Compute the empirical edge probability between a pair of nodes who share no community (epsilon), based on current community affiliations. More...
 
double SelectLambdaSum (const TIntSet &ComK)
 Compute sum of lambda_c (which is log (1 - p_c)) over C_uv (ComK). The function is used to compute edge probability P_uv. More...
 
double SelectLambdaSum (const TFltV &NewLambdaV, const TIntSet &ComK)
 COMMENT. More...
 
void RandomInit (const int &MaxK)
 COMMENT. More...
 
void RunMCMC (const int &MaxIter, const int &EvalLambdaIter, const TStr &PlotFPrx=TStr())
 Main procedure for fitting the AGM to a given graph using MCMC. More...
 
void SampleTransition (int &NID, int &JoinCID, int &LeaveCID, double &DeltaL)
 Sample MMCM transitions: Choose among (join, leave, switch), and then sample (NID, CID). More...
 
void InitNodeData ()
 COMMENT. More...
 
void LeaveCom (const int &NID, const int &CID)
 After MCMC, NID leaves community CID. More...
 
void JoinCom (const int &NID, const int &JoinCID)
 
int RemoveEmptyCom ()
 Remove all communities with no members. More...
 
double SeekLeave (const int &UID, const int &CID)
 Compute the change in likelihood (Delta) if node UID leaves community CID. More...
 
double SeekJoin (const int &UID, const int &CID)
 Compute the change in likelihood (Delta) if node UID joins community CID. More...
 
double SeekSwitch (const int &UID, const int &CurCID, const int &NewCID)
 
double GetStepSizeByLineSearchForLambda (const TFltV &DeltaV, const TFltV &GradV, const double &Alpha, const double &Beta)
 Step size search for updating P_c (which is parametarized by regularization parameter lambda). More...
 
void SetLambdaV (const TFltV &LambdaPt)
 COMMENT. More...
 
void GetLambdaV (TFltV &OutV)
 COMMENT. More...
 
void GetQV (TFltV &OutV)
 Returns QV, a vector of (1 - p_c) for each community c. More...
 
void GetCmtyVV (TVec< TIntV > &CmtyVV, const double QMax=2.0)
 Get communities whose p_c is higher than 1 - QMax. More...
 
void GetCmtyVV (TVec< TIntV > &CmtyVV, TFltV &QV, const double QMax=2.0)
 COMMENT. More...
 
void SetCmtyVV (const TVec< TIntV > &CmtyVV)
 COMMENT. More...
 
void PrintSummary ()
 COMMENT. More...
 

Private Attributes

PUNGraph G
 Graph to fit. More...
 
TVec< TIntSetCIDNSetV
 Community ID -> Member Node ID Sets. More...
 
THash< TIntPr, TIntSetEdgeComVH
 Edge -> Shared Community ID Set. More...
 
THash< TInt, TIntSetNIDComVH
 Node ID -> Communitie IDs the node belongs to. More...
 
TIntV ComEdgesV
 The number of edges in each community. More...
 
TFlt PNoCom
 Probability of edge when two nodes share no community (epsilon in the paper). More...
 
TFltV LambdaV
 Parametrization of P_c (edge probability in community c), P_c = 1 - exp(-lambda). More...
 
TRnd Rnd
 
THash< TIntPr, TFltNIDCIDPrH
 <Node ID, Community ID> pairs (for sampling MCMC moves). More...
 
THash< TIntPr, TIntNIDCIDPrS
 <Node ID, Community ID> pairs (for sampling MCMC moves). More...
 
TFlt MinLambda
 Minimum value of regularization parameter lambda (default = 1e-5). More...
 
TFlt MaxLambda
 Maximum value of regularization parameter lambda (default = 10). More...
 
TFlt RegCoef
 Regularization parameter when we fit for P_c (for finding # communities). More...
 
TInt BaseCID
 ID of the Epsilon-community (in case we fit P_c of the epsilon community). We do not fit for the Epsilon-community in general. More...
 

Detailed Description

Fitting the Affilialiton Graph Model (AGM).

Definition at line 8 of file agmfit.h.

Constructor & Destructor Documentation

TAGMFit::TAGMFit ( )
inline

Definition at line 26 of file agmfit.h.

26 { }
TAGMFit::~TAGMFit ( )
inline

Definition at line 27 of file agmfit.h.

27 { }
TAGMFit::TAGMFit ( const PUNGraph GraphPt,
const TVec< TIntV > &  CmtyVVPt,
const int  RndSeed = 0 
)
inline

COMMENT. Use to describribe parameters.

Definition at line 29 of file agmfit.h.

References SetCmtyVV().

29 : G(GraphPt), PNoCom(0.0), Rnd(RndSeed), MinLambda(0.00001), MaxLambda(10.0), RegCoef(0), BaseCID(-1) { SetCmtyVV(CmtyVVPt); }
TRnd Rnd
Definition: agmfit.h:17
TInt BaseCID
ID of the Epsilon-community (in case we fit P_c of the epsilon community). We do not fit for the Epsi...
Definition: agmfit.h:23
TFlt MinLambda
Minimum value of regularization parameter lambda (default = 1e-5).
Definition: agmfit.h:20
TFlt RegCoef
Regularization parameter when we fit for P_c (for finding # communities).
Definition: agmfit.h:22
TFlt MaxLambda
Maximum value of regularization parameter lambda (default = 10).
Definition: agmfit.h:21
void SetCmtyVV(const TVec< TIntV > &CmtyVV)
COMMENT.
Definition: agmfit.cpp:584
PUNGraph G
Graph to fit.
Definition: agmfit.h:10
TFlt PNoCom
Probability of edge when two nodes share no community (epsilon in the paper).
Definition: agmfit.h:15

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TAGMFit::TAGMFit ( const PUNGraph GraphPt,
const int  InitComs,
const int  RndSeed = 0 
)
inline

COMMENT. Use to describribe parameters.

Definition at line 31 of file agmfit.h.

References NeighborComInit().

31 : G(GraphPt), PNoCom(0.0), Rnd(RndSeed), MinLambda(0.00001), MaxLambda(10.0), RegCoef(0), BaseCID(-1) { NeighborComInit(InitComs); }//RandomInitCmtyVV(InitComs); }
TRnd Rnd
Definition: agmfit.h:17
TInt BaseCID
ID of the Epsilon-community (in case we fit P_c of the epsilon community). We do not fit for the Epsi...
Definition: agmfit.h:23
TFlt MinLambda
Minimum value of regularization parameter lambda (default = 1e-5).
Definition: agmfit.h:20
TFlt RegCoef
Regularization parameter when we fit for P_c (for finding # communities).
Definition: agmfit.h:22
void NeighborComInit(const int InitComs)
Initialize node community memberships using best neighborhood communities (see D. Gleich et al...
Definition: agmfit.cpp:186
TFlt MaxLambda
Maximum value of regularization parameter lambda (default = 10).
Definition: agmfit.h:21
PUNGraph G
Graph to fit.
Definition: agmfit.h:10
TFlt PNoCom
Probability of edge when two nodes share no community (epsilon in the paper).
Definition: agmfit.h:15

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TAGMFit::TAGMFit ( const PUNGraph GraphPt,
const TVec< TIntV > &  CmtyVVPt,
const TRnd RndPt 
)
inline

COMMENT. Use to describribe parameters.

Definition at line 33 of file agmfit.h.

References SetCmtyVV().

33 : G(GraphPt), PNoCom(0.0), Rnd(RndPt), MinLambda(0.00001), MaxLambda(10.0), RegCoef(0), BaseCID(-1) { SetCmtyVV(CmtyVVPt); }
TRnd Rnd
Definition: agmfit.h:17
TInt BaseCID
ID of the Epsilon-community (in case we fit P_c of the epsilon community). We do not fit for the Epsi...
Definition: agmfit.h:23
TFlt MinLambda
Minimum value of regularization parameter lambda (default = 1e-5).
Definition: agmfit.h:20
TFlt RegCoef
Regularization parameter when we fit for P_c (for finding # communities).
Definition: agmfit.h:22
TFlt MaxLambda
Maximum value of regularization parameter lambda (default = 10).
Definition: agmfit.h:21
void SetCmtyVV(const TVec< TIntV > &CmtyVV)
COMMENT.
Definition: agmfit.cpp:584
PUNGraph G
Graph to fit.
Definition: agmfit.h:10
TFlt PNoCom
Probability of edge when two nodes share no community (epsilon in the paper).
Definition: agmfit.h:15

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Member Function Documentation

void TAGMFit::AddBaseCmty ( )

Add Epsilon community (base community which includes all nodes) into community affiliation graph. This means that we will later fit the value of epsilon.

Definition at line 251 of file agmfit.cpp.

References TVec< TVal, TSizeTy >::Add(), BaseCID, CIDNSetV, G, GetCmtyVV(), TUNGraph::GetNIdV(), IAssert, InitNodeData(), TVec< TVal, TSizeTy >::Len(), PNoCom, and SetCmtyVV().

251  {
252  TVec<TIntV> CmtyVV;
253  GetCmtyVV(CmtyVV);
254  TIntV TmpV = CmtyVV[0];
255  CmtyVV.Add(TmpV);
256  G->GetNIdV(CmtyVV[0]);
257  IAssert(CIDNSetV.Len() + 1 == CmtyVV.Len());
258  SetCmtyVV(CmtyVV);
259  InitNodeData();
260  BaseCID = 0;
261  PNoCom = 0.0;
262 }
#define IAssert(Cond)
Definition: bd.h:262
void GetNIdV(TIntV &NIdV) const
Gets a vector IDs of all nodes in the graph.
Definition: graph.cpp:125
TSizeTy Len() const
Returns the number of elements in the vector.
Definition: ds.h:535
TInt BaseCID
ID of the Epsilon-community (in case we fit P_c of the epsilon community). We do not fit for the Epsi...
Definition: agmfit.h:23
void GetCmtyVV(TVec< TIntV > &CmtyVV, const double QMax=2.0)
Get communities whose p_c is higher than 1 - QMax.
Definition: agmfit.cpp:554
void InitNodeData()
COMMENT.
Definition: agmfit.cpp:264
TVec< TIntSet > CIDNSetV
Community ID -> Member Node ID Sets.
Definition: agmfit.h:11
void SetCmtyVV(const TVec< TIntV > &CmtyVV)
COMMENT.
Definition: agmfit.cpp:584
TSizeTy Add()
Adds a new element at the end of the vector, after its current last element.
Definition: ds.h:559
PUNGraph G
Graph to fit.
Definition: agmfit.h:10
TFlt PNoCom
Probability of edge when two nodes share no community (epsilon in the paper).
Definition: agmfit.h:15
Vector is a sequence TVal objects representing an array that can change in size.
Definition: ds.h:420

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double TAGMFit::CalcPNoComByCmtyVV ( const int &  SamplePairs = -1)

Compute the empirical edge probability between a pair of nodes who share no community (epsilon), based on current community affiliations.

Definition at line 632 of file agmfit.cpp.

References G, TAGMUtil::GetIntersection(), TUNGraph::GetNIdV(), TUNGraph::GetNodes(), TUInt64::GetStr(), TUNGraph::IsEdge(), TVec< TVal, TSizeTy >::Len(), THashSet< TKey, THashFunc >::Len(), NIDComVH, PNoCom, and TFlt::Val.

632  {
633  TIntV NIdV;
634  G->GetNIdV(NIdV);
635  uint64 PairNoCom = 0, EdgesNoCom = 0;
636  for (int u = 0; u < NIdV.Len(); u++) {
637  for (int v = u + 1; v < NIdV.Len(); v++) {
638  int SrcNID = NIdV[u], DstNID = NIdV[v];
639  TIntSet JointCom;
640  TAGMUtil::GetIntersection(NIDComVH.GetDat(SrcNID),NIDComVH.GetDat(DstNID),JointCom);
641  if(JointCom.Len() == 0) {
642  PairNoCom++;
643  if (G->IsEdge(SrcNID, DstNID)) { EdgesNoCom++; }
644  if (SamplePairs > 0 && PairNoCom >= (uint64) SamplePairs) { break; }
645  }
646  }
647  if (SamplePairs > 0 && PairNoCom >= (uint64) SamplePairs) { break; }
648  }
649  double DefaultVal = 1.0 / (double)G->GetNodes() / (double)G->GetNodes();
650  if (EdgesNoCom > 0) {
651  PNoCom = (double) EdgesNoCom / (double) PairNoCom;
652  } else {
653  PNoCom = DefaultVal;
654  }
655  printf("%s / %s edges without joint com detected (PNoCom = %f)\n", TUInt64::GetStr(EdgesNoCom).CStr(), TUInt64::GetStr(PairNoCom).CStr(), PNoCom.Val);
656  return PNoCom;
657 }
void GetNIdV(TIntV &NIdV) const
Gets a vector IDs of all nodes in the graph.
Definition: graph.cpp:125
double Val
Definition: dt.h:1293
TSizeTy Len() const
Returns the number of elements in the vector.
Definition: ds.h:535
static void GetIntersection(const THashSet< TInt > &A, const THashSet< TInt > &B, THashSet< TInt > &C)
Definition: agm.cpp:404
int GetNodes() const
Returns the number of nodes in the graph.
Definition: graph.h:165
THash< TInt, TIntSet > NIDComVH
Node ID -> Communitie IDs the node belongs to.
Definition: agmfit.h:13
unsigned long long uint64
Definition: bd.h:38
int Len() const
Definition: shash.h:1121
TStr GetStr() const
Definition: dt.h:1268
bool IsEdge(const int &SrcNId, const int &DstNId) const
Tests whether an edge between node IDs SrcNId and DstNId exists in the graph.
Definition: graph.cpp:108
PUNGraph G
Graph to fit.
Definition: agmfit.h:10
TFlt PNoCom
Probability of edge when two nodes share no community (epsilon in the paper).
Definition: agmfit.h:15

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void TAGMFit::GetCmtyVV ( TVec< TIntV > &  CmtyVV,
const double  QMax = 2.0 
)

Get communities whose p_c is higher than 1 - QMax.

Definition at line 554 of file agmfit.cpp.

Referenced by AddBaseCmty(), and TAGMUtil::FindComsByAGM().

554  {
555  TFltV TmpQV;
556  GetCmtyVV(CmtyVV, TmpQV, QMax);
557 }
void GetCmtyVV(TVec< TIntV > &CmtyVV, const double QMax=2.0)
Get communities whose p_c is higher than 1 - QMax.
Definition: agmfit.cpp:554

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void TAGMFit::GetCmtyVV ( TVec< TIntV > &  CmtyVV,
TFltV QV,
const double  QMax = 2.0 
)

COMMENT.

Definition at line 559 of file agmfit.cpp.

References TVec< TVal, TSizeTy >::Add(), THash< TKey, TDat, THashFunc >::AddDat(), BaseCID, CIDNSetV, G, TVec< TVal, TSizeTy >::Gen(), TUNGraph::GetNodes(), IAssert, LambdaV, TVec< TVal, TSizeTy >::Len(), and MinLambda.

559  {
560  CmtyVV.Gen(CIDNSetV.Len(), 0);
561  QV.Gen(CIDNSetV.Len(), 0);
562  TIntFltH CIDLambdaH(CIDNSetV.Len());
563  for (int c = 0; c < CIDNSetV.Len(); c++) {
564  CIDLambdaH.AddDat(c, LambdaV[c]);
565  }
566  CIDLambdaH.SortByDat(false);
567  for (int c = 0; c < CIDNSetV.Len(); c++) {
568  int CID = CIDLambdaH.GetKey(c);
569  IAssert(LambdaV[CID] >= MinLambda);
570  double Q = exp( - (double) LambdaV[CID]);
571  if (Q > QMax) { continue; }
572  TIntV CmtyV;
573  CIDNSetV[CID].GetKeyV(CmtyV);
574  if (CmtyV.Len() == 0) { continue; }
575  if (CID == BaseCID) { //if the community is the base community(epsilon community), discard
576  IAssert(CmtyV.Len() == G->GetNodes());
577  } else {
578  CmtyVV.Add(CmtyV);
579  QV.Add(Q);
580  }
581  }
582 }
#define IAssert(Cond)
Definition: bd.h:262
TSizeTy Len() const
Returns the number of elements in the vector.
Definition: ds.h:535
TFltV LambdaV
Parametrization of P_c (edge probability in community c), P_c = 1 - exp(-lambda). ...
Definition: agmfit.h:16
TInt BaseCID
ID of the Epsilon-community (in case we fit P_c of the epsilon community). We do not fit for the Epsi...
Definition: agmfit.h:23
int GetNodes() const
Returns the number of nodes in the graph.
Definition: graph.h:165
TFlt MinLambda
Minimum value of regularization parameter lambda (default = 1e-5).
Definition: agmfit.h:20
TVec< TIntSet > CIDNSetV
Community ID -> Member Node ID Sets.
Definition: agmfit.h:11
void Gen(const TSizeTy &_Vals)
Constructs a vector (an array) of _Vals elements.
Definition: ds.h:486
TSizeTy Add()
Adds a new element at the end of the vector, after its current last element.
Definition: ds.h:559
TDat & AddDat(const TKey &Key)
Definition: hash.h:196
PUNGraph G
Graph to fit.
Definition: agmfit.h:10

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void TAGMFit::GetEdgeJointCom ( )

For each (u, v) in edges, precompute C_uv (the set of communities nodes u and v share).

Definition at line 50 of file agmfit.cpp.

References TUNGraph::BegNI(), CIDNSetV, ComEdgesV, EdgeComVH, TUNGraph::EndNI(), G, TVec< TVal, TSizeTy >::Gen(), TUNGraph::GetEdges(), TAGMUtil::GetIntersection(), IAssert, THashSet< TKey, THashFunc >::Len(), and NIDComVH.

Referenced by InitNodeData().

50  {
51  ComEdgesV.Gen(CIDNSetV.Len());
52  EdgeComVH.Gen(G->GetEdges());
53  for (TUNGraph::TNodeI SrcNI = G->BegNI(); SrcNI < G->EndNI(); SrcNI++) {
54  int SrcNID = SrcNI.GetId();
55  for (int v = 0; v < SrcNI.GetDeg(); v++) {
56  int DstNID = SrcNI.GetNbrNId(v);
57  if (SrcNID >= DstNID) { continue; }
58  TIntSet JointCom;
59  IAssert(NIDComVH.IsKey(SrcNID));
60  IAssert(NIDComVH.IsKey(DstNID));
61  TAGMUtil::GetIntersection(NIDComVH.GetDat(SrcNID), NIDComVH.GetDat(DstNID), JointCom);
62  EdgeComVH.AddDat(TIntPr(SrcNID,DstNID),JointCom);
63  for (int k = 0; k < JointCom.Len(); k++) {
64  ComEdgesV[JointCom[k]]++;
65  }
66  }
67  }
68  IAssert(EdgeComVH.Len() == G->GetEdges());
69 }
#define IAssert(Cond)
Definition: bd.h:262
TPair< TInt, TInt > TIntPr
Definition: ds.h:83
int GetEdges() const
Returns the number of edges in the graph.
Definition: graph.cpp:74
Node iterator. Only forward iteration (operator++) is supported.
Definition: graph.h:63
static void GetIntersection(const THashSet< TInt > &A, const THashSet< TInt > &B, THashSet< TInt > &C)
Definition: agm.cpp:404
THash< TIntPr, TIntSet > EdgeComVH
Edge -> Shared Community ID Set.
Definition: agmfit.h:12
THash< TInt, TIntSet > NIDComVH
Node ID -> Communitie IDs the node belongs to.
Definition: agmfit.h:13
int Len() const
Definition: shash.h:1121
TVec< TIntSet > CIDNSetV
Community ID -> Member Node ID Sets.
Definition: agmfit.h:11
TNodeI EndNI() const
Returns an iterator referring to the past-the-end node in the graph.
Definition: graph.h:206
void Gen(const TSizeTy &_Vals)
Constructs a vector (an array) of _Vals elements.
Definition: ds.h:486
TNodeI BegNI() const
Returns an iterator referring to the first node in the graph.
Definition: graph.h:204
PUNGraph G
Graph to fit.
Definition: agmfit.h:10
TIntV ComEdgesV
The number of edges in each community.
Definition: agmfit.h:14

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void TAGMFit::GetLambdaV ( TFltV OutV)
inline

COMMENT.

Definition at line 94 of file agmfit.h.

References LambdaV.

94 {OutV = LambdaV;}
TFltV LambdaV
Parametrization of P_c (edge probability in community c), P_c = 1 - exp(-lambda). ...
Definition: agmfit.h:16
double TAGMFit::GetPNoCom ( )
inline

Definition at line 58 of file agmfit.h.

References PNoCom.

58 { return PNoCom; }
TFlt PNoCom
Probability of edge when two nodes share no community (epsilon in the paper).
Definition: agmfit.h:15
void TAGMFit::GetQV ( TFltV OutV)

Returns QV, a vector of (1 - p_c) for each community c.

Definition at line 451 of file agmfit.cpp.

References TVec< TVal, TSizeTy >::Gen(), LambdaV, and TVec< TVal, TSizeTy >::Len().

451  {
452  OutV.Gen(LambdaV.Len());
453  for (int i = 0; i < LambdaV.Len(); i++) {
454  OutV[i] = exp(- LambdaV[i]);
455  }
456 }
TSizeTy Len() const
Returns the number of elements in the vector.
Definition: ds.h:535
TFltV LambdaV
Parametrization of P_c (edge probability in community c), P_c = 1 - exp(-lambda). ...
Definition: agmfit.h:16
void Gen(const TSizeTy &_Vals)
Constructs a vector (an array) of _Vals elements.
Definition: ds.h:486

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double TAGMFit::GetStepSizeByLineSearchForLambda ( const TFltV DeltaV,
const TFltV GradV,
const double &  Alpha,
const double &  Beta 
)

Step size search for updating P_c (which is parametarized by regularization parameter lambda).

Definition at line 109 of file agmfit.cpp.

References TLinAlg::DotProduct(), IAssert, LambdaV, TVec< TVal, TSizeTy >::Len(), Likelihood(), MaxLambda, and MinLambda.

Referenced by MLEGradAscentGivenCAG().

109  {
110  double StepSize = 1.0;
111  double InitLikelihood = Likelihood();
112  IAssert(LambdaV.Len() == DeltaV.Len());
113  TFltV NewLambdaV(LambdaV.Len());
114  for (int iter = 0; ; iter++) {
115  for (int i = 0; i < LambdaV.Len(); i++) {
116  NewLambdaV[i] = LambdaV[i] + StepSize * DeltaV[i];
117  if (NewLambdaV[i] < MinLambda) { NewLambdaV[i] = MinLambda; }
118  if (NewLambdaV[i] > MaxLambda) { NewLambdaV[i] = MaxLambda; }
119  }
120  if (Likelihood(NewLambdaV) < InitLikelihood + Alpha * StepSize * TLinAlg::DotProduct(GradV, DeltaV)) {
121  StepSize *= Beta;
122  } else {
123  break;
124  }
125  }
126  return StepSize;
127 }
#define IAssert(Cond)
Definition: bd.h:262
double Likelihood()
COMMENT.
Definition: agmfit.cpp:104
TSizeTy Len() const
Returns the number of elements in the vector.
Definition: ds.h:535
TFltV LambdaV
Parametrization of P_c (edge probability in community c), P_c = 1 - exp(-lambda). ...
Definition: agmfit.h:16
TFlt MinLambda
Minimum value of regularization parameter lambda (default = 1e-5).
Definition: agmfit.h:20
TFlt MaxLambda
Maximum value of regularization parameter lambda (default = 10).
Definition: agmfit.h:21
static double DotProduct(const TFltV &x, const TFltV &y)
Definition: linalg.cpp:165

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void TAGMFit::GradLogLForLambda ( TFltV GradV)

Definition at line 595 of file agmfit.cpp.

References THashSet< TKey, THashFunc >::BegI(), CIDNSetV, ComEdgesV, EdgeComVH, THashSet< TKey, THashFunc >::EndI(), TVec< TVal, TSizeTy >::Gen(), LambdaV, TVec< TVal, TSizeTy >::Len(), THashSet< TKey, THashFunc >::Len(), PNoCom, RegCoef, and SelectLambdaSum().

Referenced by MLEGradAscentGivenCAG().

595  {
596  GradV.Gen(LambdaV.Len());
597  TFltV SumEdgeProbsV(LambdaV.Len());
598  for (int e = 0; e < EdgeComVH.Len(); e++) {
599  TIntSet& JointCom = EdgeComVH[e];
600  double LambdaSum = SelectLambdaSum(JointCom);
601  double Puv = 1 - exp(- LambdaSum);
602  if (JointCom.Len() == 0) { Puv = PNoCom; }
603  for (TIntSet::TIter SI = JointCom.BegI(); SI < JointCom.EndI(); SI++) {
604  SumEdgeProbsV[SI.GetKey()] += (1 - Puv) / Puv;
605  }
606  }
607  for (int k = 0; k < LambdaV.Len(); k++) {
608  int MaxEk = CIDNSetV[k].Len() * (CIDNSetV[k].Len() - 1) / 2;
609  int NotEdgesInCom = MaxEk - ComEdgesV[k];
610  GradV[k] = SumEdgeProbsV[k] - (double) NotEdgesInCom;
611  if (LambdaV[k] > 0.0 && RegCoef > 0.0) { //if regularization exists
612  GradV[k] -= RegCoef;
613  }
614  }
615 }
TIter BegI() const
Definition: shash.h:1105
TSizeTy Len() const
Returns the number of elements in the vector.
Definition: ds.h:535
TFltV LambdaV
Parametrization of P_c (edge probability in community c), P_c = 1 - exp(-lambda). ...
Definition: agmfit.h:16
THash< TIntPr, TIntSet > EdgeComVH
Edge -> Shared Community ID Set.
Definition: agmfit.h:12
double SelectLambdaSum(const TIntSet &ComK)
Compute sum of lambda_c (which is log (1 - p_c)) over C_uv (ComK). The function is used to compute ed...
Definition: agmfit.cpp:618
TFlt RegCoef
Regularization parameter when we fit for P_c (for finding # communities).
Definition: agmfit.h:22
TIter EndI() const
Definition: shash.h:1112
int Len() const
Definition: shash.h:1121
TVec< TIntSet > CIDNSetV
Community ID -> Member Node ID Sets.
Definition: agmfit.h:11
void Gen(const TSizeTy &_Vals)
Constructs a vector (an array) of _Vals elements.
Definition: ds.h:486
TIntV ComEdgesV
The number of edges in each community.
Definition: agmfit.h:14
TFlt PNoCom
Probability of edge when two nodes share no community (epsilon in the paper).
Definition: agmfit.h:15

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void TAGMFit::InitNodeData ( )

COMMENT.

Definition at line 264 of file agmfit.cpp.

References TUNGraph::BegNI(), CIDNSetV, ComEdgesV, TSnap::DelSelfEdges(), TUNGraph::EndNI(), G, TVec< TVal, TSizeTy >::Gen(), GetEdgeJointCom(), TAGMUtil::GetNodeMembership(), TUNGraph::GetNodes(), LambdaV, MaxLambda, MinLambda, NIDCIDPrS, and NIDComVH.

Referenced by AddBaseCmty(), NeighborComInit(), RandomInit(), RunMCMC(), and SetCmtyVV().

264  {
266  NIDComVH.Gen(G->GetNodes());
267  for (TUNGraph::TNodeI NI = G->BegNI(); NI < G->EndNI(); NI++) {
268  NIDComVH.AddDat(NI.GetId());
269  }
271  GetEdgeJointCom();
272  LambdaV.Gen(CIDNSetV.Len());
273  for (int c = 0; c < CIDNSetV.Len(); c++) {
274  int MaxE = (CIDNSetV[c].Len()) * (CIDNSetV[c].Len() - 1) / 2;
275  if (MaxE < 2) {
276  LambdaV[c] = MaxLambda;
277  }
278  else{
279  LambdaV[c] = -log((double) (MaxE - ComEdgesV[c]) / MaxE);
280  }
281  if (LambdaV[c] > MaxLambda) { LambdaV[c] = MaxLambda; }
282  if (LambdaV[c] < MinLambda) { LambdaV[c] = MinLambda; }
283  }
284  NIDCIDPrS.Gen(G->GetNodes() * 10);
285  for (int c = 0; c < CIDNSetV.Len(); c++) {
286  for (TIntSet::TIter SI = CIDNSetV[c].BegI(); SI < CIDNSetV[c].EndI(); SI++) {
287  NIDCIDPrS.AddKey(TIntPr(SI.GetKey(), c));
288  }
289  }
290 }
TPair< TInt, TInt > TIntPr
Definition: ds.h:83
static void GetNodeMembership(THash< TInt, TIntSet > &NIDComVH, const TVec< TIntV > &CmtyVV)
get hash table of
Definition: agm.cpp:335
THash< TIntPr, TInt > NIDCIDPrS
pairs (for sampling MCMC moves).
Definition: agmfit.h:19
Node iterator. Only forward iteration (operator++) is supported.
Definition: graph.h:63
TFltV LambdaV
Parametrization of P_c (edge probability in community c), P_c = 1 - exp(-lambda). ...
Definition: agmfit.h:16
void GetEdgeJointCom()
For each (u, v) in edges, precompute C_uv (the set of communities nodes u and v share).
Definition: agmfit.cpp:50
int GetNodes() const
Returns the number of nodes in the graph.
Definition: graph.h:165
TFlt MinLambda
Minimum value of regularization parameter lambda (default = 1e-5).
Definition: agmfit.h:20
THash< TInt, TIntSet > NIDComVH
Node ID -> Communitie IDs the node belongs to.
Definition: agmfit.h:13
TFlt MaxLambda
Maximum value of regularization parameter lambda (default = 10).
Definition: agmfit.h:21
TVec< TIntSet > CIDNSetV
Community ID -> Member Node ID Sets.
Definition: agmfit.h:11
TNodeI EndNI() const
Returns an iterator referring to the past-the-end node in the graph.
Definition: graph.h:206
void Gen(const TSizeTy &_Vals)
Constructs a vector (an array) of _Vals elements.
Definition: ds.h:486
TNodeI BegNI() const
Returns an iterator referring to the first node in the graph.
Definition: graph.h:204
void DelSelfEdges(const PGraph &Graph)
Removes all the self-edges from the graph.
Definition: alg.h:419
PUNGraph G
Graph to fit.
Definition: agmfit.h:10
TIntV ComEdgesV
The number of edges in each community.
Definition: agmfit.h:14

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void TAGMFit::JoinCom ( const int &  NID,
const int &  JoinCID 
)

Definition at line 309 of file agmfit.cpp.

References CIDNSetV, ComEdgesV, EdgeComVH, G, TUNGraph::TNodeI::GetDeg(), TUNGraph::TNodeI::GetNbrNId(), TUNGraph::GetNI(), TMath::Mn(), TMath::Mx(), NIDCIDPrS, and NIDComVH.

Referenced by RunMCMC().

309  {
310  TUNGraph::TNodeI NI = G->GetNI(NID);
311  for (int e = 0; e < NI.GetDeg(); e++) {
312  int VID = NI.GetNbrNId(e);
313  if (NIDComVH.GetDat(VID).IsKey(JoinCID)) {
314  TIntPr SrcDstNIDPr = TIntPr(TMath::Mn(NID,VID), TMath::Mx(NID,VID));
315  EdgeComVH.GetDat(SrcDstNIDPr).AddKey(JoinCID);
316  ComEdgesV[JoinCID]++;
317  }
318  }
319  CIDNSetV[JoinCID].AddKey(NID);
320  NIDComVH.GetDat(NID).AddKey(JoinCID);
321  NIDCIDPrS.AddKey(TIntPr(NID, JoinCID));
322 }
static const T & Mn(const T &LVal, const T &RVal)
Definition: xmath.h:36
TPair< TInt, TInt > TIntPr
Definition: ds.h:83
static const T & Mx(const T &LVal, const T &RVal)
Definition: xmath.h:32
THash< TIntPr, TInt > NIDCIDPrS
pairs (for sampling MCMC moves).
Definition: agmfit.h:19
Node iterator. Only forward iteration (operator++) is supported.
Definition: graph.h:63
THash< TIntPr, TIntSet > EdgeComVH
Edge -> Shared Community ID Set.
Definition: agmfit.h:12
int GetDeg() const
Returns degree of the current node.
Definition: graph.h:85
THash< TInt, TIntSet > NIDComVH
Node ID -> Communitie IDs the node belongs to.
Definition: agmfit.h:13
TNodeI GetNI(const int &NId) const
Returns an iterator referring to the node of ID NId in the graph.
Definition: graph.h:208
Definition: ds.h:32
TVec< TIntSet > CIDNSetV
Community ID -> Member Node ID Sets.
Definition: agmfit.h:11
int GetNbrNId(const int &NodeN) const
Returns ID of NodeN-th neighboring node.
Definition: graph.h:104
PUNGraph G
Graph to fit.
Definition: agmfit.h:10
TIntV ComEdgesV
The number of edges in each community.
Definition: agmfit.h:14

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void TAGMFit::LeaveCom ( const int &  NID,
const int &  CID 
)

After MCMC, NID leaves community CID.

Definition at line 293 of file agmfit.cpp.

References CIDNSetV, ComEdgesV, EdgeComVH, G, TUNGraph::TNodeI::GetDeg(), TUNGraph::TNodeI::GetNbrNId(), TUNGraph::GetNI(), TMath::Mn(), TMath::Mx(), NIDCIDPrS, and NIDComVH.

Referenced by RunMCMC().

293  {
294  TUNGraph::TNodeI NI = G->GetNI(NID);
295  for (int e = 0; e < NI.GetDeg(); e++) {
296  int VID = NI.GetNbrNId(e);
297  if (NIDComVH.GetDat(VID).IsKey(CID)) {
298  TIntPr SrcDstNIDPr = TIntPr(TMath::Mn(NID,VID), TMath::Mx(NID,VID));
299  EdgeComVH.GetDat(SrcDstNIDPr).DelKey(CID);
300  ComEdgesV[CID]--;
301  }
302  }
303  CIDNSetV[CID].DelKey(NID);
304  NIDComVH.GetDat(NID).DelKey(CID);
305  NIDCIDPrS.DelKey(TIntPr(NID, CID));
306 }
static const T & Mn(const T &LVal, const T &RVal)
Definition: xmath.h:36
TPair< TInt, TInt > TIntPr
Definition: ds.h:83
static const T & Mx(const T &LVal, const T &RVal)
Definition: xmath.h:32
THash< TIntPr, TInt > NIDCIDPrS
pairs (for sampling MCMC moves).
Definition: agmfit.h:19
Node iterator. Only forward iteration (operator++) is supported.
Definition: graph.h:63
THash< TIntPr, TIntSet > EdgeComVH
Edge -> Shared Community ID Set.
Definition: agmfit.h:12
int GetDeg() const
Returns degree of the current node.
Definition: graph.h:85
THash< TInt, TIntSet > NIDComVH
Node ID -> Communitie IDs the node belongs to.
Definition: agmfit.h:13
TNodeI GetNI(const int &NId) const
Returns an iterator referring to the node of ID NId in the graph.
Definition: graph.h:208
Definition: ds.h:32
TVec< TIntSet > CIDNSetV
Community ID -> Member Node ID Sets.
Definition: agmfit.h:11
int GetNbrNId(const int &NodeN) const
Returns ID of NodeN-th neighboring node.
Definition: graph.h:104
PUNGraph G
Graph to fit.
Definition: agmfit.h:10
TIntV ComEdgesV
The number of edges in each community.
Definition: agmfit.h:14

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double TAGMFit::Likelihood ( )

COMMENT.

Definition at line 104 of file agmfit.cpp.

References LambdaV.

Referenced by TAGMUtil::FindComsByAGM(), GetStepSizeByLineSearchForLambda(), MLEGradAscentGivenCAG(), PrintSummary(), and RunMCMC().

104  {
105  return Likelihood(LambdaV);
106 }
double Likelihood()
COMMENT.
Definition: agmfit.cpp:104
TFltV LambdaV
Parametrization of P_c (edge probability in community c), P_c = 1 - exp(-lambda). ...
Definition: agmfit.h:16

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double TAGMFit::Likelihood ( const TFltV NewLambdaV)
inline

Definition at line 43 of file agmfit.h.

References Likelihood().

Referenced by Likelihood().

43 { double Tmp1, Tmp2; return Likelihood(NewLambdaV, Tmp1, Tmp2); }
double Likelihood()
COMMENT.
Definition: agmfit.cpp:104

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double TAGMFit::Likelihood ( const TFltV NewLambdaV,
double &  LEdges,
double &  LNoEdges 
)

Definition at line 76 of file agmfit.cpp.

References CIDNSetV, ComEdgesV, EdgeComVH, IAssert, TVec< TVal, TSizeTy >::Len(), THashSet< TKey, THashFunc >::Len(), TFlt::Mn, PNoCom, RegCoef, SelectLambdaSum(), and TLinAlg::SumVec().

76  {
77  IAssert(CIDNSetV.Len() == NewLambdaV.Len());
78  IAssert(ComEdgesV.Len() == CIDNSetV.Len());
79  LEdges = 0.0; LNoEdges = 0.0;
80  for (int e = 0; e < EdgeComVH.Len(); e++) {
81  TIntSet& JointCom = EdgeComVH[e];
82  double LambdaSum = SelectLambdaSum(NewLambdaV, JointCom);
83  double Puv = 1 - exp(- LambdaSum);
84  if (JointCom.Len() == 0) { Puv = PNoCom; }
85  IAssert(! _isnan(log(Puv)));
86  LEdges += log(Puv);
87  }
88  for (int k = 0; k < NewLambdaV.Len(); k++) {
89  int MaxEk = CIDNSetV[k].Len() * (CIDNSetV[k].Len() - 1) / 2;
90  int NotEdgesInCom = MaxEk - ComEdgesV[k];
91  if(NotEdgesInCom > 0) {
92  if (LNoEdges >= TFlt::Mn + double(NotEdgesInCom) * NewLambdaV[k]) {
93  LNoEdges -= double(NotEdgesInCom) * NewLambdaV[k];
94  }
95  }
96  }
97  double LReg = 0.0;
98  if (RegCoef > 0.0) {
99  LReg = - RegCoef * TLinAlg::SumVec(NewLambdaV);
100  }
101  return LEdges + LNoEdges + LReg;
102 }
#define IAssert(Cond)
Definition: bd.h:262
static double SumVec(const TFltV &x)
Definition: linalg.cpp:279
TSizeTy Len() const
Returns the number of elements in the vector.
Definition: ds.h:535
THash< TIntPr, TIntSet > EdgeComVH
Edge -> Shared Community ID Set.
Definition: agmfit.h:12
double SelectLambdaSum(const TIntSet &ComK)
Compute sum of lambda_c (which is log (1 - p_c)) over C_uv (ComK). The function is used to compute ed...
Definition: agmfit.cpp:618
TFlt RegCoef
Regularization parameter when we fit for P_c (for finding # communities).
Definition: agmfit.h:22
int Len() const
Definition: shash.h:1121
TVec< TIntSet > CIDNSetV
Community ID -> Member Node ID Sets.
Definition: agmfit.h:11
TIntV ComEdgesV
The number of edges in each community.
Definition: agmfit.h:14
TFlt PNoCom
Probability of edge when two nodes share no community (epsilon in the paper).
Definition: agmfit.h:15
static const double Mn
Definition: dt.h:1295

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

Definition at line 24 of file agmfit.cpp.

References BaseCID, CIDNSetV, ComEdgesV, EdgeComVH, G, LambdaV, THash< TKey, TDat, THashFunc >::Load(), TUNGraph::Load(), TVec< TVal, TSizeTy >::Load(), TInt::Load(), TFlt::Load(), MaxLambda, MinLambda, NIDCIDPrH, NIDCIDPrS, NIDComVH, PNoCom, TRnd::PutSeed(), RegCoef, and Rnd.

24  {
25  G = TUNGraph::Load(SIn);
26  CIDNSetV.Load(SIn);
27  EdgeComVH.Load(SIn);
28  NIDComVH.Load(SIn);
29  ComEdgesV.Load(SIn);
30  PNoCom.Load(SIn);
31  LambdaV.Load(SIn);
32  NIDCIDPrH.Load(SIn);
33  NIDCIDPrS.Load(SIn);
34  MinLambda.Load(SIn);
35  MaxLambda.Load(SIn);
36  RegCoef.Load(SIn);
37  BaseCID.Load(SIn);
38  Rnd.PutSeed(RndSeed);
39 }
TRnd Rnd
Definition: agmfit.h:17
THash< TIntPr, TInt > NIDCIDPrS
pairs (for sampling MCMC moves).
Definition: agmfit.h:19
TFltV LambdaV
Parametrization of P_c (edge probability in community c), P_c = 1 - exp(-lambda). ...
Definition: agmfit.h:16
TInt BaseCID
ID of the Epsilon-community (in case we fit P_c of the epsilon community). We do not fit for the Epsi...
Definition: agmfit.h:23
THash< TIntPr, TIntSet > EdgeComVH
Edge -> Shared Community ID Set.
Definition: agmfit.h:12
void Load(TSIn &SIn)
Definition: ds.h:877
void Load(TSIn &SIn)
Definition: hash.h:137
TFlt MinLambda
Minimum value of regularization parameter lambda (default = 1e-5).
Definition: agmfit.h:20
THash< TInt, TIntSet > NIDComVH
Node ID -> Communitie IDs the node belongs to.
Definition: agmfit.h:13
TFlt RegCoef
Regularization parameter when we fit for P_c (for finding # communities).
Definition: agmfit.h:22
void Load(TSIn &SIn)
Definition: dt.h:1057
static PUNGraph Load(TSIn &SIn)
Static constructor that loads the graph from a stream SIn and returns a pointer to it...
Definition: graph.h:158
void PutSeed(const int &_Seed)
Definition: dt.cpp:18
void Load(TSIn &SIn)
Definition: dt.h:1310
TFlt MaxLambda
Maximum value of regularization parameter lambda (default = 10).
Definition: agmfit.h:21
TVec< TIntSet > CIDNSetV
Community ID -> Member Node ID Sets.
Definition: agmfit.h:11
PUNGraph G
Graph to fit.
Definition: agmfit.h:10
TIntV ComEdgesV
The number of edges in each community.
Definition: agmfit.h:14
TFlt PNoCom
Probability of edge when two nodes share no community (epsilon in the paper).
Definition: agmfit.h:15
THash< TIntPr, TFlt > NIDCIDPrH
pairs (for sampling MCMC moves).
Definition: agmfit.h:18

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int TAGMFit::MLEGradAscentGivenCAG ( const double &  Thres = 0.001,
const int &  MaxIter = 10000,
const TStr  PlotNm = TStr() 
)

Gradient descent for p_c while keeping the community affiliation graph (CAG) fixed.

Definition at line 130 of file agmfit.cpp.

References TVec< TVal, TSizeTy >::Add(), TStr::Empty(), G, TUNGraph::GetEdges(), GetStepSizeByLineSearchForLambda(), TExeTm::GetTmStr(), GradLogLForLambda(), Kilo, LambdaV, TVec< TVal, TSizeTy >::Len(), Likelihood(), MaxLambda, MinLambda, TLinAlg::Norm(), and TGnuPlot::PlotValV().

Referenced by TAGMUtil::FindComsByAGM(), and RunMCMC().

130  {
131  int Edges = G->GetEdges();
132  TExeTm ExeTm;
133  TFltV GradV(LambdaV.Len());
134  int iter = 0;
135  TIntFltPrV IterLV, IterGradNormV;
136  double GradCutOff = 1000;
137  for (iter = 0; iter < MaxIter; iter++) {
138  GradLogLForLambda(GradV); //if gradient is going out of the boundary, cut off
139  for (int i = 0; i < LambdaV.Len(); i++) {
140  if (GradV[i] < -GradCutOff) { GradV[i] = -GradCutOff; }
141  if (GradV[i] > GradCutOff) { GradV[i] = GradCutOff; }
142  if (LambdaV[i] <= MinLambda && GradV[i] < 0) { GradV[i] = 0.0; }
143  if (LambdaV[i] >= MaxLambda && GradV[i] > 0) { GradV[i] = 0.0; }
144  }
145  double Alpha = 0.15, Beta = 0.2;
146  if (Edges > Kilo(100)) { Alpha = 0.00015; Beta = 0.3;}
147  double LearnRate = GetStepSizeByLineSearchForLambda(GradV, GradV, Alpha, Beta);
148  if (TLinAlg::Norm(GradV) < Thres) { break; }
149  for (int i = 0; i < LambdaV.Len(); i++) {
150  double Change = LearnRate * GradV[i];
151  LambdaV[i] += Change;
152  if(LambdaV[i] < MinLambda) { LambdaV[i] = MinLambda;}
153  if(LambdaV[i] > MaxLambda) { LambdaV[i] = MaxLambda;}
154  }
155  if (! PlotNm.Empty()) {
156  double L = Likelihood();
157  IterLV.Add(TIntFltPr(iter, L));
158  IterGradNormV.Add(TIntFltPr(iter, TLinAlg::Norm(GradV)));
159  }
160  }
161  if (! PlotNm.Empty()) {
162  TGnuPlot::PlotValV(IterLV, PlotNm + ".likelihood_Q");
163  TGnuPlot::PlotValV(IterGradNormV, PlotNm + ".gradnorm_Q");
164  printf("MLE for Lambda completed with %d iterations(%s)\n",iter,ExeTm.GetTmStr());
165  }
166  return iter;
167 }
static double Norm(const TFltV &x)
Definition: linalg.cpp:324
Definition: tm.h:354
#define Kilo(n)
Definition: gbase.h:3
double GetStepSizeByLineSearchForLambda(const TFltV &DeltaV, const TFltV &GradV, const double &Alpha, const double &Beta)
Step size search for updating P_c (which is parametarized by regularization parameter lambda)...
Definition: agmfit.cpp:109
double Likelihood()
COMMENT.
Definition: agmfit.cpp:104
int GetEdges() const
Returns the number of edges in the graph.
Definition: graph.cpp:74
TSizeTy Len() const
Returns the number of elements in the vector.
Definition: ds.h:535
TFltV LambdaV
Parametrization of P_c (edge probability in community c), P_c = 1 - exp(-lambda). ...
Definition: agmfit.h:16
TPair< TInt, TFlt > TIntFltPr
Definition: ds.h:87
const char * GetTmStr() const
Definition: tm.h:369
void GradLogLForLambda(TFltV &GradV)
Definition: agmfit.cpp:595
TFlt MinLambda
Minimum value of regularization parameter lambda (default = 1e-5).
Definition: agmfit.h:20
bool Empty() const
Definition: dt.h:488
static void PlotValV(const TVec< TPair< TVal1, TVal2 > > &ValV, const TStr &OutFNmPref, const TStr &Desc="", const TStr &XLabel="", const TStr &YLabel="", const TGpScaleTy &ScaleTy=gpsAuto, const bool &PowerFit=false, const TGpSeriesTy &SeriesTy=gpwLinesPoints)
Definition: gnuplot.h:363
TFlt MaxLambda
Maximum value of regularization parameter lambda (default = 10).
Definition: agmfit.h:21
TSizeTy Add()
Adds a new element at the end of the vector, after its current last element.
Definition: ds.h:559
PUNGraph G
Graph to fit.
Definition: agmfit.h:10

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void TAGMFit::NeighborComInit ( const int  InitComs)

Initialize node community memberships using best neighborhood communities (see D. Gleich et al. KDD'12).

Definition at line 186 of file agmfit.cpp.

References CIDNSetV, G, TAGMUtil::GetConductance(), TUNGraph::TNodeI::GetDeg(), TUNGraph::GetEdges(), TUNGraph::TNodeI::GetId(), TAGMUtil::GetNbhCom(), TUNGraph::TNodeI::GetNbrNId(), TUNGraph::GetNI(), TUNGraph::GetNIdV(), TUNGraph::GetNodes(), TUNGraph::GetRndNI(), TExeTm::GetTmStr(), IAssert, InitNodeData(), TVec< TVal, TSizeTy >::Len(), and SetDefaultPNoCom().

Referenced by TAGMFit().

186  {
187  CIDNSetV.Gen(InitComs);
188  const int Edges = G->GetEdges();
189  TFltIntPrV NIdPhiV(G->GetNodes(), 0);
190  TIntSet InvalidNIDS(G->GetNodes());
191  TIntV ChosenNIDV(InitComs, 0); //FOR DEBUG
192  TExeTm RunTm;
193  //compute conductance of neighborhood community
194  TIntV NIdV;
195  G->GetNIdV(NIdV);
196  for (int u = 0; u < NIdV.Len(); u++) {
197  TIntSet NBCmty(G->GetNI(NIdV[u]).GetDeg() + 1);
198  double Phi;
199  if (G->GetNI(NIdV[u]).GetDeg() < 5) { //do not include nodes with too few degree
200  Phi = 1.0;
201  } else {
202  TAGMUtil::GetNbhCom(G, NIdV[u], NBCmty);
203  IAssert(NBCmty.Len() == G->GetNI(NIdV[u]).GetDeg() + 1);
204  Phi = TAGMUtil::GetConductance(G, NBCmty, Edges);
205  }
206  NIdPhiV.Add(TFltIntPr(Phi, NIdV[u]));
207  }
208  NIdPhiV.Sort(true);
209  printf("conductance computation completed [%s]\n", RunTm.GetTmStr());
210  fflush(stdout);
211  //choose nodes with local minimum in conductance
212  int CurCID = 0;
213  for (int ui = 0; ui < NIdPhiV.Len(); ui++) {
214  int UID = NIdPhiV[ui].Val2;
215  fflush(stdout);
216  if (InvalidNIDS.IsKey(UID)) { continue; }
217  ChosenNIDV.Add(UID); //FOR DEBUG
218  //add the node and its neighbors to the current community
219  CIDNSetV[CurCID].AddKey(UID);
220  TUNGraph::TNodeI NI = G->GetNI(UID);
221  fflush(stdout);
222  for (int e = 0; e < NI.GetDeg(); e++) {
223  CIDNSetV[CurCID].AddKey(NI.GetNbrNId(e));
224  }
225  //exclude its neighbors from the next considerations
226  for (int e = 0; e < NI.GetDeg(); e++) {
227  InvalidNIDS.AddKey(NI.GetNbrNId(e));
228  }
229  CurCID++;
230  fflush(stdout);
231  if (CurCID >= InitComs) { break; }
232  }
233  if (InitComs > CurCID) {
234  printf("%d communities needed to fill randomly\n", InitComs - CurCID);
235  }
236  //assign a member to zero-member community (if any)
237  for (int c = 0; c < CIDNSetV.Len(); c++) {
238  if (CIDNSetV[c].Len() == 0) {
239  int ComSz = 10;
240  for (int u = 0; u < ComSz; u++) {
241  int UID = G->GetRndNI().GetId();
242  CIDNSetV[c].AddKey(UID);
243  }
244  }
245  }
246  InitNodeData();
248 }
#define IAssert(Cond)
Definition: bd.h:262
static void GetNbhCom(const PUNGraph &Graph, const int NID, TIntSet &NBCmtyS)
Definition: agm.cpp:706
TPair< TFlt, TInt > TFltIntPr
Definition: ds.h:97
Definition: tm.h:354
void SetDefaultPNoCom()
Set Epsilon (the probability that two nodes sharing no communities connect) to the default value...
Definition: agmfit.cpp:72
void GetNIdV(TIntV &NIdV) const
Gets a vector IDs of all nodes in the graph.
Definition: graph.cpp:125
int GetEdges() const
Returns the number of edges in the graph.
Definition: graph.cpp:74
TSizeTy Len() const
Returns the number of elements in the vector.
Definition: ds.h:535
Node iterator. Only forward iteration (operator++) is supported.
Definition: graph.h:63
static double GetConductance(const PUNGraph &Graph, const TIntSet &CmtyS, const int Edges)
Definition: agm.cpp:683
int GetNodes() const
Returns the number of nodes in the graph.
Definition: graph.h:165
int GetDeg() const
Returns degree of the current node.
Definition: graph.h:85
const char * GetTmStr() const
Definition: tm.h:369
TNodeI GetNI(const int &NId) const
Returns an iterator referring to the node of ID NId in the graph.
Definition: graph.h:208
TNodeI GetRndNI(TRnd &Rnd=TInt::Rnd)
Returns an interator referring to a random node in the graph.
Definition: graph.h:243
void InitNodeData()
COMMENT.
Definition: agmfit.cpp:264
TVec< TIntSet > CIDNSetV
Community ID -> Member Node ID Sets.
Definition: agmfit.h:11
int GetNbrNId(const int &NodeN) const
Returns ID of NodeN-th neighboring node.
Definition: graph.h:104
int GetId() const
Returns ID of the current node.
Definition: graph.h:83
PUNGraph G
Graph to fit.
Definition: agmfit.h:10
Vector is a sequence TVal objects representing an array that can change in size.
Definition: ds.h:420

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void TAGMFit::PrintSummary ( )

COMMENT.

Definition at line 659 of file agmfit.cpp.

References THash< TKey, TDat, THashFunc >::AddDat(), CIDNSetV, ComEdgesV, LambdaV, TVec< TVal, TSizeTy >::Len(), Likelihood(), NIDCIDPrS, PNoCom, and TFlt::Val.

659  {
660  TIntFltH CIDLambdaH(CIDNSetV.Len());
661  for (int c = 0; c < CIDNSetV.Len(); c++) {
662  CIDLambdaH.AddDat(c, LambdaV[c]);
663  }
664  CIDLambdaH.SortByDat(false);
665  int Coms = 0;
666  for (int i = 0; i < LambdaV.Len(); i++) {
667  int CID = CIDLambdaH.GetKey(i);
668  if (LambdaV[CID] <= 0.0001) { continue; }
669  printf("P_c : %.3f Com Sz: %d, Total Edges inside: %d \n", 1.0 - exp(- LambdaV[CID]), CIDNSetV[CID].Len(), (int) ComEdgesV[CID]);
670  Coms++;
671  }
672  printf("%d Communities, Total Memberships = %d, Likelihood = %.2f, Epsilon = %f\n", Coms, NIDCIDPrS.Len(), Likelihood(), PNoCom.Val);
673 }
THash< TIntPr, TInt > NIDCIDPrS
pairs (for sampling MCMC moves).
Definition: agmfit.h:19
double Likelihood()
COMMENT.
Definition: agmfit.cpp:104
double Val
Definition: dt.h:1293
TSizeTy Len() const
Returns the number of elements in the vector.
Definition: ds.h:535
TFltV LambdaV
Parametrization of P_c (edge probability in community c), P_c = 1 - exp(-lambda). ...
Definition: agmfit.h:16
TVec< TIntSet > CIDNSetV
Community ID -> Member Node ID Sets.
Definition: agmfit.h:11
TDat & AddDat(const TKey &Key)
Definition: hash.h:196
TIntV ComEdgesV
The number of edges in each community.
Definition: agmfit.h:14
TFlt PNoCom
Probability of edge when two nodes share no community (epsilon in the paper).
Definition: agmfit.h:15

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void TAGMFit::RandomInit ( const int &  MaxK)

COMMENT.

Definition at line 169 of file agmfit.cpp.

References CIDNSetV, G, TUNGraph::TNodeI::GetDeg(), TUNGraph::TNodeI::GetId(), TUNGraph::TNodeI::GetNbrNId(), TUNGraph::GetNI(), TRnd::GetUniDevInt(), InitNodeData(), Rnd, and SetDefaultPNoCom().

169  {
170  CIDNSetV.Clr();
171  for (int c = 0; c < MaxK; c++) {
172  CIDNSetV.Add();
173  int NC = Rnd.GetUniDevInt(G -> GetNodes());
174  TUNGraph::TNodeI NI = G -> GetRndNI();
175  CIDNSetV.Last().AddKey(NI.GetId());
176  for (int v = 0; v < NC; v++) {
177  NI = G->GetNI(NI.GetNbrNId(Rnd.GetUniDevInt(NI.GetDeg())));
178  CIDNSetV.Last().AddKey(NI.GetId());
179  }
180  }
181  InitNodeData();
183 }
TRnd Rnd
Definition: agmfit.h:17
void SetDefaultPNoCom()
Set Epsilon (the probability that two nodes sharing no communities connect) to the default value...
Definition: agmfit.cpp:72
Node iterator. Only forward iteration (operator++) is supported.
Definition: graph.h:63
int GetDeg() const
Returns degree of the current node.
Definition: graph.h:85
TNodeI GetNI(const int &NId) const
Returns an iterator referring to the node of ID NId in the graph.
Definition: graph.h:208
void InitNodeData()
COMMENT.
Definition: agmfit.cpp:264
TVec< TIntSet > CIDNSetV
Community ID -> Member Node ID Sets.
Definition: agmfit.h:11
int GetNbrNId(const int &NodeN) const
Returns ID of NodeN-th neighboring node.
Definition: graph.h:104
int GetUniDevInt(const int &Range=0)
Definition: dt.cpp:39
int GetId() const
Returns ID of the current node.
Definition: graph.h:83
PUNGraph G
Graph to fit.
Definition: agmfit.h:10

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void TAGMFit::RandomInitCmtyVV ( const int  InitComs,
const double  ComSzAlpha = 1.3,
const double  MemAlpha = 1.8,
const int  MinComSz = 8,
const int  MaxComSz = 200,
const int  MinMem = 1,
const int  MaxMem = 10 
)

Randomly initialize bipartite community affiliation graph.

Definition at line 42 of file agmfit.cpp.

References G, TAGMUtil::GenCmtyVVFromPL(), TUNGraph::GetNodes(), Rnd, and SetCmtyVV().

42  {
43  TVec<TIntV> InitCmtyVV(InitComs, 0);
44  TAGMUtil::GenCmtyVVFromPL(InitCmtyVV, G, G->GetNodes(), InitComs, ComSzAlpha, MemAlpha, MinComSz, MaxComSz,
45  MinMem, MaxMem, Rnd);
46  SetCmtyVV(InitCmtyVV);
47 }
TRnd Rnd
Definition: agmfit.h:17
int GetNodes() const
Returns the number of nodes in the graph.
Definition: graph.h:165
static void GenCmtyVVFromPL(TVec< TIntV > &CmtyVV, const PUNGraph &Graph, const int &Nodes, const int &Coms, const double &ComSzAlpha, const double &MemAlpha, const int &MinSz, const int &MaxSz, const int &MinK, const int &MaxK, TRnd &Rnd)
Generate bipartite community affiliation from given power law coefficients for membership distributio...
Definition: agm.cpp:101
void SetCmtyVV(const TVec< TIntV > &CmtyVV)
COMMENT.
Definition: agmfit.cpp:584
PUNGraph G
Graph to fit.
Definition: agmfit.h:10
Vector is a sequence TVal objects representing an array that can change in size.
Definition: ds.h:420

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int TAGMFit::RemoveEmptyCom ( )

Remove all communities with no members.

Definition at line 459 of file agmfit.cpp.

References CIDNSetV, TVec< TVal, TSizeTy >::DelLast(), LambdaV, and TVec< TVal, TSizeTy >::Last().

459  {
460  int DelCnt = 0;
461  for (int c = 0; c < CIDNSetV.Len(); c++) {
462  if (CIDNSetV[c].Len() == 0) {
463  CIDNSetV[c] = CIDNSetV.Last();
464  CIDNSetV.DelLast();
465  LambdaV[c] = LambdaV.Last();
466  LambdaV.DelLast();
467  DelCnt++;
468  c--;
469  }
470  }
471  return DelCnt;
472 }
TFltV LambdaV
Parametrization of P_c (edge probability in community c), P_c = 1 - exp(-lambda). ...
Definition: agmfit.h:16
const TVal & Last() const
Returns a reference to the last element of the vector.
Definition: ds.h:539
TVec< TIntSet > CIDNSetV
Community ID -> Member Node ID Sets.
Definition: agmfit.h:11
void DelLast()
Removes the last element of the vector.
Definition: ds.h:609

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void TAGMFit::RunMCMC ( const int &  MaxIter,
const int &  EvalLambdaIter,
const TStr PlotFPrx = TStr() 
)

Main procedure for fitting the AGM to a given graph using MCMC.

MCMC fitting.

Definition at line 366 of file agmfit.cpp.

References TVec< TVal, TSizeTy >::Add(), TGnuPlot::AddPlot(), BaseCID, CIDNSetV, TStr::Fmt(), G, TUNGraph::GetEdges(), TUNGraph::GetNodes(), TExeTm::GetTmStr(), TRnd::GetUniDev(), gpwLinesPoints, InitNodeData(), JoinCom(), LambdaV, LeaveCom(), TStr::Len(), Likelihood(), MLEGradAscentGivenCAG(), TMath::Mx(), Rnd, SampleTransition(), TGnuPlot::SavePng(), TGnuPlot::SetDataPlotFNm(), TGnuPlot::SetTitle(), and TExeTm::Tick().

Referenced by TAGMUtil::FindComsByAGM().

366  {
367  TExeTm IterTm, TotalTm;
368  double PrevL = Likelihood(), DeltaL = 0;
369  double BestL = PrevL;
370  printf("initial likelihood = %f\n",PrevL);
371  TIntFltPrV IterTrueLV, IterJoinV, IterLeaveV, IterAcceptV, IterSwitchV, IterLBV;
372  TIntPrV IterTotMemV;
373  TIntV IterV;
374  TFltV BestLV;
375  TVec<TIntSet> BestCmtySetV;
376  int SwitchCnt = 0, LeaveCnt = 0, JoinCnt = 0, AcceptCnt = 0, ProbBinSz;
377  int Nodes = G->GetNodes(), Edges = G->GetEdges();
378  TExeTm PlotTm;
379  ProbBinSz = TMath::Mx(1000, G->GetNodes() / 10); //bin to compute probabilities
380  IterLBV.Add(TIntFltPr(1, BestL));
381 
382  for (int iter = 0; iter < MaxIter; iter++) {
383  IterTm.Tick();
384  int NID = -1;
385  int JoinCID = -1, LeaveCID = -1;
386  SampleTransition(NID, JoinCID, LeaveCID, DeltaL); //sample a move
387  double OptL = PrevL;
388  if (DeltaL > 0 || Rnd.GetUniDev() < exp(DeltaL)) { //if it is accepted
389  IterTm.Tick();
390  if (LeaveCID > -1 && LeaveCID != BaseCID) { LeaveCom(NID, LeaveCID); }
391  if (JoinCID > -1 && JoinCID != BaseCID) { JoinCom(NID, JoinCID); }
392  if (LeaveCID > -1 && JoinCID > -1 && JoinCID != BaseCID && LeaveCID != BaseCID) { SwitchCnt++; }
393  else if (LeaveCID > -1 && LeaveCID != BaseCID) { LeaveCnt++;}
394  else if (JoinCID > -1 && JoinCID != BaseCID) { JoinCnt++;}
395  AcceptCnt++;
396  if ((iter + 1) % EvalLambdaIter == 0) {
397  IterTm.Tick();
398  MLEGradAscentGivenCAG(0.01, 3);
399  OptL = Likelihood();
400  }
401  else{
402  OptL = PrevL + DeltaL;
403  }
404  if (BestL <= OptL && CIDNSetV.Len() > 0) {
405  BestCmtySetV = CIDNSetV;
406  BestLV = LambdaV;
407  BestL = OptL;
408  }
409  }
410  if (iter > 0 && (iter % ProbBinSz == 0) && PlotFPrx.Len() > 0) {
411  IterLBV.Add(TIntFltPr(iter, OptL));
412  IterSwitchV.Add(TIntFltPr(iter, (double) SwitchCnt / (double) AcceptCnt));
413  IterLeaveV.Add(TIntFltPr(iter, (double) LeaveCnt / (double) AcceptCnt));
414  IterJoinV.Add(TIntFltPr(iter, (double) JoinCnt / (double) AcceptCnt));
415  IterAcceptV.Add(TIntFltPr(iter, (double) AcceptCnt / (double) ProbBinSz));
416  SwitchCnt = JoinCnt = LeaveCnt = AcceptCnt = 0;
417  }
418  PrevL = OptL;
419  if ((iter + 1) % 10000 == 0) {
420  printf("\r%d iterations completed [%.2f]", iter, (double) iter / (double) MaxIter);
421  }
422  }
423 
424  // plot the likelihood and acceptance probabilities if the plot file name is given
425  if (PlotFPrx.Len() > 0) {
426  TGnuPlot GP1;
427  GP1.AddPlot(IterLBV, gpwLinesPoints, "likelihood");
428  GP1.SetDataPlotFNm(PlotFPrx + ".likelihood.tab", PlotFPrx + ".likelihood.plt");
429  TStr TitleStr = TStr::Fmt(" N:%d E:%d", Nodes, Edges);
430  GP1.SetTitle(PlotFPrx + ".likelihood" + TitleStr);
431  GP1.SavePng(PlotFPrx + ".likelihood.png");
432 
433  TGnuPlot GP2;
434  GP2.AddPlot(IterSwitchV, gpwLinesPoints, "Switch");
435  GP2.AddPlot(IterLeaveV, gpwLinesPoints, "Leave");
436  GP2.AddPlot(IterJoinV, gpwLinesPoints, "Join");
437  GP2.AddPlot(IterAcceptV, gpwLinesPoints, "Accept");
438  GP2.SetTitle(PlotFPrx + ".transition");
439  GP2.SetDataPlotFNm(PlotFPrx + "transition_prob.tab", PlotFPrx + "transition_prob.plt");
440  GP2.SavePng(PlotFPrx + "transition_prob.png");
441  }
442  CIDNSetV = BestCmtySetV;
443  LambdaV = BestLV;
444 
445  InitNodeData();
446  MLEGradAscentGivenCAG(0.001, 100);
447  printf("\nMCMC completed (best likelihood: %.2f) [%s]\n", BestL, TotalTm.GetTmStr());
448 }
int Len() const
Definition: dt.h:487
Definition: tm.h:354
TRnd Rnd
Definition: agmfit.h:17
void SavePng(const int &SizeX=1000, const int &SizeY=800, const TStr &Comment=TStr())
Definition: gnuplot.h:120
static const T & Mx(const T &LVal, const T &RVal)
Definition: xmath.h:32
void SetTitle(const TStr &PlotTitle)
Definition: gnuplot.h:70
double Likelihood()
COMMENT.
Definition: agmfit.cpp:104
int GetEdges() const
Returns the number of edges in the graph.
Definition: graph.cpp:74
TFltV LambdaV
Parametrization of P_c (edge probability in community c), P_c = 1 - exp(-lambda). ...
Definition: agmfit.h:16
TInt BaseCID
ID of the Epsilon-community (in case we fit P_c of the epsilon community). We do not fit for the Epsi...
Definition: agmfit.h:23
void SetDataPlotFNm(const TStr &DatFNm, const TStr &PltFNm)
Definition: gnuplot.h:74
int GetNodes() const
Returns the number of nodes in the graph.
Definition: graph.h:165
TPair< TInt, TFlt > TIntFltPr
Definition: ds.h:87
const char * GetTmStr() const
Definition: tm.h:369
void LeaveCom(const int &NID, const int &CID)
After MCMC, NID leaves community CID.
Definition: agmfit.cpp:293
int MLEGradAscentGivenCAG(const double &Thres=0.001, const int &MaxIter=10000, const TStr PlotNm=TStr())
Gradient descent for p_c while keeping the community affiliation graph (CAG) fixed.
Definition: agmfit.cpp:130
void Tick()
Definition: tm.h:363
Definition: dt.h:412
void InitNodeData()
COMMENT.
Definition: agmfit.cpp:264
static TStr Fmt(const char *FmtStr,...)
Definition: dt.cpp:1599
void JoinCom(const int &NID, const int &JoinCID)
Definition: agmfit.cpp:309
TVec< TIntSet > CIDNSetV
Community ID -> Member Node ID Sets.
Definition: agmfit.h:11
double GetUniDev()
Definition: dt.h:30
int AddPlot(const TIntV &YValV, const TGpSeriesTy &SeriesTy=gpwLinesPoints, const TStr &Label=TStr(), const TStr &Style=TStr())
Definition: gnuplot.cpp:182
TSizeTy Add()
Adds a new element at the end of the vector, after its current last element.
Definition: ds.h:559
PUNGraph G
Graph to fit.
Definition: agmfit.h:10
void SampleTransition(int &NID, int &JoinCID, int &LeaveCID, double &DeltaL)
Sample MMCM transitions: Choose among (join, leave, switch), and then sample (NID, CID).
Definition: agmfit.cpp:325
Vector is a sequence TVal objects representing an array that can change in size.
Definition: ds.h:420

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void TAGMFit::SampleTransition ( int &  NID,
int &  JoinCID,
int &  LeaveCID,
double &  DeltaL 
)

Sample MMCM transitions: Choose among (join, leave, switch), and then sample (NID, CID).

Definition at line 325 of file agmfit.cpp.

References BaseCID, CIDNSetV, G, TUNGraph::GetNodes(), TUNGraph::GetRndNId(), TRnd::GetUniDevInt(), TFlt::Mn, NIDCIDPrS, NIDComVH, Rnd, SeekJoin(), SeekLeave(), SeekSwitch(), TPair< TVal1, TVal2 >::Val1, and TPair< TVal1, TVal2 >::Val2.

Referenced by RunMCMC().

325  {
326  int Option = Rnd.GetUniDevInt(3); //0:Join 1:Leave 2:Switch
327  if (NIDCIDPrS.Len() <= 1) { Option = 0; } //if there is only one node membership, only join is possible.
328  int TryCnt = 0;
329  const int MaxTryCnt = G->GetNodes();
330  DeltaL = TFlt::Mn;
331  if (Option == 0) {
332  do {
333  JoinCID = Rnd.GetUniDevInt(CIDNSetV.Len());
334  NID = G->GetRndNId();
335  } while (TryCnt++ < MaxTryCnt && NIDCIDPrS.IsKey(TIntPr(NID, JoinCID)));
336  if (TryCnt < MaxTryCnt) { //if successfully find a move
337  DeltaL = SeekJoin(NID, JoinCID);
338  }
339  }
340  else if (Option == 1) {
341  do {
342  TIntPr NIDCIDPr = NIDCIDPrS.GetKey(NIDCIDPrS.GetRndKeyId(Rnd));
343  NID = NIDCIDPr.Val1;
344  LeaveCID = NIDCIDPr.Val2;
345  } while (TryCnt++ < MaxTryCnt && LeaveCID == BaseCID);
346  if (TryCnt < MaxTryCnt) {//if successfully find a move
347  DeltaL = SeekLeave(NID, LeaveCID);
348  }
349  }
350  else{
351  do {
352  TIntPr NIDCIDPr = NIDCIDPrS.GetKey(NIDCIDPrS.GetRndKeyId(Rnd));
353  NID = NIDCIDPr.Val1;
354  LeaveCID = NIDCIDPr.Val2;
355  } while (TryCnt++ < MaxTryCnt && (NIDComVH.GetDat(NID).Len() == CIDNSetV.Len() || LeaveCID == BaseCID));
356  do {
357  JoinCID = Rnd.GetUniDevInt(CIDNSetV.Len());
358  } while (TryCnt++ < G->GetNodes() && NIDCIDPrS.IsKey(TIntPr(NID, JoinCID)));
359  if (TryCnt < MaxTryCnt) {//if successfully find a move
360  DeltaL = SeekSwitch(NID, LeaveCID, JoinCID);
361  }
362  }
363 }
TPair< TInt, TInt > TIntPr
Definition: ds.h:83
TRnd Rnd
Definition: agmfit.h:17
double SeekSwitch(const int &UID, const int &CurCID, const int &NewCID)
Definition: agmfit.cpp:525
THash< TIntPr, TInt > NIDCIDPrS
pairs (for sampling MCMC moves).
Definition: agmfit.h:19
TInt BaseCID
ID of the Epsilon-community (in case we fit P_c of the epsilon community). We do not fit for the Epsi...
Definition: agmfit.h:23
int GetNodes() const
Returns the number of nodes in the graph.
Definition: graph.h:165
int GetRndNId(TRnd &Rnd=TInt::Rnd)
Returns an ID of a random node in the graph.
Definition: graph.h:241
THash< TInt, TIntSet > NIDComVH
Node ID -> Communitie IDs the node belongs to.
Definition: agmfit.h:13
Definition: ds.h:32
double SeekJoin(const int &UID, const int &CID)
Compute the change in likelihood (Delta) if node UID joins community CID.
Definition: agmfit.cpp:502
double SeekLeave(const int &UID, const int &CID)
Compute the change in likelihood (Delta) if node UID leaves community CID.
Definition: agmfit.cpp:475
TVec< TIntSet > CIDNSetV
Community ID -> Member Node ID Sets.
Definition: agmfit.h:11
TVal1 Val1
Definition: ds.h:34
TVal2 Val2
Definition: ds.h:35
int GetUniDevInt(const int &Range=0)
Definition: dt.cpp:39
PUNGraph G
Graph to fit.
Definition: agmfit.h:10
static const double Mn
Definition: dt.h:1295

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void TAGMFit::Save ( TSOut SOut)

Definition at line 8 of file agmfit.cpp.

References BaseCID, CIDNSetV, ComEdgesV, EdgeComVH, G, LambdaV, MaxLambda, MinLambda, NIDCIDPrH, NIDCIDPrS, NIDComVH, PNoCom, RegCoef, THash< TKey, TDat, THashFunc >::Save(), TUNGraph::Save(), TVec< TVal, TSizeTy >::Save(), TInt::Save(), and TFlt::Save().

8  {
9  G->Save(SOut);
10  CIDNSetV.Save(SOut);
11  EdgeComVH.Save(SOut);
12  NIDComVH.Save(SOut);
13  ComEdgesV.Save(SOut);
14  PNoCom.Save(SOut);
15  LambdaV.Save(SOut);
16  NIDCIDPrH.Save(SOut);
17  NIDCIDPrS.Save(SOut);
18  MinLambda.Save(SOut);
19  MaxLambda.Save(SOut);
20  RegCoef.Save(SOut);
21  BaseCID.Save(SOut);
22 }
void Save(TSOut &SOut) const
Definition: dt.h:1058
THash< TIntPr, TInt > NIDCIDPrS
pairs (for sampling MCMC moves).
Definition: agmfit.h:19
TFltV LambdaV
Parametrization of P_c (edge probability in community c), P_c = 1 - exp(-lambda). ...
Definition: agmfit.h:16
void Save(TSOut &SOut) const
Definition: hash.h:141
TInt BaseCID
ID of the Epsilon-community (in case we fit P_c of the epsilon community). We do not fit for the Epsi...
Definition: agmfit.h:23
void Save(TSOut &SOut) const
Saves the graph to a (binary) stream SOut.
Definition: graph.h:150
THash< TIntPr, TIntSet > EdgeComVH
Edge -> Shared Community ID Set.
Definition: agmfit.h:12
void Save(TSOut &SOut) const
Definition: ds.h:885
TFlt MinLambda
Minimum value of regularization parameter lambda (default = 1e-5).
Definition: agmfit.h:20
THash< TInt, TIntSet > NIDComVH
Node ID -> Communitie IDs the node belongs to.
Definition: agmfit.h:13
TFlt RegCoef
Regularization parameter when we fit for P_c (for finding # communities).
Definition: agmfit.h:22
TFlt MaxLambda
Maximum value of regularization parameter lambda (default = 10).
Definition: agmfit.h:21
TVec< TIntSet > CIDNSetV
Community ID -> Member Node ID Sets.
Definition: agmfit.h:11
PUNGraph G
Graph to fit.
Definition: agmfit.h:10
TIntV ComEdgesV
The number of edges in each community.
Definition: agmfit.h:14
void Save(TSOut &SOut) const
Definition: dt.h:1307
TFlt PNoCom
Probability of edge when two nodes share no community (epsilon in the paper).
Definition: agmfit.h:15
THash< TIntPr, TFlt > NIDCIDPrH
pairs (for sampling MCMC moves).
Definition: agmfit.h:18

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double TAGMFit::SeekJoin ( const int &  UID,
const int &  CID 
)

Compute the change in likelihood (Delta) if node UID joins community CID.

Definition at line 502 of file agmfit.cpp.

References CIDNSetV, EdgeComVH, G, TUNGraph::TNodeI::GetDeg(), TUNGraph::TNodeI::GetNbrNId(), TUNGraph::GetNI(), IAssert, LambdaV, THashSet< TKey, THashFunc >::Len(), TMath::Mn(), TMath::Mx(), NIDComVH, PNoCom, and SelectLambdaSum().

Referenced by SampleTransition(), and SeekSwitch().

502  {
503  IAssert(! CIDNSetV[CID].IsKey(UID));
504  double Delta = 0.0;
505  TUNGraph::TNodeI NI = G->GetNI(UID);
506  int NbhsInC = 0;
507  for (int e = 0; e < NI.GetDeg(); e++) {
508  const int VID = NI.GetNbrNId(e);
509  if (! NIDComVH.GetDat(VID).IsKey(CID)) { continue; }
510  TIntPr SrcDstNIDPr(TMath::Mn(UID,VID), TMath::Mx(UID,VID));
511  TIntSet& JointCom = EdgeComVH.GetDat(SrcDstNIDPr);
512  double CurPuv, NewPuv, LambdaSum = SelectLambdaSum(JointCom);
513  CurPuv = 1 - exp(- LambdaSum);
514  if (JointCom.Len() == 0) { CurPuv = PNoCom; }
515  NewPuv = 1 - exp(- LambdaSum - LambdaV[CID]);
516  Delta += (log(NewPuv) - log(CurPuv));
517  IAssert(!_isnan(Delta));
518  NbhsInC++;
519  }
520  Delta -= LambdaV[CID] * (CIDNSetV[CID].Len() - NbhsInC);
521  return Delta;
522 }
#define IAssert(Cond)
Definition: bd.h:262
static const T & Mn(const T &LVal, const T &RVal)
Definition: xmath.h:36
static const T & Mx(const T &LVal, const T &RVal)
Definition: xmath.h:32
Node iterator. Only forward iteration (operator++) is supported.
Definition: graph.h:63
TFltV LambdaV
Parametrization of P_c (edge probability in community c), P_c = 1 - exp(-lambda). ...
Definition: agmfit.h:16
THash< TIntPr, TIntSet > EdgeComVH
Edge -> Shared Community ID Set.
Definition: agmfit.h:12
int GetDeg() const
Returns degree of the current node.
Definition: graph.h:85
THash< TInt, TIntSet > NIDComVH
Node ID -> Communitie IDs the node belongs to.
Definition: agmfit.h:13
double SelectLambdaSum(const TIntSet &ComK)
Compute sum of lambda_c (which is log (1 - p_c)) over C_uv (ComK). The function is used to compute ed...
Definition: agmfit.cpp:618
TNodeI GetNI(const int &NId) const
Returns an iterator referring to the node of ID NId in the graph.
Definition: graph.h:208
int Len() const
Definition: shash.h:1121
Definition: ds.h:32
TVec< TIntSet > CIDNSetV
Community ID -> Member Node ID Sets.
Definition: agmfit.h:11
int GetNbrNId(const int &NodeN) const
Returns ID of NodeN-th neighboring node.
Definition: graph.h:104
PUNGraph G
Graph to fit.
Definition: agmfit.h:10
TFlt PNoCom
Probability of edge when two nodes share no community (epsilon in the paper).
Definition: agmfit.h:15

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double TAGMFit::SeekLeave ( const int &  UID,
const int &  CID 
)

Compute the change in likelihood (Delta) if node UID leaves community CID.

Definition at line 475 of file agmfit.cpp.

References CIDNSetV, EdgeComVH, G, TUNGraph::TNodeI::GetDeg(), TUNGraph::TNodeI::GetNbrNId(), TUNGraph::GetNI(), IAssert, TUNGraph::IsNode(), LambdaV, THashSet< TKey, THashFunc >::Len(), TMath::Mn(), TMath::Mx(), NIDComVH, PNoCom, and SelectLambdaSum().

Referenced by SampleTransition(), and SeekSwitch().

475  {
476  IAssert(CIDNSetV[CID].IsKey(UID));
477  IAssert(G->IsNode(UID));
478  double Delta = 0.0;
479  TUNGraph::TNodeI NI = G->GetNI(UID);
480  int NbhsInC = 0;
481  for (int e = 0; e < NI.GetDeg(); e++) {
482  const int VID = NI.GetNbrNId(e);
483  if (! NIDComVH.GetDat(VID).IsKey(CID)) { continue; }
484  TIntPr SrcDstNIDPr(TMath::Mn(UID,VID), TMath::Mx(UID,VID));
485  TIntSet& JointCom = EdgeComVH.GetDat(SrcDstNIDPr);
486  double CurPuv, NewPuv, LambdaSum = SelectLambdaSum(JointCom);
487  CurPuv = 1 - exp(- LambdaSum);
488  NewPuv = 1 - exp(- LambdaSum + LambdaV[CID]);
489  IAssert(JointCom.Len() > 0);
490  if (JointCom.Len() == 1) {
491  NewPuv = PNoCom;
492  }
493  Delta += (log(NewPuv) - log(CurPuv));
494  IAssert(!_isnan(Delta));
495  NbhsInC++;
496  }
497  Delta += LambdaV[CID] * (CIDNSetV[CID].Len() - 1 - NbhsInC);
498  return Delta;
499 }
#define IAssert(Cond)
Definition: bd.h:262
static const T & Mn(const T &LVal, const T &RVal)
Definition: xmath.h:36
static const T & Mx(const T &LVal, const T &RVal)
Definition: xmath.h:32
Node iterator. Only forward iteration (operator++) is supported.
Definition: graph.h:63
TFltV LambdaV
Parametrization of P_c (edge probability in community c), P_c = 1 - exp(-lambda). ...
Definition: agmfit.h:16
THash< TIntPr, TIntSet > EdgeComVH
Edge -> Shared Community ID Set.
Definition: agmfit.h:12
int GetDeg() const
Returns degree of the current node.
Definition: graph.h:85
THash< TInt, TIntSet > NIDComVH
Node ID -> Communitie IDs the node belongs to.
Definition: agmfit.h:13
double SelectLambdaSum(const TIntSet &ComK)
Compute sum of lambda_c (which is log (1 - p_c)) over C_uv (ComK). The function is used to compute ed...
Definition: agmfit.cpp:618
TNodeI GetNI(const int &NId) const
Returns an iterator referring to the node of ID NId in the graph.
Definition: graph.h:208
int Len() const
Definition: shash.h:1121
Definition: ds.h:32
TVec< TIntSet > CIDNSetV
Community ID -> Member Node ID Sets.
Definition: agmfit.h:11
int GetNbrNId(const int &NodeN) const
Returns ID of NodeN-th neighboring node.
Definition: graph.h:104
bool IsNode(const int &NId) const
Tests whether ID NId is a node.
Definition: graph.h:202
PUNGraph G
Graph to fit.
Definition: agmfit.h:10
TFlt PNoCom
Probability of edge when two nodes share no community (epsilon in the paper).
Definition: agmfit.h:15

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double TAGMFit::SeekSwitch ( const int &  UID,
const int &  CurCID,
const int &  NewCID 
)

Definition at line 525 of file agmfit.cpp.

References CIDNSetV, EdgeComVH, G, TUNGraph::TNodeI::GetDeg(), TUNGraph::TNodeI::GetNbrNId(), TUNGraph::GetNI(), IAssert, LambdaV, THashSet< TKey, THashFunc >::Len(), TMath::Mn(), TMath::Mx(), NIDComVH, PNoCom, SeekJoin(), SeekLeave(), SelectLambdaSum(), and TFlt::Val.

Referenced by SampleTransition().

525  {
526  IAssert(! CIDNSetV[NewCID].IsKey(UID));
527  IAssert(CIDNSetV[CurCID].IsKey(UID));
528  double Delta = SeekJoin(UID, NewCID) + SeekLeave(UID, CurCID);
529  //correct only for intersection between new com and current com
530  TUNGraph::TNodeI NI = G->GetNI(UID);
531  for (int e = 0; e < NI.GetDeg(); e++) {
532  const int VID = NI.GetNbrNId(e);
533  if (! NIDComVH.GetDat(VID).IsKey(CurCID) || ! NIDComVH.GetDat(VID).IsKey(NewCID)) {continue;}
534  TIntPr SrcDstNIDPr(TMath::Mn(UID,VID), TMath::Mx(UID,VID));
535  TIntSet& JointCom = EdgeComVH.GetDat(SrcDstNIDPr);
536  double CurPuv, NewPuvAfterJoin, NewPuvAfterLeave, NewPuvAfterSwitch, LambdaSum = SelectLambdaSum(JointCom);
537  CurPuv = 1 - exp(- LambdaSum);
538  NewPuvAfterLeave = 1 - exp(- LambdaSum + LambdaV[CurCID]);
539  NewPuvAfterJoin = 1 - exp(- LambdaSum - LambdaV[NewCID]);
540  NewPuvAfterSwitch = 1 - exp(- LambdaSum - LambdaV[NewCID] + LambdaV[CurCID]);
541  if (JointCom.Len() == 1 || NewPuvAfterLeave == 0.0) {
542  NewPuvAfterLeave = PNoCom;
543  }
544  Delta += (log(NewPuvAfterSwitch) + log(CurPuv) - log(NewPuvAfterLeave) - log(NewPuvAfterJoin));
545  if (_isnan(Delta)) {
546  printf("NS:%f C:%f NL:%f NJ:%f PNoCom:%f", NewPuvAfterSwitch, CurPuv, NewPuvAfterLeave, NewPuvAfterJoin, PNoCom.Val);
547  }
548  IAssert(!_isnan(Delta));
549  }
550  return Delta;
551 }
#define IAssert(Cond)
Definition: bd.h:262
static const T & Mn(const T &LVal, const T &RVal)
Definition: xmath.h:36
static const T & Mx(const T &LVal, const T &RVal)
Definition: xmath.h:32
double Val
Definition: dt.h:1293
Node iterator. Only forward iteration (operator++) is supported.
Definition: graph.h:63
TFltV LambdaV
Parametrization of P_c (edge probability in community c), P_c = 1 - exp(-lambda). ...
Definition: agmfit.h:16
THash< TIntPr, TIntSet > EdgeComVH
Edge -> Shared Community ID Set.
Definition: agmfit.h:12
int GetDeg() const
Returns degree of the current node.
Definition: graph.h:85
THash< TInt, TIntSet > NIDComVH
Node ID -> Communitie IDs the node belongs to.
Definition: agmfit.h:13
double SelectLambdaSum(const TIntSet &ComK)
Compute sum of lambda_c (which is log (1 - p_c)) over C_uv (ComK). The function is used to compute ed...
Definition: agmfit.cpp:618
TNodeI GetNI(const int &NId) const
Returns an iterator referring to the node of ID NId in the graph.
Definition: graph.h:208
int Len() const
Definition: shash.h:1121
Definition: ds.h:32
double SeekJoin(const int &UID, const int &CID)
Compute the change in likelihood (Delta) if node UID joins community CID.
Definition: agmfit.cpp:502
double SeekLeave(const int &UID, const int &CID)
Compute the change in likelihood (Delta) if node UID leaves community CID.
Definition: agmfit.cpp:475
TVec< TIntSet > CIDNSetV
Community ID -> Member Node ID Sets.
Definition: agmfit.h:11
int GetNbrNId(const int &NodeN) const
Returns ID of NodeN-th neighboring node.
Definition: graph.h:104
PUNGraph G
Graph to fit.
Definition: agmfit.h:10
TFlt PNoCom
Probability of edge when two nodes share no community (epsilon in the paper).
Definition: agmfit.h:15

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double TAGMFit::SelectLambdaSum ( const TIntSet ComK)

Compute sum of lambda_c (which is log (1 - p_c)) over C_uv (ComK). The function is used to compute edge probability P_uv.

Definition at line 618 of file agmfit.cpp.

References LambdaV.

Referenced by GradLogLForLambda(), Likelihood(), SeekJoin(), SeekLeave(), and SeekSwitch().

618  {
619  return SelectLambdaSum(LambdaV, ComK);
620 }
TFltV LambdaV
Parametrization of P_c (edge probability in community c), P_c = 1 - exp(-lambda). ...
Definition: agmfit.h:16
double SelectLambdaSum(const TIntSet &ComK)
Compute sum of lambda_c (which is log (1 - p_c)) over C_uv (ComK). The function is used to compute ed...
Definition: agmfit.cpp:618

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double TAGMFit::SelectLambdaSum ( const TFltV NewLambdaV,
const TIntSet ComK 
)

COMMENT.

Definition at line 622 of file agmfit.cpp.

References THashSet< TKey, THashFunc >::BegI(), THashSet< TKey, THashFunc >::EndI(), and IAssert.

622  {
623  double Result = 0.0;
624  for (TIntSet::TIter SI = ComK.BegI(); SI < ComK.EndI(); SI++) {
625  IAssert(NewLambdaV[SI.GetKey()] >= 0);
626  Result += NewLambdaV[SI.GetKey()];
627  }
628  return Result;
629 }
#define IAssert(Cond)
Definition: bd.h:262
TIter BegI() const
Definition: shash.h:1105
TIter EndI() const
Definition: shash.h:1112

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void TAGMFit::SetCmtyVV ( const TVec< TIntV > &  CmtyVV)

COMMENT.

Definition at line 584 of file agmfit.cpp.

References CIDNSetV, G, IAssert, InitNodeData(), TUNGraph::IsNode(), TVec< TVal, TSizeTy >::Len(), and SetDefaultPNoCom().

Referenced by AddBaseCmty(), RandomInitCmtyVV(), and TAGMFit().

584  {
585  CIDNSetV.Gen(CmtyVV.Len());
586  for (int c = 0; c < CIDNSetV.Len(); c++) {
587  CIDNSetV[c].AddKeyV(CmtyVV[c]);
588  for (int j = 0; j < CmtyVV[c].Len(); j++) { IAssert(G->IsNode(CmtyVV[c][j])); } // check whether the member nodes exist in the graph
589  }
590  InitNodeData();
592 }
#define IAssert(Cond)
Definition: bd.h:262
void SetDefaultPNoCom()
Set Epsilon (the probability that two nodes sharing no communities connect) to the default value...
Definition: agmfit.cpp:72
TSizeTy Len() const
Returns the number of elements in the vector.
Definition: ds.h:535
void InitNodeData()
COMMENT.
Definition: agmfit.cpp:264
TVec< TIntSet > CIDNSetV
Community ID -> Member Node ID Sets.
Definition: agmfit.h:11
bool IsNode(const int &NId) const
Tests whether ID NId is a node.
Definition: graph.h:202
PUNGraph G
Graph to fit.
Definition: agmfit.h:10

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void TAGMFit::SetDefaultPNoCom ( )

Set Epsilon (the probability that two nodes sharing no communities connect) to the default value.

Definition at line 72 of file agmfit.cpp.

References G, TUNGraph::GetNodes(), and PNoCom.

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

72  {
73  PNoCom = 1.0 / (double) G->GetNodes() / (double) G->GetNodes();
74 }
int GetNodes() const
Returns the number of nodes in the graph.
Definition: graph.h:165
PUNGraph G
Graph to fit.
Definition: agmfit.h:10
TFlt PNoCom
Probability of edge when two nodes share no community (epsilon in the paper).
Definition: agmfit.h:15

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void TAGMFit::SetLambdaV ( const TFltV LambdaPt)
inline

COMMENT.

Definition at line 92 of file agmfit.h.

References LambdaV.

92 {LambdaV = LambdaPt;}
TFltV LambdaV
Parametrization of P_c (edge probability in community c), P_c = 1 - exp(-lambda). ...
Definition: agmfit.h:16
void TAGMFit::SetPNoCom ( const double &  Epsilon)
inline

Set Epsilon (the probability that two nodes sharing no communities connect) to the default value.

Definition at line 57 of file agmfit.h.

References BaseCID, and PNoCom.

Referenced by TAGMUtil::FindComsByAGM().

57 { if (BaseCID == -1 && Epsilon > 0.0) { PNoCom = Epsilon; } }
TInt BaseCID
ID of the Epsilon-community (in case we fit P_c of the epsilon community). We do not fit for the Epsi...
Definition: agmfit.h:23
TFlt PNoCom
Probability of edge when two nodes share no community (epsilon in the paper).
Definition: agmfit.h:15

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void TAGMFit::SetRegCoef ( const double  Val)
inline

Definition at line 45 of file agmfit.h.

References RegCoef.

Referenced by TAGMUtil::FindComsByAGM().

45 { RegCoef = Val; }
TFlt RegCoef
Regularization parameter when we fit for P_c (for finding # communities).
Definition: agmfit.h:22

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Member Data Documentation

TInt TAGMFit::BaseCID
private

ID of the Epsilon-community (in case we fit P_c of the epsilon community). We do not fit for the Epsilon-community in general.

Definition at line 23 of file agmfit.h.

Referenced by AddBaseCmty(), GetCmtyVV(), Load(), RunMCMC(), SampleTransition(), Save(), and SetPNoCom().

TIntV TAGMFit::ComEdgesV
private

The number of edges in each community.

Definition at line 14 of file agmfit.h.

Referenced by GetEdgeJointCom(), GradLogLForLambda(), InitNodeData(), JoinCom(), LeaveCom(), Likelihood(), Load(), PrintSummary(), and Save().

THash<TIntPr,TIntSet> TAGMFit::EdgeComVH
private

Edge -> Shared Community ID Set.

Definition at line 12 of file agmfit.h.

Referenced by GetEdgeJointCom(), GradLogLForLambda(), JoinCom(), LeaveCom(), Likelihood(), Load(), Save(), SeekJoin(), SeekLeave(), and SeekSwitch().

TFltV TAGMFit::LambdaV
private
TFlt TAGMFit::MaxLambda
private

Maximum value of regularization parameter lambda (default = 10).

Definition at line 21 of file agmfit.h.

Referenced by GetStepSizeByLineSearchForLambda(), InitNodeData(), Load(), MLEGradAscentGivenCAG(), and Save().

TFlt TAGMFit::MinLambda
private

Minimum value of regularization parameter lambda (default = 1e-5).

Definition at line 20 of file agmfit.h.

Referenced by GetCmtyVV(), GetStepSizeByLineSearchForLambda(), InitNodeData(), Load(), MLEGradAscentGivenCAG(), and Save().

THash<TIntPr,TFlt> TAGMFit::NIDCIDPrH
private

<Node ID, Community ID> pairs (for sampling MCMC moves).

Definition at line 18 of file agmfit.h.

Referenced by Load(), and Save().

THash<TIntPr,TInt> TAGMFit::NIDCIDPrS
private

<Node ID, Community ID> pairs (for sampling MCMC moves).

Definition at line 19 of file agmfit.h.

Referenced by InitNodeData(), JoinCom(), LeaveCom(), Load(), PrintSummary(), SampleTransition(), and Save().

THash<TInt, TIntSet> TAGMFit::NIDComVH
private

Node ID -> Communitie IDs the node belongs to.

Definition at line 13 of file agmfit.h.

Referenced by CalcPNoComByCmtyVV(), GetEdgeJointCom(), InitNodeData(), JoinCom(), LeaveCom(), Load(), SampleTransition(), Save(), SeekJoin(), SeekLeave(), and SeekSwitch().

TFlt TAGMFit::PNoCom
private

Probability of edge when two nodes share no community (epsilon in the paper).

Definition at line 15 of file agmfit.h.

Referenced by AddBaseCmty(), CalcPNoComByCmtyVV(), GetPNoCom(), GradLogLForLambda(), Likelihood(), Load(), PrintSummary(), Save(), SeekJoin(), SeekLeave(), SeekSwitch(), SetDefaultPNoCom(), and SetPNoCom().

TFlt TAGMFit::RegCoef
private

Regularization parameter when we fit for P_c (for finding # communities).

Definition at line 22 of file agmfit.h.

Referenced by GradLogLForLambda(), Likelihood(), Load(), Save(), and SetRegCoef().

TRnd TAGMFit::Rnd
private

Definition at line 17 of file agmfit.h.

Referenced by Load(), RandomInit(), RandomInitCmtyVV(), RunMCMC(), and SampleTransition().


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