int main(int argc, char* argv[]) {
Env = TEnv(argc, argv, TNotify::StdNotify);
Env.PrepArgs(TStr::Fmt("ragm. build: %s, %s. Time: %s", __TIME__, __DATE__, TExeTm::GetCurTm()));
TExeTm ExeTm;
Try
TStr OutFPrx = Env.GetIfArgPrefixStr("-o:", "", "Output Graph data prefix");
const TStr InFNm = Env.GetIfArgPrefixStr("-i:", "../as20graph.txt", "Input edgelist file name");
const TStr LabelFNm = Env.GetIfArgPrefixStr("-l:", "", "Input file name for node names (Node ID, Node label) ");
int OptComs = Env.GetIfArgPrefixInt("-c:", -1, "The number of communities to detect (-1: detect automatically)");
const int MinComs = Env.GetIfArgPrefixInt("-mc:", 5, "Minimum number of communities to try");
const int MaxComs = Env.GetIfArgPrefixInt("-xc:", 100, "Maximum number of communities to try");
const int DivComs = Env.GetIfArgPrefixInt("-nc:", 10, "How many trials for the number of communities");
const int NumThreads = Env.GetIfArgPrefixInt("-nt:", 1, "Number of threads for parallelization");
const double StepAlpha = Env.GetIfArgPrefixFlt("-sa:", 0.3, "Alpha for backtracking line search");
const double StepBeta = Env.GetIfArgPrefixFlt("-sb:", 0.3, "Beta for backtracking line search");
PUNGraph G;
TIntStrH NIDNameH;
if (InFNm.IsStrIn(".ungraph")) {
TFIn GFIn(InFNm);
G = TUNGraph::Load(GFIn);
} else {
G = TAGMUtil::LoadEdgeListStr<PUNGraph>(InFNm, NIDNameH);
}
if (LabelFNm.Len() > 0) {
TSsParser Ss(LabelFNm, ssfTabSep);
while (Ss.Next()) {
if (Ss.Len() > 0) { NIDNameH.AddDat(Ss.GetInt(0), Ss.GetFld(1)); }
}
}
else {
}
printf("Graph: %d Nodes %d Edges\n", G->GetNodes(), G->GetEdges());
TVec<TIntV> EstCmtyVV;
TExeTm RunTm;
TAGMFast RAGM(G, 10, 10);
if (OptComs == -1) {
printf("finding number of communities\n");
OptComs = RAGM.FindComsByCV(NumThreads, MaxComs, MinComs, DivComs, OutFPrx, StepAlpha, StepBeta);
}
RAGM.NeighborComInit(OptComs);
if (NumThreads == 1 || G->GetEdges() < 1000) {
RAGM.MLEGradAscent(0.0001, 1000 * G->GetNodes(), "", StepAlpha, StepBeta);
} else {
RAGM.MLEGradAscentParallel(0.0001, 1000, NumThreads, "", StepAlpha, StepBeta);
}
RAGM.GetCmtyVV(EstCmtyVV);
TAGMUtil::DumpCmtyVV(OutFPrx + "cmtyvv.txt", EstCmtyVV, NIDNameH);
TAGMUtil::SaveGephi(OutFPrx + "graph.gexf", G, EstCmtyVV, 1.5, 1.5, NIDNameH);
Catch
printf("\nrun time: %s (%s)\n", ExeTm.GetTmStr(), TSecTm::GetCurTm().GetTmStr().CStr());
return 0;
}
// Test GetCmnNbrs: the number of neighbors in common
TEST(triad, TestGetCmnNbrs) {
// Test TUNGraph
PUNGraph GraphTUN = TriadGetTestTUNGraph();
for (int i = 0; i < GraphTUN->GetNodes(); i++) {
for (int j = i + 1; j < GraphTUN->GetNodes(); j++) {
VerifyCmnNbrs(i, j, TSnap::GetCmnNbrs(GraphTUN, i, j));
}
}
// Test TNGraph which is same as undirected.
PNGraph GraphTN = TriadGetTestTNGraph();
for (int i = 0; i < GraphTN->GetNodes(); i++) {
for (int j = i + 1; j < GraphTN->GetNodes(); j++) {
VerifyCmnNbrs(i, j, TSnap::GetCmnNbrs(GraphTN, i, j));
}
}
// Test TNEGraph which is same as undirected.
PNEGraph GraphTNE = TriadGetTestTNEGraph();
for (int i = 0; i < GraphTNE->GetNodes(); i++) {
for (int j = i + 1; j < GraphTNE->GetNodes(); j++) {
VerifyCmnNbrs(i, j, TSnap::GetCmnNbrs(GraphTNE, i, j));
}
}
}
// Test GetLen2Paths: Number of path lengths 2 between pair of nodes
TEST(triad, TestGetLen2Paths) {
// Test TUNGraph
PUNGraph GraphTUN = TriadGetTestTUNGraph();
for (int i = 0; i < GraphTUN->GetNodes(); i++) {
for (int j = i + 1; j < GraphTUN->GetNodes(); j++) {
VerifyLen2Paths(i, j, TSnap::GetLen2Paths(GraphTUN, i, j), 0);
}
}
// Test TNGraph which is different from undirected due to out neighbors.
PNGraph GraphTN = TriadGetTestTNGraph();
for (int i = 0; i < GraphTN->GetNodes(); i++) {
for (int j = i + 1; j < GraphTN->GetNodes(); j++) {
VerifyLen2Paths(i, j, TSnap::GetLen2Paths(GraphTN, i, j), 1);
}
}
// Test TNEGraph which is different from undirected due to out neighbors.
PNEGraph GraphTNE = TriadGetTestTNEGraph();
for (int i = 0; i < GraphTNE->GetNodes(); i++) {
for (int j = i + 1; j < GraphTNE->GetNodes(); j++) {
VerifyLen2Paths(i, j, TSnap::GetLen2Paths(GraphTNE, i, j), 2);
}
}
}
int ComputeKCore(const PUNGraph& G) {
int cnt = 0;
for(TUNGraph::TNodeI NI = G->BegNI(); NI < G->EndNI(); NI++)
cnt = max(cnt, NI.GetOutDeg());
THashSet <TInt> D[cnt+1];
THash <TInt, TInt> deg;
for(TUNGraph::TNodeI NI = G->BegNI(); NI < G->EndNI(); NI++) {
TInt tmp = NI.GetOutDeg() - G->IsEdge(NI.GetId(), NI.GetId() );
D[tmp.Val].AddKey(NI.GetId());
deg.AddDat(NI.GetId()) = tmp;
}
int max_k = 0;
for(int num_iters = 0;num_iters < G->GetNodes(); num_iters++)
for(int i = 0; i < cnt; i++)
if(D[i].Empty() == 0) {
max_k = max(max_k, i);
TInt a = *(D[i].BegI());
D[i].DelKey(a);
deg.AddDat(a.Val) = -1; // Hope overwriting works
TUNGraph::TNodeI NI = G->GetNI(a.Val);
for(int e = 0; e < NI.GetOutDeg(); e++) {
TInt b = NI.GetOutNId(e);
if(deg.GetDat(b) >= 0) {
int Id = deg.GetKeyId(b);
D[deg[Id].Val].DelKey(b);
deg[Id] = deg[Id] - 1; //Hope the overwriting works
D[deg[Id]].AddKey(b);
}
}
break;
}
return max_k;
}
/// Clique Percolation method communities
void TCliqueOverlap::GetCPMCommunities(const PUNGraph& G, int MinMaxCliqueSize, TVec<TIntV>& NIdCmtyVV) {
printf("Clique Percolation Method\n");
TExeTm ExeTm;
TVec<TIntV> MaxCliques;
TCliqueOverlap::GetMaxCliques(G, MinMaxCliqueSize, MaxCliques);
// op RS 2012/05/15, commented out next line, a parameter is missing,
// creating a warning on OS X
// printf("...%d cliques found\n");
// get clique overlap matrix (graph)
PUNGraph OverlapGraph = TCliqueOverlap::CalculateOverlapMtx(MaxCliques, MinMaxCliqueSize-1);
printf("...overlap matrix (%d, %d)\n", G->GetNodes(), G->GetEdges());
// connected components are communities
TCnComV CnComV;
TSnap::GetWccs(OverlapGraph, CnComV);
NIdCmtyVV.Clr(false);
TIntSet CmtySet;
for (int c = 0; c < CnComV.Len(); c++) {
CmtySet.Clr(false);
for (int i = 0; i <CnComV[c].Len(); i++) {
const TIntV& CliqueNIdV = MaxCliques[CnComV[c][i]];
CmtySet.AddKeyV(CliqueNIdV);
}
NIdCmtyVV.Add();
CmtySet.GetKeyV(NIdCmtyVV.Last());
NIdCmtyVV.Last().Sort();
}
printf("done [%s].\n", ExeTm.GetStr());
}
///Generate graph using the AGM model. CProbV = vector of Pc
PUNGraph TAGM::GenAGM(TVec<TIntV>& CmtyVV, const TFltV& CProbV, TRnd& Rnd, const double PNoCom) {
PUNGraph G = TUNGraph::New(100 * CmtyVV.Len(), -1);
printf("AGM begins\n");
for (int i = 0; i < CmtyVV.Len(); i++) {
TIntV& CmtyV = CmtyVV[i];
for (int u = 0; u < CmtyV.Len(); u++) {
if ( G->IsNode(CmtyV[u])) {
continue;
}
G->AddNode(CmtyV[u]);
}
double Prob = CProbV[i];
RndConnectInsideCommunity(G, CmtyV, Prob, Rnd);
}
if (PNoCom > 0.0) { //if we want to connect nodes that do not share any community
TIntSet NIDS;
for (int c = 0; c < CmtyVV.Len(); c++) {
for (int u = 0; u < CmtyVV[c].Len(); u++) {
NIDS.AddKey(CmtyVV[c][u]);
}
}
TIntV NIDV;
NIDS.GetKeyV(NIDV);
RndConnectInsideCommunity(G,NIDV,PNoCom,Rnd);
}
printf("AGM completed (%d nodes %d edges)\n",G->GetNodes(),G->GetEdges());
G->Defrag();
return G;
}
void TAGMFast::SetGraph(const PUNGraph& GraphPt) {
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;
}
// Test GetNodeClustCf (Specific Node)
TEST(triad, TestGetNodeClustCfSpecific) {
// Test TUNGraph
PUNGraph GraphTUN = TriadGetTestTUNGraph();
for (int i = 0; i < GraphTUN->GetNodes(); i++) {
double ClustCf = TSnap::GetNodeClustCf(GraphTUN, i);
VerifyNodeClustCf(i, ClustCf);
}
// TNGraph should be treated as TUNGraph for calculations
PNGraph GraphTN = TriadGetTestTNGraph();
for (int i = 0; i < GraphTN->GetNodes(); i++) {
double ClustCf = TSnap::GetNodeClustCf(GraphTN, i);
VerifyNodeClustCf(i, ClustCf);
}
// TNEGraph should be treated as TUNGraph for calculations
PNEGraph GraphTNE = TriadGetTestTNEGraph();
for (int i = 0; i < GraphTNE->GetNodes(); i++) {
double ClustCf = TSnap::GetNodeClustCf(GraphTNE, i);
VerifyNodeClustCf(i, ClustCf);
}
}
double GetGroupFarnessCentr(const PUNGraph& Graph, const TIntH& GroupNodes) {
TIntH* NDistH = new TIntH[GroupNodes.Len()];
for (int i = 0; i<GroupNodes.Len(); i++){
NDistH[i](Graph->GetNodes());
TSnap::GetShortPath<PUNGraph>(Graph, GroupNodes.GetDat(i), NDistH[i], true, TInt::Mx);
}
int min, dist, sum = 0, len = 0;
for (PUNGraph::TObj::TNodeI NI = Graph->BegNI(); NI < Graph->EndNI(); NI++){
if (NDistH[0].IsKey(NI.GetId()))
min = NDistH[0].GetDat(NI.GetId());
else
min = -1;
for (int j = 1; j<GroupNodes.Len(); j++){
if (NDistH[j].IsKey(NI.GetId()))
dist = NDistH[j].GetDat(NI.GetId());
else
dist = -1;
if ((dist < min && dist != -1) || (dist > min && min == -1))
min = dist;
}
if (min>0){
sum += min;
len++;
}
}
if (len > 0) { return sum / double(len); }
else { return 0.0; }
}
// to get first few eigenvectors
void GetEigVec(const PUNGraph& Graph, const int& EigVecs, TFltV& EigValV, TVec<TFltV>& EigVecV) {
const int Nodes = Graph->GetNodes();
// Lanczos
TUNGraphMtx GraphMtx(Graph);
int CalcVals = int(2*EigVecs);
if (CalcVals > Nodes) { CalcVals = Nodes; }
TFltVV EigVecVV;
//while (EigValV.Len() < EigVecs && CalcVals < 10*EigVecs) {
try {
TSparseSVD::Lanczos(GraphMtx, EigVecs, 2*EigVecs, ssotFull, EigValV, EigVecVV, false); }
catch(...) {
printf("\n ***EXCEPTION: TRIED %d GOT %d values** \n", CalcVals, EigValV.Len()); }
if (EigValV.Len() < EigVecs) {
printf(" ***TRIED %d GOT %d values** \n", CalcVals, EigValV.Len()); }
// CalcVals += EigVecs;
//}
TFltIntPrV EigValIdV;
for (int i = 0; i < EigValV.Len(); i++) {
EigValIdV.Add(TFltIntPr(EigValV[i], i));
}
EigValIdV.Sort(false);
EigValV.Sort(false);
for (int v = 0; v < EigValIdV.Len(); v++) { // vector components are not sorted!!!
EigVecV.Add();
EigVecVV.GetCol(EigValIdV[v].Val2, EigVecV.Last());
}
IsAllValVNeg(EigVecV[0], true);
}
// Test GetNodeClustCf (Vector)
TEST(triad, TestGetNodeClustCfVector) {
// Test TUNGraph
PUNGraph GraphTUN = TriadGetTestTUNGraph();
TIntFltH NIdCCfH;
TSnap::GetNodeClustCf(GraphTUN, NIdCCfH);
for (int i = 0; i < GraphTUN->GetNodes(); i++) {
double ClustCf = NIdCCfH.GetDat(i);
VerifyNodeClustCf(i, ClustCf);
}
// TNGraph should be treated as TUNGraph for calculations
PNGraph GraphTN = TriadGetTestTNGraph();
NIdCCfH.Clr();
TSnap::GetNodeClustCf(GraphTN, NIdCCfH);
for (int i = 0; i < GraphTN->GetNodes(); i++) {
double ClustCf = NIdCCfH.GetDat(i);
VerifyNodeClustCf(i, ClustCf);
}
// TNEGraph should be treated as TUNGraph for calculations
PNEGraph GraphTNE = TriadGetTestTNEGraph();
NIdCCfH.Clr();
TSnap::GetNodeClustCf(GraphTNE, NIdCCfH);
for (int i = 0; i < GraphTNE->GetNodes(); i++) {
double ClustCf = NIdCCfH.GetDat(i);
VerifyNodeClustCf(i, ClustCf);
}
}
// Test GetNodeTriads (Open and Closed)
TEST(triad, TestGetNodeCOTriads) {
// Test TUNGraph
PUNGraph GraphTUN = TriadGetTestTUNGraph();
for (int i = 0; i < GraphTUN->GetNodes(); i++) {
int ClosedTr = -1, OpenTr = -1;
TSnap::GetNodeTriads(GraphTUN, i, ClosedTr, OpenTr);
VerifyClosedTriads(i, ClosedTr);
VerifyOpenTriads(i, OpenTr);
}
// Test TNGraph which is treated same as undirected.
PNGraph GraphTN = TriadGetTestTNGraph();
for (int i = 0; i < GraphTN->GetNodes(); i++) {
int ClosedTr = -1, OpenTr = -1;
TSnap::GetNodeTriads(GraphTN, i, ClosedTr, OpenTr);
VerifyClosedTriads(i, ClosedTr);
VerifyOpenTriads(i, OpenTr);
}
// Test TNEGraph which is treated same as undirected.
PNEGraph GraphTNE = TriadGetTestTNEGraph();
for (int i = 0; i < GraphTNE->GetNodes(); i++) {
int ClosedTr = -1, OpenTr = -1;
TSnap::GetNodeTriads(GraphTNE, i, ClosedTr, OpenTr);
VerifyClosedTriads(i, ClosedTr);
VerifyOpenTriads(i, OpenTr);
}
}
void GetEigenVectorCentr(const PUNGraph& Graph, TIntFltH& EigenH, const double& Eps, const int& MaxIter) {
const int NNodes = Graph->GetNodes();
EigenH.Gen(NNodes);
for (TUNGraph::TNodeI NI = Graph->BegNI(); NI < Graph->EndNI(); NI++) {
EigenH.AddDat(NI.GetId(), 1.0/NNodes);
IAssert(NI.GetId() == EigenH.GetKey(EigenH.Len()-1));
}
TFltV TmpV(NNodes);
double diff = TFlt::Mx;
for (int iter = 0; iter < MaxIter; iter++) {
int j = 0;
for (TUNGraph::TNodeI NI = Graph->BegNI(); NI < Graph->EndNI(); NI++, j++) {
TmpV[j] = 0;
for (int e = 0; e < NI.GetOutDeg(); e++) {
TmpV[j] += EigenH.GetDat(NI.GetOutNId(e)); }
}
double sum = 0;
for (int i = 0; i < TmpV.Len(); i++) {
EigenH[i] = TmpV[i];
sum += EigenH[i];
}
for (int i = 0; i < EigenH.Len(); i++) {
EigenH[i] /= sum; }
if (fabs(diff-sum) < Eps) { break; }
//printf("\tdiff:%f\tsum:%f\n", fabs(diff-sum), sum);
diff = sum;
}
}
// Test node subgraph conversion
void TestConvertSubGraphs() {
PNGraph NGraph;
PUNGraph UNGraph;
int N1, N2, N3;
int E1, E2, E3;
TIntV NIdV;
int i;
NGraph = GetTestTNGraph();
N1 = NGraph->GetNodes();
E1 = NGraph->GetEdges();
for (i = 0; i < 20; i += 2) {
NIdV.Add(i);
}
// TODO: fix TSnap::ConvertSubGraph<PUNGraph>(NGraph, NIdV, true), it fails
// UNGraph = TSnap::ConvertSubGraph<PUNGraph>(NGraph, NIdV, true);
UNGraph = TSnap::ConvertSubGraph<PUNGraph>(NGraph, NIdV);
N2 = UNGraph->GetNodes();
E2 = UNGraph->GetEdges();
NGraph = TSnap::ConvertSubGraph<PNGraph>(UNGraph, NIdV);
N3 = NGraph->GetNodes();
E3 = NGraph->GetEdges();
printf("---- TestConvertSubGraphs -----\n");
printf("nodes: %d,%d,%d, edges: %d,%d,%d\n", N1, N2, N3, E1, E2, E3);
printf("\n");
}
/////////////////////////////////////////////////
// Spectral graph properties
void PlotEigValRank(const PUNGraph& Graph, const int& EigVals, const TStr& FNmPref, TStr DescStr) {
TFltV EigValV;
TSnap::GetEigVals(Graph, EigVals, EigValV);
EigValV.Sort(false);
if (DescStr.Empty()) { DescStr = FNmPref; }
TGnuPlot::PlotValV(EigValV, "eigVal."+FNmPref, TStr::Fmt("%s. G(%d, %d). Largest eig val = %f",
DescStr.CStr(), Graph->GetNodes(), Graph->GetEdges(), EigValV[0].Val), "Rank", "Eigen value", gpsLog10XY, false, gpwLinesPoints);
}
double GetDegreeCentralization(const PUNGraph& Graph) {
int MaxDeg = -1;
int N = Graph->GetNodes();
int Sum = 0;
if (Graph->GetNodes() > 1 && (double(N - 2.0)*double(N - 1)) > 0) {
for (TUNGraph::TNodeI NI = Graph->BegNI(); NI < Graph->EndNI(); NI++) {
int deg = NI.GetDeg();
if (deg > MaxDeg) {
MaxDeg = deg;
}
}
for (TUNGraph::TNodeI NI = Graph->BegNI(); NI < Graph->EndNI(); NI++) {
Sum += MaxDeg - NI.GetDeg();
}
return double(Sum) / (double(N - 2.0)*double(N - 1));
}
else { return 0.0; }
}
double GetAsstyCor(const PUNGraph& Graph) {
TIntFltH deg(Graph->GetNodes()), deg_sq(Graph->GetNodes());
for (TUNGraph::TNodeI NI = Graph->BegNI(); NI < Graph->EndNI(); NI++) {
deg.AddDat(NI.GetId()) = NI.GetOutDeg();
deg_sq.AddDat(NI.GetId()) = NI.GetOutDeg() * NI.GetOutDeg();
}
double m = Graph->GetEdges(), num1 = 0.0, num2 = 0.0, den1 = 0.0;
for (TUNGraph::TEdgeI EI = Graph->BegEI(); EI < Graph->EndEI(); EI++) {
double t1 = deg.GetDat(EI.GetSrcNId()).Val, t2 = deg.GetDat(EI.GetDstNId()).Val;
num1 += t1 * t2;
num2 += t1 + t2;
den1 += deg_sq.GetDat(EI.GetSrcNId()).Val + deg_sq.GetDat(EI.GetDstNId()).Val;
}
num1 /= m;
den1 /= (2.0 * m);
num2 = (num2 / (2.0 * m)) * (num2 / (2.0 * m));
return (num1 - num2) / (den1 - num2);
}
// Inverse participation ratio: normalize EigVec to have L2=1 and then I=sum_k EigVec[i]^4
// see Spectra of "real-world" graphs: Beyond the semicircle law by Farkas, Derenyi, Barabasi and Vicsek
void PlotInvParticipRat(const PUNGraph& Graph, const int& MaxEigVecs, const int& TimeLimit, const TStr& FNmPref, TStr DescStr) {
TFltPrV EigIprV;
GetInvParticipRat(Graph, MaxEigVecs, TimeLimit, EigIprV);
if (DescStr.Empty()) { DescStr = FNmPref; }
if (EigIprV.Empty()) { DescStr+=". FAIL"; EigIprV.Add(TFltPr(-1,-1)); return; }
TGnuPlot::PlotValV(EigIprV, "eigIPR."+FNmPref, TStr::Fmt("%s. G(%d, %d). Largest eig val = %f (%d values)",
DescStr.CStr(), Graph->GetNodes(), Graph->GetEdges(), EigIprV.Last().Val1(), EigIprV.Len()),
"Eigenvalue", "Inverse Participation Ratio of corresponding Eigenvector", gpsLog10Y, false, gpwPoints);
}
double GetFarnessCentr(const PUNGraph& Graph, const int& NId) {
TIntH NDistH(Graph->GetNodes());
TSnap::GetShortPath<PUNGraph>(Graph, NId, NDistH, true, TInt::Mx);
double sum = 0;
for (TIntH::TIter I = NDistH.BegI(); I < NDistH.EndI(); I++) {
sum += I->Dat();
}
if (NDistH.Len() > 1) { return sum / double(NDistH.Len() - 1); }
else { return 0.0; }
}
std::vector<int> obtenerVerticesOrdenados(PUNGraph G){
Visitor vis(G->GetNodes());
TCnCom::GetDfsVisitor(G, vis);
std::vector<int> nodos = vis.getVertices();
ordenarAsc(nodos, int(nodos.size()));
return nodos;
}
// Test the default constructor
TEST(TUNGraph, DefaultConstructor) {
PUNGraph Graph;
Graph = TUNGraph::New();
EXPECT_EQ(0,Graph->GetNodes());
EXPECT_EQ(0,Graph->GetEdges());
EXPECT_EQ(1,Graph->IsOk());
EXPECT_EQ(1,Graph->Empty());
EXPECT_EQ(0,Graph->HasFlag(gfDirected));
}
// Test small graph
TEST(TUNGraph, GetSmallGraph) {
PUNGraph Graph;
Graph = TUNGraph::GetSmallGraph();
EXPECT_EQ(5,Graph->GetNodes());
EXPECT_EQ(5,Graph->GetEdges());
EXPECT_EQ(1,Graph->IsOk());
EXPECT_EQ(0,Graph->Empty());
EXPECT_EQ(0,Graph->HasFlag(gfDirected));
}
int main(int argc, char* argv[]) {
Env = TEnv(argc, argv, TNotify::StdNotify);
Env.PrepArgs(TStr::Fmt("Cascades. build: %s, %s. Time: %s", __TIME__, __DATE__, TExeTm::GetCurTm()));
TExeTm ExeTm;
Try
const TStr InFNm = Env.GetIfArgPrefixStr("-i:", "demo", "Input undirected graph");
const TStr OutFNm = Env.GetIfArgPrefixStr("-o:", "demo", "Output file name prefix");
const double Beta = Env.GetIfArgPrefixFlt("-b:", 0.1, "Beta (infection (i.e., cascade propagation) probability)");
// load
printf("Loading %s...", InFNm.CStr());
PUNGraph Graph;
if (InFNm == "demo") { Graph = TSnap::GenRndGnm<PUNGraph>(100, 200); }
else { Graph = TSnap::LoadEdgeList<PUNGraph>(InFNm); }
printf("nodes:%d edges:%d\n", Graph->GetNodes(), Graph->GetEdges());
// Simulate SI model
Graph = TSnap::GetMxWcc(Graph);
bool DivByM = true;
TCascadeStat CascStat;
printf("\nGraph:%s -- Beta: %g\n", OutFNm.CStr(), Beta);
for (int Run = 0; Run < 10; Run++) { // number of runs
TIntH NIdInfTmH;
// incluence cascade
PNGraph InfCasc = RunSICascade(Graph, Beta, 100, NIdInfTmH);
if (InfCasc->GetNodes() < 10) { printf("."); continue; } // min cascade size
// network cascade
PNGraph NetCasc = AddSpuriousEdges(Graph, InfCasc, NIdInfTmH);
// sample the cascade
CascStat.SampleCascade(InfCasc, NetCasc, NIdInfTmH, 0.1, 10, DivByM); // div-by-M
printf(".");
}
CascStat.PlotAll(TStr::Fmt("%s-B%03d", OutFNm.CStr(), int(100*Beta)), TStr::Fmt("%s N=%d E=%d Beta=%g",
OutFNm.CStr(), Graph->GetNodes(), Graph->GetEdges(), Beta), DivByM);
Catch
printf("\nrun time: %s (%s)\n", ExeTm.GetTmStr(), TSecTm::GetCurTm().GetTmStr().CStr());
return 0;
}
int main(int argc, char* argv[]) {
Env = TEnv(argc, argv, TNotify::StdNotify);
Env.PrepArgs(TStr::Fmt("Network community detection. build: %s, %s. Time: %s", __TIME__, __DATE__, TExeTm::GetCurTm()));
TExeTm ExeTm;
Try
const TStr InFNm = Env.GetIfArgPrefixStr("-i:", "graph.txt", "Input graph (undirected graph)");
const TStr OutFNm = Env.GetIfArgPrefixStr("-o:", "communities.txt", "Output file");
const int CmtyAlg = Env.GetIfArgPrefixInt("-a:", 2, "Algorithm: 1:Girvan-Newman, 2:Clauset-Newman-Moore, 3:Infomap");
PUNGraph Graph = TSnap::LoadEdgeList<PUNGraph>(InFNm, false);
//PUNGraph Graph = TSnap::LoadEdgeList<PUNGraph>("../as20graph.txt", false);
//PUNGraph Graph = TSnap::GenRndGnm<PUNGraph>(5000, 10000); // generate a random graph
TSnap::DelSelfEdges(Graph);
TCnComV CmtyV;
double Q = 0.0;
TStr CmtyAlgStr;
if (CmtyAlg == 1) {
CmtyAlgStr = "Girvan-Newman";
Q = TSnap::CommunityGirvanNewman(Graph, CmtyV); }
else if (CmtyAlg == 2) {
CmtyAlgStr = "Clauset-Newman-Moore";
Q = TSnap::CommunityCNM(Graph, CmtyV); }
else if (CmtyAlg == 3) {
CmtyAlgStr = "Infomap";
Q = TSnap::Infomap(Graph, CmtyV); }
else { Fail; }
FILE *F = fopen(OutFNm.CStr(), "wt");
fprintf(F, "# Input: %s\n", InFNm.CStr());
fprintf(F, "# Nodes: %d Edges: %d\n", Graph->GetNodes(), Graph->GetEdges());
fprintf(F, "# Algoritm: %s\n", CmtyAlgStr.CStr());
if (CmtyAlg!=3) {
fprintf(F, "# Modularity: %f\n", Q);
} else {
fprintf(F, "# Average code length: %f\n", Q);
}
fprintf(F, "# Communities: %d\n", CmtyV.Len());
fprintf(F, "# NId\tCommunityId\n");
for (int c = 0; c < CmtyV.Len(); c++) {
for (int i = 0; i < CmtyV[c].Len(); i++) {
fprintf(F, "%d\t%d\n", CmtyV[c][i].Val, c);
}
}
fclose(F);
Catch
printf("\nrun time: %s (%s)\n", ExeTm.GetTmStr(), TSecTm::GetCurTm().GetTmStr().CStr());
return 0;
}
TUNGraphMtx::TUNGraphMtx(const PUNGraph& GraphPt) : Graph() {
Graph = GraphPt;
if (! CheckNodeIds()) {
printf(" Renumbering %d nodes....", GraphPt->GetNodes());
TExeTm ExeTm;
Graph = TSnap::ConvertGraph<PUNGraph>(GraphPt, true);
/*TIntSet NIdSet;
for (TUNGraph::TNodeI NI = Graph->BegNI(); NI < Graph->EndNI(); NI++) {
NIdSet.AddKey(NI.GetId());
}
Graph = TUNGraph::New(); *Graph = *GraphPt; */
printf("done [%s]\n", ExeTm.GetStr());
}
}
int main(int argc, char* argv[]) {
Env = TEnv(argc, argv, TNotify::StdNotify);
Env.PrepArgs(TStr::Fmt("agmgen. build: %s, %s. Time: %s", __TIME__, __DATE__, TExeTm::GetCurTm()));
TExeTm ExeTm;
Try
const TStr InFNm = Env.GetIfArgPrefixStr("-i:", "DEMO", "Community affiliation data");
const TStr OutFPrx = Env.GetIfArgPrefixStr("-o:", "agm", "out file name prefix");
const int RndSeed = Env.GetIfArgPrefixInt("-rs:",10,"Rnd Seed");
const double DensityCoef= Env.GetIfArgPrefixFlt("-a:",0.6,"Power-law Coefficient a of density (density ~ N^(-a)");
const double ScaleCoef= Env.GetIfArgPrefixFlt("-c:",1.3,"Scaling Coefficient c of density (density ~ c");
TRnd Rnd(RndSeed);
TVec<TIntV> CmtyVV;
if(InFNm=="DEMO") {
CmtyVV.Gen(2);
TIntV NIdV;
for(int i=0;i<25;i++) {
TIntV& CmtyV = CmtyVV[0];
CmtyV.Add(i+1);
}
for(int i=15;i<40;i++) {
TIntV& CmtyV = CmtyVV[1];
CmtyV.Add(i+1);
}
}
else {
TVec<TIntV> CmtyVV;
TSsParser Ss(InFNm, ssfWhiteSep);
while (Ss.Next()) {
if(Ss.GetFlds()>0) {
TIntV CmtyV;
for(int i=0;i<Ss.GetFlds();i++) {
if(Ss.IsInt(i)){CmtyV.Add(Ss.GetInt(i));}
}
CmtyVV.Add(CmtyV);
}
}
printf("community loading completed (%d communities)\n",CmtyVV.Len());
}
PUNGraph AG = TAGM::GenAGM(CmtyVV,DensityCoef,ScaleCoef,Rnd);
TSnap::SaveEdgeList(AG,OutFPrx + ".edgelist.txt");
if(AG->GetNodes()<50) {
TAGM::GVizComGraph(AG,CmtyVV,OutFPrx + ".graph.gif");
}
Catch
printf("\nrun time: %s (%s)\n", ExeTm.GetTmStr(), TSecTm::GetCurTm().GetTmStr().CStr());
return 0;
}
// Test graph conversion
TEST(subgraph, TestConvertGraphs) {
PNGraph NGraph;
PUNGraph UNGraph;
NGraph = GetTestTNGraph();
EXPECT_EQ(20,NGraph->GetNodes());
EXPECT_EQ(60,NGraph->GetEdges());
UNGraph = TSnap::ConvertGraph<PUNGraph>(NGraph);
EXPECT_EQ(20,UNGraph->GetNodes());
EXPECT_EQ(60,UNGraph->GetEdges());
NGraph = TSnap::ConvertGraph<PNGraph>(UNGraph);
EXPECT_EQ(20,NGraph->GetNodes());
EXPECT_EQ(120,NGraph->GetEdges());
}
void GetEigenVectorCentr(const PUNGraph& Graph, TIntFltH& NIdEigenH, const double& Eps, const int& MaxIter) {
const int NNodes = Graph->GetNodes();
NIdEigenH.Gen(NNodes);
// initialize vector values
for (TUNGraph::TNodeI NI = Graph->BegNI(); NI < Graph->EndNI(); NI++) {
NIdEigenH.AddDat(NI.GetId(), 1.0 / NNodes);
IAssert(NI.GetId() == NIdEigenH.GetKey(NIdEigenH.Len() - 1));
}
TFltV TmpV(NNodes);
for (int iter = 0; iter < MaxIter; iter++) {
int j = 0;
// add neighbor values
for (TUNGraph::TNodeI NI = Graph->BegNI(); NI < Graph->EndNI(); NI++, j++) {
TmpV[j] = 0;
for (int e = 0; e < NI.GetOutDeg(); e++) {
TmpV[j] += NIdEigenH.GetDat(NI.GetOutNId(e));
}
}
// normalize
double sum = 0;
for (int i = 0; i < TmpV.Len(); i++) {
sum += (TmpV[i] * TmpV[i]);
}
sum = sqrt(sum);
for (int i = 0; i < TmpV.Len(); i++) {
TmpV[i] /= sum;
}
// compute difference
double diff = 0.0;
j = 0;
for (TUNGraph::TNodeI NI = Graph->BegNI(); NI < Graph->EndNI(); NI++, j++) {
diff += fabs(NIdEigenH.GetDat(NI.GetId()) - TmpV[j]);
}
// set new values
j = 0;
for (TUNGraph::TNodeI NI = Graph->BegNI(); NI < Graph->EndNI(); NI++, j++) {
NIdEigenH.AddDat(NI.GetId(), TmpV[j]);
}
if (diff < Eps) {
break;
}
}
}
void TCliqueOverlap::GetMaximalCliques(const PUNGraph& G, int MinMaxCliqueSize, TVec<TIntV>& MaxCliques) {
if (G->GetNodes() == 0) return;
//
m_G = G;
m_minMaxCliqueSize = MinMaxCliqueSize;
m_maxCliques =& MaxCliques;
m_Q.Clr();
//
THashSet<TInt> SUBG;
THashSet<TInt> CAND;
for (TUNGraph::TNodeI NI=m_G->BegNI(); NI<m_G->EndNI(); NI++) {
TInt nId = NI.GetId();
SUBG.AddKey(nId);
CAND.AddKey(nId);
}
//
Expand(SUBG, CAND);
}
/// Rewire the network. Keeps node degrees as is but randomly rewires the edges.
/// Use this function to generate a random graph with the same degree sequence
/// as the OrigGraph.
/// See: On the uniform generation of random graphs with prescribed degree
/// sequences by R. Milo, N. Kashtan, S. Itzkovitz, M. E. J. Newman, U. Alon
/// URL: http://arxiv.org/abs/cond-mat/0312028
PUNGraph GenRewire(const PUNGraph& OrigGraph, const int& NSwitch, TRnd& Rnd) {
const int Nodes = OrigGraph->GetNodes();
const int Edges = OrigGraph->GetEdges();
PUNGraph GraphPt = TUNGraph::New();
TUNGraph& Graph = *GraphPt;
Graph.Reserve(Nodes, -1);
TExeTm ExeTm;
// generate a graph that satisfies the constraints
printf("Randomizing edges (%d, %d)...\n", Nodes, Edges);
TIntPrSet EdgeSet(Edges);
for (TUNGraph::TNodeI NI = OrigGraph->BegNI(); NI < OrigGraph->EndNI(); NI++) {
const int NId = NI.GetId();
for (int e = 0; e < NI.GetOutDeg(); e++) {
if (NId <= NI.GetOutNId(e)) { continue; }
EdgeSet.AddKey(TIntPr(NId, NI.GetOutNId(e)));
}
Graph.AddNode(NI.GetId());
}
// edge switching
uint skip=0;
for (uint swps = 0; swps < 2*uint(Edges)*uint(NSwitch); swps++) {
const int keyId1 = EdgeSet.GetRndKeyId(Rnd);
const int keyId2 = EdgeSet.GetRndKeyId(Rnd);
if (keyId1 == keyId2) { skip++; continue; }
const TIntPr& E1 = EdgeSet[keyId1];
const TIntPr& E2 = EdgeSet[keyId2];
TIntPr NewE1(E1.Val1, E2.Val1), NewE2(E1.Val2, E2.Val2);
if (NewE1.Val1 > NewE1.Val2) { Swap(NewE1.Val1, NewE1.Val2); }
if (NewE2.Val1 > NewE2.Val2) { Swap(NewE2.Val1, NewE2.Val2); }
if (NewE1!=NewE2 && NewE1.Val1!=NewE1.Val2 && NewE2.Val1!=NewE2.Val2 && ! EdgeSet.IsKey(NewE1) && ! EdgeSet.IsKey(NewE2)) {
EdgeSet.DelKeyId(keyId1); EdgeSet.DelKeyId(keyId2);
EdgeSet.AddKey(TIntPr(NewE1));
EdgeSet.AddKey(TIntPr(NewE2));
} else { skip++; }
if (swps % Edges == 0) {
printf("\r %uk/%uk: %uk skip [%s]", swps/1000u, 2*uint(Edges)*uint(NSwitch)/1000u, skip/1000u, ExeTm.GetStr());
if (ExeTm.GetSecs() > 2*3600) { printf(" *** Time limit!\n"); break; } // time limit 2 hours
}
}
printf("\r total %uk switchings attempted, %uk skiped [%s]\n", 2*uint(Edges)*uint(NSwitch)/1000u, skip/1000u, ExeTm.GetStr());
for (int e = 0; e < EdgeSet.Len(); e++) {
Graph.AddEdge(EdgeSet[e].Val1, EdgeSet[e].Val2); }
return GraphPt;
}
