void TSubGraphsEnum::RecurBfs1(const int& NId, const int& Depth) {
if (Depth == 0) {
TIntPrV EdgeV;
EdgeH.GetKeyV(EdgeV);
EdgeV.Sort();
SgV.Add(EdgeV);
return;
}
const TNGraph::TNodeI NI = NGraph ->GetNI(NId);
for (int e = 0; e < NI.GetOutDeg(); e++) {
const TIntPr Edge(NId, NI.GetOutNId(e));
if (! EdgeH.IsKey(Edge)) {
EdgeH.AddKey(Edge);
RecurBfs1(NI.GetOutNId(e), Depth-1);
EdgeH.DelKey(Edge);
}
}
for (int e = 0; e < NI.GetInDeg(); e++) {
const TIntPr Edge(NI.GetInNId(e), NId);
if (! EdgeH.IsKey(Edge)) {
EdgeH.AddKey(Edge);
RecurBfs1(NI.GetInNId(e), Depth-1);
EdgeH.DelKey(Edge);
}
}
}
// improved version
void GetMergeSortedV1(TIntV& NeighbourV, TNGraph::TNodeI NI) {
int j = 0;
int k = 0;
int prev = -1;
int indeg = NI.GetInDeg();
int outdeg = NI.GetOutDeg();
//while (j < NI.GetInDeg() && k < NI.GetOutDeg()) {
if (indeg > 0 && outdeg > 0) {
int v1 = NI.GetInNId(j);
int v2 = NI.GetOutNId(k);
while (1) {
if (v1 <= v2) {
if (prev != v1) {
NeighbourV.Add(v1);
prev = v1;
}
j += 1;
if (j >= indeg) {
break;
}
v1 = NI.GetInNId(j);
} else {
if (prev != v2) {
NeighbourV.Add(v2);
prev = v2;
}
k += 1;
if (k >= outdeg) {
break;
}
v2 = NI.GetOutNId(k);
}
}
}
while (j < indeg) {
int v = NI.GetInNId(j);
if (prev != v) {
NeighbourV.Add(v);
prev = v;
}
j += 1;
}
while (k < outdeg) {
int v = NI.GetOutNId(k);
if (prev != v) {
NeighbourV.Add(v);
prev = v;
}
k += 1;
}
}
void MergeNbrs(TIntV* NeighbourV, TIntV* list1, TNGraph::TNodeI NI2) {
int j = 0;
int k = 0;
int prev = -1;
int lenA = list1->Len();
int lenB = NI2.GetInDeg();
if (lenA > 0 && lenB > 0) {
int v1 = (*list1)[j];
int v2 = NI2.GetInNId(k);
while (1) {
if (v1 <= v2) {
if (prev != v1) {
NeighbourV->Add(v1);
prev = v1;
}
j += 1;
if (j >= lenA) {
break;
}
v1 = (*list1)[j];
} else {
if (prev != v2) {
NeighbourV->Add(v2);
prev = v2;
}
k += 1;
if (k >= lenB) {
break;
}
v2 = NI2.GetInNId(k);
}
}
}
while (j < lenA) {
int v = (*list1)[j];
if (prev != v) {
NeighbourV->Add(v);
prev = v;
}
j += 1;
}
while (k < lenB) {
int v = NI2.GetInNId(k);
if (prev != v) {
NeighbourV->Add(v);
prev = v;
}
k += 1;
}
}
void TGraphCascade::PruneGraph() {
// iterate over nodes
int Nodes = NodeNmIdH.Len();
TIntV NodeIdV; NodeNmIdH.GetDatV(NodeIdV);
TStrV NodeNmV; NodeNmIdH.GetKeyV(NodeNmV);
for (int NodeN = 0; NodeN < Nodes; NodeN++) {
int NodeId = NodeIdV[NodeN];
if (!EnabledNodeIdH.IsKey(NodeId)) {
// if a node is not enabled:
// - connect its parents to its children
TNGraph::TNodeI NI = Graph.GetNI(NodeId);
for (int ParentN = 0; ParentN < NI.GetInDeg(); ParentN++) {
for (int ChildN = 0; ChildN < NI.GetOutDeg(); ChildN++) {
if (!Graph.IsEdge(NI.GetInNId(ParentN), NI.GetOutNId(ChildN))) {
Graph.AddEdge(NI.GetInNId(ParentN), NI.GetOutNId(ChildN));
}
}
}
//printf("deleting node %s %d\n", NodeNmV[NodeN].CStr(), NodeId);
// - delete it (deletes edges)
Graph.DelNode(NodeId);
}
}
// generate search sequence from sinks to sources
TopologicalSort(NIdSweep);
//Print(NIdSweep);
}
int getNumOfIndependentPaths(const PNGraph& graph, int srcNodeID, int dstNodeID) {
int ret = 0;
while (true) {
PNGraph bfsGraph = TSnap::GetBfsTree(graph, srcNodeID, true, false);
if (!bfsGraph->IsNode(dstNodeID)) {
return ret;
}
printf("%d hops\n", TSnap::GetShortPath(bfsGraph, srcNodeID, dstNodeID, true));
// Go back from dstNode to src
int itrNodeId = dstNodeID;
while (itrNodeId != srcNodeID) {
TNGraph::TNodeI curNode = bfsGraph->GetNI(itrNodeId);
int parentNodeId = curNode.GetInNId(0);
// Delete Edges
// graph->DelEdge(parentNodeId, itrNodeId, true);
// Delete Node
if (itrNodeId != dstNodeID && itrNodeId != srcNodeID) {
graph->DelNode(itrNodeId);
}
itrNodeId = parentNodeId;
}
++ret;
}
}
// burn each link independently (forward with FwdBurnProb, backward with BckBurnProb)
void TForestFire::BurnExpFire() {
const double OldFwdBurnProb = FwdBurnProb;
const double OldBckBurnProb = BckBurnProb;
const int NInfect = InfectNIdV.Len();
const TNGraph& G = *Graph;
TIntH BurnedNIdH; // burned nodes
TIntV BurningNIdV = InfectNIdV; // currently burning nodes
TIntV NewBurnedNIdV; // nodes newly burned in current step
bool HasAliveNbrs; // has unburned neighbors
int NBurned = NInfect, NDiedFire=0;
for (int i = 0; i < InfectNIdV.Len(); i++) {
BurnedNIdH.AddDat(InfectNIdV[i]); }
NBurnedTmV.Clr(false); NBurningTmV.Clr(false); NewBurnedTmV.Clr(false);
for (int time = 0; ; time++) {
NewBurnedNIdV.Clr(false);
// for each burning node
for (int node = 0; node < BurningNIdV.Len(); node++) {
const int& BurningNId = BurningNIdV[node];
const TNGraph::TNodeI Node = G.GetNI(BurningNId);
HasAliveNbrs = false;
NDiedFire = 0;
// burn forward links (out-links)
for (int e = 0; e < Node.GetOutDeg(); e++) {
const int OutNId = Node.GetOutNId(e);
if (! BurnedNIdH.IsKey(OutNId)) { // not yet burned
HasAliveNbrs = true;
if (Rnd.GetUniDev() < FwdBurnProb) {
BurnedNIdH.AddDat(OutNId); NewBurnedNIdV.Add(OutNId); NBurned++; }
}
}
// burn backward links (in-links)
if (BckBurnProb > 0.0) {
for (int e = 0; e < Node.GetInDeg(); e++) {
const int InNId = Node.GetInNId(e);
if (! BurnedNIdH.IsKey(InNId)) { // not yet burned
HasAliveNbrs = true;
if (Rnd.GetUniDev() < BckBurnProb) {
BurnedNIdH.AddDat(InNId); NewBurnedNIdV.Add(InNId); NBurned++; }
}
}
}
if (! HasAliveNbrs) { NDiedFire++; }
}
NBurnedTmV.Add(NBurned);
NBurningTmV.Add(BurningNIdV.Len() - NDiedFire);
NewBurnedTmV.Add(NewBurnedNIdV.Len());
//BurningNIdV.AddV(NewBurnedNIdV); // node is burning eternally
BurningNIdV.Swap(NewBurnedNIdV); // node is burning just 1 time step
if (BurningNIdV.Empty()) break;
FwdBurnProb = FwdBurnProb * ProbDecay;
BckBurnProb = BckBurnProb * ProbDecay;
}
BurnedNIdV.Gen(BurnedNIdH.Len(), 0);
for (int i = 0; i < BurnedNIdH.Len(); i++) {
BurnedNIdV.Add(BurnedNIdH.GetKey(i)); }
FwdBurnProb = OldFwdBurnProb;
BckBurnProb = OldBckBurnProb;
}
void TempMotifCounter::GetAllNeighbors(int node, TIntV& nbrs) {
nbrs = TIntV();
TNGraph::TNodeI NI = static_graph_->GetNI(node);
for (int i = 0; i < NI.GetOutDeg(); i++) { nbrs.Add(NI.GetOutNId(i)); }
for (int i = 0; i < NI.GetInDeg(); i++) {
int nbr = NI.GetInNId(i);
if (!NI.IsOutNId(nbr)) { nbrs.Add(nbr); }
}
}
uint64 TGraphCascade::SampleNodeTimestamp(const int& NodeId, const uint64& Time, const int& SampleN) {
if (Timestamps.GetDat(NodeId) > 0) {
return Timestamps.GetDat(NodeId);
} else if (Sample.GetDat(NodeId).Len() > SampleN) {
return Sample.GetDat(NodeId)[SampleN];
}
TNGraph::TNodeI NI = Graph.GetNI(NodeId);
int Parents = NI.GetInDeg();
if (Parents == 0) {
throw TExcept::New("Root node has not been observed yet - cannot run simulation");
}
uint64 MaxParentTime = 0;
for (int ParentN = 0; ParentN < Parents; ParentN++) {
int ParentId = NI.GetInNId(ParentN);
// check if parent was observed or has samples available
if (Timestamps.GetDat(ParentId) == 0 && Sample.GetDat(ParentId).Empty()) {
throw TExcept::New("Parent node unobserved and sample not available! Missing data or bad graph");
}
// get SampleN from each parent
uint64 ParentTime = SampleNodeTimestamp(ParentId, Time, SampleN);
// update max
MaxParentTime = (MaxParentTime > ParentTime) ? MaxParentTime : ParentTime;
}
int TimeDiff = (int)(((int64)(Time)-(int64)(MaxParentTime)) / TimeUnit);
int MinDuration = MAX(TimeDiff, 0);
if (!CDF.IsKey(NodeId)) {
// model is missing and the node has not been observed
// this probably indicates that the node is always missing
// model its duration as 0, so it should have been observed after
// its last parent
return MaxParentTime;
}
TFltV& NodeCDF = CDF.GetDat(NodeId);
int MaxDuration = NodeCDF.Len();
if (TimeDiff > MaxDuration) { return Time + 1; } // out of model bounds
double CDFRemain = MinDuration == 0 ? 1.0 : (1.0 - NodeCDF[MinDuration - 1]);
if (CDFRemain < 1e-16) { return Time + 1; } // numerically out of model bounds
// inverse cdf sample, conditioned on elapsed time
double Samp = (1.0 - CDFRemain) + Rnd.GetUniDev() * CDFRemain;
// find the first CDF bin that exceeds Samp
// SPEEDUP possible with bisection
int BinIdx = MaxDuration;
for (int BinN = MinDuration; BinN < MaxDuration; BinN++) {
if (NodeCDF[BinN] >= Samp) {
BinIdx = BinN;
break;
}
}
// compute time
return MaxParentTime + (uint64)((BinIdx)* TimeUnit);
}
void TSubGraphsEnum::RecurBfs(const int& NId, const int& Depth, TSimpleGraph& PrevG) {
if (Depth == 0) {
TIntPrV& EdgeV = PrevG();
EdgeV.Sort();
for (int i = 1; i < EdgeV.Len(); i++) {
if (EdgeV[i-1] == EdgeV[i]) { return; }
}
SgV.Add(PrevG);
return;
}
const TNGraph::TNodeI NI = NGraph ->GetNI(NId);
for (int e = 0; e < NI.GetOutDeg(); e++) {
TSimpleGraph CurG = PrevG;
CurG.AddEdge(NI.GetId(), NI.GetOutNId(e));
RecurBfs(NI.GetOutNId(e), Depth-1, CurG);
}
for (int e = 0; e < NI.GetInDeg(); e++) {
TSimpleGraph CurG = PrevG;
CurG.AddEdge(NI.GetInNId(e), NI.GetId());
RecurBfs(NI.GetInNId(e), Depth-1, CurG);
}
}
// initial version
void GetMergeSortedV(TIntV& NeighbourV, TNGraph::TNodeI NI) {
int ind, j, k;
ind = j = k = 0;
while (j < NI.GetInDeg() && k < NI.GetOutDeg()) {
int v1 = NI.GetInNId(j);
int v2 = NI.GetOutNId(k);
if (v1 <= v2) {
if ((ind == 0) || (NeighbourV[ind-1] != v1)) {
NeighbourV.Add(v1);
ind += 1;
}
j += 1;
}
else {
if ((ind == 0) || (NeighbourV[ind-1] != v2)) {
NeighbourV.Add(v2);
ind += 1;
}
k += 1;
}
}
while (j < NI.GetInDeg()) {
int v = NI.GetInNId(j);
if ((ind == 0) || (NeighbourV[ind-1] != v)) {
NeighbourV.Add(v);
ind += 1;
}
j += 1;
}
while (k < NI.GetOutDeg()) {
int v = NI.GetOutNId(k);
if ((ind == 0) || (NeighbourV[ind-1] != v)) {
NeighbourV.Add(v);
ind += 1;
}
k += 1;
}
}
// Rok #5
void GetMergeSortedV(TIntV& NeighbourV, TNGraph::TNodeI NI) {
int j = 0;
int k = 0;
int prev = -1;
while (j < NI.GetInDeg() && k < NI.GetOutDeg()) {
int v1 = NI.GetInNId(j);
int v2 = NI.GetOutNId(k);
if (v1 <= v2) {
if (prev != v1) {
NeighbourV.Add(v1);
prev = v1;
}
j += 1;
} else {
if (prev != v2) {
NeighbourV.Add(v2);
prev = v2;
}
k += 1;
}
}
while (j < NI.GetInDeg()) {
int v = NI.GetInNId(j);
if (prev != v) {
NeighbourV.Add(v);
prev = v;
}
j += 1;
}
while (k < NI.GetOutDeg()) {
int v = NI.GetOutNId(k);
if (prev != v) {
NeighbourV.Add(v);
prev = v;
}
k += 1;
}
}
PJsonVal TGraphCascade::GetGraph() const {
PJsonVal G = TJsonVal::NewObj();
for (TNGraph::TNodeI NI = Graph.BegNI(); NI < Graph.EndNI(); NI++) {
TStr NodeNm = NodeIdNmH.GetDat(NI.GetId());
PJsonVal ParentsArr = TJsonVal::NewArr();
int InDeg = NI.GetInDeg();
for (int ParentN = 0; ParentN < InDeg; ParentN++) {
TStr ParentNm = NodeIdNmH.GetDat(NI.GetInNId(ParentN));
ParentsArr->AddToArr(ParentNm);
}
G->AddToObj(NodeNm, ParentsArr);
}
return G;
}
void getInNeighborNodeIDs(const PNGraph& graph, int destNodeID, std::set<int>& nodeIdSet) {
std::queue<int> q;
q.push(destNodeID);
nodeIdSet.insert(destNodeID);
for (int level = 0; level < 2; ++level) {
int levelCount = q.size();
for (int i = 0; i < levelCount; ++i) {
int curNodeId = q.front();
q.pop();
// Scan neigbors;
TNGraph::TNodeI curNode = graph->GetNI(curNodeId);
int inDeg = curNode.GetInDeg();
for (int j = 0; j < inDeg; ++j) {
int curNeighborNodeID = curNode.GetInNId(j);
q.push(curNeighborNodeID);
nodeIdSet.insert(curNeighborNodeID);
}
}
}
}
double TCascade::GetProb(const PNGraph& G) {
double P = 0;
for (int n = 0; n < Len(); n++) {
const int DstNId = GetNode(n);
const double DstTm = GetTm(DstNId);
TNGraph::TNodeI NI = G->GetNI(DstNId);
double MxProb = log(Eps);
int BestParent = -1;
for (int e = 0; e < NI.GetInDeg(); e++) {
const int SrcNId = NI.GetInNId(e);
if (IsNode(SrcNId) && GetTm(SrcNId) < DstTm) {
const double Prob = log(TransProb(SrcNId, DstNId));
if (MxProb < Prob) { MxProb = Prob; BestParent = SrcNId; }
}
}
NIdHitH.GetDat(DstNId).Parent = BestParent;
P += MxProb;
}
return P;
}
int main(int argc, char* argv[]) {
// create a graph and save it
{ PNGraph Graph = TNGraph::New();
for (int i = 0; i < 10; i++) {
Graph->AddNode(i); }
for (int i = 0; i < 10; i++) {
Graph->AddEdge(i, TInt::Rnd.GetUniDevInt(10)); }
TSnap::SaveEdgeList(Graph, "graph.txt", "Edge list format"); }
// load a graph
PNGraph Graph;
Graph = TSnap::LoadEdgeList<PNGraph>("graph.txt", 0, 1);
// traverse nodes
for (TNGraph::TNodeI NI = Graph->BegNI(); NI < Graph->EndNI(); NI++) {
printf("NodeId: %d, InDegree: %d, OutDegree: %d\n", NI.GetId(), NI.GetInDeg(), NI.GetOutDeg());
printf("OutNodes: ");
for (int e = 0; e < NI.GetOutDeg(); e++) { printf(" %d", NI.GetOutNId(e)); }
printf("\nInNodes: ");
for (int e = 0; e < NI.GetInDeg(); e++) { printf(" %d", NI.GetInNId(e)); }
printf("\n\n");
}
// graph statistic
TSnap::PrintInfo(Graph, "Graph info");
PNGraph MxWcc = TSnap::GetMxWcc(Graph);
TSnap::PrintInfo(MxWcc, "Largest Weakly connected component");
// random graph
PNGraph RndGraph = TSnap::GenRndGnm<PNGraph>(100, 1000);
TGStat GraphStat(RndGraph, TSecTm(1), TGStat::AllStat(), "Gnm graph");
GraphStat.PlotAll("RndGraph", "Random graph on 1000 nodes");
// Forest Fire graph
{ TFfGGen ForestFire(false, 1, 0.35, 0.30, 1.0, 0.0, 0.0);
ForestFire.GenGraph(100);
PNGraph FfGraph = ForestFire.GetGraph(); }
// network
TPt<TNodeEDatNet<TStr, TStr> > Net = TNodeEDatNet<TStr, TStr>::New();
Net->AddNode(0, "zero");
Net->AddNode(1, "one");
Net->AddEdge(0, 1, "zero to one");
return 0;
}
// Node selects N~geometric(1.0-FwdBurnProb)-1 out-links and burns them. Then same for in-links.
// geometirc(p) has mean 1/(p), so for given FwdBurnProb, we burn 1/(1-FwdBurnProb)
void TForestFire::BurnGeoFire() {
const double OldFwdBurnProb = FwdBurnProb;
const double OldBckBurnProb = BckBurnProb;
const int& NInfect = InfectNIdV.Len();
const TNGraph& G = *Graph;
TIntH BurnedNIdH; // burned nodes
TIntV BurningNIdV = InfectNIdV; // currently burning nodes
TIntV NewBurnedNIdV; // nodes newly burned in current step
bool HasAliveInNbrs, HasAliveOutNbrs; // has unburned neighbors
TIntV AliveNIdV; // NIds of alive neighbors
int NBurned = NInfect, time;
for (int i = 0; i < InfectNIdV.Len(); i++) {
BurnedNIdH.AddDat(InfectNIdV[i]);
}
NBurnedTmV.Clr(false); NBurningTmV.Clr(false); NewBurnedTmV.Clr(false);
for (time = 0;; time++) {
NewBurnedNIdV.Clr(false);
for (int node = 0; node < BurningNIdV.Len(); node++) {
const int& BurningNId = BurningNIdV[node];
const TNGraph::TNodeI Node = G.GetNI(BurningNId);
// find unburned links
HasAliveOutNbrs = false;
AliveNIdV.Clr(false); // unburned links
for (int e = 0; e < Node.GetOutDeg(); e++) {
const int OutNId = Node.GetOutNId(e);
if (!BurnedNIdH.IsKey(OutNId)) {
HasAliveOutNbrs = true; AliveNIdV.Add(OutNId);
}
}
// number of links to burn (geometric coin). Can also burn 0 links
const int BurnNFwdLinks = Rnd.GetGeoDev(1.0 - FwdBurnProb) - 1;
if (HasAliveOutNbrs && BurnNFwdLinks > 0) {
AliveNIdV.Shuffle(Rnd);
for (int i = 0; i < TMath::Mn(BurnNFwdLinks, AliveNIdV.Len()); i++) {
BurnedNIdH.AddDat(AliveNIdV[i]);
NewBurnedNIdV.Add(AliveNIdV[i]); NBurned++;
}
}
// backward links
if (BckBurnProb > 0.0) {
// find unburned links
HasAliveInNbrs = false;
AliveNIdV.Clr(false);
for (int e = 0; e < Node.GetInDeg(); e++) {
const int InNId = Node.GetInNId(e);
if (!BurnedNIdH.IsKey(InNId)) {
HasAliveInNbrs = true; AliveNIdV.Add(InNId);
}
}
// number of links to burn (geometric coin). Can also burn 0 links
const int BurnNBckLinks = Rnd.GetGeoDev(1.0 - BckBurnProb) - 1;
if (HasAliveInNbrs && BurnNBckLinks > 0) {
AliveNIdV.Shuffle(Rnd);
for (int i = 0; i < TMath::Mn(BurnNBckLinks, AliveNIdV.Len()); i++) {
BurnedNIdH.AddDat(AliveNIdV[i]);
NewBurnedNIdV.Add(AliveNIdV[i]); NBurned++;
}
}
}
}
NBurnedTmV.Add(NBurned); NBurningTmV.Add(BurningNIdV.Len()); NewBurnedTmV.Add(NewBurnedNIdV.Len());
// BurningNIdV.AddV(NewBurnedNIdV); // node is burning eternally
BurningNIdV.Swap(NewBurnedNIdV); // node is burning just 1 time step
if (BurningNIdV.Empty()) break;
FwdBurnProb = FwdBurnProb * ProbDecay;
BckBurnProb = BckBurnProb * ProbDecay;
}
BurnedNIdV.Gen(BurnedNIdH.Len(), 0);
for (int i = 0; i < BurnedNIdH.Len(); i++) {
BurnedNIdV.Add(BurnedNIdH.GetKey(i));
}
FwdBurnProb = OldFwdBurnProb;
BckBurnProb = OldBckBurnProb;
}