void PrintNewBestSub(Substructure *sub, SubList *subList,
Parameters *parameters)
{
ULONG outputLevel = parameters->outputLevel;
if ((subList->head == NULL) ||
(sub->value > subList->head->sub->value))
{
parameters->outputLevel = 1; // turn off instance printing
printf("\nNew best ");
PrintSub(sub, parameters);
printf("\n");
parameters->outputLevel = outputLevel;
}
}
void SuffixTree<Symb,NSymb>::Print(std::ostream& str, uint flags, PNode n, PNode prev, int ind)
{
if(n == NIL) { n = ROOT; prev = NIL; }
Node& node = GetNode(n);
//if(IsInternal(n)) {
int len = (n==ROOT) ? 0 : node.len;
PrintInd(str, ind);
if(flags & 1) {
PrintSub(str, node.pos, node.pos + len);
str << ' ';
}
if(flags & 2)
str << len << ' ';
//if(flags & 4)
// str << node.dep << ' ';
if(flags & 8)
str << node.count << ' ';
str << " [" << n << "]->[" << node.suf << "]" << std::endl;
ind += len;
for(int i = 1; i <= NSymb; i++) {
PNode ch = GetChild(n, i % NSymb);
if(ch != NIL)
Print(str, flags, ch, n, ind);
}
//}
//else {
// int pos = GetLeafPos(prev, n);
//
// PrintInd(str, ind);
// if(flags & 1) {
// PrintSub(str, pos);
// str << ' ';
// }
// if(flags & 2)
// str << (dlen - pos) << ' ';
// if(flags & 4)
// str << dlen - node.dep << ' ';
// if(flags & 8)
// str << node.count << ' ';
// str << " (" << node.dep << ")" << endl;
//}
}
void PrintSubList(SubList *subList, Parameters *parameters)
{
ULONG counter = 1;
SubListNode *subListNode = NULL;
if (subList != NULL)
{
subListNode = subList->head;
while (subListNode != NULL)
{
printf("(%lu) ", counter);
counter++;
PrintSub(subListNode->sub, parameters);
printf("\n");
subListNode = subListNode->next;
}
}
}
SubList *DiscoverSubs(Parameters *parameters)
{
SubList *parentSubList;
SubList *childSubList;
SubList *extendedSubList;
SubList *discoveredSubList;
SubListNode *parentSubListNode;
SubListNode *extendedSubListNode;
Substructure *parentSub;
Substructure *extendedSub;
Substructure *recursiveSub = NULL;
// parameters used
ULONG limit = parameters->limit;
ULONG numBestSubs = parameters->numBestSubs;
ULONG beamWidth = parameters->beamWidth;
BOOLEAN valueBased = parameters->valueBased;
LabelList *labelList = parameters->labelList;
BOOLEAN prune = parameters->prune;
ULONG maxVertices = parameters->maxVertices;
ULONG minVertices = parameters->minVertices;
ULONG outputLevel = parameters->outputLevel;
BOOLEAN recursion = parameters->recursion;
ULONG evalMethod = parameters->evalMethod;
// get initial one-vertex substructures
parentSubList = GetInitialSubs(parameters);
discoveredSubList = AllocateSubList();
while ((limit > 0) && (parentSubList->head != NULL))
{
parentSubListNode = parentSubList->head;
childSubList = AllocateSubList();
// extend each substructure in parent list
while (parentSubListNode != NULL)
{
parentSub = parentSubListNode->sub;
parentSubListNode->sub = NULL;
if (outputLevel > 4)
{
parameters->outputLevel = 1; // turn off instance printing
printf("\nConsidering ");
PrintSub(parentSub, parameters);
printf("\n");
parameters->outputLevel = outputLevel;
}
if ((((parentSub->numInstances > 1) && (evalMethod != EVAL_SETCOVER)) ||
(parentSub->numNegInstances > 0)) &&
(limit > 0))
{
limit--;
if (outputLevel > 3)
printf("%lu substructures left to be considered\n", limit);
fflush(stdout);
extendedSubList = ExtendSub(parentSub, parameters);
extendedSubListNode = extendedSubList->head;
while (extendedSubListNode != NULL)
{
extendedSub = extendedSubListNode->sub;
extendedSubListNode->sub = NULL;
if (extendedSub->definition->numVertices <= maxVertices)
{
// evaluate each extension and add to child list
EvaluateSub(extendedSub, parameters);
if (prune && (extendedSub->value < parentSub->value))
{
FreeSub(extendedSub);
}
else
{
SubListInsert(extendedSub, childSubList, beamWidth,
valueBased, labelList);
}
}
else
{
FreeSub(extendedSub);
}
extendedSubListNode = extendedSubListNode->next;
}
FreeSubList(extendedSubList);
}
// add parent substructure to final discovered list
if (parentSub->definition->numVertices >= minVertices)
{
if (! SinglePreviousSub(parentSub, parameters))
{
// consider recursive substructure, if requested
if (recursion)
recursiveSub = RecursifySub(parentSub, parameters);
if (outputLevel > 3)
PrintNewBestSub(parentSub, discoveredSubList, parameters);
SubListInsert(parentSub, discoveredSubList, numBestSubs, FALSE,
labelList);
if (recursion && (recursiveSub != NULL))
{
if (outputLevel > 4)
{
parameters->outputLevel = 1; // turn off instance printing
printf("\nConsidering Recursive ");
PrintSub(recursiveSub, parameters);
printf ("\n");
parameters->outputLevel = outputLevel;
}
if (outputLevel > 3)
PrintNewBestSub(recursiveSub, discoveredSubList, parameters);
SubListInsert(recursiveSub, discoveredSubList, numBestSubs,
FALSE, labelList);
}
}
}
else
{
FreeSub (parentSub);
}
parentSubListNode = parentSubListNode->next;
}
FreeSubList(parentSubList);
parentSubList = childSubList;
}
if ((limit > 0) && (outputLevel > 2))
printf ("\nSubstructure queue empty.\n");
// try to insert any remaining subs in parent list on to discovered list
parentSubListNode = parentSubList->head;
while (parentSubListNode != NULL)
{
parentSub = parentSubListNode->sub;
parentSubListNode->sub = NULL;
if (parentSub->definition->numVertices >= minVertices)
{
if (! SinglePreviousSub(parentSub, parameters))
{
if (outputLevel > 3)
PrintNewBestSub(parentSub, discoveredSubList, parameters);
SubListInsert(parentSub, discoveredSubList, numBestSubs, FALSE,
labelList);
}
}
else
{
FreeSub(parentSub);
}
parentSubListNode = parentSubListNode->next;
}
FreeSubList(parentSubList);
return discoveredSubList;
}
int main(int argc, char **argv)
{
struct tms tmsstart, tmsend;
clock_t startTime, endTime;
static long clktck = 0;
time_t iterationStartTime;
time_t iterationEndTime;
SubList *subList;
Substructure *normSub = NULL;
Parameters *parameters;
FILE *outputFile;
ULONG iteration;
BOOLEAN done;
clktck = sysconf(_SC_CLK_TCK);
startTime = times(&tmsstart);
printf("GBAD %s\n\n", GBAD_VERSION);
parameters = GetParameters(argc, argv);
// compress positive graphs with predefined subs, if given
if (parameters->numPreSubs > 0)
CompressWithPredefinedSubs(parameters);
PrintParameters(parameters);
if (parameters->iterations > 1)
printf("----- Iteration 1 -----\n\n");
iteration = 1;
parameters->currentIteration = iteration;
done = FALSE;
while ((iteration <= parameters->iterations) && (!done))
{
iterationStartTime = time(NULL);
if (iteration > 1)
printf("----- Iteration %lu -----\n\n", iteration);
printf("%lu positive graphs: %lu vertices, %lu edges",
parameters->numPosEgs, parameters->posGraph->numVertices,
parameters->posGraph->numEdges);
if (parameters->evalMethod == EVAL_MDL)
printf(", %.0f bits\n", parameters->posGraphDL);
else
printf("\n");
printf("%lu unique labels\n", parameters->labelList->numLabels);
printf("\n");
if ((parameters->prob) && (iteration > 1))
{
//
// If GBAD-P option chosen, after the first iteration, we no longer
// care about minsize of maxsize after the first iteration (if the
// user specified these parameters), as we are just dealing with
// single extensions from the normative - so set it to where we
// just look at substructures that are composed of the normative
// pattern (SUB_) and the single vertex extension.
//
parameters->minVertices = 1;
parameters->maxVertices = 2;
}
//
// If the user has specified a normative pattern, on the first iteration
// need to save the top-N substructures, where N is what the user
// specified with the -norm parameter.
//
ULONG saveNumBestSubs = parameters->numBestSubs;
if ((iteration == 1) && (!parameters->noAnomalyDetection) &&
(parameters->norm > parameters->numBestSubs))
parameters->numBestSubs = parameters->norm;
//
// -prune is useful to get to the initial normative pattern, but
// possibly detremental to discovering anomalies... so, turn off
// pruning (in case it was turned on), so that it is not used in
// future iterations.
//
if ((parameters->prob) && (iteration > 1))
{
parameters->prune = FALSE;
}
subList = DiscoverSubs(parameters, iteration);
//
// Now that we have the best substructure(s), return the user
// specified number of best substructures to its original value.
//
if (iteration == 1)
parameters->numBestSubs = saveNumBestSubs;
if (subList->head == NULL)
{
done = TRUE;
printf("No substructures found.\n\n");
}
else
{
//
// GBAD-MDL
//
if (parameters->mdl)
GBAD_MDL(subList,parameters);
//
// GBAD-MPS
//
if (parameters->mps)
{
GBAD_MPS(subList,parameters);
}
//
// GBAD-P
//
if (parameters->prob)
{
normSub = GBAD_P(subList,iteration,parameters);
}
// write output to stdout
if (parameters->outputLevel > 1)
{
printf("\nBest %lu substructures:\n\n", CountSubs (subList));
PrintSubList(subList, parameters);
}
else
{
printf("\nBest substructure: ");
if ((CountSubs(subList) > 0) && (subList->head->sub != NULL))
PrintSub(subList->head->sub, parameters);
else
printf("None.");
printf("\n\n");
}
// write machine-readable output to file, if given
if (parameters->outputToFile)
{
outputFile = fopen(parameters->outFileName, "a");
if (outputFile == NULL)
{
printf("WARNING: unable to write to output file %s,",
parameters->outFileName);
printf("disabling\n");
parameters->outputToFile = FALSE;
}
WriteGraphToFile(outputFile, subList->head->sub->definition,
parameters->labelList, 0, 0,
subList->head->sub->definition->numVertices,
TRUE);
fclose(outputFile);
}
if (iteration < parameters->iterations)
{ // Another iteration?
if (parameters->evalMethod == EVAL_SETCOVER)
{
printf("Removing positive examples covered by");
printf(" best substructure.\n\n");
RemovePosEgsCovered(subList->head->sub, parameters);
}
else
{
//
// For the GBAD-P algorithm, multiple iterations will need
// to be performed, and if it is the first iteration
// AND the user has specified a different normative
// pattern (other than the best one), we need to
// use the substructure that was set above.
//
if ((iteration == 1) && (parameters->prob))
{
printf("Compressing graph by best substructure (%lu):\n",
parameters->norm);
PrintSub(normSub,parameters);
printf("\n");
CompressFinalGraphs(normSub, parameters,
iteration, FALSE);
} else
CompressFinalGraphs(subList->head->sub, parameters,
iteration, FALSE);
}
// check for stopping condition
// if set-covering, then no more positive examples
// if MDL or size, then positive graph contains no edges
if (parameters->evalMethod == EVAL_SETCOVER)
{
if (parameters->numPosEgs == 0)
{
done = TRUE;
printf("Ending iterations - ");
printf("all positive examples covered.\n\n");
}
}
else
{
if (parameters->posGraph->numEdges == 0)
{
done = TRUE;
printf("Ending iterations - graph fully compressed.\n\n");
}
}
}
if ((iteration == parameters->iterations) && (parameters->compress))
{
if (parameters->evalMethod == EVAL_SETCOVER)
WriteUpdatedGraphToFile(subList->head->sub, parameters);
else
WriteCompressedGraphToFile(subList->head->sub, parameters,
iteration);
}
}
//
// Need to store information regarding initial best substructure, for use
// in future GBAD-P calculations
//
if ((parameters->prob) && (iteration == 1) && (subList->head != NULL))
{
parameters->numPreviousInstances = subList->head->sub->numInstances;
}
if ((parameters->prob) && (iteration > 1) && (subList->head != NULL))
parameters->numPreviousInstances = subList->head->sub->numInstances;
FreeSubList(subList);
if (parameters->iterations > 1)
{
iterationEndTime = time(NULL);
printf("Elapsed time for iteration %lu = %lu seconds.\n\n",
iteration, (iterationEndTime - iterationStartTime));
}
iteration++;
parameters->currentIteration = iteration;
}
FreeParameters(parameters);
endTime = times(&tmsend);
printf("\nGBAD done (elapsed CPU time = %7.2f seconds).\n",
(endTime - startTime) / (double) clktck);
return 0;
}
