Matt Stabeler

the HGCE algorithm has a number of parameters to it, summarised below:

 Usage: gce_serial.py [options]

Options:
  -h, --help            show this help message and exit
  -f FILE, --file=FILE  Input filename for edgelist.  If not provided, then
                        input will be piped in from STDIN
  -o OUTFILE, --outfile=OUTFILE
                        Filename for output.  If not provided, then found
                        communities will be piped to STDOUT
  -k MINCLIQUESIZE, --minCliqueSize=MINCLIQUESIZE
                        Minimum size that a clique must have to be considered
                        as a seed.  Must be an integer with value 3 or larger.
                        Default: 4.
  -a ALPHA, --alpha=ALPHA
                        Scaling parameter for GCE (smaller alpha leads to
                        larger comms). Default: 1.0
  -e EPSILON, --epsilon=EPSILON
                        Minimum distance that seeds and communities must be
                        from all larger or previously accepted seeds or
                        communities. Default: 0.25
  -p PHI, --phi=PHI     Minimum proportion of a seed that must not be
                        containted in a previously accepted seed (a.k.a.
                        Clique Coverage Heuristic parameter). Default: 0.25
  -i, --intNodeIDs      If this flag is included, then node IDs must already
                        be integers (this may save memory---ignore except for
                        huge graphs)
  -t THREADS, --threads=THREADS
                        Number of threads to run concurrently for clique
                        finding and sorting. Default: 1
  -m MINCLIQUEEDGEWEIGHT, --minCliqueEdgeWeight=MINCLIQUEEDGEWEIGHT
                        Minimum weight that an edge must have for it to be
                        eligible for membership in a clique. default = 0.0,
  -s MAX_TIMES_SPOKEN_FOR, --maxTimesSpokenFor=MAX_TIMES_SPOKEN_FOR
                        Number of times a node/edge must be already included
                        in accepted seeds for it to be considered spoken for. default = 1,
  -r NUM_REALIZATIONS, --numRealizations=NUM_REALIZATIONS
                        Number of perturbed graphs to create. default = 100,
  --minAppearanceProp=MIN_APPEARANCE_PROP
                        Proportion of perturbed graphs in which a similar set
                        must appear for that set to be considered significant. default = 0.9,
  --similarityThreshold=SIMILARITY_THRESHOLD
                        Given two sets, the proportion of items that must be
                        common to both sets for those sets to be considered
                        similar. default = 0.8,
  -z PERTURB_ALPHA, --perturbAlpha=PERTURB_ALPHA
                        Proportion of edges randomized in perturbed graphs. default = 0.1,