Sleipnir
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Cliquer mines an interaction network for dense subgraphs, i.e. clusters. These can be (by default) heavily weighted subgraphs (clusters) based on a greedy algorithm due to Charikar 2000 or full cliques above some cutoff (computationally expensive!)
Cliquer -i <network.dab> -r <initial_specificity> -w <final_specificity_ratio>
Output (to standard output) all heavy subgraphs (clusters) in network.dab
with initial specificity ratio at least initial_specificity
and final specificity ratio at least final_specificity_ratio
fraction of the initial value.
Cliquer -i <network.dab> -r 0 -s <subgraphs> -S <size>
Output at most subgraphs
cliques of non-missing, non-zero edges in network.dab
of size size
.
package "Cliquer"
version "1.0"
purpose "Find heavy subgraphs in a DAT graph"
section "Main"
option "input" i "Input DAT/DAB file"
string typestr="filename"
option "heavy" w "Final/initial specificity ratio for heavy subgraphs"
double default="0.5"
option "specificity" r "Minimum subgraph specificity"
double default="25"
section "Miscellaneous"
option "subgraphs" s "Number of subgraphs to output"
int default="100"
option "size" S "Size of subgraphs to find"
int default="3"
option "motifs" f "Extract programmatically defined network motifs"
double default="0"
section "Preprocessing"
option "knowns" k "Known interactions (DAT/DAB) to ignore"
string typestr="filename"
option "normalize" n "Normalize input file"
flag off
option "cutoff" c "Exclude edges below cutoff"
double default="-1e30"
section "Optional"
option "memmap" m "Memory map input"
flag off
option "verbosity" v "Message verbosity"
int default="5"
Flag | Default | Type | Description |
---|---|---|---|
-i | stdin | DAT/DAB file | Interaction network which will be mined for dense subgraphs (clusters/cliques). |
-w | 0.5 | Double | Ratio of initial to final specificity scores for heavy subgraphs. For example, if searching for dense subgraphs with a seed specificity of 25, a ratio of 0.5 will stop building the subgraph when a specificity of 12.5 is reached. Value should not exceed -r or fall below 1 / -r . |
-r | 25 | Double | Initial specificity score for heavy subgraphs. Guarantees that the ratio of in- to out-connectivity for a cluster seed is at least the given value. A value of 0 will find full cliques of edges above -c instead of dense subgraphs. |
-s | 100 | Integer | Number of cliques (not dense subgraphs) to output. |
-S | 3 | Integer | Size of cliques (not dense subgraphs) to output. Use with caution; exponential growth is not your friend. |
-k | None | DAT/DAB file | If given, ignore all edges present in the given DAT/DAB file during clique finding. |
-n | off | Flag | If on, normalize input edges to the range [0,1] before processing. |
-c | None | Double | If given, remove all input edges below the given cutoff (after optional normalization). |
-m | off | Flag | If given, memory map the input files when possible. DAT and PCL inputs cannot be memmapped. |