Cliquer

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!)

Usage

Basic Usage

 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.

Detailed Usage

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.