Command line

The orbitsi command has two subcommands, search and count-orbits.

Subgraph isomorphism search

orbitsi search --data DATA --pattern PATTERN
               [--orbit-counter evoke|orca] [--graphlet-size 4|5] [--order auto|core]
               [--arc-consistency] [--no-contraction] [--no-edge-thinning] [--no-tail]
               [--published] [--backend cpp|python] [--count-only]

Prints the number of embeddings of the pattern in the data graph and, without --count-only, each embedding as a {pattern vertex: data vertex} dict.

--data, --pattern: Paths of the data graph and the pattern (required).
--orbit-counter: evoke (default) or orca.
--graphlet-size: 4 (default) or 5; orca supports 4 only.
--order: auto (default): OrbitSI’s orbit-strength order. core: the pattern’s 2-core first, then the vertex with the most already-matched neighbours, ties by fewest candidates.
--arc-consistency: Also run arc consistency after NLF and after the orbit filter. Off by default, as in OrbitSI as published.
--no-contraction: Leave out the NLF rounds on the candidate subgraph before the orbit filter.
--no-edge-thinning: Count orbits on every edge of the candidate subgraph.
--no-tail: Search the last pattern vertices one by one instead of counting them together.
--published: OrbitSI’s algorithm as published: the orbit-strength order, no arc consistency, and none of contraction, edge thinning or tail counting.
--backend: Implementation of --count-only: cpp (default) or python. cpp applies only with --orbit-counter evoke; with orca the count runs in Python. Listing embeddings always runs in Python.
--count-only: Print only the number of embeddings, counted without storing them.

Contraction, edge thinning and tail counting are on by default; none of them changes the result. See How OrbitSI works.

Example:

orbitsi search --data HPRD.graph --pattern query_dense_16_1.graph --count-only

Orbit counting

orbitsi count-orbits --graph GRAPH [--orbit-counter evoke|orca] [--graphlet-size 4|5] [--induced]

Prints the matrix of vertex orbit counts, one row per vertex in sorted vertex order.

--graph: Path of the graph (required).
--orbit-counter: evoke (default) or orca.
--graphlet-size: 4 (default, 15 orbits) or 5 (73 orbits); orca supports 4 only.
--induced: Induced orbit counts instead of non-induced ones.

Example:

orbitsi count-orbits --graph HPRD.graph --graphlet-size 5 --induced