simrank-cmp 1.0.3

Exact SimRank similarities for small graphs

SimRank-CMP

This is an implementation of SimRank for comparing small, undirected graphs. Notably, it can be used for augmenting pairwise similarities calculated using just the node labels alone, with structural similarity information from the edges.

The algorithm used is exact and non-iterative, and is based on a matrix formulation of SimRank. The main complexity comes from calculating the full eigendecomposition of the adjacency matrices and then doing matrix multiplication. As such, it is not meant to be used on graphs much larger than a few thousand nodes. A derivation can be found here.

For larger graphs and where 1) you don't need exact results, or 2) you don't need pairwise similarities, only similarities for specific node-pairs, there are alternative algorithms.

Installation and Usage

Install with pip install simrank_cmp.

Usage is straightforward:

from simrank_cmp import compute_similarities

updated_similarities = compute_similarities(f_adj, g_adj, initial_similarities, decay=0.8)

initial_similarities should be the pairwise node similarities calculated using some other metric (such as Jaccard). It is important for there to be some signal here in this matrix; SimRank will propagate this information across the graphs.

Examples

In examples/similarity_propagation.py, we visualize the propagation of similarity information across the graph from a single node (the center one in this picture). Darker means more similar.

In examples/match_robustness.py, we are trying to match nodes from two identical graphs. Only 10% of the nodes are labeled, resulting in a ~10% baseline if you were to match nodes at random. The rest of the other nodes are indistinguishable.

By propagating the similarity information from the 10% across the two graphs, we are able to achieve a perfect 100% match of all nodes. We then slowly remove edges from one of the graphs and see that, as expected, accuracy drops until we hit the baseline.

In examples/symmetry.py, we use the algorithm to detect symmetries in the graph. Nodes that have the same color can be swapped without affecting the structure of the graph. This can be useful, for example, during constrained optimization, where symmetry points to redundant solutions that can be pruned.