necom Documentation

Cluster entries using Markov Clustering (MCL).

Input:

• A pairwise similarity TSV file (name1\tname2\tsimilarity). Higher scores indicate higher similarity.

Output:

• --format cluster (default): each line contains points of one cluster.
• --format pair: each line contains a (representative, member) pair.

Notes:

• The input must contain similarities, not distances.
• --inflation <V> / -I: inflation parameter (default: 2.0).
• --prune <V>: pruning threshold; matrix entries smaller than or equal to this are set to zero (default: 1e-5).
• --max-iter <N>: maximum number of iterations (default: 100). Must be greater than 0.
• --same <V>: default score of identical element pairs (default: 1.0).
• --missing <V>: default score of missing pairs (default: 0.0).
• The representative point is selected by --rep:
  • medoid (default): point with maximum sum of similarities to other cluster members.
  • first: alphabetically first member.
• In cluster format, the representative is placed first; in pair format, it is the first column.
• During initialization, input similarities smaller than or equal to 1e-5 (including negative values) are treated as zero and ignored. This initial filtering threshold is independent of the --prune threshold used during iterations.
• Reference: Stijn van Dongen, Graph Clustering by Flow Simulation. PhD thesis, University of Utrecht, May 2000.

Examples:

1. Run MCL with defaults necom clust mcl similarities.tsv

2. Adjust inflation necom clust mcl similarities.tsv --inflation 3.0

3. Output as pairs necom clust mcl similarities.tsv --format pair