necom Documentation

Cluster entries using K-Medoids (PAM / Lloyd-like).

Input:

• A pairwise distance TSV file (name1\tname2\tdistance). Lower distances 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 distances, not similarities.
• --k <N>: number of clusters (required). Must not exceed the number of samples.
• --runs <N>: number of random initializations (default: 10).
• --max-iter <N>: maximum number of iterations (default: 100).
• --seed <N>: random seed for reproducible initialization.
• --same <V>: default score of identical element pairs (default: 0.0).
• --missing <V>: default score of missing pairs (default: 1.0).
• Alias: necom clust km is equivalent to necom clust k-medoids.
• The representative point is selected by --rep:
  • medoid (default): point with minimum sum of distances to other cluster members.
  • first: alphabetically first member.
• In cluster format, the representative is placed first; in pair format, it is the first column.
• If a cluster becomes empty during iteration, it is omitted from the output, so the final number of clusters may be less than k.

Examples:

1. Run K-Medoids with K=3 necom clust k-medoids pairs.tsv --k 3

2. Output as pairs necom clust k-medoids pairs.tsv --k 3 --format pair

3. Reproducible run with seed necom clust k-medoids pairs.tsv --k 3 --seed 42