Example Commands
CM++
python3 -m hm01.cm
-i network.tsv
-e clustering.tsv
-o output.tsv
-c leiden
-g 0.5
-t 1log10
--nprocs 4
--quiet
- Runs CM++ on a Leiden with resolution 0.5 clustering with connectivity threshold
log10(n)(Every cluster with connectivity over the log of the number of nodesnis considered "well-connected")
python3 -m hm01.cm
-i network.tsv
-e clustering.tsv
-o output.tsv
-c ikc
-k 10
-t 1log10
--nprocs 4
--quiet
- Similar idea but with IKC having hyperparameter
k=10.
CM Pipeline
- Suppose we have a network and a clustering
- We can then construct the following
pipeline.json:
{
"title": "example",
"name": "example",
"input_file": "network.tsv",
"output_dir": "samples/",
"algorithm": "leiden",
"params": [{
"res": 0.5,
"i": 2,
"existing_clustering": "clustering.tsv"
}],
"stages": [
{
"name": "connectivity_modifier",
"memprof": false,
"threshold": "1log10",
"nprocs": 1,
"quiet": true
}
]
}
- Then from the root of this repository run:
python -m main pipeline.json