Hierarchical Modularity

Hierarchical organization of modularity in metabolic networks

E. Ravasz, A. L. Somera, D. A. Mongru, Z. N. Oltvai and A.-L. Barabási · Science 297(5586), 1551–1555 (2002)

Read source material

Study modular organization in metabolic networks through modularity scoring and greedy community detection.

What you will implement

Implement modularity scoring and deterministic greedy community detection; this exercise does not reproduce the paper's full hierarchy or results on real metabolic networks.

• 119. Community Detection and Candidate Biological Modules

  Score a graph partition with modularity, find candidate modules with a deterministic greedy algorithm, and understand that results depend on the algorithm and its resolution parameter and are not validated pathways.

  Newman modularity (with a resolution parameter) and greedy agglomerative community detection on a simple undirected graph, with explicit tie and stopping rules; Louvain, hierarchical clustering and statistical tests are not implemented.