Question: Clustering in directed gene networks
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3 months ago by
The Last Word190
The Last Word190 wrote:


I have a directed transcriptional regulatory network. I would like to partition it, but most of the clustering algorithm do clustering assuming that the network is undirected. Would it be an issue partitioning a directed, bipartite network as undirected? Kindly advice.

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ADD COMMENTlink modified 3 months ago by Jean-Karim Heriche21k • written 3 months ago by The Last Word190
gravatar for Jean-Karim Heriche
3 months ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche21k wrote:

Clustering for an undirected graph often assumes a symmetric adjacency matrix. You can always convert your directed graph to an undirected one if you accept the corresponding loss of information. This is a common approach and works well enough in many cases. Otherwise, there are specific algorithms for directed graphs. For example, spectral clustering can be applied to directed graphs by adapting the graph Laplacian (for details, see this master thesis on spectral clustering algorithms for directed graphs). Modularity-based algorithms have also been extended to directed graphs (e.g. paper on the directed Louvain algorithm).

ADD COMMENTlink modified 3 months ago • written 3 months ago by Jean-Karim Heriche21k
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