The research I do revolves around how to break down protein interaction networks (PINs) into functional modules, or communities, using community detection methods. These communities are groups of proteins which interact more with one another than with the rest of the network. We decompose the PINs in this manner, as it is very difficult to determine how a protein functions through its interactions by simply looking at the entire network. The sheer amount of data in one of these networks, clouds the information we would actually like to see, as explained in my previous blog post.
In a journal club in August, I presented the overlapping community detection method Link Clustering by Ahn et al. which is the first community detection method I am aware of that assigns nodes to communities by clustering the edges between the nodes. I contrasted Link Clustering with the Affiliation Graph Model method proposed by Yang and Leskovec, as the authors use the same comparison technique to validate their methods. In a world where studies usually only work on a single network using a specific method, having two independent papers that use the same validation method is something that gets me much more excited than it probably should.
Instead of assigning nodes to communities, Link Clustering focusses on the edges in a network. Clustering edges is essentially an equivalent problem to clustering nodes. This becomes obvious if you take a graph, decide to call all the edges “blobs” and say two of your new “blobs” have an edge between them if they share a node in the original network. This is called creating the “line graph” of the network and performing “blob” clustering on this is the same as performing edge clustering on the initial network.
To come back from my tangent, if an edge is assigned to community A, this means the nodes on either side of this edge are assigned community A by association. By assigning each edge to an individual community, Link Clustering creates overlapping node communities as shown in Figure 1 below.In Link Clustering, edges are placed into the same community, based on similarity scores computed between all connected edges. Edge clusters are computed from these similarity scores using single-linkage clustering, where the edges with the highest similarity scores are iteratively merged into the same community. Using this method all edges end up in the same community in the end, so a threshold for the similarity score needs to be found at which the network is partitioned into communities in the best way. This threshold value represents a type of resolution parameter of the for community detection. At a low threshold there are few, large communities as many edges have been clustered together, while at a high threshold only highly similar edges are in the same community and there are many, small communities. Ahn et al. propose maximizing a function called the partition density to find the optimal resolution threshold. This function is simply a weighted average of the density of the communities. For those incredibly keen, it is given by the equation:
Here, represents the total number of edges in the network and and represent the number of edges and nodes in the community respectively.
All of this partitioning is based on a similarity score between two edges. The crux of this method, the scoring measure, is explained in Figure 2.
Affiliation Graph Model
The method which I would like to compare Link Clustering to is the Affiliation Graph Model (AGM). Briefly, this is a statistical community detection algorithm which generates overlapping communities. Node affiliations are recorded in the Community Affiliation Matrix shown in Figure 2.The AGM has a probability of interaction for each community, denoted for community . For nodes and , which may share several community affiliations, the probability of interaction, is given by the equation:
where denotes a community in the set of communities shared by nodes and , . This model is be fitted to the network using a Metropolis-Hastings algorithm with a Markov chain constructed by pre-defined defined steps in the space of possible Community Affiliation Matrices (c.f. Yang and Leskovec 2012).
Result Comparison Method
Link Clustering itself has some very interesting results, especially relating to looking at real-world networks at different resolutions (which can be found in the paper). However, I want to focus on the validation method used in the paper which compares results generated from Link Clustering with that of other methods. This comparison method evaluates four different aspects of the partitions generated by different methods. These four aspects are: Community Quality, Overlap Quality, Community Coverage, and Overlap Coverage. The “Quality” aspects relate to network metadata indicating how good the obtained communities are, and the “Coverage” aspects relate to the amount of information extracted from a network.
The metadata referred to above is a general term for additional data available about the nodes in a network. In the case of PINs this metadata is related to the function of proteins in the network (their Gene Ontology annotations). Loosely, proteins with similar functions should be placed in the same community to improve the Community Quality measure. Overlap Quality concerns the boundaries between generated communities. If the functions assigned to proteins show similar boundaries between groups of functions, the Overlap Quality is high.
The “Coverage” values are more basic calculations. A partition has a high Community Coverage if the fraction of nodes assigned to communities with three or more nodes is high (non-trivial communities). A community of size two is uninformative, as it is the result of a single edge being in a community by itself. Overlap Coverage is simply the number of non-trivial community memberships per node. The two “Coverage” values are thus equal for non-overlapping community detection methods.
When comparing community detection methods, these four measures are computed for a partition generated by each method, and then rescaled so that the maximum score achieved by any method is 1 for each measure independently. These values are then added to give a score between 0 and 4 for each community detection method.
The results shown in Figure 4 were generated by Yang and Leskovec to show their AGM outperforms Link Clustering (and other methods) on a variety of networks. While it is noteable that they used the same metric and networks used by Ahn et al. when proposing Link Clustering, this Figure must be taken with a pinch of salt. Yang and Leskovec acknowledge that the metric proposed by Ahn et al. rewards methods which find more communities in a network and thus do not fit the number of communities judged to be best by the AGM, but instead fit the same number as fitted in Link Clustering. Furthermore, it is peculiar that half of the networks used for comparison by Ahn et al. have disappeared in this comparison.To conclude we can say that while it is very interesting that two papers use the same method to compare their methods to others for validation purposes, it wasn’t done completely accurately here. The comparison metric is however an interesting development to create a gold standard for method comparison. For my purposes, Community Quality is the most important, so maybe a weighted version of this may be more interesting.