The performance of modularity maximization in practical contexts

Although widely used in practice, the behavior and accuracy of the popular module identification technique called modularity maximization is not well understood in practical contexts. Here, we present a broad characterization of its performance in such situations. First, we revisit and clarify the resolution limit phenomenon for modularity maximization. Second, we show that the modularity function Q exhibits extreme degeneracies: it typically admits an exponential number of distinct high-scoring solutions and typically lacks a clear global maximum. Third, we derive the limiting behavior of the maximum modularity Q_max for one model of infinitely modular networks, showing that it depends strongly both on the size of the network and on the number of modules it contains. Finally, using three real-world metabolic networks as examples, we show that the degenerate solutions can fundamentally disagree on many, but not all, partition properties such as the composition of the largest modules and the distribution of module sizes. These results imply that the output of any modularity maximization procedure should be interpreted cautiously in scientific contexts. They also explain why many heuristics are often successful at finding high-scoring partitions in practice and why different heuristics can disagree on the modular structure of the same network. We conclude by discussing avenues for mitigating some of these behaviors, such as combining information from many degenerate solutions or using generative models.Comment: 20 pages, 14 figures, 6 appendices; code available at http://www.santafe.edu/~aaronc/modularity

On Spectral Graph Embedding: A Non-Backtracking Perspective and Graph Approximation

Graph embedding has been proven to be efficient and effective in facilitating graph analysis. In this paper, we present a novel spectral framework called NOn-Backtracking Embedding (NOBE), which offers a new perspective that organizes graph data at a deep level by tracking the flow traversing on the edges with backtracking prohibited. Further, by analyzing the non-backtracking process, a technique called graph approximation is devised, which provides a channel to transform the spectral decomposition on an edge-to-edge matrix to that on a node-to-node matrix. Theoretical guarantees are provided by bounding the difference between the corresponding eigenvalues of the original graph and its graph approximation. Extensive experiments conducted on various real-world networks demonstrate the efficacy of our methods on both macroscopic and microscopic levels, including clustering and structural hole spanner detection.Comment: SDM 2018 (Full version including all proofs

Tool support for reasoning in display calculi

We present a tool for reasoning in and about propositional sequent calculi. One aim is to support reasoning in calculi that contain a hundred rules or more, so that even relatively small pen and paper derivations become tedious and error prone. As an example, we implement the display calculus D.EAK of dynamic epistemic logic. Second, we provide embeddings of the calculus in the theorem prover Isabelle for formalising proofs about D.EAK. As a case study we show that the solution of the muddy children puzzle is derivable for any number of muddy children. Third, there is a set of meta-tools, that allows us to adapt the tool for a wide variety of user defined calculi