Metrics for Graph Comparison: A Practitioner's Guide

Comparison of graph structure is a ubiquitous task in data analysis and machine learning, with diverse applications in fields such as neuroscience, cyber security, social network analysis, and bioinformatics, among others. Discovery and comparison of structures such as modular communities, rich clubs, hubs, and trees in data in these fields yields insight into the generative mechanisms and functional properties of the graph. Often, two graphs are compared via a pairwise distance measure, with a small distance indicating structural similarity and vice versa. Common choices include spectral distances (also known as $\lambda$ distances) and distances based on node affinities. However, there has of yet been no comparative study of the efficacy of these distance measures in discerning between common graph topologies and different structural scales. In this work, we compare commonly used graph metrics and distance measures, and demonstrate their ability to discern between common topological features found in both random graph models and empirical datasets. We put forward a multi-scale picture of graph structure, in which the effect of global and local structure upon the distance measures is considered. We make recommendations on the applicability of different distance measures to empirical graph data problem based on this multi-scale view. Finally, we introduce the Python library NetComp which implements the graph distances used in this work

Defining and Evaluating Network Communities based on Ground-truth

Nodes in real-world networks organize into densely linked communities where edges appear with high concentration among the members of the community. Identifying such communities of nodes has proven to be a challenging task mainly due to a plethora of definitions of a community, intractability of algorithms, issues with evaluation and the lack of a reliable gold-standard ground-truth. In this paper we study a set of 230 large real-world social, collaboration and information networks where nodes explicitly state their group memberships. For example, in social networks nodes explicitly join various interest based social groups. We use such groups to define a reliable and robust notion of ground-truth communities. We then propose a methodology which allows us to compare and quantitatively evaluate how different structural definitions of network communities correspond to ground-truth communities. We choose 13 commonly used structural definitions of network communities and examine their sensitivity, robustness and performance in identifying the ground-truth. We show that the 13 structural definitions are heavily correlated and naturally group into four classes. We find that two of these definitions, Conductance and Triad-participation-ratio, consistently give the best performance in identifying ground-truth communities. We also investigate a task of detecting communities given a single seed node. We extend the local spectral clustering algorithm into a heuristic parameter-free community detection method that easily scales to networks with more than hundred million nodes. The proposed method achieves 30% relative improvement over current local clustering methods.Comment: Proceedings of 2012 IEEE International Conference on Data Mining (ICDM), 201

A Novel Joint Brain Network Analysis Using Longitudinal Alzheimer's Disease Data.

There is well-documented evidence of brain network differences between individuals with Alzheimer's disease (AD) and healthy controls (HC). To date, imaging studies investigating brain networks in these populations have typically been cross-sectional, and the reproducibility of such findings is somewhat unclear. In a novel study, we use the longitudinal ADNI data on the whole brain to jointly compute the brain network at baseline and one-year using a state of the art approach that pools information across both time points to yield distinct visit-specific networks for the AD and HC cohorts, resulting in more accurate inferences. We perform a multiscale comparison of the AD and HC networks in terms of global network metrics as well as at the more granular level of resting state networks defined under a whole brain parcellation. Our analysis illustrates a decrease in small-worldedness in the AD group at both the time points and also identifies more local network features and hub nodes that are disrupted due to the progression of AD. We also obtain high reproducibility of the HC network across visits. On the other hand, a separate estimation of the networks at each visit using standard graphical approaches reveals fewer meaningful differences and lower reproducibility

Graph analysis of functional brain networks: practical issues in translational neuroscience

The brain can be regarded as a network: a connected system where nodes, or units, represent different specialized regions and links, or connections, represent communication pathways. From a functional perspective communication is coded by temporal dependence between the activities of different brain areas. In the last decade, the abstract representation of the brain as a graph has allowed to visualize functional brain networks and describe their non-trivial topological properties in a compact and objective way. Nowadays, the use of graph analysis in translational neuroscience has become essential to quantify brain dysfunctions in terms of aberrant reconfiguration of functional brain networks. Despite its evident impact, graph analysis of functional brain networks is not a simple toolbox that can be blindly applied to brain signals. On the one hand, it requires a know-how of all the methodological steps of the processing pipeline that manipulates the input brain signals and extract the functional network properties. On the other hand, a knowledge of the neural phenomenon under study is required to perform physiological-relevant analysis. The aim of this review is to provide practical indications to make sense of brain network analysis and contrast counterproductive attitudes