The Hidden Convexity of Spectral Clustering

In recent years, spectral clustering has become a standard method for data analysis used in a broad range of applications. In this paper we propose a new class of algorithms for multiway spectral clustering based on optimization of a certain "contrast function" over the unit sphere. These algorithms, partly inspired by certain Independent Component Analysis techniques, are simple, easy to implement and efficient. Geometrically, the proposed algorithms can be interpreted as hidden basis recovery by means of function optimization. We give a complete characterization of the contrast functions admissible for provable basis recovery. We show how these conditions can be interpreted as a "hidden convexity" of our optimization problem on the sphere; interestingly, we use efficient convex maximization rather than the more common convex minimization. We also show encouraging experimental results on real and simulated data.Comment: 22 page

How to Round Subspaces: A New Spectral Clustering Algorithm

A basic problem in spectral clustering is the following. If a solution obtained from the spectral relaxation is close to an integral solution, is it possible to find this integral solution even though they might be in completely different basis? In this paper, we propose a new spectral clustering algorithm. It can recover a $k$-partition such that the subspace corresponding to the span of its indicator vectors is $O(\sqrt{opt})$ close to the original subspace in spectral norm with $opt$ being the minimum possible ($opt \le 1$ always). Moreover our algorithm does not impose any restriction on the cluster sizes. Previously, no algorithm was known which could find a $k$-partition closer than $o(k \cdot opt)$. We present two applications for our algorithm. First one finds a disjoint union of bounded degree expanders which approximate a given graph in spectral norm. The second one is for approximating the sparsest $k$-partition in a graph where each cluster have expansion at most $\phi_k$ provided $\phi_k \le O(\lambda_{k+1})$ where $\lambda_{k+1}$ is the $(k+1)^{st}$ eigenvalue of Laplacian matrix. This significantly improves upon the previous algorithms, which required $\phi_k \le O(\lambda_{k+1}/k)$.Comment: Appeared in SODA 201

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

Multiscale Feature Analysis of Salivary Gland Branching Morphogenesis

Pattern formation in developing tissues involves dynamic spatio-temporal changes in cellular organization and subsequent evolution of functional adult structures. Branching morphogenesis is a developmental mechanism by which patterns are generated in many developing organs, which is controlled by underlying molecular pathways. Understanding the relationship between molecular signaling, cellular behavior and resulting morphological change requires quantification and categorization of the cellular behavior. In this study, tissue-level and cellular changes in developing salivary gland in response to disruption of ROCK-mediated signaling by are modeled by building cell-graphs to compute mathematical features capturing structural properties at multiple scales. These features were used to generate multiscale cell-graph signatures of untreated and ROCK signaling disrupted salivary gland organ explants. From confocal images of mouse submandibular salivary gland organ explants in which epithelial and mesenchymal nuclei were marked, a multiscale feature set capturing global structural properties, local structural properties, spectral, and morphological properties of the tissues was derived. Six feature selection algorithms and multiway modeling of the data was performed to identify distinct subsets of cell graph features that can uniquely classify and differentiate between different cell populations. Multiscale cell-graph analysis was most effective in classification of the tissue state. Cellular and tissue organization, as defined by a multiscale subset of cell-graph features, are both quantitatively distinct in epithelial and mesenchymal cell types both in the presence and absence of ROCK inhibitors. Whereas tensor analysis demonstrate that epithelial tissue was affected the most by inhibition of ROCK signaling, significant multiscale changes in mesenchymal tissue organization were identified with this analysis that were not identified in previous biological studies. We here show how to define and calculate a multiscale feature set as an effective computational approach to identify and quantify changes at multiple biological scales and to distinguish between different states in developing tissues