Spectral partitioning, eigenvalue bounds, and circle packings for graphs of bounded genus

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2005.Includes bibliographical references (leaves 37-39).In this paper, we address two longstanding questions about finding good separators in graphs of bounded genus and degree: 1. It is a classical result of Gilbert, Hutchinson, and Tarjan [12] that one can find asymptotically optimal separators on these graphs if he is given both the graph and an embedding of it onto a low genus surface. Does there exist a simple, efficient algorithm to find these separators given only the graph and not the embedding? 2. In practice, spectral partitioning heuristics work extremely well on these graphs. Is there a theoretical reason why this should be the case? We resolve these two questions by showing that a simple spectral algorithm finds separators of cut ratio O(sqrt(g/n)) and vertex bisectors of size O(sqrt(gn)) in these graphs, both of which are optimal. As our main technical lemma, we prove an O(g/n) bound on the second smallest eigenvalue of the Laplacian of such graphs and show that this is tight, thereby resolving a conjecture of Spielman and Teng. While this lemma is essentially combinatorial in nature, its proof comes from continuous mathematics, drawing on the theory of circle packings and the geometry of compact Riemann surfaces.by Jonathan Kelner.S.M

Many Sparse Cuts via Higher Eigenvalues

Cheeger's fundamental inequality states that any edge-weighted graph has a vertex subset $S$ such that its expansion (a.k.a. conductance) is bounded as follows: \phi(S) \defeq \frac{w(S,\bar{S})}{\min \set{w(S), w(\bar{S})}} \leq 2\sqrt{\lambda_2} where $w$ is the total edge weight of a subset or a cut and $\lambda_2$ is the second smallest eigenvalue of the normalized Laplacian of the graph. Here we prove the following natural generalization: for any integer $k \in [n]$, there exist $ck$ disjoint subsets $S_1, ..., S_{ck}$, such that $$\max_i \phi(S_i) \leq C \sqrt{\lambda_{k} \log k}$$ where $\lambda_i$ is the $i^{th}$ smallest eigenvalue of the normalized Laplacian and $c0$ are suitable absolute constants. Our proof is via a polynomial-time algorithm to find such subsets, consisting of a spectral projection and a randomized rounding. As a consequence, we get the same upper bound for the small set expansion problem, namely for any $k$, there is a subset $S$ whose weight is at most a \bigO(1/k) fraction of the total weight and $\phi(S) \le C \sqrt{\lambda_k \log k}$. Both results are the best possible up to constant factors. The underlying algorithmic problem, namely finding $k$ subsets such that the maximum expansion is minimized, besides extending sparse cuts to more than one subset, appears to be a natural clustering problem in its own right

New geometric techniques for linear programming and graph partitioning

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2006.Includes bibliographical references (leaves 79-82).In this thesis, we advance a collection of new geometric techniques for the analysis of combinatorial algorithms. Using these techniques, we resolve several longstanding questions in the theory of linear programming, polytope theory, spectral graph theory, and graph partitioning. The thesis consists of two main parts. In the first part, which is joint work with Daniel Spielman, we present the first randomized polynomial-time simplex algorithm for linear programming, answering a question that has been open for over fifty years. Like the other known polynomial-time algorithms for linear programming, its running time depends polynomially on the number of bits used to represent its input. To do this, we begin by reducing the input linear program to a special form in which we merely need to certify boundedness of the linear program. As boundedness does not depend upon the right-hand-side vector, we run a modified version of the shadow-vertex simplex method in which we start with a random right-hand-side vector and then modify this vector during the course of the algorithm. This allows us to avoid bounding the diameter of the original polytope.(cont.) Our analysis rests on a geometric statement of independent interest: given a polytope ... in isotropic position, if one makes a polynomially small perturbation to b then the number of edges of the projection of the perturbed polytope onto a random 2-dimensional subspace is expected to be polynomial. In the second part of the thesis, we address two long-open questions about finding good separators in graphs of bounded genus and degree: 1. It is a classical result of Gilbert, Hutchinson, and Tarjan [25] that one can find asymptotically optimal separators on these graphs if he is given both the graph and an embedding of it onto a low genus surface. Does there exist a simple, efficient algorithm to find these separators given only the graph and not the embedding? 2. In practice, spectral partitioning heuristics work extremely well on these graphs. Is there a theoretical reason why this should be the case? We resolve these two questions by showing that a simple spectral algorithm finds separators of cut ratio O( g/n) and vertex bisectors of size O(Vng) in these graphs, both of which are optimal. As our main technical lemma, we prove an O(g/n) bound on the second smallest eigenvalue of the Laplacian of such graphs and show that this is tight, thereby resolving a conjecture of Spielman and Teng.(cont.) While this lemma is essentially combinatorial in nature, its proof comes from continuous mathematics, drawing on the theory of circle packings and the geometry of compact Riemann surfaces. While the questions addressed in the two parts of the thesis are quite different, we show that a common methodology runs through their solutions. We believe that this methodology provides a powerful approach to the analysis of algorithms that will prove useful in a variety of broader contexts.by Jonathan A. Kelner.Ph.D

A transfer principle and applications to eigenvalue estimates for graphs

In this paper, we prove a variant of the Burger-Brooks transfer principle which, combined with recent eigenvalue bounds for surfaces, allows to obtain upper bounds on the eigenvalues of graphs as a function of their genus. More precisely, we show the existence of a universal constants $C$ such that the $k$-th eigenvalue $\lambda_k^{nr}$ of the normalized Laplacian of a graph $G$ of (geometric) genus $g$ on $n$ vertices satisfies $$\lambda_k^{nr}(G) \leq C \frac{d_{\max}(g+k)}{n},$$ where $d_{\max}$ denotes the maximum valence of vertices of the graph. This result is tight up to a change in the value of the constant $C$, and improves recent results of Kelner, Lee, Price and Teng on bounded genus graphs. To show that the transfer theorem might be of independent interest, we relate eigenvalues of the Laplacian on a metric graph to the eigenvalues of its simple graph models, and discuss an application to the mesh partitioning problem, extending pioneering results of Miller-Teng-Thurston-Vavasis and Spielman-Tang to arbitrary meshes.Comment: Major revision, 16 page

Finding local communities in protein networks

<p>Abstract</p> <p>Background</p> <p>Protein-protein interactions (PPIs) play fundamental roles in nearly all biological processes, and provide major insights into the inner workings of cells. A vast amount of PPI data for various organisms is available from BioGRID and other sources. The identification of communities in PPI networks is of great interest because they often reveal previously unknown functional ties between proteins. A large number of global clustering algorithms have been applied to protein networks, where the entire network is partitioned into clusters. Here we take a different approach by looking for local communities in PPI networks.</p> <p>Results</p> <p>We develop a tool, named Local Protein Community Finder, which quickly finds a community close to a queried protein in any network available from BioGRID or specified by the user. Our tool uses two new local clustering algorithms Nibble and PageRank-Nibble, which look for a good cluster among the most popular destinations of a short random walk from the queried vertex. The quality of a cluster is determined by proportion of outgoing edges, known as conductance, which is a relative measure particularly useful in undersampled networks. We show that the two local clustering algorithms find communities that not only form excellent clusters, but are also likely to be biologically relevant functional components. We compare the performance of Nibble and PageRank-Nibble to other popular and effective graph partitioning algorithms, and show that they find better clusters in the graph. Moreover, Nibble and PageRank-Nibble find communities that are more functionally coherent.</p> <p>Conclusion</p> <p>The Local Protein Community Finder, accessible at <url>http://xialab.bu.edu/resources/lpcf</url>, allows the user to quickly find a high-quality community close to a queried protein in any network available from BioGRID or specified by the user. We show that the communities found by our tool form good clusters and are functionally coherent, making our application useful for biologists who wish to investigate functional modules that a particular protein is a part of.</p

Improved Cheeger's Inequality: Analysis of Spectral Partitioning Algorithms through Higher Order Spectral Gap

Let \phi(G) be the minimum conductance of an undirected graph G, and let 0=\lambda_1 <= \lambda_2 <=... <= \lambda_n <= 2 be the eigenvalues of the normalized Laplacian matrix of G. We prove that for any graph G and any k >= 2, \phi(G) = O(k) \lambda_2 / \sqrt{\lambda_k}, and this performance guarantee is achieved by the spectral partitioning algorithm. This improves Cheeger's inequality, and the bound is optimal up to a constant factor for any k. Our result shows that the spectral partitioning algorithm is a constant factor approximation algorithm for finding a sparse cut if \lambda_k$ is a constant for some constant k. This provides some theoretical justification to its empirical performance in image segmentation and clustering problems. We extend the analysis to other graph partitioning problems, including multi-way partition, balanced separator, and maximum cut