Kyle Kloster

Heat kernel based community detection

The heat kernel is a type of graph diffusion that, like the much-used personalized PageRank diffusion, is useful in identifying a community nearby a starting seed node. We present the first deterministic, local algorithm to compute this diffusion and use that algorithm to study the communities that it produces. Our algorithm is formally a relaxation method for solving a linear system to estimate the matrix exponential in a degree-weighted norm. We prove that this algorithm stays localized in a large graph and has a worst-case constant runtime that depends only on the parameters of the diffusion, not the size of the graph. On large graphs, our experiments indicate that the communities produced by this method have better conductance than those produced by PageRank, although they take slightly longer to compute. On a real-world community identification task, the heat kernel communities perform better than those from the PageRank diffusion.

A Nearly-Sublinear Method for Approximating a Column of the Matrix Exponential for Matrices from Large, Sparse Networks

We consider random-walk transition matrices from large social and information networks. For these matrices, we describe and evaluate a fast method to estimate one column of the matrix exponential. Our method runs in sublinear time on networks where the maximum degree grows doubly logarithmic with respect to the number of nodes. For collaboration networks with over 5 million edges, we find it runs in less than a second on a standard desktop machine.

Sublinear Column-wise Actions of the Matrix Exponential on Social Networks

We consider stochastic transition matrices from large social and information networks. For these matrices, we describe and evaluate three fast methods to estimate one column of the matrix exponential. The methods are designed to exploit the properties inherent in social networks, such as a power-law degree distribution. Using only this property, we prove that one of our three algorithms has a sublinear runtime. We present further experimental evidence showing that all three of them run quickly on social networks with billions of edges, and they accurately identify the largest elements of the column.

Seeded PageRank solution paths

Seeded PageRank is an important network analysis tool for identifying and studying regions nearby a given set of nodes, which are called seeds. The seeded PageRank vector is the stationary distribution of a random walk that randomly resets at the seed nodes. Intuitively, this vector is concentrated nearby the given seeds, but is mathematically non-zero for all nodes in a connected graph. We study this concentration, or localization, and show a sublinear upper bound on the number of entries required to approximate seeded PageRank on all graphs with a natural type of skewed-degree sequence---similar to those that arise in many real-world networks. Experiments with both real-world and synthetic graphs give further evidence to the idea that the degree sequence of a graph has a major influence on the localization behavior of seeded PageRank. Moreover, we establish that this localization is non-trivial by showing that complete-bipartite graphs produce seeded PageRank vectors that cannot be approximated with a sublinear number of non-zeros.We study the behaviour of network diffusions based on the PageRank random walk from a set of seed nodes. These diffusions are known to reveal small, localized clusters (or communities), and also large macro-scale clusters by varying a parameter that has a dual-interpretation as an accuracy bound and as a regularization level. We propose a new method that quickly approximates the result of the diffusion for all values of this parameter. Our method efficiently generates an approximate solution path or regularization path associated with a PageRank diffusion, and it reveals cluster structures at multiple size-scales between small and large. We formally prove a runtime bound on this method that is independent of the size of the network, and we investigate multiple optimizations to our method that can be more practical in some settings. We demonstrate that these methods identify refined clustering structure on a number of real-world networks with up to 2 billion edges.

Strong Localization in Personalized PageRank Vectors

The personalized PageRank diffusion is a fundamental tool in network analysis tasks like community detection and link prediction. It models the spread of a quantity from a set of seed nodes, and it has been observed to stay localized near this seed set. We derive an upper-bound on the number of entries necessary to approximate a personalized PageRank vector in graphs with skewed degree sequences. This bound shows localization under mild assumptions on the maximum and minimum degrees. Experimental results on random graphs with these degree sequences show the bound is loose and support a conjectured bound.

AptRank: an adaptive PageRank model for protein function prediction on bi-relational graphs

Motivation: Diffusion‐based network models are widely used for protein function prediction using protein network data and have been shown to outperform neighborhood‐based and module‐based methods. Recent studies have shown that integrating the hierarchical structure of the Gene Ontology (GO) data dramatically improves prediction accuracy. However, previous methods usually either used the GO hierarchy to refine the prediction results of multiple classifiers, or flattened the hierarchy into a function‐function similarity kernel. No study has taken the GO hierarchy into account together with the protein network as a two‐layer network model. Results: We first construct a Bi‐relational graph (Birg) model comprised of both protein‐protein association and function‐function hierarchical networks. We then propose two diffusion‐based methods, BirgRank and AptRank, both of which use PageRank to diffuse information on this two‐layer graph model. BirgRank is a direct application of traditional PageRank with fixed decay parameters. In contrast, AptRank utilizes an adaptive diffusion mechanism to improve the performance of BirgRank. We evaluate the ability of both methods to predict protein function on yeast, fly and human protein datasets, and compare with four previous methods: GeneMANIA, TMC, ProteinRank and clusDCA. We design four different validation strategies: missing function prediction, de novo function prediction, guided function prediction and newly discovered function prediction to comprehensively evaluate predictability of all six methods. We find that both BirgRank and AptRank outperform the previous methods, especially in missing function prediction when using only 10% of the data for training. Availability and Implementation: The MATLAB code is available at https://github.rcac.purdue.edu/mgribsko/aptrank. Contact: gribskov@purdue.edu Supplementary information: Supplementary data are available at Bioinformatics online.