Probabilistic Random Walk Models for Comparative Network Analysis

Graph-based systems and data analysis methods have become critical tools in many fields as they can provide an intuitive way of representing and analyzing interactions between variables. Due to the advances in measurement techniques, a massive amount of labeled data that can be represented as nodes on a graph (or network) have been archived in databases. Additionally, novel data without label information have been gradually generated and archived. Labeling and identifying characteristics of novel data is an important first step in utilizing the valuable data in an effective and meaningful way. Comparative network analysis is an effective computational means to identify and predict the properties of the unlabeled data by comparing the similarities and differences between well-studied and less-studied networks. Comparative network analysis aims to identify the matching nodes and conserved subnetworks across multiple networks to enable a prediction of the properties of the nodes in the less-studied networks based on the properties of the matching nodes in the well-studied networks (i.e., transferring knowledge between networks). One of the fundamental and important questions in comparative network analysis is how to accurately estimate node-to-node correspondence as it can be a critical clue in analyzing the similarities and differences between networks. Node correspondence is a comprehensive similarity that integrates various types of similarity measurements in a balanced manner. However, there are several challenges in accurately estimating the node correspondence for large-scale networks. First, the scale of the networks is a critical issue. As networks generally include a large number of nodes, we have to examine an extremely large space and it can pose a computational challenge due to the combinatorial nature of the problem. Furthermore, although there are matching nodes and conserved subnetworks in different networks, structural variations such as node insertions and deletions make it difficult to integrate a topological similarity. In this dissertation, novel probabilistic random walk models are proposed to accurately estimate node-to-node correspondence between networks. First, we propose a context-sensitive random walk (CSRW) model. In the CSRW model, the random walker analyzes the context of the current position of the random walker and it can switch the random movement to either a simultaneous walk on both networks or an individual walk on one of the networks. The context-sensitive nature of the random walker enables the method to effectively integrate different types of similarities by dealing with structural variations. Second, we propose the CUFID (Comparative network analysis Using the steady-state network Flow to IDentify orthologous proteins) model. In the CUFID model, we construct an integrated network by inserting pseudo edges between potential matching nodes in different networks. Then, we design the random walk protocol to transit more frequently between potential matching nodes as their node similarity increases and they have more matching neighboring nodes. We apply the proposed random walk models to comparative network analysis problems: global network alignment and network querying. Through extensive performance evaluations, we demonstrate that the proposed random walk models can accurately estimate node correspondence and these can lead to improved and reliable network comparison results

BioFabric Visualization of Network Alignments

Background Dozens of global network alignment algorithms have been developed over the past fifteen years. Effective network visualization tools are lacking and would enhance our ability to gain an intuitive understanding of the strengths and weaknesses of these algorithms. Results We have created a plugin to the existing network visualization tool BioFabric, called VISNAB: Visualization of Network Alignments using BioFabric . We leverage BioFabric’s unique approach to layout (nodes are horizontal lines connected by vertical lines representing edges) to improve understanding of network alignment performance. Our visualization tool allows the user to clearly spot deficiencies in alignments that cannot be detected through simply evaluating and comparing standard numerical topological measures such as the Edge Coverage ( EC ) or Symmetric Substructure Score ( S 3 ). Furthermore, we provide new automatic layouts that allow researchers to identify problem areas in an alignment. Finally, our new definitions of node groups and link groups that arise from our visualization technique allows us to also introduce novel numeric measures for assessing alignment quality. Conclusions Our new approach to visualize network alignments will allow researchers to gain a new, and better, understanding of the strengths and shortcomings of the many available network alignment algorithms

Graphettes: Constant-time determination of graphlet and orbit identity including (possibly disconnected) graphlets up to size 8

Graphlets are small connected induced subgraphs of a larger graph $G$. Graphlets are now commonly used to quantify local and global topology of networks in the field. Methods exist to exhaustively enumerate all graphlets (and their orbits) in large networks as efficiently as possible using orbit counting equations. However, the number of graphlets in $G$ is exponential in both the number of nodes and edges in $G$. Enumerating them all is already unacceptably expensive on existing large networks, and the problem will only get worse as networks continue to grow in size and density. Here we introduce an efficient method designed to aid statistical sampling of graphlets up to size $k=8$ from a large network. We define graphettes as the generalization of graphlets allowing for disconnected graphlets. Given a particular (undirected) graphette $g$, we introduce the idea of the canonical graphette $\mathcal K(g)$ as a representative member of the isomorphism group $Iso(g)$ of $g$. We compute the mapping $\mathcal K$, in the form of a lookup table, from all $2^{k(k-1)/2}$ undirected graphettes $g$ of size $k\le 8$ to their canonical representatives $\mathcal K(g)$, as well as the permutation that transforms $g$ to $\mathcal K(g)$. We also compute all automorphism orbits for each canonical graphette. Thus, given any $k\le 8$ nodes in a graph $G$, we can in constant time infer which graphette it is, as well as which orbit each of the $k$ nodes belongs to. Sampling a large number $N$ of such $k$-sets of nodes provides an approximation of both the distribution of graphlets and orbits across $G$, and the orbit degree vector at each node.Comment: 13 pages, 4 figures, 2 tables. Accepted to PLOS ON