Persistent Homology Lower Bounds on High Order Network Distances

There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

Abstract

High order networks are weighted hypergraphs col- lecting relationships between elements of tuples, not necessarily pairs. Valid metric distances between high order networks have been defined but they are difficult to compute when the number of nodes is large. The goal here is to find tractable approximations of these network distances. The paper does so by mapping high order networks to filtrations of simplicial complexes and showing that the distance between networks can be lower bounded by the difference between the homological features of their respective filtrations. Practical implications are explored by classifying weighted pairwise networks constructed from different gener- ative processes and by comparing the coauthorship networks of engineering and mathematics academic journals. The persistent homology methods succeed in identifying different generative models, in discriminating engineering and mathematics commu- nities, as well as in differentiating engineering communities with different research interests.

Related collections

Most cited references 9

Record: found
Abstract: found
Article: not found

Global alignment of multiple protein interaction networks with application to functional orthology detection.

Rohit Singh, Bonnie Berger, Jinbo Xu (2008)

Protein-protein interactions (PPIs) and their networks play a central role in all biological processes. Akin to the complete sequencing of genomes and their comparative analysis, complete descriptions of interactomes and their comparative analysis is fundamental to a deeper understanding of biological processes. A first step in such an analysis is to align two or more PPI networks. Here, we introduce an algorithm, IsoRank, for global alignment of multiple PPI networks. The guiding intuition here is that a protein in one PPI network is a good match for a protein in another network if their respective sequences and neighborhood topologies are a good match. We encode this intuition as an eigenvalue problem in a manner analogous to Google's PageRank method. Using IsoRank, we compute a global alignment of the Saccharomyces cerevisiae, Drosophila melanogaster, Caenorhabditis elegans, Mus musculus, and Homo sapiens PPI networks. We demonstrate that incorporating PPI data in ortholog prediction results in improvements over existing sequence-only approaches and over predictions from local alignments of the yeast and fly networks. Previous methods have been effective at identifying conserved, localized network patterns across pairs of networks. This work takes the further step of performing a global alignment of multiple PPI networks. It simultaneously uses sequence similarity and network data and, unlike previous approaches, explicitly models the tradeoff inherent in combining them. We expect IsoRank-with its simultaneous handling of node similarity and network similarity-to be applicable across many scientific domains.

0 comments Cited 163 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: found

Is Open Access

Biological network comparison using graphlet degree distribution

Nataša Pržulj (2009)

Analogous to biological sequence comparison, comparing cellular networks is an important problem that could provide insight into biological understanding and therapeutics. For technical reasons, comparing large networks is computationally infeasible, and thus heuristics such as the degree distribution have been sought. It is easy to demonstrate that two networks are different by simply showing a short list of properties in which they differ. It is much harder to show that two networks are similar, as it requires demonstrating their similarity in all of their exponentially many properties. Clearly, it is computationally prohibitive to analyze all network properties, but the larger the number of constraints we impose in determining network similarity, the more likely it is that the networks will truly be similar. We introduce a new systematic measure of a network's local structure that imposes a large number of similarity constraints on networks being compared. In particular, we generalize the degree distribution, which measures the number of nodes 'touching' k edges, into distributions measuring the number of nodes 'touching' k graphlets, where graphlets are small connected non-isomorphic subgraphs of a large network. Our new measure of network local structure consists of 73 graphlet degree distributions (GDDs) of graphlets with 2-5 nodes, but it is easily extendible to a greater number of constraints (i.e. graphlets). Furthermore, we show a way to combine the 73 GDDs into a network 'agreement' measure. Based on this new network agreement measure, we show that almost all of the 14 eukaryotic PPI networks, including human, are better modeled by geometric random graphs than by Erdos-Reny, random scale-free, or Barabasi-Albert scale-free networks.