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128
Random Walks in PeertoPeer Networks
, 2004
"... We quantify the effectiveness of random walks for searching and construction of unstructured peertopeer (P2P) networks. For searching, we argue that random walks achieve improvement over flooding in the case of clustered overlay topologies and in the case of reissuing the same request several tim ..."
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Cited by 208 (2 self)
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We quantify the effectiveness of random walks for searching and construction of unstructured peertopeer (P2P) networks. For searching, we argue that random walks achieve improvement over flooding in the case of clustered overlay topologies and in the case of reissuing the same request several times. For construction, we argue that an expander can be maintained dynamically with constant operations per addition. The key technical ingredient of our approach is a deep result of stochastic processes indicating that samples taken from consecutive steps of a random walk can achieve statistical properties similar to independent sampling (if the second eigenvalue of the transition matrix is bounded away from 1, which translates to good expansion of the network; such connectivity is desired, and believed to hold, in every reasonable network and network model). This property has been previously used in complexity theory for construction of pseudorandom number generators. We reveal another facet of this theory and translate savings in random bits to savings in processing overhead.
Statistical properties of community structure in large social and information networks
"... A large body of work has been devoted to identifying community structure in networks. A community is often though of as a set of nodes that has more connections between its members than to the remainder of the network. In this paper, we characterize as a function of size the statistical and structur ..."
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Cited by 181 (12 self)
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A large body of work has been devoted to identifying community structure in networks. A community is often though of as a set of nodes that has more connections between its members than to the remainder of the network. In this paper, we characterize as a function of size the statistical and structural properties of such sets of nodes. We define the network community profile plot, which characterizes the “best ” possible community—according to the conductance measure—over a wide range of size scales, and we study over 70 large sparse realworld networks taken from a wide range of application domains. Our results suggest a significantly more refined picture of community structure in large realworld networks than has been appreciated previously. Our most striking finding is that in nearly every network dataset we examined, we observe tight but almost trivial communities at very small scales, and at larger size scales, the best possible communities gradually “blend in ” with the rest of the network and thus become less “communitylike.” This behavior is not explained, even at a qualitative level, by any of the commonlyused network generation models. Moreover, this behavior is exactly the opposite of what one would expect based on experience with and intuition from expander graphs, from graphs that are wellembeddable in a lowdimensional structure, and from small social networks that have served as testbeds of community detection algorithms. We have found, however, that a generative model, in which new edges are added via an iterative “forest fire” burning process, is able to produce graphs exhibiting a network community structure similar to our observations.
Community structure in large networks: Natural cluster sizes and the absence of large welldefined clusters
, 2008
"... A large body of work has been devoted to defining and identifying clusters or communities in social and information networks, i.e., in graphs in which the nodes represent underlying social entities and the edges represent some sort of interaction between pairs of nodes. Most such research begins wit ..."
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Cited by 133 (12 self)
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A large body of work has been devoted to defining and identifying clusters or communities in social and information networks, i.e., in graphs in which the nodes represent underlying social entities and the edges represent some sort of interaction between pairs of nodes. Most such research begins with the premise that a community or a cluster should be thought of as a set of nodes that has more and/or better connections between its members than to the remainder of the network. In this paper, we explore from a novel perspective several questions related to identifying meaningful communities in large social and information networks, and we come to several striking conclusions. Rather than defining a procedure to extract sets of nodes from a graph and then attempt to interpret these sets as a “real ” communities, we employ approximation algorithms for the graph partitioning problem to characterize as a function of size the statistical and structural properties of partitions of graphs that could plausibly be interpreted as communities. In particular, we define the network community profile plot, which characterizes the “best ” possible community—according to the conductance measure—over a wide range of size scales. We study over 100 large realworld networks, ranging from traditional and online social networks, to technological and information networks and
On Cubical Graphs
 JOURNAL OF COMBINATORIAL THEORY (B) 18, 86 % (1975)
, 1975
"... It is frequently of interest to represent a given graph G as a subgraph of a graph H which has some special structure. A particularly useful class of graphs in which to embed G is the class of ndimensional cubes. This has found applications, for example, in coding theory, data transmission, and lin ..."
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Cited by 78 (6 self)
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It is frequently of interest to represent a given graph G as a subgraph of a graph H which has some special structure. A particularly useful class of graphs in which to embed G is the class of ndimensional cubes. This has found applications, for example, in coding theory, data transmission, and linguistics. In this note, we study the structure of those graphs 6, called cubical graphs (not to be confused with cubic graphs, those graphs for which all vertices have degree 3), which can be embedded into an ndimensional cube. A basic technique used is the investigation of graphs which are critically nonembeddable, i.e., which can not be embedded but all of whose subgrapbs can be embedded.
Epidemic Thresholds in Real Networks
"... How will a virus propagate in a real network? How long does it take to disinfect a network given particular values of infection rate and virus death rate? What is the single best node to immunize? Answering these questions is essential for devising networkwide strategies to counter viruses. In addi ..."
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Cited by 70 (10 self)
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How will a virus propagate in a real network? How long does it take to disinfect a network given particular values of infection rate and virus death rate? What is the single best node to immunize? Answering these questions is essential for devising networkwide strategies to counter viruses. In addition, viral propagation is very similar in principle to the spread of rumors, information, and “fads, ” implying that the solutions for viral propagation would also offer insights into these other problem settings. We answer these questions by developing a nonlinear dynamical system (NLDS) that accurately models viral propagation in any arbitrary network, including real and synthesized network graphs. We propose a general epidemic threshold condition for the NLDS system: we prove that the epidemic threshold for a network is exactly the inverse of the largest eigenvalue of its adjacency matrix. Finally, we show that below the epidemic threshold, infections die out at an exponential rate. Our epidemic threshold model subsumes many known thresholds for specialcase graphs (e.g., Erdös–Rényi, BA powerlaw, homogeneous). We demonstrate the predictive power of our model with extensive experiments on real and synthesized graphs, and show that our threshold condition holds for arbitrary graphs. Finally, we show how to utilize our threshold condition for practical uses: It can dictate which nodes to immunize; it can assess the effects of a throttling
Concentration inequalities and martingale inequalities – a survey
 Internet Math
"... Abstract. We examine a number of generalized and extended versions of concentration inequalities and martingale inequalities. These inequalities are effective for analyzing processes with quite general conditions as illustrated in an example for an infinite Polya process and web graphs. 1. ..."
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Cited by 45 (1 self)
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Abstract. We examine a number of generalized and extended versions of concentration inequalities and martingale inequalities. These inequalities are effective for analyzing processes with quite general conditions as illustrated in an example for an infinite Polya process and web graphs. 1.
Pairwise alignment of protein interaction networks
 Journal of Computational Biology
, 2006
"... With an everincreasing amount of available data on protein–protein interaction (PPI) networks and research revealing that these networks evolve at a modular level, discovery of conserved patterns in these networks becomes an important problem. Although available data on protein–protein interactions ..."
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Cited by 31 (3 self)
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With an everincreasing amount of available data on protein–protein interaction (PPI) networks and research revealing that these networks evolve at a modular level, discovery of conserved patterns in these networks becomes an important problem. Although available data on protein–protein interactions is currently limited, recently developed algorithms have been shown to convey novel biological insights through employment of elegant mathematical models. The main challenge in aligning PPI networks is to define a graph theoretical measure of similarity between graph structures that captures underlying biological phenomena accurately. In this respect, modeling of conservation and divergence of interactions, as well as the interpretation of resulting alignments, are important design parameters. In this paper, we develop a framework for comprehensive alignment of PPI networks, which is inspired by duplication/divergence models that focus on understanding the evolution of protein interactions. We propose a mathematical model that extends the concepts of match, mismatch, and gap in sequence alignment to that of match, mismatch, and duplication in network alignment and evaluates similarity between graph structures through a scoring function that accounts for evolutionary events. By relying on evolutionary models, the proposed framework facilitates interpretation of resulting alignments in terms of not only conservation but also divergence of modularity in PPI networks. Furthermore, as in the case of sequence alignment, our model allows flexibility in adjusting parameters to quantify underlying evolutionary relationships. Based on the proposed model, we formulate PPI network alignment as an optimization problem and present fast algorithms to solve this problem. Detailed experimental results from an implementation of the proposed framework show that our algorithm is able to discover conserved interaction patterns very effectively, in terms of both accuracies and computational cost. Key words: protein–protein interactions, network alignment, evolutionary models. 1.