Results 1  10
of
46
Comparing community structure identification
 Journal of Statistical Mechanics: Theory and Experiment
, 2005
"... ..."
(Show Context)
On partial contraction analysis for coupled nonlinear oscillators
 technical Report, Nonlinear Systems Laboratory, MIT
, 2003
"... We describe a simple but general method to analyze networks of coupled identical nonlinear oscillators, and study applications to fast synchronization, locomotion, and schooling. Specifically, we use nonlinear contraction theory to derive exact and global (rather than linearized)results on synchroni ..."
Abstract

Cited by 85 (39 self)
 Add to MetaCart
(Show Context)
We describe a simple but general method to analyze networks of coupled identical nonlinear oscillators, and study applications to fast synchronization, locomotion, and schooling. Specifically, we use nonlinear contraction theory to derive exact and global (rather than linearized)results on synchronization, antisynchronization and oscillatordeath. The method can be applied to coupled networks of various structures and arbitrary size. For oscillators with positivedefinite diffusion coupling, it can be shown that synchronization always occur globally for strong enough coupling strengths, and an explicit upper bound on the corresponding threshold can be computed through eigenvalue analysis. The discussion also extends to the case when network structure varies abruptly and asynchronously, as in “flocks ” of oscillators or dynamic elements.
Graph theory and networks in biology
 IET Systems Biology, 1:89 – 119
, 2007
"... In this paper, we present a survey of the use of graph theoretical techniques in Biology. In particular, we discuss recent work on identifying and modelling the structure of biomolecular networks, as well as the application of centrality measures to interaction networks and research on the hierarch ..."
Abstract

Cited by 30 (0 self)
 Add to MetaCart
In this paper, we present a survey of the use of graph theoretical techniques in Biology. In particular, we discuss recent work on identifying and modelling the structure of biomolecular networks, as well as the application of centrality measures to interaction networks and research on the hierarchical structure of such networks and network motifs. Work on the link between structural network properties and dynamics is also described, with emphasis on synchronization and disease propagation. 1
Modular Stability Tools for Distributed Computation and Control
 TO BE PUBLISHED IN INT. J. ADAPTIVE CONTROL AND SIGNAL PROCESSING, 17(6)
, 2002
"... Much recent functional modelling of the central nervous system, beyond traditional “neural net” approaches, focuses on its distributed computational architecture. This paper discusses extensions of our recent work aimed at understanding this architecture from an overall nonlinear stability and conve ..."
Abstract

Cited by 25 (16 self)
 Add to MetaCart
Much recent functional modelling of the central nervous system, beyond traditional “neural net” approaches, focuses on its distributed computational architecture. This paper discusses extensions of our recent work aimed at understanding this architecture from an overall nonlinear stability and convergence point of view, and at constructing artificial devices exploiting similar modularity. Applications to synchronisation and to schooling are also described. The development makes extensive use of nonlinear contraction theory.
The Graph Analysis Toolbox: Image Processing on Arbitrary Graphs
, 2003
"... We present a theoretical and computational framework for the analysis of data associated with the node set of an arbitrary graph. The algorithms described here are collected in a TM MATLAB software package named the Graph Analysis Toolbox. Our purpose is to describe the functionality of the Graph An ..."
Abstract

Cited by 13 (5 self)
 Add to MetaCart
(Show Context)
We present a theoretical and computational framework for the analysis of data associated with the node set of an arbitrary graph. The algorithms described here are collected in a TM MATLAB software package named the Graph Analysis Toolbox. Our purpose is to describe the functionality of the Graph Analysis Toolbox and the associated theoretical framework in the context of biologically inspired, spacevariant computer vision. 1
A molecular model for intercellular synchronization in the mammalian circadian clock
 Biophysical Journal
, 2007
"... ABSTRACT The mechanisms and consequences of synchrony among heterogeneous oscillators are poorly understood in biological systems. We present a multicellular, molecular model of the mammalian circadian clock that incorporates recent data implicating the neurotransmitter vasoactive intestinal polypep ..."
Abstract

Cited by 12 (0 self)
 Add to MetaCart
(Show Context)
ABSTRACT The mechanisms and consequences of synchrony among heterogeneous oscillators are poorly understood in biological systems. We present a multicellular, molecular model of the mammalian circadian clock that incorporates recent data implicating the neurotransmitter vasoactive intestinal polypeptide (VIP) as the key synchronizing agent. The model postulates that synchrony arises among circadian neurons because they release VIP rhythmically on a daily basis and in response to ambient light. Two basic cell types, intrinsically rhythmic pacemakers and damped oscillators, are assumed to arise from a distribution of Period gene transcription rates. Postsynaptic neurons show timeofday dependent responses to VIP binding through a signaling cascade that activates Period mRNA transcription. The heterogeneous cell ensemble model selfsynchronizes, entrains to ambient lightdark cycles, and desynchronizes in constant bright light or upon removal of VIP signaling. The degree of synchronicity observed depends on cellspecific features (e.g., mean and variability of parameters within the rhythmgenerating loop), in addition to the more commonly studied effect of intercellular coupling strength. These simulations closely replicate experimental data and predict that heterogeneous oscillations (e.g., sustained, damped, and arrhythmic) arise from small differences in the molecular parameters between cells, that damped oscillators participate in entrainment and synchrony of the ensemble of cells, and that constant light desynchronizes oscillators by maximizing VIP release.
Critical Values in Asynchronous Random Boolean Networks
 Advances in Artificial Life, ECAL2003
, 2003
"... Wherever we see life, we see dierent kinds of complex networks, reason why they are studied across various elds of science. Random Boolean Networks (RBNs) form a special class in which the links between the nodes and the boolean functions are speci ed at random. ..."
Abstract

Cited by 9 (1 self)
 Add to MetaCart
Wherever we see life, we see dierent kinds of complex networks, reason why they are studied across various elds of science. Random Boolean Networks (RBNs) form a special class in which the links between the nodes and the boolean functions are speci ed at random.
Periodicity, MixedMode Oscillations, and Quasiperiodicity in a RhythmGenerating Neural Network
, 2002
"... ABSTRACT We studied patterns of oscillatory neural activity in the network that generates respiratory rhythm in mammals. When isolated in vitro, this network spontaneously generates an inspiratoryrelated motor rhythm, with stable amplitude from cycle to cycle. We show that progressively elevating n ..."
Abstract

Cited by 8 (0 self)
 Add to MetaCart
ABSTRACT We studied patterns of oscillatory neural activity in the network that generates respiratory rhythm in mammals. When isolated in vitro, this network spontaneously generates an inspiratoryrelated motor rhythm, with stable amplitude from cycle to cycle. We show that progressively elevating neuronal excitability in vitro causes periodic modulation of this inspiratory rhythm, evoking (in order): mixedmode oscillations, quasiperiodicity, and ultimately disorganized aperiodic activity. Thus, the respiratory network oscillator follows a well defined sequence of behavioral states characterized by dynamical systems theory, which includes discrete stages of periodic and quasiperiodic amplitude modulation and progresses (according to theory) to aperiodic chaoslike behavior. We also observed periodic, mixedmode periodic, and quasiperiodic breathing patterns in neonatal rodents and human infants in vivo, suggesting that breathing patterns generated by the intact nervous system reflect deterministic neural activity patterns in the underlying rhythmgenerating network.
A rolebased trust model for peertopeer communities and dynamic coalitions
 In Proceedings of the Second IEEE International Information Assurance Workshop
, 2004
"... Although P2P systems are usually used for information exchange between peers, they have either protected peers ’ anonymity, or required transacting peers to trust each other implicitly. Both these approaches are vulnerable to attacks by malicious peers who could abuse the P2P system to spread viruse ..."
Abstract

Cited by 6 (0 self)
 Add to MetaCart
(Show Context)
Although P2P systems are usually used for information exchange between peers, they have either protected peers ’ anonymity, or required transacting peers to trust each other implicitly. Both these approaches are vulnerable to attacks by malicious peers who could abuse the P2P system to spread viruses, incorrect, or damaging information. In this paper, we propose an approach for trust management in P2P systems. We introduce an optimistic rolebased model for trust amongst peers and show that it is scalable, dynamic, revocable, secure and transitive. Our proposed solution permits asymmetric trust relationships that can be verified by any peer in the system through a simple, lowcost algorithm. This paper introduces a metric known as iComplex that combines a peer’s trust value for each of its roles into a single, relative, probabilistic guarantee of trust. Finally, we discuss how our trust model allows peers to revoke relationships with malicious peers, and the nonrepudiation of peer relations. We use simulations to illustrate the trust value distribution amongst peers in the network. Our analysis and experiments demonstrates the lowcost involved to verify and validate trust values. Lastly, we establish the effectiveness of using sum as the aggregation function to combine trust values of a peer.
Modeling FoodWeb Dynamics: ComplexityStability Implications
"... Abstract: We discuss theoretical aspects of the broader foodweb research agenda, particularly the background and various approaches used for modeling foodweb dynamics in abstract systems with more than two taxa. Much of this type of modeling has oriented itself around the classic and enduring comp ..."
Abstract

Cited by 4 (3 self)
 Add to MetaCart
Abstract: We discuss theoretical aspects of the broader foodweb research agenda, particularly the background and various approaches used for modeling foodweb dynamics in abstract systems with more than two taxa. Much of this type of modeling has oriented itself around the classic and enduring complexitystability debate in ecology, especially those aspects which relate to the theoretical and associated empirical foodweb research into the relationships between ecosystem complexity, often characterized as number of links and/or number of species in a community, and various aspects of ecosystem stability. “Stability ” in ecology is a catchall term that has been variously defined to reflect aspects of population and/or system equilibrium, persistence, resilience, resistance, and robustness. In some cases stability refers to the outcome of internal dynamics while in other cases it reflects the response of a population or system to a perturbation. The very notion of what is a plausible definition of ecosystem stability has Understanding the structure and dynamics of ecological networks is critical for understanding the persistence and stability of ecosystems. Determining the interplay