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Systematic topology analysis and generation using degree correlations

Priya Mahadevan, Dmitri Krioukov, Kevin Fall, Amin Vahdat
2006 Computer communication review  
We hope that a systematic method to analyze and synthesize topologies offers a significant improvement to the set of tools available to network topology and protocol researchers.  ...  We first introduce the dK-series of probability distributions specifying all degree correlations within d-sized subgraphs of a given graph G.  ...  Acknowledgements We would like to thank Walter Willinger and Lun Li for their HOT topology data; Bradley Huffaker, David Moore, Marina Fomenkov, and kc claffy for their contributions at different stages  ... 
doi:10.1145/1151659.1159930 fatcat:ald4cnmtdrbqpccifyzshzslei

Systematic topology analysis and generation using degree correlations

Priya Mahadevan, Dmitri Krioukov, Kevin Fall, Amin Vahdat
2006 Proceedings of the 2006 conference on Applications, technologies, architectures, and protocols for computer communications - SIGCOMM '06  
We hope that a systematic method to analyze and synthesize topologies offers a significant improvement to the set of tools available to network topology and protocol researchers.  ...  We first introduce the dK-series of probability distributions specifying all degree correlations within d-sized subgraphs of a given graph G.  ...  Acknowledgements We would like to thank Walter Willinger and Lun Li for their HOT topology data; Bradley Huffaker, David Moore, Marina Fomenkov, and kc claffy for their contributions at different stages  ... 
doi:10.1145/1159913.1159930 dblp:conf/sigcomm/MahadevanKFV06 fatcat:adtk2mux3rhjplafih3ogjpdoa

Transition to reconstructibility in weakly coupled networks

Benedict J. Lünsmann, Christoph Kirst, Marc Timme, Michal Zochowski
2017 PLoS ONE  
We explicate how local common cause and relay structures, heterogeneous in-degrees and non-local structural properties of the network generally hinder reconstructibility.  ...  Here we systematically study the problem of reconstructing direct physical interaction networks from thresholding correlations.  ...  In particular, what do correlations generally tell us about direct physical interactions in network dynamical systems?  ... 
doi:10.1371/journal.pone.0186624 pmid:29053744 pmcid:PMC5650155 fatcat:hfwste54ajfvhktjbt344wb5dq

Hexagonal Patterning of the Insect Compound Eye: Facet Area Variation, Defects, and Disorder

Sangwoo Kim, Justin J. Cassidy, Boyuan Yang, Richard W. Carthew, Sascha Hilgenfeldt
2016 Biophysical Journal  
This work develops formalisms of size-topology correlation that are very general and can be potentially applied to other cellular structures near the onset of disorder.  ...  Without free parameters, the simulation predicts the size-topology correlation for both wild-type and mutant eyes.  ...  ACKNOWLEDGMENTS We thank Salvatore Torquato and Duyu Chen for fruitful conversations and helpful suggestions on order parameter analysis.  ... 
doi:10.1016/j.bpj.2016.11.004 pmid:28002749 pmcid:PMC5194618 fatcat:xciy3tuuybc7tb2uuaqjgxziqu

Rates of evolution and homoplasy

David L. Hauser, George E. Boyajian, N.H. Shubin
1992 The Paleontological Society Special Publications  
Homoplasy is present in virtually every known systematic analysis and exists at all levels of the Linnaean hierarchy.  ...  In order to control for results that were unique to a given tree topology, the same data sets were generated onto two very different tree topologies (a extensively bifurcated tree and a Hennigian comb)  ...  Homoplasy is present in virtually every known systematic analysis and exists at all levels of the Ilnnaean hierarchy.  ... 
doi:10.1017/s2475262200006845 fatcat:d3ar46cobrdqnddl4blatxkfom

Gene essentiality and the topology of protein interaction networks

S. Coulomb, M. Bauer, D. Bernard, M.-C. Marsolier-Kergoat
2005 Proceedings of the Royal Society of London. Biological Sciences  
Gene essentiality and more generally cell resistance against mutations thus seem largely unrelated to many parameters of protein network topology.  ...  We also found that yeast protein interaction networks lack degree correlation, i.e. a propensity for their vertices to associate according to their degrees.  ...  We would like to thank Jean-Louis Sikorav and Arach Goldar for critical comments on the manuscript, and Raphaël Guérois for the automatic retrieval of the numbers of SGD curated references.  ... 
doi:10.1098/rspb.2005.3128 pmid:16087428 pmcid:PMC1559853 fatcat:d4ofyzeijvcnjheda73pdp6wne

Effect of dataset selection on the topological interpretation of protein interaction networks

Luke Hakes, David L Robertson, Stephen G Oliver
2005 BMC Genomics  
When performing network-based studies, it is essential to define what is meant by the term "interaction" and this must be taken into account when interpreting the topologies of the networks generated.  ...  Studies of the yeast protein interaction network have revealed distinct correlations between the connectivity of individual proteins within the network and the average connectivity of their neighbours.  ...  Simon Lovell and for insights and discussions. LH is supported by a CASE Studentship from the Biotechnology & Biological Sciences Research Council (BBSRC) and AstraZeneca.  ... 
doi:10.1186/1471-2164-6-131 pmid:16174296 pmcid:PMC1249571 fatcat:mrde7vpnibhghixn47vb5lilma

Classification of Complex Networks Based on Topological Properties

Burcu Kantarci, Vincent Labatut
2013 2013 International Conference on Cloud and Green Computing  
However, each one of these studies generally focuses on a very small number of topological measures and networks. In this work, we aim at using a more systematic approach.  ...  However, each one of these studies generally focuses on a very small number of topological measures and networks. In this work, we aim at using a more systematic approach.  ...  The first contribution of our work was to tackle the problem of identifying discriminant topological measures by using a systematic approach, in terms of amount of data, topological measures and analysis  ... 
doi:10.1109/cgc.2013.54 dblp:conf/cgc/KantarciL13 fatcat:c5vx5fgw7fgcripvxmmabeigea

Resting-state fMRI Signals of Intelligent People Wander in a Larger Space: Supplementary Material [article]

Aslan S Dizaji, Mohammad-Reza Khodaei, Hamid Soltanian-Zadeh
2019 bioRxiv   pre-print
In the general framework of topological data analysis, using a well-established non-linear dimensionality reduction method, we show that indeed resting-state fMRI signals of intelligent individuals occupy  ...  This may be interpreted as the functional equivalence of one of the most celebrated structural correlates of intelligence, its positive association with the total brain volume.  ...  topological data analysis.  ... 
doi:10.1101/529362 fatcat:jwbvwgxporadvns5oosbpjfvau

A comparative analysis of knowledge acquisition performance in complex networks [article]

Lucas Guerreiro and Filipi N. Silva and Diego R. Amancio
2020 arXiv   pre-print
While some studies have analyzed the performance of the knowledge acquisition process in particular network topologies, here we performed a systematic performance analysis in well-known dynamics and topologies  ...  We also found ambiguities in the feature space describing the learning curves, meaning that the same knowledge acquisition curve can be generated in different combinations of network topology and dynamics  ...  To our knowledge, no previous study focused on a systematic analysis among the dynamics, networks, and the sequences generated by them.  ... 
arXiv:2007.12028v1 fatcat:srejchpuvzbrvalslciljjlo5u

Spectral Graph Partitioning Analysis of In Vitro Synthesized RNA Structural Folding [chapter]

Stanley NG Kwang Loong, Santosh K. Mishra
2006 Lecture Notes in Computer Science  
Our analysis shows that the majority of synthetic RNAs possess between two to six vertices and their second eigenvalues lie between one and two.  ...  Our statistical analysis (at 95 percentile) also reveals three criteria important for designing novel functional RNAs.  ...  Fig. 4 depicts how the non-topological properties of the primary sequence (i.e., L and G/C) and of the secondary structure (i.e., PB and MFE) are correlated with varying degrees to the topological measures  ... 
doi:10.1007/11818564_10 fatcat:676pjmxyvbgc3oasa5neqfpjuy

Addressing head motion dependencies for small-world topologies in functional connectomics

Chao-Gan Yan, R. Cameron Craddock, Yong He, Michael P. Milham
2013 Frontiers in Human Neuroscience  
This study provides a comprehensive examination of motion correction strategies on the relationship between motion and commonly used topological parameters.  ...  At the individual-level, we evaluated different models of head motion regression and scrubbing, as well as the potential benefits of using partial correlation (estimated via graphical lasso) instead of  ...  Milham), Brain and Behavior Research Foundation (R.  ... 
doi:10.3389/fnhum.2013.00910 pmid:24421764 pmcid:PMC3872728 fatcat:dkx6rg4vufaovjzldzivbtj5xi

Regularizing capacity of metabolic networks

Carsten Marr, Mark Müller-Linow, Marc-Thorsten Hütt
2007 Physical Review E  
Here, we expose metabolic network topologies to binary dynamics generated by simple local rules.  ...  We find that the networks' response is highly specific: Complex dynamics are systematically reduced on metabolic networks compared to randomized networks with identical degree sequences.  ...  ] with degree correlations of 0.05, 0, +0.3, and −0.3, respectively.  ... 
doi:10.1103/physreve.75.041917 pmid:17500931 fatcat:acew3cadsbafbhzc7y3l3765ii

Effects of Different Correlation Metrics and Preprocessing Factors on Small-World Brain Functional Networks: A Resting-State Functional MRI Study

Xia Liang, Jinhui Wang, Chaogan Yan, Ni Shu, Ke Xu, Gaolang Gong, Yong He, Pedro Antonio Valdes-Sosa
2012 PLoS ONE  
Analysis of nodal degree revealed differing hub distributions for brain networks derived from Pearson's correlation versus partial correlation.  ...  TRT analysis revealed that the reliability of both global and local topological properties are modulated by correlation metrics and the global signal, with the highest reliability observed for Pearson's-correlation-based  ...  Yufeng Zang and Dr. Michael P. Milham for kindly providing the Datasets. Author Contributions  ... 
doi:10.1371/journal.pone.0032766 pmid:22412922 pmcid:PMC3295769 fatcat:witoa4otcrewja6w6fxxavjl7q

Protein Networks Reveal Detection Bias and Species Consistency When Analysed by Information-Theoretic Methods

Luis P. Fernandes, Alessia Annibale, Jens Kleinjung, Anthony C. C. Coolen, Franca Fraternali, Kumar Selvarajoo
2010 PLoS ONE  
These measures are used to quantify topological network features via macroscopic statistical properties.  ...  We present the results of a large-scale analysis of protein-protein interaction networks. Precise null models are used in our analyses, allowing for reliable interpretation of the results.  ...  We find that degree-degree correlations provide important and consistent information on PPIN topologies, but it is crucial that they are normalised correctly and that one uses robust and systematic methods  ... 
doi:10.1371/journal.pone.0012083 pmid:20805870 pmcid:PMC2923596 fatcat:lhyz7riojfbqtetiwqlmg76kei
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