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CABDyN Network Journal Club

Hilary Term 2010
Co-ordinators: Eduardo López and Nick Jones
 

The Network Journal Club meets weekly to discuss interesting, recent papers mostly in the field of complex networks, although occasionally we will select papers related to complex systems in general. The first half an hour is reserved for the speaker to guide the attendants through the paper and the remaining half an hour is meant for informal discussions. Anyone interested in the current paper is welcome to attend. If you would like to come and give a talk on a network paper yourself, please do not hesitate to contact the club coordinator. To add your name to the Network Journal Club mailing list email info.cabdyn@sbs.ox.ac.uk


Forthcoming Network Journal Club meetings

Monday 8th February 2010 13:30
Mendelssohn Room of the Clarendon Physics Laboratory
Speaker: Sumeet Agarwal
Active Learning for Hidden Attributes in Networks
Authors: X. Ran Yan, Y. J. Zhu, J.B. Rouquier, C. Moore



Previous Network Journal Club meetings

Monday 1st February 2010 13:30
Mendelssohn Room of the Clarendon Physics Laboratory
Speaker: Puck Rombach
Community detection in networks with positive and negative links
Author: V.A Traag, J. Bruggeman

Monday 25th January 2010 13:30
Mendelssohn Room of the Clarendon Physics Laboratory
Speaker: Sergey Melnik (Limerick)
Cascades on correlated and modular random networks
Author: J.P Gleeson

Monday 30th November 2009 13:30
Mendelssohn Room of the Clarendon Physics Laboratory
Speaker: Luke Heaton
Transoport and dispersion in random networks with percolation disorder
Authors: J. Koplik, S. Redner, D. Wilkinson

Monday 9th November 2009 13:30
Mendelssohn Room of the Clarendon Physics Laboratory
Speaker: David Smith
Diffusion-based method for producing density-equalizing maps
Authors: Michael T. Gastner and M. E. J. Newman

Monday 26th October 2009 13:30
Mendelssohn Room of the Clarendon Physics Laboratory
Speaker: Martin Gould
Elegance and Error: The Strengths and Weaknesses of Networks
Techniques as Tools for Data Mining

Authors: Mark McDonald, Omer Suleman, Stacy Williams, Sam Howison, Neil F. Johnson

Monday 19th October 2009 13:30
Mendelssohn Room of the Clarendon Physics Laboratory
Speaker: Sumeet Agarwal
A Markov model of the Indus script
Authors: Rajesh P. N. Raoa,1, Nisha Yadavb,c, Mayank N. Vahiab,c, Hrishikesh Joglekard, R. Adhikarie and Iravatham Mahadevanf

Monday 12th October 2009 13:30
Mendelssohn Room of the Clarendon Physics Laboratory
Speaker: Max Little
The Power of Convex Relaxation: Near-Optimal Matrix Completion
Authors: Emmanuel J. Candes, Terence Tao

Monday 5th October
11.00am
Audrey Wood Room on the first floor of the Clarendon Physics Lab
Speakers: Erik Bollt and Jie Sun
 
Tuesday 25th August 2009
11.30am
Audrey Wood Room in the Clarendon Lab in Physics
Speaker: Anna Lewis
Tailored graph ensembles as proxies or null models for real networks I: tools for quantifying structure
by A. Annibale, A.C.C. Coolen, L.P. Fernandes, F. Fraternali, J. Kleinjung

Monday 6th July 2009
11.30am
Seminar Room 501, Denys Wilkinson Building, Physics Department
Speaker 1: Guido Klingebeil
Efficient Parallelization of Stochastic Simulation Algorithm for Chemically Reacting Systems on the Graphics Processing Unit
by Hong Li & Linda Petzold
 
Speaker 2: Luke Heaton
Sizing Up Allometric Scaling Theory
by Van M. Savage, Eric J. Deeds, Walter Fontana
 
 
Monday 22nd June 2009
11.30am
Seminar Room 501, Denys Wilkinson Building, Physics Department
Speaker: Thanasis Athanasios
"Tracking Parkinson's disease progression using speech signal
processing in a telemonitoring framework
"
by Athanasios Tsanas, Max A. Little, Patrick E. McSharry, Lorraine
Ramig.
 
 
Monday 8th June 2009
11.30am
Seminar Room 501, Denys Wilkinson Building, Physics Department
Speaker: Sumeet Agarwal
Learning Nonlinear Dynamic Models
by John Langford, Ruslan Salakhutdinov, Tong Zhang
 
 
Monday 1st June 2009
11.30am
Speaker: Tim Evans (Imperial)
Line Graphs, Link Partitions and Overlapping Communities
by T.S.Evans, R.Lambiotteminar Room 501, Denys Wilkinson Building, Physics Department

Monday 18th May 2009
11.30am
Seminar Room 501, Denys Wilkinson Building, Physics Department
Speaker: Ben Fulcher
"Distilling Free-Form Natural Laws from Experimental Data"
by Michael Schmidt & Hod Lipson

Monday 27th April 2009
Speaker: Antonis Papachristodoulou
"Efficient, Sparse, Biological Network Determination"
by E. August & A. Papachristodoulou

Monday 20th April 2009
Speaker: Max Little
"Reconstructing the topology of sparsely connected dynamical networks"
by D. Napoletani and T. D. Saue

Monday 6th April 2009
Speaker: Nick Jones
"The discovery of the structural form" [Supporting Information pdf]
by C. Kemp and J. B. Tenenbaum

Monday 2nd March 2009
Speaker: Phillip Staniczenko
"Network structure and biodiversity loss in food webs: robustness increases with connectance"
by Dunne, J. A., Williams, R. J., and Martinez, N. D.

Monday 23rd February 2009
Speaker: Alex Fletcher
"The transition from differential equations to Boolean networks: A case study in simplifying a regulatory network model"
by Davidich, M. and Bornholdt, S.


Monday, 16th February 2009
Speaker: David Smith
"Characterization of complex networks: A survey of measurements"
by Luciano da F. Costa, Francisco A. Rodrigues, Gonzalo Travieso, P. R. Villas Boas

Monday 9th February 2009
Speaker: Anna Lewis
"A likelihood approach to analysis of network data"
by Carsten Wiuf, Markus Brameier, Oskar Hagberg and Michael P. H. Stumpf

Monday, 2nd February 2009
Speaker: Sumeet Agarwal
"Kronecker Graphs: an approach to modeling networks"
by Jure Leskovec, Deepayan Chakrabarti, Jon Kleinberg, Christos Faloutsos, Zoubin Gharamani

Monday, 26th January 2009
Speaker: Max Little
"Efficiency and Cost of Economical Brain Functional Networks"
by Sophie Achard, Ed Bullmore

Monday, 19th January 2009
Speaker: Renaud Lambiotte
"Dynamics and Modular Structure in Networks"
by R. Lambiotte, J.-C. Delvenne and M. Barahona

Monday, 5th January 2009
Speaker: Ben Fulcher
"Modeling the impact of impulsive stimuli on sleep-wake dynamics"
by B. D. Fulcher, A. J. K. Phillips, and P. A. Robinson

Wednesday, 17th December 2008
Speaker: Chiu Fan Lee
"Scaling of Fluctuations in Traffic on Complex Networks"
by Jordi Duch and Alex Arenas

Monday, 8th December 2008
Speaker: Rebecca Hamer
"Rhodobacter sphaeroides: complexity in chemotactic signalling"
by Steven L. Porter, George H. Wadhams and Judith P. Armitage

Monday, 1st December 2008
Speaker: Anna Lewis will discuss her work on:
" Function and Community structure in the yeast protein interaction network"
Speaker: Luke Heaton
"Anomalous Transport in Scale-Free Networks"
by Eduardo López, Sergey V. Buldyrev, Shlomo Havlin, and H. Eugene Stanley


Monday, 24th November 2008
Speaker: Daniel Stouffer
"A robust measure of food web intervality"
by Daniel B. Stouffer, Juan Camacho, and Luís A. Nunes Amaral
Speaker: Jonathan Doye
"Power-law distributions for the areas of the basins of attraction on a potential energy landscape"
by Claire P. Massen and Jonathan P. K. Doye

Monday, 17th November 2008
Speaker: Pau Creixell
"High-Quality Binary Protein Interaction map of the Yeast Interactome Network"
by Haiyuan Yu et al

Monday, 3rd November 2008
Speaker: Dan Fenn will discuss his recent paper -
"Dynamic Communities in Multichannel Data"

Monday, 27th October 2008
Speaker: Eduardo López
Paper: "Effects of epidemic threshold definition on disease spread statistics"
by C. Lagorio, M. V. Migueles, L. A. Braunstein, E. López, and P. A. Macri

Monday, 20th October 2008
Speaker: Anna Lewis
Paper: "Community Structure in Large Networks: Natural Cluster Sizes and the Absence of Large Well-Defined Clusters"
by Jure Leskovec, Kevin J. Lang, Anirban Dasgupta, Michael W. Mahoney

Monday, 13th October 2008
Speaker: Sumeet Agarwal
Paper: "Hierarchical structure and the prediction of missing links in networks"
by Aaron Clauset et al
DOI: doi:10.1038/nature06830


Friday, 13th June 2008
Speaker: Chiu Fan Lee
Paper: "Scaling Breakdown in Flow Fluctuations on Complex Networks"
by Sandro Meloni et al
DOI: 10.1103/PhysRevLett.100.208701

Friday, 23rd May 2008
Speaker: Mariano Beguerisse Dias
Paper: "Exact solution for the time evolution of network rewiring models"
by T. S. Evans and A. D. K. Plato
DOI: 10.1103/PhysRevE.75.056101

Friday, 16th May 2008
Speaker: Eduardo Lopez
Paper: "Resilience of the Internet to Random Breakdowns"
by Reuven Cohen et al
DOI: 10.1103/PhysRevLett.85.4626

Friday, 9th May 2008
Speaker: Stephen Reid
This week Stephen will talk about his M. Phys. project entitled, "Legislatures as spin glasses".
Time and Venue: 1.00pm, Mendelssohn Room, Clarendon Laboratory, Department of Physics

Friday, 11th April 2008
Speaker: Chiu Fan Lee
Paper: "Random Vibrational Networks and the Renormalization Group"
by M. B. Hastings
DOI: 10.1103/PhysRevLett.90.148702/

Friday, 7th March 2008
Speaker: Phillip Staniczenko
Paper: "Classes of complex networks defined by role-to-role connectivity profiles"
by Roger Guimerà, Marta Sales-Pardo and Luís A. N. Amaral
Nature Physics 3, 63 - 69 (2007) doi:10.1038/nphys489

Friday, 22nd February 2008
Speaker: Pau Creixell
Paper: "Evidence for dynamically organized modularity
in the yeast protein-protein interaction network
"
by Jing-Dong J. Han, Nicolas Bertin, Tong Hao, Debra S. Goldberg, Gabriel F. Berriz, Lan V. Zhang, Denis Dupuy, Albertha J.M. Walhout, Michael E. Cusick, Frederick P. Roth
and Marc Vidal
Nature 430, 88-93 (1 July 2004) | doi:10.1038/nature02555

Friday, 15th February 2008
Speaker: Jari Saramäki
Paper: "A model of large-scale proteome evolution"
by Ricard V. Solé, Romualdo Pastor-Satorras, Eric Smith, and Thomas B. Kepler
Paper PDF


Friday, 8th February 2008
Speaker: Nick Jones
Paper: "Community Structure in Graphs"
by Santo Fortunato and Claudio Castellano
Paper PDF

Friday, 25th January 2008
Speaker: Jukka-Pekka Onnela
Paper: "Emergence of Communities in Weighted Networks"
by Jussi M. Kumpula, Jukka-Pekka Onnela, Jari Saramäki, Kimmo Kaski and János Kertész
Paper PDF

Friday, 30th November 2007
Speaker: Nick Jones
Paper: "Spontaneous evolution of modularity and network motifs"
by Nadav Kashtan and Uri Alon
PNAS | September 27, 2005 | vol. 102 | no. 39 | 13773-13778

Friday, 23rd November 2007
Speaker: Jukka-Pekka Onnela
Paper: "Separating Internal and External Dynamics of Complex Systems"
by M. Argollo do Menezes and A.-L. Barabási
Paper PDF

Friday, 2nd November 2007
Speaker: Chiu Fan Lee
Paper: "Power-law distributions in empirical data"
by Aaron Clauset, Cosma Rohilla Shalizi, and M. E. J. Newman
Paper PDF

Friday, 12th October 2007
Speaker: Rui Carvalho
Paper: "Socioeconomic Networks with Long-Range Interactions"
by Rui Carvalho and Giulia Iori
Paper PDF

Friday, 21st September 2007
Speaker: Jukka-Pekka Onnela
Paper: "Fluctuation scaling in complex systems: Taylor's law and beyond"
by Zoltán Eisler, Imre Bartos and János Kertész
Paper PDF

Friday, 24th August 2007
Speaker: Sean Gourley
Paper: "A Gap in the Community-Size Distribution of a Large-Scale Social Networking Site"
by Kikuo Yuta, Naoaki Ono and Yoshi Fujiwara
Paper PDF

Friday, 17th August 2007
Speaker: Chiu Fan Lee
Paper: "Perturbation analysis of multi-asset portfolio optimization with transaction cost"
by Siu Lung Law, Chiu Fan Lee, Sam Howison, and Jeff N. Dewynne
Paper PDF

13th July 2007
“Kalman Filtering in the Presence of State Space Equality Constraints"
by Nachi Gupta
Paper PDF

6th July 2007
In this week's journal club Chiu Fan will talk about polymers.
The talk is not based on any particular paper but deals with the basic assumptions in polymer physics and how network structure affects the mechanical properties of polymers.

29th June 2007
"Weak pairwise correlations imply strongly correlated network states in a neural population"
by Elad Schneidman, Michael J. Berry II, Ronen Segev and William Bialek
Nature 440, 1007-1012 (20 April 2006) | doi:10.1038/nature04701

7th June 2007
"Network analysis of the state space of discrete dynamical systems"
by Amer Shreim, Peter Grassberger, Walter Nadler, Björn Samuelsson, Joshua E. S. Socolar, and Maya Paczuski
Paper PDF

18th May 2007
"Optimal Network Topologies for Local Search with Congestion"
by R. Guimerá, A. Díaz-Guilera, F. Vega-Redondo, A. Cabrales, and A. Arenas
Paper PDF

8th May 2007
"Exact Results for Cultural Transmission and Network Rewiring"
by Tim Evans
Paper PDF

20th April 2007
"Common Interaction Patterns across Biological and Organizational Networks"
by Serguei Saavedra (working paper)

"Quantitative patterns in the structure of model and empirical food webs"
by D. B. Stouffer, J. Camacho, R. Guimerá, C. A. Ng, and L. A. Nunes Amaral
Paper PDF

30th March 2007
"Clogging and self-organized criticality in complex networks"
by Ginestra Bianconi and Matteo Marsili
Phys Rev E Stat Nonlin Soft Matter Phys. 2004 Sep ;70 (3 Pt 2):035105 15524569

"Self-organized criticality and coevolution of network structure and dynamics"
by Piotr Fronczak, Agata Fronczak, and Janusz A. Holyst
Phys. Rev. E 73, 046117 (2006)

23rd March 2007
"Resolution limit in community detection"
by Santo Fortunato and Marc Barthelemy
Paper PDF

16th March 2007
"Evolving networks through deletion and duplication"
by Nadia Farid and Kim Christensen
Paper PDF