@article{automatic_filters, author = {Cosma Rohilla Shalizi and Robert Haslinger and Jean-Baptiste Rouquier and Kristina Lisa Klinkner and Cristopher Moore}, title = {Automatic Filters for the Detection of Coherent Structure in Spatiotemporal Systems}, url = {http://www.cscs.umich.edu/research/projects/AFICS/}, url2 = {http://www.cscs.umich.edu/~crshalizi/research/AFICS.pdf}, arxiv = {nlin.CG/0508001}, keywords = {filtering; local sensitivity; local statistical complexity; elementary cellular automata; cyclic cellular automata; coherent structures}, url3 = {http://link.aps.org/abstract/PRE/v73/e036104}, doi = {10.1103/PhysRevE.73.036104}, journal = {Physical Review E}, impactfactor = {2.4}, year = {2005}, month = {March}, volume = 73, number = 3, pages = {036104}, isbn = {3-540-34383-0}, abstract = {Most current methods for identifying coherent structures in spatially-extended systems rely on prior information about the form which those structures take. Here we present two new approaches to automatically filter the changing configurations of spatial dynamical systems and extract coherent structures. One, local sensitivity filtering, is a modification of the local Lyapunov exponent approach suitable to cellular automata and other discrete spatial systems. The other, local statistical complexity filtering, calculates the amount of information needed for optimal prediction of the system's behavior in the vicinity of a given point. By examining the changing spatiotemporal distributions of these quantities, we can find the coherent structures in a variety of pattern-forming cellular automata, without needing to guess or postulate the form of that structure. We apply both filters to elementary and cyclical cellular automata (ECA and CCA) and find that they readily identify particles, domains and other more complicated structures. We compare the results from ECA with earlier ones based upon the theory of formal languages, and the results from CCA with a more traditional approach based on an order parameter and free energy. While sensitivity and statistical complexity are equally adept at uncovering structure, they are based on different system properties (dynamical and probabilistic, respectively), and provide complementary information.}, importance = {International journals with review committee}, type_publi = {irevcomlec}, contribution = {I suggested to use statistical complexity as a visual filter, designed the local sensitivity measure, wrote the code and ran the simulations.} }

@inproceedings{Coalescing_CA_conf, title = {Coalescing Cellular Automata}, author = {Jean-Baptiste Rouquier and Michel Morvan}, booktitle = {Proceedings of the 6th International Conference on Computational Science (ICCS)}, year = 2006, doi = {10.1007/11758532_44}, editor = {Vassil N. Alexandrov and G. Dick van Albada and Peter M. A. Sloot and Jack Dongarra}, publisher = {Springer Berlin}, series = {Lectures Notes in Computer Science}, month = {May}, location = {Reading, UK}, volume = {3993}, part = {III}, pages = {321--328}, arxiv = {nlin.CG/0610009}, keywords = {cellular automata; directed percolation; asynchronous cellular automata; phase transition}, url = {http://prunel.ccsd.cnrs.fr/ensl-00103510/fr/}, old_crossref = {DBLP:conf/iccS/2006-3_rouquier.bib}, abstract = {We say that a Cellular Automata (CA) is coalescing when its execution on two distinct (random) initial configurations in the same asynchronous mode (the same cells are updated in each configuration at each time step) makes both configurations become identical after a reasonable time. We prove coalescence for two elementary rules and show that there exists infinitely many coalescing CA. We then conduct an experimental study on all elementary CA and show that some rules exhibit a phase transition, which belongs to the universality class of directed percolation.}, isbn = {3-540-34383-0}, importance = {International conferences with review committee}, type_publi = {icolcomlec}, paragraph_note = {There is an extended journal version in~\cite{Coalescing_CA_journal}.}, contribution = {Michel Morvan suggested research directions, I did the rest.} }

@article{Coalescing_CA_journal, author = {Jean-Baptiste Rouquier and Michel Morvan}, title = {Coalescing Cellular Automata: Synchronization by Common Random Source for Asynchronous Updating}, journal = {Journal of Cellular Automata}, impactfactor = {0.325}, year = {2009}, volume = {4}, umber = 1, pages = {55-78}, url = {http://oldcitypublishing.com/JCA/JCA.html}, arxiv = {0712.1992}, abstract = {We say that a Cellular Automata (CA) is coalescing when its execution on two distinct (random) initial configurations in the same asynchronous mode (the same cells are updated in each configuration at each time step) makes both configurations become identical after a reasonable time. We prove coalescence for two elementary rules, non coalescence for two other, and show that there exists infinitely many coalescing CA. We then conduct an experimental study on all elementary CA and show that some rules exhibit a phase transition, which belongs to the universality class of directed percolation.}, importance = {International journals with review committee}, type_publi = {irevcomlec}, contribution = {Michel Morvan suggested research directions, I did the rest.} }

@inproceedings{synchronization_by_forcing, title = {An Exhaustive experimental study of synchronization by forcing on elementary cellular automata}, author = {Jean-Baptiste Rouquier}, booktitle = {Proceedings of the First Symposium on Cellular Automata}, year = 2008, editor = {Bruno Durand}, publisher = {MCCME Publishing House, Moscow}, isbn = {978-5-94057-377-7}, month = {April}, pages = {250--261}, url = {http://hal.archives-ouvertes.fr/hal-00274006/en/}, url2 = {http://www.lif.univ-mrs.fr/jac/actes/250-261.pdf}, abstract = {We study a way of coupling two configurations of the same cellular automaton rule for all elementary cellular automata (ECA). We experimentally show that there are only two possible behaviors: either synchronization for all coupling strength, or a phase transition. This transition is shown to belong to the directed percolation universality class, even for a non chaotic rule and for rules with particles.}, importance = {International conferences with review committee}, type_publi = {icolcomlec} }

@comment{{publisher="Москва Издательство МЦНМО"}}

@inproceedings{topo_synchro_perturbation, title = {Combined Effect of Topology and Synchronism Perturbation on Cellular Automata: Preliminary Results}, author = {Jean-Baptiste Rouquier and Michel Morvan}, booktitle = {ACRI}, year = 2008, editor = {Hiroshi Umeo and Shin Morishita and Katsuhiro Nishinari}, publisher = {Springer Berlin}, series = {LNCS}, volume = {5191}, doi = {10.1007/978-3-540-79992-4_28}, url = {http://www.rouquier.org/jb/research/papers/2008_topology_perturbation/topology_perturbation.pdf}, url2 = {http://www.springerlink.com/content/j6t671003226nl2n/}, url3 = {http://hal.archives-ouvertes.fr/hal-00541474/fr/}, keywords = {cellular automata; perturbation; topology perturbation; synchronism; synchronism perturbation; complex system}, abstract = {The aim of this paper is to experimentally study the combined effect of the introduction of two kinds of structural perturbations to the behavior of cellular automata. We present the results obtained by simultaneously perturbing synchronism and topology of elementary cellular automata. We show that very interesting and different behaviors appear, including phase transitions and non monotonicity (i.e. introduction of both perturbations is less effective than the introduction of only one of them). These results lead us to think that this study is worth to be now developed more accurately.}, importance = {International conferences with review committee}, type_publi = {icolcomlec}, contribution = {Michel Morvan suggested research directions, I did the rest.} }

@article{bibliometry-vs-promotion, title = {Testing bibliometric indicators by their prediction of scientists promotions}, author = {Pablo Jensen and Jean-Baptiste Rouquier and Yves Croissant}, journal = {Scientometrics}, impactfactor = {2.167}, year = 2009, volume = 78, number = 3, month = {March}, doi = {10.1007/s11192-007-2014-3}, issn_online = {1588-2861}, issn = {0138-9130}, hal = {ensl-00336140}, arxiv = {0811.0237}, keywords = {bibliometric indicators; h-index; Hirsch index; career; scientific career; academic career; promotion; citations}, abstract = {We have developed a method to obtain robust quantitative bibliometric indicators for several thousand scientists. This allows us to study the dependence of bibliometric indicators (such as number of publications, number of citations, Hirsch index...) on the age, position, etc. of CNRS scientists. Our data suggests that the normalized $h$ index ($h$ divided by the career length) is not constant for scientists with the same productivity but differents ages. We also compare the predictions of several bibliometric indicators on the promotions of about 600 CNRS researchers. Contrary to previous publications, our study encompasses most disciplines, and shows that no single indicator is the best predictor for all disciplines. Overall, however, the Hirsch index $h$ provides the least bad correlations, followed by the number of papers published. It is important to realize however that even $h$ is able to recover only half of the actual promotions. The number of citations or the mean number of citations per paper are definitely not good predictors of promotion.}, importance = {International journals with review committee}, type_publi = {irevcomlec}, contribution = {Pablo Jensen had the original idea, obtained some data and did part of the analysis. I collected the bibliometric data and did part of the analysis.} }

@article{bibliometry_and_vulgarization, title = {Scientists who engage with society perform better academically}, oldtitle = {Scientists connected with society are more active academically}, author = {Pablo Jensen and Jean-Baptiste Rouquier and Pablo Kreimer and Yves Croissant}, journal = {Science and Public Policy}, year = 2008, month = {Aug}, day = {20}, url = {http://www.ingentaconnect.com/content/beech/spp/2008/00000035/00000007/art00006}, volume = 35, number = 7, issn = {0302-3427}, issn_online = {1471-5430}, pages = {527--541}, doi = {10.3152/030234208X329130}, arxiv = {0810.4672}, keywords = {popularization; vulgarization:dissemination; h-index; bibliometry; bibliometric indicator; promotion; scientific career; academic career; teaching; industrial collaboration}, hal = {ensl-00334363}, abstract = {Most scientific institutions acknowledge the importance of opening the so-called 'ivory tower' of academic research through popularization, industrial collaboration or teaching. However, little is known about the actual openness of scientific institutions and how their proclaimed priorities translate into concrete measures. This paper gives an idea of some actual practices by studying three key points: the proportion of researchers who are active in wider dissemination, the academic productivity of these scientists, and the institutional recognition of their wider dissemination activities in terms of their careers. We analyze extensive data about the academic production, career recognition and teaching or public/industrial outreach of several thousand of scientists, from many disciplines, from France's Centre National de la Recherche Scientifique. We find that, contrary to what is often suggested, scientists active in wider dissemination are also more active academically. However, their dissemination activities have almost no impact (positive or negative) on their careers.}, importance = {International journals with review committee}, type_publi = {irevcomlec}, contribution = {Pablo Jensen had the original idea, obtained some data and did part of the analysis. I collected the bibliometric data and did part of the analysis.} }

@phdthesis{rouquier_phd, author = {Jean-Baptiste Rouquier}, year = 2008, month = {December}, title = {Robustesse et émergence dans les systèmes complexes: le modèle des automates cellulaires}, school = {École Normale Supérieure de Lyon}, url = {http://rouquier.org/jb/recherche/these.php}, hal = {tel-00354042}, importance = {Misc.}, type_publi = {autre}, paragraph_note = {See the dedicated page.} }

@inproceedings{Velov_ECCS09, title = {Studying {L}yon's {V}\'elo'v: A Statistical Cyclic Model}, author = {Pierre Borgnat and Patrice Abry and Patrick Flandrin and Jean-Baptiste Rouquier}, booktitle = {Proceedings of the European Conference on Complex Systems (ECCS)}, year = 2009, month = {September}, location = {Warwick, UK}, publisher = {Complex System Society}, keywords = {Complex System; Community bicycle program ; {V}{\'e}lo'v; Cyclostationarity; Auto-Regressive Process}, affiliation = {Laboratoire de Physique de l'{ENS} {L}yon - {CNRS} : {UMR}5672 - {\'E}cole normale sup{\'e}rieure de {L}yon - {ENS} {L}yon - Laboratoire de l'Informatique du Parall{\'e}lisme - {LIP} - {INRIA} - {CNRS} : {UMR}5668 - Universit{\'e} {C}laude {B}ernard {L}yon {I} - Institut Rh{\^o}ne-Alpin des syst{\`e}mes complexes - {IXXI} - Institut National des Sciences Appliqu{\'e}es de Lyon - Ecole Normale Sup{\'e}rieure Lettres et Sciences Humaines - Universit{\'e} {J}oseph {F}ourier {G}renoble {I} - {IRD} }, abstract = {Lyon's community bicycle program called V\'elo'v is a major initiative in shared public transportation, in activity since May 2005. It is studied here at a global level, to assess the evolution with time of the number of hired bikes. Based on the entire V\'elo'v data set, up to December 2007, a statistical model is proposed to describe the daily and weekly patterns in a cyclostationary manner, jointly with the non-stationary evolutions over larger time-scales larger. Combining this model with linear statistical regression, a procedure is developed for the prediction of the number of bikes hired per hour. This prediction method involves several explanation factors such as the number of subscribed users, the time in the week, the occurrence of holidays or strikes, and weather parameters (temperature, volume of rain). The conclusion is that, for most days, the observation of the number of actually hired bicyles is satisfyingly explained and predicted by the model proposed here.}, url = {http://prunel.ccsd.cnrs.fr/ensl-00408147/en/}, importance = {International conferences with review committee}, type_publi = {icolcomlec}, contribution = {Pierre Borgnat led the research and did part of the analysis, Patrice Abry obtained the data and did part of the analysis, I collected complementary data and did part of the analysis.} }

@article{Velov_ACS, title = {Shared Bicycles in a City: A Signal Processing and Data Analysis Perspective}, url = {http://hal.archives-ouvertes.fr/ensl-00490325/}, author = {Pierre Borgnat and C\'eline Robardet and Jean-Baptiste Rouquier and \'Eric Fleury and Patrice Abry and Patrick Flandrin}, abstract = {Community shared bicycle systems, like the V\'elo'v program launched in Lyon in May 2005, are public transportation programs that can be studied as a complex system composed of interconnected stations that exchange bicycles. They generate digital footprints that reveal the activity in the city over time and space, making possible a quantitative analysis of people’s movements. A careful study relying on nonstationary statistical modeling and data mining is done to first model the time evolution of the dynamics of movements with V\'elo'v, that is mostly cyclostationary over the week with nonstationary evolutions over larger time-scales, and second to disentangle the spatial patterns to understand and visualize the flows of V\'elo'v bicycles in the city. This study gives insights about social behaviors of the users of this intermodal transportation system, the objective being to help in designing and planning policy in urban transportation.}, journal = {Advances in Complex Systems}, impactfactor = {0.723}, year = 2010, note = {Accepted}, importance = {International journals with review committee}, type_publi = {irevcomlec}, contribution = {Pierre Borgnat led the research and did part of the analysis, Patrice Abry obtained the data and did part of the analysis, I collected complementary data and did part of the analysis.} }

@techreport{minority-on-trees_techreport, author = {Damien Regnault and Jean-Baptiste Rouquier and \'Eric Thierry}, title = {Stochastic Minority on Graphs}, url = {http://hal.archives-ouvertes.fr/hal-00272271/}, year = 2008, month = {April}, institution = {LIP, ENS Lyon, Université de Lyon}, abstract = {Cellular automata have been mainly studied on very regular graphs carrying the cells (like lines or grids) and under synchronous dynamics (all cells update simultaneously). In this paper we study how the asynchronism and the topology of cells act upon the dynamics of the classical Minority rule. Beyond its apparent simplicity, this rule yields complex behaviors which are clearly linked to the structure of the graph carrying the cells.}, importance = {Misc.}, type_publi = {autre}, paragraph_note = {There is an extended journal version in~\cite{stochastic_minority_on_graphs}.}, contribution = {Alphabetical author list. Damien Regnault authored biased trees, I coauthored binary trees with \'Eric Thierry and authored both appendices.} }

@inproceedings{active_learning, title = {Active Learning for Hidden Attributes in Networks}, booktitle = {22nd Annual Conference on Neural Information Processing Systems, Workshop on Analyzing Networks and Learning with Graphs}, author = {Xiao Ran Yan and Yao Jia Zhu and Jean-Baptiste Rouquier and Cristopher Moore}, year = 2009, editor = {Edoardo Airoldi and Jon Kleinberg and Jure Leskovec and Josh Tenenbaum}, url = {http://snap.stanford.edu/nipsgraphs2009/papers/yan-paper.pdf}, url2 = {http://www.santafe.edu/media/workingpapers/10-02-003.pdf}, url3 = {http://hal.archives-ouvertes.fr/hal-00541417}, keywords = {active learning; collective classification; machine learning; foodweb; complex networks; node label; mutual information}, location = {Whistler, BC, Canada}, month = {December}, day = 11, arxiv = {1005.0794}, abstract = {In many networks, vertices have hidden attributes that are correlated with the network’s topology. For instance, in social networks, people are more likely to be friends if they are demographically similar. In food webs, predators typically eat prey of lower body mass. We explore a setting in which the network’s topology is known, but these attributes are not. If each vertex can be queried, learning the value of its hidden attributes— but only at some cost—then we need an algorithm which chooses which vertex to query next, in order to learn as much as possible about the attributes of the remaining vertices. We assume that the network is generated by a probabilistic model, but we make no assumptions about the assortativity or disassortativity of the network. We then query the vertex with the largest mutual information between its type and that of the others (a well-known approach in active learning) or with the largest average agreement between two independent samples of the Gibbs distribution which agree on its type. We test these approaches on two networks with known attributes, the Karate Club network and a food web of species in the Weddell Sea. We find that the average agreement algorithm performs better than mutual information, and that both perform better than simpler heuristics. The algorithms appear to explore the network intelligently, first querying vertices at the centers of communities, and then vertices along the boundaries between communities.}, importance = {International conferences with review committee}, type_publi = {icolcomlec}, contribution = {I designed one of both heuristics, the average agreement.} }

@article{velov_speed_paths, title = {Characterizing the speed and paths of shared bicycles in {L}yon}, author = {Pablo Jensen and Jean-Baptiste Rouquier and Nicolas Ovtracht and Céline Robardet}, journal = {Transportation Research Part D: Transport and Environment}, impactfactor = {1.214}, volume = {15}, number = {8}, pages = {522 - 524}, year = {2010}, issn = {1361-9209}, doi = {10.1016/j.trd.2010.07.002}, arxiv = {1011.6266}, url = {http://liris.cnrs.fr/Documents/Liris-4800.pdf}, url2 = {http://www.sciencedirect.com/science/article/B6VH8-50NH66M-1/2/04fe18899f4465e443e02c2d05f9ba01}, url3 = {http://hal.archives-ouvertes.fr/hal-00541307}, keywords = {Vélov; transport; average speed; bike; cycling; bike lane; cycleway; bike path; path; car}, url4 = {http://www.ens-lyon.eu/1278323836875/0/fiche___article/&RH=ENS-LYON-FR-LETTREIN}, abstract = {Thanks to numerical data gathered by Lyon's shared bicycling system Vélo'v, we are able to analyze 11.6 millions bicycle trips, leading to the first robust characterization of urban bikers' behaviors. We show that bicycles outstrip cars in downtown Lyon, by combining high speed and short paths.These data also allows us to calculate Vélo'v fluxes on all streets, pointing to interesting locations for bike paths.}, importance = {International journals with review committee}, type_publi = {irevcomlec}, contribution = {Pablo Jensen led the research. I did the data analysis on the average speed.} }

@article{stochastic_minority_on_graphs, title = {Stochastic Minority on Graphs}, author = {Damien Regnault and Jean-Baptiste Rouquier and Eric Thierry}, journal = {Theoretical Computer Science}, impactfactor = {0.943}, volume = {Special issue on Cellular automata and Discrete dynamical systems}, year = {2011}, arxiv = {1011.5119}, doi = {10.1016/j.tcs.2011.02.028}, keywords = {cellular automata; minority; asynchronism; graph; perturbation}, abstract = {Cellular automata have been mainly studied on very regular graphs carrying the vertices (like lines or grids) and under synchronous dynamics (all vertices update simultaneously). In this paper, we study how the asynchronism and the graph act upon the dynamics of the classical Minority rule. Minority has been well-studied for synchronous updates and is thus a reasonable choice to begin with. Yet, beyond its apparent simplicity, this rule yields complex behaviors when asynchronism is introduced. We investigate the transitory part as well as the asymptotic behavior of the dynamics under full asynchronism (also called sequential: only one random vertex updates at each time step) for several types of graphs. Such a comparative study is a first step in understanding how the asynchronous dynamics is linked to the topology (the graph). Previous analyses on the grid have observed that Minority seems to induce fast stabilization We investigate here this property on arbitrary graph using tools such as energy, particles and random walks. We show that the convergence time is, in fact, strongly dependent on the topology. In particular, we observe that the case of trees is non trivial.}, note = {In press}, importance = {International journals with review committee}, type_publi = {irevcomlec}, contribution = {Alphabetical author list. Damien Regnault authored biased trees, I coauthored binary trees with \'Eric Thierry and authored both appendices.} }

@article{PCA-ising-coalescing-time-is-gumbel, title = {Time-to-Coalescence for Interacting Particle Systems: Parallel versus Sequential Updating}, author = {Pierre-Yves Louis and Jean-Baptiste Rouquier}, journal = {Statistics and Computing}, note = {In preparation}, year = 2010, importance = {In preparation}, type_publi = {inprep} }

@article{Topological-phase-transition-in-complex-networks, title = {Topological phase transition in complex networks}, author = {Cris Moore and Jean-Baptiste Rouquier and David Sherrington}, journal = {European Physics Journal B}, note = {In preparation}, year = 2010, importance = {In preparation}, type_publi = {inprep}, contribution = {Alphabetical author list. I did part of the proofs and ran the simulations.} }

@article{velov_carto, title = {L'usage des vélos en libre service ({VLS}) comme révélateur des rythmes urbains~: le cas des stations de {V}élo'v à {L}yon}, author = {Luc Merchez and Jean-Baptiste Rouquier}, journal = {Données Urbaines}, note = {Submitted}, year = 2010, importance = {In preparation}, type_publi = {inprep}, contribution = {I collected the data and did part of the analysis. Luc Merchez had the original idea, made the maps, did part of the analysis.} }

@article{complex_systems_scientometry, title = {Complex systems science: dreams of universality, reality of interdisciplinarity}, author = {Sébastian Grauwin and Guillaume Beslon and Eric Fleury and Sara Franceschelli and Céline Robardet and Jean-Baptiste Rouquier and Pablo Jensen}, journal = {PlosOne}, impactfactor = {4.351}, note = {Accepted}, year = 2011, abstract = {Thanks to a large database (215 000 records) of relevant articles, we empirically study the ``complex systems'' field and its claims to find universal principles applying to systems in general. Study of the references shared by the papers allows us to obtain a global point of view on the structure of this highly interdisciplinary field. We show that its overall coherence does not arise from a universal theory but instead from computational techniques and fruitful adaptations of the idea of self-organization to specific systems. At a more local level, specifically interdisciplinary, we find that understanding between vastly different scientific cultures is possible thanks to ``trading zones'', i.e. sub-communities that manage to work at the interface around specific tools (a DNA microchip) or concepts (a network).}, importance = {International journals with review committee}, type_publi = {irevcomlec}, contribution = {I collected the data and did part of the analysis.} }

@inproceedings{active_learning_KDD, title = {Active Learning for Hidden Attributes in Networks}, author = {Cristopher Moore and Xiaoran Yan and Yaojia Zhu and Jean-Baptiste Rouquier and Terran Lane}, year = 2011, booktitle = {KDD (International Conference on Knowledge Discovery and Data Mining)}, note = {Accepted. Acceptance rate: 17.5\%}, abstract = {Preferential attachment is a popular model of growing networks. We consider a generalized model with random node removal, and a combination of preferential and random attachment. Using a high-degree expansion of the master equation, we identify a topological phase transition depending on the rate of node removal and the relative strength of preferential vs. random attachment, where the degree distribution goes from a power law to one with an exponential tail.}, importance = {International conferences with review committee}, type_publi = {icolcomlec}, contribution = {I designed one of both heuristics, the average agreement.} }

@article{quadtree_viability, title = {A kd-tree algorithm to find and store hypervolumes}, author = {Jean-Baptiste Rouquier and Isabelle Alvarez and Pierre-Henri Wuillemin and Romain Reuillon}, year = 2011, importance = {In preparation}, type_publi = {inprep}, contribution = {I designed the algorithm, determined its complexity, and wrote the paper.} }

@article{publications_europe, title = {Quelques éléments sur la géographie de la recherche en Europe}, author = {Pablo Jensen, Andrea Apolloni, Jean-Baptiste Rouquier}, journal = {Données Urbaines}, note = {Submitted}, year = 2011, importance = {In preparation}, type_publi = {inprep}, contribution = {I did part of the analysis.} }

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