Network Seminar

Since December 2018, we are organizing along with Liubov Tupikina a network seminar series at CRI Paris. Talks showcase the use of network science in a wide range of disciplines, from physics to mathematics, biology, social sciences or neurosciences, and are intended for a broad, interdisciplinary audience.

Below you can find the past and upcoming speakers. Please contact us if you know someone working with networks who would be a great speaker for this event! Talks are 45 min + 15 min questions, and are usually held on Thursdays at 5pm in room 5.11 at CRI Paris, 8bis rue Charles V 75004 Paris (now online during the COVID19 pandemic).

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18 Feb 2020 – Laura Cantini (CNRS, ENS)

Network-guided integration of multi-omics data: towards a comprehensive view of cancer

Abstract: Due to the advent of high-throughput technologies, high-dimensional “omics” data are produced at an increasing pace. In cancer biology, national and international consortia have profiled thousands of tumors at multiple molecular levels (“multi-omics”) allowing to gather a comprehensive molecular picture of this disease. Moreover, multi-omics profiling approaches are currently being transposed at single-cell resolution, further increasing the information accessible from cancer samples. The current main challenge is to design appropriate methods to integrate this wealth of information and translate it into actionable biological knowledge. In this talk I will give some examples on the use of networks to mine and integrate multi-omics data with the ultimate aim of revealing new insights into cancer biology.

Bio: Laura Cantini is a CNRS permanent researcher at the Institut de Biologie de l’Ecole Normale Supérieure (IBENS). She develops machine learning methods for the integration of bulk and single-cell data. In addition, she closely collaborates with biologists to address specific biological questions by applying the developed methods. Mathematician by training, Laura received her PhD in cancer systems biology from the University of Turin (Italy). She then pursed a postdoc in the cancer system biology group at Institut Curie (Paris). In 2018, awarded of the L’Oréal-UNESCO for Women in Science and EMBO fellowship, she joined CSAIL at MIT (USA), before being selected as CNRS permanent researcher. In 2020, She is recipient of an ANR JCJC and Sanofi iTech Awards funding which gave her the possibility to start her independent research line.

21 Jan 2021 – Jürgen Kurths (Humboldt University)

Quantifying Stability in Deterministic and Stochastic Complex Networks and its Application to Power Grids
Network seminar "Quantifying Stability in Deterministic and Stochastic Complex Networks and its Application to Power Grids"

Abstract: Power grids, the human brain, arrays of coupled lasers, genetic networks, or the Amazon rainforest are all characterized by multistability. The likelihood that these systems will remain in the most desirable of their many stable states depends on their stability against significant perturbations, particularly in a state space populated by undesirable states. Here we claim that the traditional linearization-based approach to stability is in several cases too local to adequately assess how stable a state is. Instead, we quantify it in terms of basin stability, a new measure related to the volume of the basin of attraction. Basin stability is non-local, nonlinear and easily applicable, even to high-dimensional systems. It provides a long-sought-after explanation for the surprisingly regular topologies of neural networks and power grids, which have eluded theoretical description based solely on linear stability. Remarkably, when taking physical losses in the network into account, the back-reaction of the network induces new exotic solitary states in the individual actors, and the stability characteristics of the synchronous state are dramatically altered. These novel effects will have to be explicitly taken into account in the design of future power grids, and their existence poses a challenge for control.

Bio: Jürgen Kurths studied mathematics at the University of Rostock. He received the Ph.D.degree from the GDR Academy of Sciences, in 1983. He was a Full Professor with the University of Potsdam, from 1994 to 2008. He has been a Professor of nonlinear dynamics at the Humboldt University, Berlin, and the Chair of the Research Domain Complexity Science of the Potsdam Institute for Climate Impact Research, since 2008. He has published more than 600 articles that are cited more than 48,000 times (H-factor: 99). His primary research interests include synchronization, complex networks, and time series analysis and their applications in Earth Sciences, Physiology, infrastructure and others. He is a Fellow of the American Physical Society. He became a member of the Academia Europaea, in 2010. He received the Alexander von Humboldt Research Award from CSIR, India, in 2005, and the Richardson award from the European Geoscience Union in 2013. He got eight Honory Doctorates and Honorary Professors. He is Editor-in-chief of the Journal of Nonlinear Science, and Chaos and editor of about 10 further journals, such as Europ. Physics Lett.

References:
P. Menck, J. Heitzig, N. Marwan, and J. Kurths, Nature Physics 9, 89 (2013)
P. Menck, J. Heitzig, J. Kurths, and H. Schellnhuber, Nature Communication 5, 3969 (2014)
Y. Zou, T. Pereira, M. Small, Z. Liu, and J. Kurths, Phys. Rev. Lett. 112, 114102 (2014)
F. Hellmann, P. Schultz, C. Grabow, J. Heitzig, and J. Kurths, Scient. Rep. 6, 29654 (2016)
Y. Xu, Y. Li, H. Zhang, X. Li, and J. Kurths, Scient. Rep. 6, 31505 (2016)
J. Nitzbon, P. Schultz, J. Heitzig, J. Kurths, and F. Hellmann, New J. Phys. 19, 033028 (2017)
F. Hellmann, P. Schultz, P. Jaros, R. Levchenko, T. Kapitaniak, J. Kurths, and Y. Maistrenko, Nature Communications 11, 592 (2020)

10 Dec 2020 – Tiago P. Peixoto (CEU)

Network reconstruction from indirect observations

Abstract: The observed functional behavior of a wide variety of large-scale systems is often the result of a network of pairwise interactions. However, in many cases these interactions are hidden from us, either because they are impossible or very costly to be measured directly, or, in the best case, are measured with some degree of uncertainty. In such situations, we are required to infer the network of interactions from indirect information.

In this talk, I present a scalable Bayesian method to perform network reconstruction from indirect data, including noisy measurements and observed network dynamics. This kind of approach allows us to convey in a principled manner the uncertainty present in the measurement, and combined with versatile modelling assumptions can yield good results even when data are scarce. In particular, I describe how the reconstruction approach can be combined with community detection, allowing us to tap into multiple sources of evidence available for the task. I show how this combined approach provides a twofold improvement, by increasing not only the reconstruction accuracy, but also the identification of communities in networks. The latter improvement is possible even in situations where at first we might imagine that reconstruction is superfluous, for example when direct network data are available and measurement errors can be neglected.

Bio: Tiago P. Peixoto is an Associate Professor at the Department of Network and Data Science at the Central European University (https://networkdatascience.ceu.edu/people/tiago-peixoto). His research focuses on characterizing, identifying and explaining large-scale patterns found in the structure and function of complex network systems — representing diverse phenomena with physical, biological, technological, or social origins — using principled approaches from statistical physics, nonlinear dynamics and Bayesian inference. Peixoto develops and maintains graph-tool — an efficient Python module for manipulation and statistical analysis of graphs and networks. He has a PhD in Physics from the University of São Paulo, and a Habilitation in Theoretical Physics from the University of Bremen. In 2019 he was the recipient of the Erdős–Rényi Prize in Network Science, awarded by the Network Science Society.

19 Nov 2020 – Michele Starnini (ISI Foundation)

Emergence of echo chambers and polarization dynamics in social networks

Abstract: Echo chambers and opinion polarization, recently quantified in several sociopolitical contexts and across different social media, raise concerns on their potential impact on the spread of misinformation and on the openness of debates. Despite increasing efforts, the dynamics leading to the emergence of these phenomena stay unclear. In this talk, we will first review empirical evidence for the presence of echo chambers across social media platforms, by performing a comparative analysis among Gab, Facebook, Reddit, and Twitter. Then, we will present a simple modeling framework able to reproduce the observed opinion segregation in the social network. We consider networked agents characterized by heterogeneous activities and homophily, whose opinions can be reinforced by interactions with like-minded peers. We show that the transition between a global consensus and emerging polarized states in the network can be analytically characterized as a function of the social influence of the agents and the controversialness of the topic discussed. Finally, we consider a generalization to multiple opinions with respect to different topics. Inspired by skew coordinate systems recently proposed in natural language processing models, we frame this problem in a formalism in which opinions evolve in a multidimensional space where topics form a non-orthogonal basis. We show that this approach can reproduce the correlations between extreme opinions on different topics found in survey data.

Bio: Michele Starnini is currently Research Fellow in Network and Data Science at ISI Foundation. Before, he was Principal Investigator of a project funded by the J. S. McDonnell Foundation, at the University of Barcelona. His interests are the understanding of emerging socio-economic phenomena, such as the epidemic spreading of behaviors or ideas in a population, the dynamics of physical interactions in social gatherings, or cooperation/collaboration among individuals. At a more theoretical level, he studies the behavior of dynamical processes on static and time-varying networks.

12 Nov 2020 – Geoffroy Berthelot (INSEP)

Pseudo-Darwinian network evolution

Abstract:

The paper which we will present you is from our recent publications [1,2] and is related to the topic of extreme cost optimization and network fragility/vulnerability.

Variety of natural and human-engineered processes  including biological, societal and technological  ones can be presented as transportation networks.
Common examples include blood vessel networks and the lung airway tree that deliver blood and oxygen molecules.

In our work the evolution of complex transport networks is investigated under three strategies of link removal: random, intentional attack and “Pseudo-Darwinian” strategy. At each evolution step and regarding the selected strategy, one removes either a randomly chosen link, or the link carrying the strongest flux, or the link with the weakest flux, respectively. We study how the network structure and the total flux between randomly chosen source and drain nodes evolve. We discover a universal power- law decrease of the total flux, followed by an abrupt transport collapse. The time of collapse is shown to be determined by the average number of links per node in the initial network, highlighting the importance of this network property for ensuring safe and robust transport against random failures, intentional attacks and maintenance cost optimizations

[1] https://www.nature.com/articles/s41598-019-44701-6

[2] https://www.nature.com/articles/s41598-020-72379-8.epdf?sharing_token=mbk1IDqUeNUR7adSeHXjfNRgN0jAjWel9jnR3ZoTv0Oi1H-B424AS93IwP7vT72wDLz4low6XTqv–xoSw3KkXzcq8igrHUR_n5UM6ki0W7_0ZDtW8RbfeNBzu2p3npznled1YWY4MFRB8ZN6rxd3oLj0fEb4W62aNr4JEQwIU4%3D

5 Nov 2020 –  Massimo Stella (University of Exeter)

Cognitive network science as a proxy for accessing key ideas and emotions in people’s minds

Abstract: This talk focuses on recent applications of network science to the quantification of cognitive patterns about people’s perceptions. The recent field of cognitive network science, at the intersection between computer science, psycholinguistics and complex systems, provides novel tools for reconstructing how people frame and perceive events by means of conceptual associations, sentiment analysis and emotional profiling. Different case studies will be investigated, such as: (i) identifying subjective perceptions of STEM subjects in students and researchers, (ii) reconstructing the emotional profiles of social discourse around the gender gap in science and (iii) the identification of emotional patterns over time within the social discourse of COVID-19. Research gaps and potential bridges with natural language processing and AI will be highlighted, as well as theoretical motivations brought up by the current literature in cognitive science. Cognitive networks provide a transparent access to knowledge structure and its perceptions, opening the way to important future applications for policy making, interpretable AIs and social good.

8 Oct 2020 – Elisa Omodei (World Food Programme’s Research)

Who, where, why: non-traditional data and predictive analytics to map socio-economic vulnerabilities

Abstract: In a rapidly changing world, severely affected by extreme weather events, epidemic outbreaks, economic shocks and conflicts, it is of fundamental importance to understand where the most vulnerable people are, how many they are, and to identify what it is that makes them more vulnerable than others to these threats. During the last decade, research has shown that data such as digital traces, phone metadata and satellite imagery carry relevant information beyond their original purpose and can be used as a proxy to measure socio-economic characteristics and detect vulnerabilities when traditional data is not available. Following an overview of these studies, the talk will deep dive into the UN World Food Programme’s original work on predicting food security. We will then conclude by discussing challenges and limitations, but also opportunities, that come with these approaches.

Bio:  Elisa Omodei is the Predictive Analytics Lead of the Hunger Monitoring Unit at the World Food Programme’s Research, Assessment and Monitoring division. She also serves as Vice-President Secretary of the Complex Systems Society. She holds a BSc and a MSc in Physics and a PhD in Applied Mathematics for the Social Sciences. After her PhD, she spent a few years in academia before joining the United Nations in 2017, first at UNICEF’s Office of Innovation and now at the World Food Programme.

9 July 2020 – Petter Holme (Tokyo Tech)

Freedom of choice adds value to public goods

Abstract: Public goods, ranging from judiciary to sanitation to parkland, permeate daily life. They have been a subject of intense interdisciplinary study, with a traditional focus being on participation levels in isolated public goods games (PGGs) as opposed to a more recent focus on participation in PGGs embedded into complex social networks. We merged the two perspectives by arranging voluntary participants into one of three network configurations, upon which volunteers played a number of iterated PGGs within their network neighborhood. The purpose was to test whether the topology of social networks or a freedom to express preferences for some local public goods over others affect participation. The results show that changes in social networks are of little consequence, yet volunteers significantly increase participation when they freely express preferences. Surprisingly, the increase in participation happens from the very beginning of the game experiment, before any information about how others play can be gathered. Such information does get used later in the game as volunteers seek to correlate contributions with higher returns, thus adding significant value to public goods overall. These results are ascribable to a small number of behavioral phenotypes, and suggest that societies may be better off with bottom-up schemes for public goods provision.

28 May 2020 – Luca Aiello (Bell Labs, Cambridge)

Ten Dimensions of Social Relationships

Abstract: Social relationships are the key determinant of crucial societal outcomes, including diffusion of innovation, productivity, happiness, and life expectancy. To better attain such outcomes at scale, it is therefore paramount to have technologies that can effectively capture the type of social relationships from digital data. NLP researchers have tried to do so from conversational text but mostly focusing on sentiment or topic mining, techniques that fall short on either conciseness or exhaustiveness. We propose a theoretical model of 10 dimensions of social relationships that is backed by decades of research in social sciences and that captures most of common relationship types. We trained a deep-learning model to classify text along these ten dimensions, and we reached performance up to 0.98 AUC. By applying this tool on large-scale conversational data, we show that the combination of the predicted dimensions suggests both the types of relationships people entertain and the types of real-world communities they shape. As a use case, we show how this technology can be used in the domain of employer care by predicting Nokia employee satisfaction from online review text

Bio: Luca Maria Aiello is a Senior Research Scientist in the Social Dynamics team at Nokia Bell Labs Cambridge, UK. Formerly, he has been a Research Scientist at Yahoo Labs for almost 5 years and a research Fellow of the ISI Foundation in Torino, Italy. He conducts interdisciplinary research in computational social science and network science. His work has been covered by hundreds of news articles published by news outlets worldwide including Wired, WSJ, and BBC. He is currently working on NLP research to model fundamental aspects of human relationships from conversational text.

27 Feb 2020 – Jean-philippe Cointet (Sciences Po Media Lab)

The structure of the French media space and the Yellow vest movement

Abstract: I will start by outlining the main results of the structural description of the French media sphere we are working on at médialab. We are collecting data at two distinct levels of the media system: the daily publication of articles by the 400 main news outlets, and the interactions that these articles incite (citations to media sources) on Twitter. The morphology of the media space that is emerging is characterized by a very high concentration of authority (particularly visible in the distribution of hypertext links) and a rather limited ideological polarization. This first result is in stark contrast with the structure of the media space as observed in the United States. We will finally consider how this organization is being challenged at another layer of the public space: conversations on Facebook. We will show, in particular, how Yellow Vests group pages redistribute order between the different media.

Bio: Jean-Philippe Cointet is working at the Sciences Po médialab, where he designs innovative computational sociology methods. He is specialized in text analysis, and is working on various kinds of corpora and sources questioning their socio-political dynamics. His research areas are diverse, ranging from social media analysis (Facebook public posts and comments) to science of science (data turn in oncology)or political processes mapping (political discourses, international negotiations) and frame analysis (press coverage of migration processes). He also participates in developing the CorText platform. He holds a PhD in Complex Systems and was trained as an engineer at Ecole Polytechnique. He is also affiliated with the research center INCITE, from Columbia University.

28 Nov 2019Blaise Delmotte (CNRS, LadHyX, Ecole Polytechnique)

Leveraging Collective Effects in Active Fluids

Abstract: We have all witnessed the flocking of starlings in the sky and the schools of fish that form in the ocean. This kind of organization of living systems is not limited to those that we see, but also occurs for those that we don’t: swimming micro-organisms. Collections of micro-swimmers, such as bacteria or sperm cells, exhibit a rich dynamics. They can form coherent structures due to collective motion, mix the surrounding fluid or tune some of its effective physical properties. These fascinating phenomena raise a fundamental question: how can a living system self-organize without any sensorial or cognitive functions ?

Beyond the fundamental interest in the physical understanding of such “active fluids”, their precise modeling is also likely to have applications to the design of new fluid systems with synthetic controllable properties. More recently, artificial micro-swimmers have been developed to mimic these behaviors, but also to achieve specific functions, such as targeted drug delivery or transport in microfluidic systems. 

Active matter therefore offers promising perspectives for the design of smart meta-materials, but also for miniaturized and medical technologies.

In this talk, I will show how to combine experiments, numerical modeling and theoretical calculations to explore different ways to use and control biologic and synthetic micro-swimmers for self-assembly, enhanced fluid mixing and particle transport at the microscopic level. 

17 Oct 2019Brennan Klein (Network Science Institute, Northeastern University)

The structure is the story: How the right representation can bring forth new theories in complex systems

The effectiveness of a network at modeling a given system is intrinsically linked to its ability to express potential or counterfactual interactions in the system. If these neurons fired, would you observe a certain behavior? If I start a rumor, would you hear about it? This ability to encode counterfactual information in their structure makes complex networks rich philosophical objects as well. In this talk, I explore the role—and power—of representation in science and, in particular, complex systems science. To do this, I will primarily focus primarily on two recent projects about representation in network science. First, I will describe a general framework for coarse-graining complex networks to their most informative scale, a phenomenon known as causal emergence. Second, I will describe recent work that compares dozens of tools that are commonly used to infer network structure from time series data. This project is the culmination of a months-long “Collabathon” based out of the Network Science Institute at Northeastern University, and it features contributions from 33 different network scientists from around the world. I will close by briefly describing the structure of this style of research, encouraging more of these large, rigorous, and fun collaborations.

Bio: Brennan is a fifth-year PhD student studying surprise in complex systems. He is focused on understanding how complex systems are able to represent, predict, and intervene on their surroundings across a number of different scales—all in ways that minimize the surprisal experienced in the future. This approach is used to study a range of phenomena from decision making, to experimental design, to causation and emergence in networks. He is currently working with Alessandro Vespignani on a dissertation examining the teleology of networks, or why there appears to be an apparent purpose or goal-directedness to the dynamics and structure of networks. Brennan received his BA in Cognitive Science and Psychology from Swarthmore College in 2014, where he studied the relationship between perception, action, and cognition. He makes art under the pseudonym JK Rofling.

9 Oct 2019Ray Rivers (Imperial College)

Myth and Math: A network approach to Atlantis

The Aegean archaeologist Carl Knappett, Tim Evans and myself have used network models to try to understand the effect of the eruption of Thera on the demise of the MBA Minoan thalassocracy. The destruction of Thera is often taken to be the basis for the Atlantis legend in popular culture (see D.Duck). I have been fascinated (and appalled) by the continuing potency of this myth, particularly with the European Alt-Right (Google ‘aryan atlantis’ to see). In this talk I will argue that disaster myths have their contradictions and reconsider Thera. I shall also briefly put this network modelling in the context of networking of text-based myths and stories.

Bio: Ray Rivers is Emeritus Professor in Theoretical Physics and a member of The Centre for Complexity Science at Imperial College London. However, in addition to continuing to work on fundamental quantum physics, for the last decade and more he has been active in archaeological network modelling, particularly of the Bronze Age Aegean. Most recently he is concerned with more epistemic issues such as how we impose the present on the past.

3 Oct 2019Elizabeth Vergu (INRA)

Data analysis and model-based indicators of nodes criticality for epidemic spread and control on a cattle trade network

Informing prevention and control of infectious diseases in livestock populations at regional level necessitates the investigation of the underlying structure of spread represented by animal trade network and the coupling of intra-herd infection dynamics. Despite an abundant literature about dynamical epidemics on contact networks, generic tools are still needed when nodes are subpopulations, to characterize the impact on the infection dynamics of the interplay between network structure and local demography.

In this talk, I will first show some results from the analysis of the French cattle movement network over several years to investigate the fidelity over time of transaction partners. Proxies for pathogen spread, such as reachability ratio, accounting for network time-varying properties, were also computed, using efficient algorithms of network exploration, to assess spread and control of epidemics for various assumptions. In the second part, I will present theoretical results based on a model coupling metapopulation and epidemic dynamics on an explicit network and applied to the French data on cattle trade to build and assess graph vulnerability indicators and explore control strategies.

26 Sept 2019Vincent Hakim (CNRS, ENS)

Puzzles about long term memory and neuronal learning
Network Seminar - Puzzles about long term memory and neuronal learning

Synapses are important biological structures that serve to transmit information between neurons and are thought to be the sites of learning and memory. Yet, it has remained enigmatic how memory can be retained for years while synaptic components turnover over the course of hours. Similarly, when learning a complex task, the received feedback seems most often global and poorly informative. It is then quite unclear how the strengths of different synapses belonging to numerous different neurons can be properly adjusted, the so called « credit assignment problem ». After recalling some element of synapse biophysics and relevant experimental findings, I will discuss our recent work in collaboration with the teams of A Triller and B Barbour at IBENS, aiming at addressing these two puzzles. 

Bio: Vincent Hakim holds a CNRS Research Director position at Ecole Normale Supérieure (ENS) in Paris, France. He is a theoretical physicist specialised in statistical physics and nonlinear dynamics. During the last twenty years, he has carried out theoretical work in theoretical neuroscience and developmental biology, much of it in close collaboration with experimental teams.

12 Sept 2019Federico Battiston (CEU)

New emergent behavior in generalized networks

Networks constitute the backbone of many complex systems, on top of which collective behavior can emerge: from epileptic seizures in the human brain to the viral spread of rumours in a social network. When are simple network representations not enough? In this talk I introduce the topic of generalized networks, richer architectures which allow to consider the temporal and multiplex dimensions of relationships, and to go beyond simple pairwise interactions. Building on my contributions to the field, I focus on how to measure multiplexity in real-world systems from the micro to the macro scale, with examples from social, transportation and biological networks. I will then provide a short perspective on dynamical processes on generalized networks, searching for new emergent collective behavior and warning against overly optimistic statements associated to the multiplex, temporal and non-dyadic nature of interactions.

Bio: Federico is an Assistant Professor at the Department of Network and Data Science at Central European University. Federico studies the structure and the dynamics of complex systems, using his background as statistical physicist (B.Sc. and M.Sc. from Sapienza University of Rome) to look into biological problems, model social systems, and find new solutions for the design of man-made networks. He holds a PhD in Applied Mathematics from Queen Mary University of London, where he was a member of the Complex Systems and Networks Group and worked under the supervision of Vito Latora as part of the EU-FP7 project LASAGNE on multilayer networks. Federico is an elected member of the council of the Complex Systems Society and a former Chair of the Young Researchers of the Society. Before joining DNDS, Federico held postdoctoral positions at the Brain & Spine Institute in Paris, and at the Department of Anthropology at University College London.

14 July 2019Jennifer Dunne (Santa Fe Institute)

Examining human-centered ecological networks across the world

Abstract: Some of our best opportunities for generalizing and enhancing ecological understanding come from studies of ancient ecosystems. One frontier of such research focuses on ecological networks. In this talk, I’ll take a deep-time perspective on food web structure and dynamics. First I’ll briefly discuss the organization of food webs from ecosystems 100s to 10s of millions of years old. Second I’ll discuss a new research agenda to study archaeo-ecological networks from the last several thousand years that include pre-industrial humans. These types of deep-time data sets and analyses provide important perspectives on ecosystem stability, robustness and sustainability as we move further into the Anthropocene.

Bio: Jennifer Dunne is the Vice President for Science at the Santa Fe Institute, where she has been on the faculty since 2007. Dunne has degrees in philosophy (A.B., Harvard), ecology and systematic biology (M.A., San Francisco State University), and energy and resources (Ph.D., University of California, Berkeley). Her research interests are in analysis, modeling and theory related to the organization, dynamics, stability and function of ecological networks at multiple spatial and temporal scales. Dunne was named a Fellow of the Ecological Society of America in 2017. Her publications have appeared in journals such as Proceedings of the National Academy of Sciences USA, Trends in Ecology and Evolution, PLoS Biology, Philosophical Transactions of the Royal Society B, Proceedings of the Royal Society B, Ecology Letters, Ecology, and Ecological Monographs. Media outlets including Scientific American, Wired, SmartPlanet, ScienceNow, Nature News, and Quanta have reported on Dunne’s research.

27 June 2019Daniele Marinazzo (Ghent University, Belgium)

Synergy and Redundancy: a Network Perspective  
 Synergy and Redundancy: a Network Perspective

Synergy and redundancy are ubiquitous yet elusive concepts. Frameworks rooted in information theory allow to quantitatively define them, in particular quantifying the joint information shared by two drivers on a target. In this contribution, we will add networks to the picture in three aspects:

1. Synergy and redundancy in building networks: higher order interactions are often ignored when computing dynamical interactions in multivariate systems. I will try to convince you that this is both necessary and informative.

2. Synergy and redundancy as networks: defining a pairwise synergy index we can define networks in which the nodes are pairs of drivers, and the links determine whether they share joint information on a given target. The resulting network has a hierarchical structure, and we can see shared information mapped on graph theory quantities.

3. Synergy and redundancy between networks: we address the information transferred between networks, in a directed way, or mediated by another network. We will present a simple theory and two simple applications, to social media, and neural data.  

Figure from The Neuron Doctrine [Cajal, 1894]

20 June 2019Charles Baroud (Ecole Polytechnique, Pasteur, France)

Abstract: In this presentation I will discuss our work on 3D cell culture in droplet microfluidics. I will begin by explaining the technique and how it allows us to make, manipulate, and observe hundreds spheroids or organoids in parallel. Then I will show some new biological insights we have gained by generating very large sets of single-cell data within model organoids. Finally, I will describe some recent work to understand the interactions between immune cells and cancer models, and how network theory can help us understand the biology of the 3D spheroids.

Bio: Charles Baroud studied physics and mechanical engineering at MIT then U. Texas at Austin. In 2001 he joined the Laboratoire de Physique Statistique at ENS as a post-doc, working on reaction-diffusion experiments. Since 2002 he has held a faculty position at Ecole Polytechnique, where he has worked on different problems in microfluidics, first covering the physical aspects and more recently working on biological applications. Since 2018 he has also led a research unit at Institut Pasteur, focusing on the use of droplet techniques to learn new biology.

13 June 2019Henry C. W. Price (Imperial College, London)

From Local to Global: Nested Interaction and Community in Late Bronze Age Crete. A network approach. 

Abstract: Using as series of null models, we attempt to reconcile complex systems and the simple models that come to characterize much of the explained distribution of artifacts and settlement relationships to the wider Mediterranean. We also try and describe when these models are inappropriate.

Bio: Henry C. W. Price is currently a doctoral candidate in Theoretical Physics at Imperial College London. Working on a diverse number of topics in network theory and applied mathematics. Mainly Complexity Science, Complex Networks and Directed Acyclic Graphs. Actively researching Cryptocurrency and distributed ledger technology with University of London research groups and others bodies, he also works on machine learning and data science projects in Reg/Fin-tech. With an undergraduate degree in Theoretical Physics at Imperial. Henry also studied Mathematics and Financial Modelling and wrote his MSc thesis on Volatility. His most recent research also concerns computational methods in the digital humanities, social and life sciences, in addition to derivatives and futures contracts on Bitcoin.

6 June 2019Janet Bennion (Vermont University)

Polyamory in Paris: A Social Network Theory Application

Abstract: This research applies social network theory to the polyamory networks (polycules) of Paris, where participants in multiple loving relationships (both partners and metamours) share an exchange of information, ideas, and an assortment of valued prestations such as sexuality, friendship, and money. In such non-monogamous networks, there exists a vast web of nodes connected in much more intimate and complex ways than one finds in the mononormative landscape. This study seeks to evaluate the specific social capital exchanged by 45 individuals in the Polyamour/Polyamorie Paris Facebook group, assessing the strengths and weaknesses of their ties, and better understanding how they navigate the web to simultaneously live intimately with others and still fulfill their own selfish needs and desires.

Bio: Janet Bennion is a Professor of Anthropology from Northern Vermont University. She is the preeminent scholar on polygyny among Mormon Fundamentalist groups, having published extensively on female networking and the variability of poly lifestyles, including Women of Principle (University of Oxford Press, 1998) and Polygamy in Primetime (Brandeis University Press 2012). Her latest publication is collaborative and international, stemming from several international conference discussions about how to handle the poly world legally, compiled in the volume, The Polygamy Question (Utah State and Colorado Presses, 2015). Her most recent research explores polyamory networks in Paris where she is testing the efficacy of network theory on 45 subjects involved in 24 polycules.

23 May 2019Guillaume Dumas (Pasteur Institute)

Networks and Machine Learning in Biomedical Research: from Generative Models in Social Neurosciences to Multi-Scale Priors in Precision Medicine

Abstract: With the recent development of –omics fields, multiple sub-disciplines in life sciences have embraced networks as a valuable formalism. This presentation will present two projects illustrating how –omics networks can be used in biomedical research: 1) whole brain neuro-computational modelling with Connectomics, and 2) network-based stratification (NBS) with Genomics. The first example builds on the importance of anatomical and functional interactions in neuroscience; through modelling, numerical simulation provides insight into the basic mechanisms that enable integrative neural processes and how structural brain networks generate spatially and temporally organised brain activity at both intra- and inter-individual levels. The second example was originally designed for cancer research; the NBS combines genetic mutation profiles of patients with protein-protein interaction (PPI) networks to uncover clusters of patients with similar tumour subtypes. Here we will review the original results through a case study of reproducibility in bioinformatics and then explain the challenges to apply it to autism.

Bio: Guillaume Dumas is a researcher in the department of neuroscience of the Institut Pasteur in Paris. Originally from engineering and theoretical physics, he did a Ph.D. on cognitive neuroscience at the University of Paris 6 (UPMC) and then moved in a postdoc at the Center for Complex System and Brain Science of Florida Atlantic University. He came back to France for working in the “Human Genetics and Cognitive Functions” unit of the Institut Pasteur, where he started as a postdoc before receiving his permanent position. He then created the platform SoNeTAA (Social Neuroscience for Therapeutic Approaches of Autism) at the child and adolescent psychiatric department of the Robert Debré hospital in Paris. His interdisciplinary research is focused on integrative accounts of neural, behavioural and social coordination dynamics. Methods used range from both intra- and inter-individual neuroimaging techniques to neurocomputational simulations. He is also a science writer and journalist and is engaged with multiple projects at the cross-road of Art and Science. He has, for instance, co-founded HackYourPhD, a community advocating internationally the use of openness in Science and Knowledge as a common good, and ALIUS, an international and interdisciplinary research group dedicated to the investigation of the diversity of consciousness.

18 April 2019Alexey Medvedev (Université de Namur and Université catholique de Louvain)

Predicting discussion dynamics in online forums using Hawkes processes: case study of Reddit
Network seminar: predictions in online communities

Abstract: Online forums provide rich environments where users may post questions and comments about different topics. Understanding how people behave in online forums may shed light on the fundamental mechanisms by which collective thinking emerges in a group of individuals, but it has also important practical applications, for instance to improve user experience and increase engagement. Communication in online forums mostly happen through the open discussions, potentially available for all members of a particular platform. Cascading patterns, often emerging and well studied in online social media, are represented in forums in the form of threads, or, otherwise called, discussion trees. The two main questions arise: what is the shape and what is the dynamics of evolution of these trees? In this talk I will present an overview of the main research directions that arose in recent years and focus primarily on the most popular platform, Reddit. Then I will present a model of discussion trees generation based on the self-exciting Hawkes processes, which represents both the tree structure and temporal information. This model was applied to Reddit discussion trees and showed better accuracy in predicting future flow of the discussion, in comparison with the contemporary dynamic cascade models.

28 Feb 2019Chiara Poletto (INSERM)

Accounting for variable and heterogeneous human behaviour in the assessment of an epidemic

Abstract: Mathematical and computational approaches based on network theory and complex system dynamics are becoming increasingly effective in tackling open problems in infectious disease epidemiology. I will review my recent research work in this direction presenting studies on both fundamental problems and specific epidemic events. On the theoretical side, I will show how the structure and dynamics of human-to-human contacts alter the risk of an outbreak. This effect can be captured by the epidemic threshold, the critical transmissibility below which extinction is certain, that quantifies the vulnerability of a population to an infection. In order to compute this indicator we developed the infection propagator approach, where we used the multilayer framework to describe a temporal network and the Markov-chain formalism to solve the spreading dynamics in the critical regime close to the threshold. On the applicative side I will show how health seeking behavior, daily social contacts, and daily mobility patterns affect the initial transmission of an emerging disease and the propagation dynamics of recurrent epidemics at the city and regional level. These understandings were important for the epidemiological assessment of the MERS global dissemination, the recent outbreak of Zika and the seasonal influenza circulation.

Bio: Chiara Poletto is a researcher at the National Institute of Health and Medical Research (INSERM) in Paris (France), working on the spreading of infectious diseases seen as a complex system phenomenon. Epidemics are mediated by human contacts and, on a different scale, by human mobility patterns. Therefore, the role of network structure on infection risk, its persistence and impact on the population is a central question of her research work. Within this broad context, she is dedicating increasing attention to the physics of interacting spreading processes underlying important problems in disease ecology. Poletto received her PhD in Physics from the University of Padova (Italy) in 2009 and was then Post Doc at the Computational Epidemiology Laboratory, ISI Foundation, Torino (Italy), before joining the INSERM in 2012. She is recipient of the Junior Scientific Award of the Complex Systems Society for extraordinary scientific achievements, and of the starting grant from the program Emergence de la Ville de Paris. Her studies on emerging pathogens’ epidemics (from Ebola outbreak to Zika) have translated into expert advices for public health decision makers.

6 Dec 2018Christian Vestergaard (Pasteur Institute)

Randomized reference models for temporal networks
Seminar on complex networks theory

Abstract: Many complex systems can successfully be described as networks. This abstracts away most particularities of individual units in the system and allows to highlight and study the effects of the complex structure of their connections. Notable examples are human interaction networks and the spread of contagions and information in these, biological networks, including biotic interactions in ecosystems and neural connections in the brain, infrastructural networks, and world trade. The structure and dynamics of most empirically measured networks are complex and intrinsically correlated, making it particularly challenging to study them using traditional generative models.

As an alternative to the bottom-up approach of generative models, randomized reference models (RRMs) constitute a top-down approach to studying complex networks. RRMs deal with the controlled destruction of given temporal or topological structures in a complex network in order to create a distribution of reference networks retaining certain features of the original network. They are typically implemented as procedures that shuffle the edges of the network while retaining the features in question. This makes RRMs very generally applicable, and in particular in cases where we are not able to specify a realistic generative model. However, the effects of most shuffling procedures on network features remain poorly understood, complicating the interpretation of results, and the lack of a common framework has made it difficult to compare different RRMs.

I will describe a unified framework for the important class of RRMs generated by uniform shuffling procedures, which we by analogy to statistical physics will name microcanonical RRMs (MRRMs). Our framework lets us build a taxonomy of MRRMs that orders them and deduces their effects on important network features. It additionally tells us how we may generate new MRRMs by combining existing ones. I will discuss how MRRMs may be used as null models to identify statistically significant features in empirical networks. I will show how our framework can be used when we do not know how to choose the correct null model, and will apply this to characterize computational motifs in the Drosophila larval brain. I will finally show how series of different MRRMs may be used to pick apart the effects of different features of a network on dynamical processes unfolding on it.

Reference: https://arxiv.org/pdf/1806.04032.pdf

Bio: I am a statistical physicist and biophysicist with a main interest in data-driven modeling and in developing methods for the analysis of complex dynamical systems. The focus of my research has been on time-varying (temporal) social networks and single molecule dynamics in intracellular processes. I currently work on linking the physical structure and function of the brain to behavior.

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