arXiv subjects

Antoine Allard

Publications and source records attributed to Antoine Allard.

At least 55 records · Page 3Linked to original sources

arXiv2020

Master equation analysis of mesoscopic localization in contagion dynamics on higher-order networks

Simple models of infectious diseases tend to assume random mixing of individuals, but real interactions are not random pairwise encounters: they occur within various types of gatherings such as workplaces, households, schools, and concerts, best described by a higher-order network structure. We model contagions on higher-order networks using group-based approximate master equations, in which we track all states and interactions within a group of nodes and assume a mean-field coupling between them. Using the Susceptible-Infected-Susceptible dynamics, our approach reveals the existence of a mesoscopic localization regime, where a disease can concentrate and self-sustain only around large groups in the network overall organization. In this regime, the phase transition is smeared, characterized by an inhomogeneous activation of the groups. At the mesoscopic level, we observe that the distribution of infected nodes within groups of a same size can be very dispersed, even bimodal. When considering heterogeneous networks, both at the level of nodes and groups, we characterize analytically the region associated with mesoscopic localization in the structural parameter space. We put in perspective this phenomenon with eigenvector localization and discuss how a focus on higher-order structures is needed to discern the more subtle localization at the mesoscopic level. Finally, we discuss how mesoscopic localization affects the response to structural interventions and how this framework could provide important insights for a broad range of dynamics.

physics.soc-ph↗

arXiv2020

Geometric renormalization unravels self-similarity of the multiscale human connectome

Structural connectivity in the brain is typically studied by reducing its observation to a single spatial resolution. However, the brain possesses a rich architecture organized over multiple scales linked to one another. We explored the multiscale organization of human connectomes using datasets of healthy subjects reconstructed at five different resolutions. We found that the structure of the human brain remains self-similar when the resolution of observation is progressively decreased by hierarchical coarse-graining of the anatomical regions. Strikingly, a geometric network model, where distances are not Euclidean, predicts the multiscale properties of connectomes, including self-similarity. The model relies on the application of a geometric renormalization protocol which decreases the resolution by coarse-graining and averaging over short similarity distances. Our results suggest that simple organizing principles underlie the multiscale architecture of human structural brain networks, where the same connectivity law dictates short- and long-range connections between different brain regions over many resolutions. The implications are varied and can be substantial for fundamental debates, such as whether the brain is working near a critical point, as well as for applications including advanced tools to simplify the digital reconstruction and simulation of the brain.

physics.soc-ph↗

arXiv2020

Fluctuations of a membrane nanotube covered with an actin sleeve

Many biological functions rely on the reshaping of cell membranes, in particular into nanotubes, which are covered in vivo by dynamic actin networks. Nanotubes are subject to thermal fluctuations, but the effect of these on cell functions is unknown. Here, we form nanotubes from liposomes using an optically trapped bead adhering to the liposome membrane. From the power spectral density of this bead, we study the nanotube fluctuations in the range of membrane tensions measured in vivo. We show that an actin sleeve covering the nanotube damps its high frequency fluctuations because of the network viscoelasticity. Our work paves the way for further studies on the effect of nanotube fluctuations in cellular functions.

physics.bio-ph↗

arXiv2020

Stochasticity and heterogeneity in the transmission dynamics of SARS-CoV-2

SARS-CoV-2 causing COVID-19 disease has moved rapidly around the globe, infecting millions and killing hundreds of thousands. The basic reproduction number, which has been widely used and misused to characterize the transmissibility of the virus, hides the fact that transmission is stochastic, is dominated by a small number of individuals, and is driven by super-spreading events (SSEs). The distinct transmission features, such as high stochasticity under low prevalence, and the central role played by SSEs on transmission dynamics, should not be overlooked. Many explosive SSEs have occurred in indoor settings stoking the pandemic and shaping its spread, such as long-term care facilities, prisons, meat-packing plants, fish factories, cruise ships, family gatherings, parties and night clubs. These SSEs demonstrate the urgent need to understand routes of transmission, while posing an opportunity that outbreak can be effectively contained with targeted interventions to eliminate SSEs. Here, we describe the potential types of SSEs, how they influence transmission, and give recommendations for control of SARS-CoV-2.

q-bio.PE↗

arXiv2020

Beyond $R_0$: Heterogeneity in secondary infections and probabilistic epidemic forecasting

The basic reproductive number -- $R_0$ -- is one of the most common and most commonly misapplied numbers in public health. Although often used to compare outbreaks and forecast pandemic risk, this single number belies the complexity that two different pathogens can exhibit, even when they have the same $R_0$. Here, we show how to predict outbreak size using estimates of the distribution of secondary infections, leveraging both its average $R_0$ and the underlying heterogeneity. To do so, we reformulate and extend a classic result from random network theory that relies on contact tracing data to simultaneously determine the first moment ($R_0$) and the higher moments (representing the heterogeneity) in the distribution of secondary infections. Further, we show the different ways in which this framework can be implemented in the data-scarce reality of emerging pathogens. Lastly, we demonstrate that without data on the heterogeneity in secondary infections for emerging infectious diseases like COVID-19, the uncertainty in outbreak size ranges dramatically. Taken together, our work highlights the critical need for contact tracing during emerging infectious disease outbreaks and the need to look beyond $R_0$ when predicting epidemic size.

q-bio.PE↗

arXiv2020

Navigable maps of structural brain networks across species

Connectomes are spatially embedded networks whose architecture has been shaped by physical constraints and communication needs throughout evolution. Using a decentralized navigation protocol, we investigate the relationship between the structure of the connectomes of different species and their spatial layout. As a navigation strategy, we use greedy routing where nearest neighbors, in terms of geometric distance, are visited. We measure the fraction of successful greedy paths and their length as compared to shortest paths in the topology of connectomes. In Euclidean space, we find a striking difference between the navigability properties of mammalian and non-mammalian species, which implies the inability of Euclidean distances to fully explain the structural organization of their connectomes. In contrast, we find that hyperbolic space, the effective geometry of complex networks, provides almost perfectly navigable maps of connectomes for all species, meaning that hyperbolic distances are exceptionally congruent with the structure of connectomes. Hyperbolic maps therefore offer a quantitative meaningful representation of connectomes that suggests a new cartography of the brain based on the combination of its connectivity with its effective geometry rather than on its anatomy only. Hyperbolic maps also provide a universal framework to study decentralized communication processes in connectomes of different species and at different scales on an equal footing.

q-bio.NC↗

arXiv2019

On the accuracy of message-passing approaches to percolation in complex networks

The Message-Passing Approach (MPA) is the state-of-the-art technique to obtain quasi-analytical predictions for percolation on real complex networks. Besides being intuitive and straightforward, it has the advantage of being mathematically principled: it is exact on trees, while yielding generally good predictions on networks containing cycles as do most real complex networks. Here we show that the MPA does not perform its calculations on some ill-defined tree-like approximation of the network, as its formulation leads to believe, but rather considers a random network ensemble in which the original network is cloned and shuffled an infinite number of times. We conclude that the fact that the MPA is exact on trees does not imply that it is nearly exact on tree-like networks. In fact we find that the closer a non-tree network is to a tree, the worse the MPA accuracy becomes.

physics.soc-ph↗

arXiv2019

Mercator: uncovering faithful hyperbolic embeddings of complex networks

We introduce Mercator, a reliable embedding method to map real complex networks into their hyperbolic latent geometry. The method assumes that the structure of networks is well described by the Popularity$\times$Similarity $\mathbb{S}^1/\mathbb{H}^2$ static geometric network model, which can accommodate arbitrary degree distributions and reproduces many pivotal properties of real networks, including self-similarity patterns. The algorithm mixes machine learning and maximum likelihood approaches to infer the coordinates of the nodes in the underlying hyperbolic disk with the best matching between the observed network topology and the geometric model. In its fast mode, Mercator uses a model-adjusted machine learning technique performing dimensional reduction to produce a fast and accurate map, whose quality already outperform other embedding algorithms in the literature. In the refined Mercator mode, the fast-mode embedding result is taken as an initial condition in a Maximum Likelihood estimation, which significantly improves the quality of the final embedding. Apart from its accuracy as an embedding tool, Mercator has the clear advantage of systematically inferring not only node orderings, or angular positions, but also the hidden degrees and global model parameters, and has the ability to embed networks with arbitrary degree distributions. Overall, our results suggest that mixing machine learning and maximum likelihood techniques in a model-dependent framework can boost the meaningful mapping of complex networks.

physics.soc-ph↗

arXiv2018

Smeared phase transitions in percolation on real complex networks

Percolation on complex networks is used both as a model for dynamics on networks, such as network robustness or epidemic spreading, and as a benchmark for our models of networks, where our ability to predict percolation measures our ability to describe the networks themselves. In many applications, correctly identifying the phase transition of percolation on real-world networks is of critical importance. Unfortunately, this phase transition is obfuscated by the finite size of real systems, making it hard to distinguish finite size effects from the inaccuracy of a given approach that fails to capture important structural features. Here, we borrow the perspective of smeared phase transitions and argue that many observed discrepancies are due to the complex structure of real networks rather than to finite size effects only. In fact, several real networks often used as benchmarks feature a smeared phase transition where inhomogeneities in the topological distribution of the order parameter do not vanish in the thermodynamic limit. We find that these smeared transitions are sometimes better described as sequential phase transitions within correlated subsystems. Our results shed light not only on the nature of the percolation transition in complex systems, but also provide two important insights on the numerical and analytical tools we use to study them. First, we propose a measure of local susceptibility to better detect both clean and smeared phase transitions by looking at the topological variability of the order parameter. Second, we highlight a shortcoming in state-of-the-art analytical approaches such as message passing, which can detect smeared transitions but not characterize their nature.

physics.soc-ph↗

arXiv2018

Percolation and the effective structure of complex networks

Analytical approaches to model the structure of complex networks can be distinguished into two groups according to whether they consider an intensive (e.g., fixed degree sequence and random otherwise) or an extensive (e.g., adjacency matrix) description of the network structure. While extensive approaches---such as the state-of-the-art Message Passing Approach---typically yield more accurate predictions, intensive approaches provide crucial insights on the role played by any given structural property in the outcome of dynamical processes. Here we introduce an intensive description that yields almost identical predictions to the ones obtained with MPA for bond percolation. Our approach distinguishes nodes according to two simple statistics: their degree and their position in the core-periphery organization of the network. Our near-exact predictions highlight how accurately capturing the long-range correlations in network structures allows to easily and effectively compress real complex network data.

physics.soc-ph↗

arXiv2017

Geometric evolution of complex networks

We present a general class of geometric network growth mechanisms by homogeneous attachment in which the links created at a given time $t$ are distributed homogeneously between a new node and the exising nodes selected uniformly. This is achieved by creating links between nodes uniformly distributed in a homogeneous metric space according to a Fermi-Dirac connection probability with inverse temperature $β$ and general time-dependent chemical potential $μ(t)$. The chemical potential limits the spatial extent of newly created links. Using a hidden variable framework, we obtain an analytical expression for the degree sequence and show that $μ(t)$ can be fixed to yield any given degree distributions, including a scale-free degree distribution. Additionally, we find that depending on the order in which nodes appear in the network---its $\textit{history}$---the degree-degree correlation can be tuned to be assortative or disassortative. The effect of the geometry on the structure is investigated through the average clustering coefficient $\langle c \rangle$. In the thermodynamic limit, we identify a phase transition between a random regime where $\langle c \rangle \rightarrow 0$ when $β< β_\mathrm{c}$ and a geometric regime where $\langle c \rangle > 0$ when $β> β_\mathrm{c}$.

physics.soc-ph↗

arXiv2017

Strategic tradeoffs in competitor dynamics on adaptive networks

Recent empirical work highlights the heterogeneity of social competitions such as political campaigns: proponents of some ideologies seek debate and conversation, others create echo chambers. While symmetric and static network structure is typically used as a substrate to study such competitor dynamics, network structure can instead be interpreted as a signature of the competitor strategies, yielding competition dynamics on adaptive networks. Here we demonstrate that tradeoffs between aggressiveness and defensiveness (i.e., targeting adversaries vs. targeting like-minded individuals) creates paradoxical behaviour such as non-transitive dynamics. And while there is an optimal strategy in a two competitor system, three competitor systems have no such solution; the introduction of extreme strategies can easily affect the outcome of a competition, even if the extreme strategies have no chance of winning. Not only are these results reminiscent of classic paradoxical results from evolutionary game theory, but the structure of social networks created by our model can be mapped to particular forms of payoff matrices. Consequently, social structure can act as a measurable metric for social games which in turn allows us to provide a game theoretical perspective on online political debates.

physics.soc-ph↗

arXiv2017

Asymmetric percolation drives a double transition in sexual contact networks

Zika virus (ZIKV) exhibits unique transmission dynamics in that it is concurrently spread by a mosquito vector and through sexual contact. We show that this sexual component of ZIKV transmission induces novel processes on networks through the highly asymmetric durations of infectiousness between males and females -- it is estimated that males are infectious for periods up to ten times longer than females -- leading to an asymmetric percolation process on the network of sexual contacts. We exactly solve the properties of this asymmetric percolation on random sexual contact networks and show that this process exhibits two epidemic transitions corresponding to a core-periphery structure. This structure is not present in the underlying contact networks, which are not distinguishable from random networks, and emerges because of the asymmetric percolation. We provide an exact analytical description of this double transition and discuss the implications of our results in the context of ZIKV epidemics. Most importantly, our study suggests a bias in our current ZIKV surveillance as the community most at risk is also one of the least likely to get tested.

physics.soc-ph↗

arXiv2017

The hidden geometry of weighted complex networks

The topology of many real complex networks has been conjectured to be embedded in hidden metric spaces, where distances between nodes encode their likelihood of being connected. Besides of providing a natural geometrical interpretation of their complex topologies, this hypothesis yields the recipe for sustainable Internet's routing protocols, sheds light on the hierarchical organization of biochemical pathways in cells, and allows for a rich characterization of the evolution of international trade. We present empirical evidence that this geometric interpretation also applies to the weighted organisation of real complex networks. We introduce a very general and versatile model and use it to quantify the level of coupling between their topology, their weights, and an underlying metric space. Our model accurately reproduces both their topology and their weights, and our results suggest that the formation of connections and the assignment of their magnitude are ruled by different processes.

physics.soc-ph↗

arXiv2016

Growing networks of overlapping communities with internal structure

We introduce an intuitive model that describes both the emergence of community structure and the evolution of the internal structure of communities in growing social networks. The model comprises two complementary mechanisms: One mechanism accounts for the evolution of the internal link structure of a single community, and the second mechanism coordinates the growth of multiple overlapping communities. The first mechanism is based on the assumption that each node establishes links with its neighbors and introduces new nodes to the community at different rates. We demonstrate that this simple mechanism gives rise to an effective maximal degree within communities. This observation is related to the anthropological theory known as Dunbar's number, i.e., the empirical observation of a maximal number of ties which an average individual can sustain within its social groups. The second mechanism is based on a recently proposed generalization of preferential attachment to community structure, appropriately called structural preferential attachment (SPA). The combination of these two mechanisms into a single model (SPA+) allows us to reproduce a number of the global statistics of real networks: The distribution of community sizes, of node memberships and of degrees. The SPA+ model also predicts (a) three qualitative regimes for the degree distribution within overlapping communities and (b) strong correlations between the number of communities to which a node belongs and its number of connections within each community. We present empirical evidence that support our findings in real complex networks.

physics.soc-ph↗

arXiv2016

The hidden hyperbolic geometry of international trade: World Trade Atlas 1870-2013

Here, we present the World Trade Atlas 1870-2013, a collection of annual world trade maps in which distance combines economic size and the different dimensions that affect international trade beyond mere geography. Trade distances, which are based on a gravity model predicting the existence of significant trade channels, are such that the closer countries are in trade space, the greater their chance of becoming connected. The atlas provides us with information regarding the long-term evolution of the international trade system and demonstrates that, in terms of trade, the world is not flat but hyperbolic, as a reflection of its complex architecture. The departure from flatness has been increasing since World War I, meaning that differences in trade distances are growing and trade networks are becoming more hierarchical. Smaller-scale economies are moving away from other countries except for the largest economies; meanwhile those large economies are increasing their chances of becoming connected worldwide. At the same time, Preferential Trade Agreements do not fit in perfectly with natural communities within the trade space and have not necessarily reduced internal trade barriers. We discuss an interpretation in terms of globalization, hierarchization, and localization; three simultaneous forces that shape the international trade system.

physics.soc-ph↗

arXiv2016

Multi-scale structure and topological anomaly detection via a new network statistic: The onion decomposition

We introduce a new network statistic that measures diverse structural properties at the micro-, meso-, and macroscopic scales, while still being easy to compute and easy to interpret at a glance. Our statistic, the onion spectrum, is based on the onion decomposition, which refines the k-core decomposition, a standard network fingerprinting method. The onion spectrum is exactly as easy to compute as the k-cores: It is based on the stages at which each vertex gets removed from a graph in the standard algorithm for computing the k-cores. But the onion spectrum reveals much more information about a network, and at multiple scales; for example, it can be used to quantify node heterogeneity, degree correlations, centrality, and tree- or lattice-likeness of the whole network as well as of each k-core. Furthermore, unlike the k-core decomposition, the combined degree-onion spectrum immediately gives a clear local picture of the network around each node which allows the detection of interesting subgraphs whose topological structure differs from the global network organization. This local description can also be leveraged to easily generate samples from the ensemble of networks with a given joint degree-onion distribution. We demonstrate the utility of the onion spectrum for understanding both static and dynamic properties on several standard graph models and on many real-world networks.

physics.soc-ph↗

arXiv2016

On the constrained growth of complex scale-independent systems

Scale independence is a ubiquitous feature of complex systems which implies a highly skewed distribution of resources with no characteristic scale. Research has long focused on why systems as varied as protein networks, evolution and stock actions all feature scale independence. Assuming that they simply do, we focus here on describing how this behaviour emerges, in contrast to more idealized models usually considered. We arrive at the conjecture that a minimal model to explain the growth towards scale independence involves only two coupled dynamical features: the first is the well-known preferential attachment principle and the second is a general form of delayed temporal scaling. While the first is sufficient, the second is present in all studied data and appears to maximize the speed of convergence to true scale independence. The delay in this temporal scaling acts as a coupling between population growth and individual activity. Together, these two dynamical properties appear to pave a precise evolution path, such that even an instantaneous snapshot of a distribution is enough to reconstruct the past of the system and predict its future. We validate our approach and confirm its usefulness on diverse spheres of human activities ranging from scientific and artistic productivity, to sexual relations and online traffic.

physics.soc-ph↗