arXiv subjects

Laurent Hébert-Dufresne

Publications and source records attributed to Laurent Hébert-Dufresne.

At least 55 records · Page 3Linked to original sources

arXiv2023

Accurately summarizing an outbreak using epidemiological models takes time

Recent outbreaks of monkeypox and Ebola, and worrying waves of COVID-19, influenza and respiratory syncytial virus, have all led to a sharp increase in the use of epidemiological models to estimate key epidemiological parameters. The feasibility of this estimation task is known as the practical identifiability (PI) problem. Here, we investigate the PI of eight commonly reported statistics of the classic Susceptible-Infectious-Recovered model using a new measure that shows how much a researcher can expect to learn in a model-based Bayesian analysis of prevalence data. Our findings show that the basic reproductive number and final outbreak size are often poorly identified, with learning exceeding that of individual model parameters only in the early stages of an outbreak. The peak intensity, peak timing, and initial growth rate are better identified, being in expectation over 20 times more probable having seen the data by the time the underlying outbreak peaks. We then test PI for a variety of true parameter combinations, and find that PI is especially problematic in slow-growing or less-severe outbreaks. These results add to the growing body of literature questioning the reliability of inferences from epidemiological models when limited data are available.

q-bio.PE↗

arXiv2023

TRACE-Omicron: Policy Counterfactuals to Inform Mitigation of COVID-19 Spread in the United States

The Omicron wave was the largest wave of COVID-19 pandemic to date, more than doubling any other in terms of cases and hospitalizations in the United States. In this paper, we present a large-scale agent-based model of policy interventions that could have been implemented to mitigate the Omicron wave. Our model takes into account the behaviors of individuals and their interactions with one another within a nationally representative population, as well as the efficacy of various interventions such as social distancing, mask wearing, testing, tracing, and vaccination. We use the model to simulate the impact of different policy scenarios and evaluate their potential effectiveness in controlling the spread of the virus. Our results suggest the Omicron wave could have been substantially curtailed via a combination of interventions comparable in effectiveness to extreme and unpopular singular measures such as widespread closure of schools and workplaces, and highlight the importance of early and decisive action.

cs.SI↗

arXiv2022

The penumbra of open source: projects outside of centralized platforms are longer maintained, more academic and more collaborative

GitHub has become the central online platform for much of open source, hosting most open source code repositories. With this popularity, the public digital traces of GitHub are now a valuable means to study teamwork and collaboration. In many ways, however, GitHub is a convenience sample, and may not be representative of open source development off the platform. Here we develop a novel, extensive sample of public open source project repositories outside of centralized platforms. We characterized these projects along a number of dimensions, and compare to a time-matched sample of corresponding GitHub projects. Our sample projects tend to have more collaborators, are maintained for longer periods, and tend to be more focused on academic and scientific problems.

cs.CY↗

arXiv2022

Limits of Individual Consent and Models of Distributed Consent in Online Social Networks

Personal data are not discrete in socially-networked digital environments. A user who consents to allow access to their profile can expose the personal data of their network connections to non-consented access. Therefore, the traditional consent model (informed and individual) is not appropriate in social networks where informed consent may not be possible for all users affected by data processing and where information is distributed across users. Here, we outline the adequacy of consent for data transactions. Informed by the shortcomings of individual consent, we introduce both a platform-specific model of "distributed consent" and a cross-platform model of a "consent passport." In both models, individuals and groups can coordinate by giving consent conditional on that of their network connections. We simulate the impact of these distributed consent models on the observability of social networks and find that low adoption would allow macroscopic subsets of networks to preserve their connectivity and privacy.

physics.soc-ph↗

arXiv2022

The OCEAN mailing list data set: Network analysis spanning mailing lists and code repositories

Communication surrounding the development of an open source project largely occurs outside the software repository itself. Historically, large communities often used a collection of mailing lists to discuss the different aspects of their projects. Multimodal tool use, with software development and communication happening on different channels, complicates the study of open source projects as a sociotechnical system. Here, we combine and standardize mailing lists of the Python community, resulting in 954,287 messages from 1995 to the present. We share all scraping and cleaning code to facilitate reproduction of this work, as well as smaller datasets for the Golang (122,721 messages), Angular (20,041 messages) and Node.js (12,514 messages) communities. To showcase the usefulness of these data, we focus on the CPython repository and merge the technical layer (which GitHub account works on what file and with whom) with the social layer (messages from unique email addresses) by identifying 33% of GitHub contributors in the mailing list data. We then explore correlations between the valence of social messaging and the structure of the collaboration network. We discuss how these data provide a laboratory to test theories from standard organizational science in large open source projects.

cs.CY↗

arXiv2022

Hierarchical team structure and multidimensional localization (or siloing) on networks

Knowledge silos emerge when structural properties of organizational interaction networks limit the diffusion of information. These structural barriers are known to take many forms at different scales - hubs in otherwise sparse organisations, large dense teams, or global core-periphery structure - but we lack an understanding of how these different structures interact. Here we bridge the gap between the mathematical literature on localization of spreading dynamics and the more applied literature on knowledge silos in organizational interaction networks. To do so, we introduce a new model that considers a layered structure of teams to unveil a new form of hierarchical localization (i.e., the localization of information at the top or center of an organization) and study its interplay with known phenomena of mesoscopic localization (i.e., the localization of information in large groups), $k$-core localization (i.e., around denser $k$-cores) and hub localization (i.e., around high degree stars). We also include a complex contagion mechanism by considering a general infection kernel which can depend on hierarchical level (influence), degree (popularity), infectious neighbors (social reinforcement) or team size (importance). This general model allows us to study the multifaceted phenomenon of information siloing in complex organizational interaction networks and opens the door to new optimization problems to promote or hinder the emergence of different localization regimes.

physics.soc-ph↗

arXiv2022

Predicting the diversity of early epidemic spread on networks

The interplay of biological, social, structural and random factors makes disease forecasting extraordinarily complex. The course of an epidemic exhibits average growth dynamics determined by features of the pathogen and the population, yet also features significant variability reflecting the stochastic nature of disease spread. In this work, we reframe a stochastic branching process analysis in terms of probability generating functions and compare it to continuous time epidemic simulations on networks. In doing so, we predict the diversity of emerging epidemic courses on both homogeneous and heterogeneous networks. We show how the challenge of inferring the early course of an epidemic falls on the randomness of disease spread more so than on the heterogeneity of contact patterns. We provide an analysis which helps quantify, in real time, the probability that an epidemic goes supercritical or conversely, dies stochastically. These probabilities are often assumed to be one and zero, respectively, if the basic reproduction number, or R0, is greater than 1, ignoring the heterogeneity and randomness inherent to disease spread. This framework can give more insight into early epidemic spread by weighting standard deterministic models with likelihood to inform pandemic preparedness with probabilistic forecasts.

q-bio.PE↗

arXiv2022

The role of directionality, heterogeneity and correlations in epidemic risk and spread

Most models of epidemic spread, including many designed specifically for COVID-19, implicitly assume mass-action contact patterns and undirected contact networks, meaning that the individuals most likely to spread the disease are also the most at risk to receive it from others. Here, we review results from the theory of random directed graphs which show that many important quantities, including the reproduction number and the epidemic size, depend sensitively on the joint distribution of in- and out-degrees ("risk" and "spread"), including their heterogeneity and the correlation between them. By considering joint distributions of various kinds, we elucidate why some types of heterogeneity cause a deviation from the standard Kermack-McKendrick analysis of SIR models, i.e., so-called mass-action models where contacts are homogeneous and random, and some do not. We also show that some structured SIR models informed by realistic complex contact patterns among types of individuals (age or activity) are simply mixtures of Poisson processes and tend not to deviate significantly from the simplest mass-action model. Finally, we point out some possible policy implications of this directed structure, both for contact tracing strategy and for interventions designed to prevent superspreading events. In particular, directed graphs have a forward and backward version of the classic "friendship paradox" -- forward edges tend to lead to individuals with high risk, while backward edges lead to individuals with high spread -- such that a combination of both forward and backward contact tracing is necessary to find superspreading events and prevent future cascades of infection.

physics.soc-ph↗

arXiv2022

Spatial epidemiology and adaptive targeted sampling to manage the Chagas disease vector Triatoma dimidiata

Widespread application of insecticide remains the primary form of control for Chagas disease in Central America, despite only temporarily reducing domestic levels of the endemic vector Triatoma dimidiata and having little long-term impact. Recently, an approach emphasizing community feedback and housing improvements has been shown to yield lasting results. However, the additional resources and personnel required by such an intervention likely hinders its widespread adoption. One solution to this problem would be to target only a subset of houses in a community while still eliminating enough infestations to interrupt disease transfer. Here we develop a sequential sampling framework that adapts to information specific to a community as more houses are visited, thereby allowing us to efficiently find homes with domiciliary vectors while minimizing sampling bias. The method fits Bayesian geostatistical models to make spatially informed predictions, while gradually transitioning from prioritizing houses based on prediction uncertainty to targeting houses with a high risk of infestation. A key feature of the method is the use of a single exploration parameter, $α$, to control the rate of transition between these two design targets. In a simulation study using empirical data from five villages in southeastern Guatemala, we test our method using a range of values for $α$, and find it can consistently select fewer homes than random sampling, while still bringing the village infestation rate below a given threshold. We further find that when additional socioeconomic information is available, much larger savings are possible, but that meeting the target infestation rate is less consistent, particularly among the less exploratory strategies. Our results suggest new options for implementing long-term T. dimidiata control.

stat.AP↗

arXiv2021

The network epidemiology of an Ebola epidemic

Connecting the different scales of epidemic dynamics, from individuals to communities to nations, remains one of the main challenges of disease modeling. Here, we revisit one of the largest public health efforts deployed against a localized epidemic: the 2014-2016 Ebola Virus Disease (EVD) epidemic in Sierra Leone. We leverage the data collected by the surveillance and contact tracing protocols of the Sierra Leone Ministry of Health and Sanitation, the US Centers for Disease Control and Prevention, and other responding partners to validate a network epidemiology framework connecting the population (incidence), community (local forecasts), and individual (secondary infections) scales of disease transmission. In doing so, we gain a better understanding of what brought the EVD epidemic to an end: Reduction of introduction in new clusters (primary cases), and not reduction in local transmission patterns (secondary infections). We also find that the first 90 days of the epidemic contained enough information to produce probabilistic forecasts of EVD cases; forecasts which we show are confirmed independently by both disease surveillance and contact tracing. Altogether, using data available two months before the start of the international support to the local response, network epidemiology could have inferred heterogeneity in local transmissions, the risk for superspreading events, and probabilistic forecasts of eventual cases per community. We expect that our framework will help connect large data collection efforts with individual behavior, and help reduce uncertainty during health emergencies and emerging epidemics.

q-bio.PE↗

arXiv2021

Influential groups for seeding and sustaining nonlinear contagion in heterogeneous hypergraphs

Several biological and social contagion phenomena, such as superspreading events or social reinforcement, are the results of multi-body interactions, for which hypergraphs offer a natural mathematical description. In this paper, we develop a novel mathematical framework based on approximate master equations to study contagions on random hypergraphs with a heterogeneous structure, both in terms of group size (hyperedge cardinality) and of membership of nodes to groups (hyperdegree). The characterization of the inner dynamics of groups provides an accurate description of the contagion process, without losing the analytical tractability. Using a contagion model where multi-body interactions are mapped onto a nonlinear infection rate, our two main results show how large groups are influential, in the sense that they drive both the early spread of a contagion and its endemic state (i.e., its stationary state). First, we provide a detailed characterization of the phase transition, which can be continuous or discontinuous with a bistable regime, and derive analytical expressions for the critical and tricritical points. We find that large values of the third moment of the membership distribution suppress the emergence of a discontinuous phase transition. Furthermore, the combination of heterogeneous group sizes and nonlinear contagion facilitates the onset of a mesoscopic localization phase, where contagion is sustained only by the largest groups, thereby inhibiting bistability as well. Second, we formulate the problem of optimal seeding for hypergraph contagion, and we compare two strategies: tuning the allocation of seeds according to either individual node or group properties. We find that, when the contagion is sufficiently nonlinear, groups are more effective seeds of contagion than individual nodes.

physics.soc-ph↗

arXiv2021

Immunity-induced criticality of the genotype network of influenza A (H3N2) hemagglutinin

Seasonal influenza kills hundreds of thousands every year, with multiple constantly-changing strains in circulation at any given time. A high mutation rate enables the influenza virus to evade recognition by the human immune system, including immunity acquired through past infection and vaccination. Here, we capture the genetic similarity of influenza strains and their evolutionary dynamics with genotype networks. We show that the genotype networks of influenza A (H3N2) hemagglutinin are characterized by heavy-tailed distributions of module sizes and connectivity, suggesting critical-like behavior. We argue that: (i) genotype networks are driven by mutation and host immunity to explore a subspace of networks predictable in structure, and (ii) genotype networks provide an underlying structure necessary to capture the rich dynamics of multistrain epidemic models. In particular, inclusion of strain-transcending immunity in epidemic models is dependent upon the structure of an underlying genotype network. This interplay suggests a self-organized criticality where the epidemic dynamics of influenza locates critical-like regions of its genotype network. We conclude that this interplay between disease dynamics and network structure might be key for future network analysis of pathogen evolution and realistic multistrain epidemic models.

q-bio.PE↗

arXiv2021

Source-sink cooperation dynamics constrain institutional evolution in a group-structured society

Societies change through time, entailing changes in behaviors and institutions. We ask how social change occurs when behaviors and institutions are interdependent. We model a group-structured society in which the transmission of individual behavior occurs in parallel with the selection of group-level institutions. We consider a cooperative behavior that generates collective benefits for groups but does not spread between individuals on its own. Groups exhibit institutions that increase the diffusion of the behavior within the group, but also incur a group cost. Groups adopt institutions in proportion to their fitness. Finally, cooperative behavior may also spread globally. As expected, we find that cooperation and institutions are mutually reinforcing. But the model also generates behavioral source-sink dynamics when cooperation generated in institutional groups spreads to non-institutional groups, boosting their fitness. Consequently, the global diffusion of cooperation creates a pattern of institutional free-riding that limits the evolution of group-beneficial institutions. Our model suggests that, in a group-structured society, large-scale change in behavior and institutions (i.e. social change) can be best achieved when the two remain correlated, such as through the spread successful pilot programs.

physics.soc-ph↗

arXiv2021

Impact and dynamics of hate and counter speech online

Citizen-generated counter speech is a promising way to fight hate speech and promote peaceful, non-polarized discourse. However, there is a lack of large-scale longitudinal studies of its effectiveness for reducing hate speech. To this end, we perform an exploratory analysis of the effectiveness of counter speech using several different macro- and micro-level measures to analyze 180,000 political conversations that took place on German Twitter over four years. We report on the dynamic interactions of hate and counter speech over time and provide insights into whether, as in `classic' bullying situations, organized efforts are more effective than independent individuals in steering online discourse. Taken together, our results build a multifaceted picture of the dynamics of hate and counter speech online. While we make no causal claims due to the complexity of discourse dynamics, our findings suggest that organized hate speech is associated with changes in public discourse and that counter speech -- especially when organized -- may help curb hateful rhetoric in online discourse.

cs.SI↗

arXiv2021

Universal nonlinear infection kernel from heterogeneous exposure on higher-order networks

The colocation of individuals in different environments is an important prerequisite for exposure to infectious diseases on a social network. Standard epidemic models fail to capture the potential complexity of this scenario by (1) neglecting the higher-order structure of contacts which typically occur through environments like workplaces, restaurants, and households; and by (2) assuming a linear relationship between the exposure to infected contacts and the risk of infection. Here, we leverage a hypergraph model to embrace the heterogeneity of environments and the heterogeneity of individual participation in these environments. We find that combining heterogeneous exposure with the concept of minimal infective dose induces a universal nonlinear relationship between infected contacts and infection risk. Under nonlinear infection kernels, conventional epidemic wisdom breaks down with the emergence of discontinuous transitions, super-exponential spread, and hysteresis.

physics.soc-ph↗

arXiv2021

When the Echo Chamber Shatters: Examining the Use of Community-Specific Language Post-Subreddit Ban

Community-level bans are a common tool against groups that enable online harassment and harmful speech. Unfortunately, the efficacy of community bans has only been partially studied and with mixed results. Here, we provide a flexible unsupervised methodology to identify in-group language and track user activity on Reddit both before and after the ban of a community (subreddit). We use a simple word frequency divergence to identify uncommon words overrepresented in a given community, not as a proxy for harmful speech but as a linguistic signature of the community. We apply our method to 15 banned subreddits, and find that community response is heterogeneous between subreddits and between users of a subreddit. Top users were more likely to become less active overall, while random users often reduced use of in-group language without decreasing activity. Finally, we find some evidence that the effectiveness of bans aligns with the content of a community. Users of dark humor communities were largely unaffected by bans while users of communities organized around white supremacy and fascism were the most affected. Altogether, our results show that bans do not affect all groups or users equally, and pave the way to understanding the effect of bans across communities.

cs.SI↗

arXiv2021

Localization, epidemic transitions, and unpredictability of multistrain epidemics with an underlying genotype network

Mathematical disease modelling has long operated under the assumption that any one infectious disease is caused by one transmissible pathogen spreading among a population. This paradigm has been useful in simplifying the biological reality of epidemics and has allowed the modelling community to focus on the complexity of other factors such as population structure and interventions. However, there is an increasing amount of evidence that the strain diversity of pathogens, and their interplay with the host immune system, can play a large role in shaping the dynamics of epidemics. Here, we introduce a disease model with an underlying genotype network to account for two important mechanisms. One, the disease can mutate along network pathways as it spreads in a host population. Two, the genotype network allows us to define a genetic distance across strains and therefore to model the transcendence of immunity often observed in real world pathogens. We study the emergence of epidemics in this model, through its epidemic phase transitions, and highlight the role of the genotype network in driving cyclicity of diseases, large scale fluctuations, sequential epidemic transitions, as well as localization around specific strains of the associated pathogen. More generally, our model illustrates the richness of behaviours that are possible even in well-mixed host populations once we consider strain diversity and go beyond the "one disease equals one pathogen" paradigm.

q-bio.PE↗

arXiv2021

Containing Future Epidemics with Trustworthy Federated Systems for Ubiquitous Warning and Response

In this paper, we propose a global digital platform to avoid and combat epidemics by providing relevant real-time information to support selective lockdowns. It leverages the pervasiveness of wireless connectivity while being trustworthy and secure. The proposed system is conceptualized to be decentralized yet federated, based on ubiquitous public systems and active citizen participation. Its foundations lie on the principle of informational self-determination. We argue that only in this way it can become a trustworthy and legitimate public good infrastructure for citizens by balancing the asymmetry of the different hierarchical levels within the federated organization while providing highly effective detection and guiding mitigation measures towards graceful lockdown of the society. To exemplify the proposed system, we choose the remote patient monitoring as use case. In which, the integration of distributed ledger technologies with narrowband IoT technology is evaluated considering different number of endorsed peers. An experimental proof of concept setup is used to evaluate the performance of this integration, in which the end-to-end latency is slightly increased when a new endorsed element is added. However, the system reliability, privacy, and interoperability are guaranteed. In this sense, we expect active participation of empowered citizens to supplement the more usual top-down management of epidemics.

cs.DC↗