News

2021.08.05 — New paper in Nat. Commun.: Deep learning of contagion dynamics on complex networks.

2021.07.07 — New manuscript on the arXiv: Predicting the diversity of early epidemic spread on networks.

2021.07.05 — Patrick Desrosiers, Charles Murphy, Guillaume St-Onge, Vincent Thibeault, Marina Vegué Llorente and myself are presenting our latest results at the Networks 2021 conference.

2021.05.23 — Charles Murphy, Guillaume St-Onge, Vincent Thibeault and Marina Vegué Llorente are presenting our latest results at the SIAM Conference on Applications of Dynamical Systems (DS21).

2021.05.18 — New manuscript on the arXiv: Influential groups for seeding and sustaining hypergraph contagions.

2021.05.03 — Olivier Lapointe-Gagné, Pierre-Luc Larouche and Jérémi Lesage join the group as summer interns.

2021.04.09 — Immensely honored to have been awarded the 2021 ADEPUL prize for ``Teacher of the year'' (elected by the Physics undergraduate students).

2021.04.01 — Guillaume St-Onge, Vincent Thibeault and Marina Vegué Llorente are presenting our latest results at the Fourth Northeast Regional Conference on Complex Systems (NERCCS 2021).

2021.03.01 — New paper in Phys. Rev. Lett.: Social confinement and mesoscopic localization of epidemics on networks.

2021.03.01 — New paper in Phys. Rev. E: Master equation analysis of mesoscopic localization in contagion dynamics on higher-order networks.

2021.02.11 — Immensely honored to have been nominated as an external faculty member of the Vermont Complex Systems Center at the University of Vermont.

2021.01.19 — New manuscript on the arXiv: Universal nonlinear infection kernel from heterogeneous exposure on higher-order networks.

2020.11.12 — New paper in PLOS Biol.: Superspreading events in the transmission dynamics of SARS-CoV-2: Opportunities for interventions and control.

2020.11.04 — New paper in J. R. Soc. Interface: Beyond R0: heterogeneity in secondary infections and probabilistic epidemic forecasting.

2020.11.02 — Dr. Ilhem Bouderbala joins the group as postdoctoral fellow.

2020.09.23 — Just published an essay in ACFAS Magazine on the role mathematical modeling plays in understanding the behavior of complex systems.

2020.08.31 — François Thibault and Olivier Ribordy join the group as MSc students.

2019.08.06 — New paper in PNAS: Geometric renormalization unravels self-similarity of the multiscale human connectome.


Research group

My Research Chair is part of the Dynamica Research Lab on Complex Systems that I lead alongside Patrick Desrosiers and Louis J. Dubé. I also co-supervise students or postdoctoral researchers affiliated with other research groups.

Students/postdocs currently under my (co-)supervision

Marina Vegué Llorente
Postdoctoral fellow

Ilhem Bouderbala
Postdoctoral fellow

Charles Murphy
PhD student

Guillaume St-Onge
PhD student

Vincent Thibeault
PhD student

Francis Normand
MSc student

Béatrice Désy
MSc student

Simon Lizotte
MSc student

François Thibault
MSc student

Olivier Ribordy
MSc student

Heikel Jarras
MSc student

Former members
Olivier Lapointe-Gagné, Undergraduate intern (summer 2021)
Pierre-Luc Larouche, Undergraduate intern (summer 2021)
Jérémi Lesage, Undergraduate intern (summer 2021)
Bastian Raulier, Undergraduate intern (summer-fall 2020)
Simon Lizotte, Undergraduate intern (winter 2020)
Olivier Ribordy, Undergraduate intern (summer 2019)
François Thibault, Undergraduate intern (summer 2019, winter 2020)

Code

Mercator
A C++/Python code embedding real complex netwoks in hyperbolic space. The algorithm is presented here and can be downloaded here.

Onion Decomposition
A C++ code extracting the Onion Decomposition of a graph as introduced here (and used here and here) can be downloaded here.


Publications

Listed in inverse chronological order; equal contributions are denoted by *.
Most of the publications below can also be found on arXiv or on Google Scholar.

— Submitted manuscripts —

Predicting the diversity of early epidemic spread on networks
A. J. Allen, M. C. Boudreau, N. J. Roberts, A. Allard and L. Hébert-Dufresne
arXiv

Influential groups for seeding and sustaining hypergraph contagions
G. St-Onge, I. Iacopini, V. Latora, A. Barrat, G. Petri, A. Allard and L. Hébert-Dufresne
arXiv

The unintended consequences of inconsistent pandemic control policies
B. M. Althouse, B. Case, S. V. Scarpino, A. Allard, A. M. Berdahl, E. R. White and L. Hébert-Dufresne
medRxiv

Limits of individual consent and models of distributed consent in online social networks
J. Lovato, A. Allard, R. Harp and L. Hébert-Dufresne
arXiv

The role of directionality, heterogeneity and correlations in epidemic risk and spread
A. Allard, C. Moore, S. V. Scarpino, B. M. Althouse and L. Hébert-Dufresne
arXiv

On the accuracy of message-passing approaches to percolation in complex networks
A. Allard and L. Hébert-Dufresne
arXiv

— 2021 —

Universal nonlinear infection kernel from heterogeneous exposure on higher-order networks
G. St-Onge, H. Sun, A. Allard, L. Hébert-Dufresne and G. Bianconi
To appear in Physical Review Letters
arXiv

Deep learning of contagion dynamics on complex networks
C. Murphy, E. Laurence and A. Allard
Nature Communications 12, 4720 (2021)
Full text | arXiv | code | data

Social confinement and mesoscopic localization of epidemics on networks
G. St-Onge, V. Thibeault, A. Allard, L. J. Dubé and L. Hébert-Dufresne
Physical Review Letters 126, 098301 (2021)
Full text | arXiv

Master equation analysis of mesoscopic localization in contagion dynamics on higher-order networks
G. St-Onge, V. Thibeault, A. Allard, L. J. Dubé and L. Hébert-Dufresne
Physical Review E 103, 032301 (2021)
Full text | arXiv

— 2020 —

La modélisation mathématique pour cartographier le complexe et l'inconnu
(Mapping the complex and the unknown with mathematical modeling)
A. Allard, L. J. Dubé and L. Hébert-Dufresne
ACFAS Magazine (2020)

Superspreading events in the transmission dynamics of SARS-CoV-2: Opportunities for interventions and control
B. M. Althouse, E. A. Wenger, J. C. Miller, S. V. Scarpino, A. Allard, L. Hébert-Dufresne and H. Hu
PLOS Biology 18, e3000897 (2020)
Full text | arXiv

Beyond R0: heterogeneity in secondary infections and probabilistic epidemic forecasting
L. Hébert-Dufresne, B. M. Althouse, S. V. Scarpino and A. Allard
Journal of the Royal Society Interface 17, 20200393 (2020)
Full text | arXiv | medRxiv

Geometric renormalization unravels self-similarity of the multiscale human connectome
M. Zheng, A. Allard, P. Hagmann, Y. Alemán-Gómez and M. Á. Serrano
Proceedings of the National Academy of Sciences USA 117, 20244 (2020)
Full text | arXiv

COVID-19: Cancel your next large event, and tell your friends to cancel theirs
G. St-Onge, V. Thibeault, A. Allard, L. J. Dubé and L. Hébert-Dufresne
medium.com

Genome-scale modeling of metabolism in the polar diatom Fragilariopsis cylindrus underscores the strong robustness of growth rate in response to cellular perturbations
M. Lavoie, B. Saint-Béat, J. Strauss, S. Guérin, A. Allard, S. V. Hardy, A. Falciatore and J. Lavaud
Biology 9, 30 (2020)
Full text

Navigable maps of structural brain networks across species
A. Allard and M. Á. Serrano
PLOS Computational Biology 16, e1007584 (2020)
Full text | arXiv | data

— 2019 —

Mercator: uncovering faithful hyperbolic embeddings of complex networks
G. García-Pérez*, A. Allard*, M. Á. Serrano and M. Boguñá
New Journal of Physics 21, 123033 (2019)
Full text | arXiv | code

Smeared phase transition of percolation on real complex networks
L. Hébert-Dufresne and A. Allard
Physical Review Research 1, 013009 (2019)
Full text | arXiv

Percolation and the effective structure of complex networks
A. Allard and L. Hébert-Dufresne
Physical Review X 9, 011023 (2019)
Full text | arXiv | code

— 2018 —

A new approach to international trade from Network Geometry: The World Trade Atlas 1870-2013
G. García-Pérez, M. Boguñá, A. Allard, and M. Á. Serrano
S. Gorgoni, A. Amighini, and M. Smith (Eds.), Vernon Press, ISBN 978-1622730650
Table of contents

Geometric evolution of complex networks with degree correlations
C. Murphy, A. Allard, E. Laurence, G. St-Onge and L. J. Dubé
Physical Review E 97, 032309 (2018)
Full text | arXiv

— 2017 —

The risk of sustained sexual transmission of Zika is underestimated
A. Allard*, B. M. Althouse*, L. Hébert-Dufresne* and S. V. Scarpino*
PLOS Pathogens 13, e1006633 (2017)
Full text | bioRxiv

Asymmetric percolation drives a double transition in sexual contact networks
A. Allard, B. M. Althouse, S. V. Scarpino and L. Hébert-Dufresne
Proceedings of the National Academy of Sciences USA 114, 8969-8973 (2017)
Full text | arXiv

Strategic tradeoffs in competitor dynamics on adaptive networks
L. Hébert-Dufresne, A. Allard, P.-A. Noël, J.-G. Young and E. Libby
Scientific Reports 7, 7576 (2017)
Full text | arXiv

The geometric nature of weights in real complex networks
A. Allard, M. Á. Serrano, G. García-Pérez and M. Boguñá
Nature Communications 8, 14103 (2017)
Full text | arXiv
Nature Phys. Research Highlights
Features in Nature Communications' web collection on complex systems

— 2016 —

Growing networks of overlapping communities with internal structure
J.-G. Young, L. Hébert-Dufresne, A. Allard, and L. J. Dubé
Physical Review E 94, 022317 (2016)
Full text | arXiv

Multi-scale structure and topological anomaly detection via a new network statistic: The onion decomposition
L. Hébert-Dufresne, J. A. Grochow, and A. Allard
Scientific Reports 6, 31708 (2016)
Full text | arXiv

The effect of a prudent adaptive behaviour on disease transmission
S. V. Scarpino, A. Allard, L. Hébert-Dufresne
Nature Physics 12, 1042-1046 (2016)
Full text | arXiv | Media coverage
Nature Phys. News & Views

Constrained growth of complex scale-independent systems
L. Hébert-Dufresne, A. Allard, J.-G. Young, and L. J. Dubé
Physical Review E 93, 032304 (2016)
Full text | arXiv
★ In the Editors' Suggestions section of Physical Review E.

The hidden hyperbolic geometry of international trade: World Trade Atlas 1870-2013
G. García-Pérez, M. Boguñá, A. Allard, and M. Á. Serrano
Scientific Reports 6, 33441 (2016)
Full text | arXiv | Interactive map
★ Featured in the section Economía of the newspaper El Periódico.

— 2015 —

Complex networks as an emerging property of hierarchical preferential attachment
L. Hébert-Dufresne, E. Laurence, A. Allard, J.-G. Young and L. J. Dubé
Physical Review E 92, 062809 (2015)
Full text | arXiv

General and exact approach to percolation on random graphs
A. Allard, L. Hébert-Dufresne, J.-G. Young and L. J. Dubé
Physical Review E 92, 062807 (2015)
Full text | arXiv

A shadowing problem in the detection of overlapping communities: lifting the resolution limit through a cascading procedure
J.-G. Young, A. Allard, L. Hébert-Dufresne and L. J. Dubé
PLOS ONE 10, e0140133 (2015)
Full text | arXiv | code

— 2014 —

The Social Zombie: Modelling undead outbreaks on social networks
L. Hébert-Dufresne, V. Marceau, P.-A. Noël, A. Allard, and L. J. Dubé
Robert Smith? (Ed.), University of Ottawa Press, ISBN 978-0776622101
Table of contents

Spreading dynamics on complex networks: a general stochastic approach
P.-A. Noël, A. Allard, L. Hébert-Dufresne, V. Marceau and L. J. Dubé
Journal of Mathematical Biology 69, 1627 (2014)
Full text | arXiv

A system-level model for the microbial regulatory genome
A. N. Brooks, D. J. Reiss, A. Allard, W.-J. Wu, D. M. Salvanha, C. L. Plaisier, S. Chandrasekaran, M. Pan, A. Kaur and N. S. Baliga
Molecular Systems Biology 10, 740 (2014)
Full text

Coexistence of phases and the observability of random graphs
A. Allard, L. Hébert-Dufresne, J.-G. Young and L. J. Dubé
Physical Review E 89, 022801 (2014)
Full text | arXiv
★ In the Editors' Suggestions section of Physical Review E.

Percolation sur graphes aléatoires: Modélisation et description analytique
(Percolation on random graphs: Modelling and analytical description)
Ph.D. Thesis, Université Laval (2014)
Full text

— 2013 —

Percolation on random networks with arbitrary k-core structure
L. Hébert-Dufresne*, A. Allard*, J.-G. Young and L. J. Dubé
Physical Review E 88, 062820 (2013)
Full text | arXiv

Global efficiency of local immunization of complex networks
L. Hébert-Dufresne*, A. Allard*, J.-G. Young* and L. J. Dubé
Scientific Reports 3, 2171 (2013)
Full text | arXiv

— 2012 —

Bond percolation on a class of correlated and clustered random graphs
A. Allard, L. Hébert-Dufresne, P.-A. Noël, V. Marceau and L. J. Dubé
Journal of Physics A 45, 405005 (2012)
Full text | arXiv

Exact solution of bond percolation on small arbitrary graphs
A. Allard, L. Hébert-Dufresne, P.-A. Noël, V. Marceau and L. J. Dubé
Europhysics Letters (EPL) 98, 16001 (2012)
Full text | arXiv

Propagation on networks: An exact alternative perspective
P.-A. Noël, A. Allard, L. Hébert-Dufresne, V. Marceau and L. J. Dubé
Physical Review E 85, 031118 (2012)
Full text | arXiv

Structural preferential attachment: Stochastic process for the growth of scale-free, modular and self-similar systems
L. Hébert-Dufresne, A. Allard, V. Marceau, P.-A. Noël and L. J. Dubé
Physical Review E 85, 026108 (2012)
Full text | arXiv

— 2011 —

Structural Preferential Attachment: Network Organization beyond the Link
L. Hébert-Dufresne, A. Allard, V. Marceau, P.-A. Noël and L. J. Dubé
Physical Review Letters 107, 158702 (2011)
Full text | arXiv

Modeling the dynamical interaction between epidemics on overlay networks
V. Marceau, P.-A. Noël, L. Hébert-Dufresne, A. Allard and L. J. Dubé
Physical Review E 84, 026105 (2011)
Full text | arXiv

— 2010 —

Propagation dynamics on networks featuring complex topologies
L. Hébert-Dufresne, P.-A. Noël, V. Marceau, A. Allard and L. J. Dubé
Physical Review E 82, 036115 (2010)
Full text | arXiv
★ Also in the Virtual Journal of Biological Physics Research, issue 7, vol. 20 (2010)

Adaptive networks: Coevolution of disease and topology
V. Marceau, P.-A. Noël, L. Hébert-Dufresne, A. Allard and L. J. Dubé
Physical Review E 82, 036116 (2010)
Full text | arXiv
★ Also in the Virtual Journal of Biological Physics Research, issue 7, vol. 20 (2010)

— 2009 —

Heterogeneous Bond Percolation on Multitype Networks with an Application to Epidemic Dynamics
A. Allard, P.-A. Noël, L. J. Dubé and B. Pourbohloul
Physical Review E 79, 036113 (2009)
Full text | arXiv
★ Also in the Virtual Journal of Biological Physics Research, issue 7, vol. 17 (2009)

Des Ponts d'Euler à la Grippe Aviaire: De l'abstraction mathématique à la réalité sociale des épidémies
(From Euler Bridges to the Avian Flu: From Mathematical Abstraction to the Social Reality of Epidemics)
A. Allard, P.-A. Noël, and L. J. Dubé
Accromath 4, 24-29 (2009)
Full text

— 2008 —

Modélisation Mathématique en Epidémiologie par Réseaux de Contacts: Introduction de l'Hétérogénéité dans la Transmissibilité
(Mathematical Modelling in Contact Networks for Epidemiology: Introduction of Heterogenity in Transmissibility)
M.Sc. Thesis, Université Laval (2008)
Full text