News

2023.03.15 — New paper in PLOS Clim.: Long-term effect of forest harvesting on boreal species assemblages under climate change.

2023.02.27 — New manuscript on the arXiv: Heterogeneous transmission in groups induces a superlinear force of infection.

2023.02.19 — New manuscript on the arXiv: Geometric description of clustering in directed networks.

2023.02.08 — New manuscript on the arXiv: Temporal and probabilistic forecasts of epidemic interventions.

2023.01.27 — Olivier Ribordy successfully completed his Master's degree in Physics with the final acceptation of his thesis titled De la densité spectrale des réseaux extrêmement creux. Congratulations!

2023.01.25 — New manuscript on the arXiv: Exact and rapid linear clustering of networks with dynamic programming.

2022.12.20 — François Thibault successfully completed his Master's degree in Physics with the final acceptation of his thesis titled Modèles de graphes aléatoires avec séquences de degrés et de centralité fixes. Congratulations!

2022.12.15 — Béatrice Désy successfully completed her Master's degree in Physics with the final acceptation of her thesis titled Effets de la dimension des réseaux hyperboliques sur la modélisation de la structure communautaire. Her thesis was added to the Board of Honour, the highest distinction at Université Laval. Congratulations!

2022.12.01 — Simon Lizotte successfully completed his Master's degree in Physics with the final acceptation of his thesis titled Inférence de la structure d’interactions de données bruitées. His thesis was added to the Board of Honour, the highest distinction at Université Laval. Congratulations!

2022.09.19 — New manuscript on the arXiv: Dimension matters when modeling network communities in hyperbolic spaces.

2022.09.01 — New manuscript on bioRxiv: NBS-SNI, an extension of the Network-based statistic: Investigating differences in functional connections between important structural actors in case-control studies.

2022.08.15 — New manuscript on the arXiv: Hypergraph reconstruction from noisy pairwise observations.

2022.08.09 — New manuscript on the arXiv: The low-rank hypothesis of complex systems.

2022.07.25 — Béatrice Désy, François Thibault and Simon Lizotte are presenting our latest results at the NetSci 2022 conference.

2022.07.07 — The slides from my seminar at Universitat de Barcelona Institute of Complex Systems titled Dynamics on networks through the lens of spectral and information theories are available here.

2022.06.23 — New manuscript on the arXiv: Dimension reduction of dynamics on modular and heterogeneous directed networks.

2022.06.21 — New paper published in FAccT '22 proceedings: Limits of Individual Consent and Models of Distributed Consent in Online Social Networks.

2022.06.09 — New manuscript on the arXiv: Duality between predictability and reconstructability in complex systems.

2022.05.19 — Francis Normand successfully completed his Master's degree in Biophotonics with the final acceptation of his thesis titled Network-based approaches for case-control studies diagnostic/investigations. Congratulations!

2022.04.18 — New manuscript on the arXiv: Network Onion Divergence: Network representation and comparison using nested configuration models with fixed connectivity, correlation and centrality patterns.

2022.04.01 — The slides from my presentation at CIMMUL's seminar dedicated to the scientific contribution of Siméon Denis Poisson titled Graphe poissonnien, un oxymore? are available here.

Research group

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

Students/postdocs currently under my (co-)supervision

Former members

Ilhem Bouderbala (Postdoc 2020–2022)

Marina Vegué Llorente (Postdoc 2020–2022)

Guillaume St-Onge ( PhD 2022)

Béatrice Désy ( MSc 2022; internship 2019–2020)

Simon Lizotte ( MSc 2022; internship 2020)

Francis Normand ( MSc 2022)

Olivier Ribordy ( MSc 2022; internship 2019)

François Thibault ( MSc 2022; internship 2019–2020)

Émile Baril (internship 2022)

Olivier Lapointe-Gagné (internship 2021)

Pierre-Luc Larouche (internship 2021)

Jérémi Lesage (internship 2021)

Bastian Raulier (internship 2020)

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 and preprints —

Heterogeneous transmission in groups induces a superlinear force of infection
G. St-Onge, L. Hébert-Dufresne and A. Allard
arXiv

Geometric description of clustering in directed networks
A. Allard, M. Á. Serrano and M. Boguñá
arXiv

Temporal and probabilistic forecasts of epidemic interventions
M. C. Boudreau, A. J. Allen, N. J. Roberts, A. Allard and L. Hébert-Dufresne
arXiv

Exact and rapid linear clustering of networks with dynamic programming
A. Patania, A. Allard and J.-G. Young
arXiv

NBS-SNI, an extension of the Network-based statistic: Investigating differences in functional connections between important structural actors in case-control studies
F. Normand, D. C. Côté and A. Allard
bioRxiv

Hypergraph reconstruction from noisy pairwise observations
S. Lizotte, J.-G. Young and A. Allard
arXiv

The low-rank hypothesis of complex systems
V. Thibeault, A. Allard and P. Desrosiers
arXiv

Dimension reduction of dynamics on modular and heterogeneous directed networks
M. Vegué, V. Thibeault, P. Desrosiers and A. Allard
arXiv

Duality between predictability and reconstructability in complex systems
C. Murphy, V. Thibeault, A. Allard and P. Desrosiers
arXiv

Network Onion Divergence: Network representation and comparison using nested configuration models with fixed connectivity, correlation and centrality patterns
L. Hébert-Dufresne, J.-G. Young, A. Daniels and A. Allard
arXiv

Hierarchical team structure and multidimensional localization (or siloing) on networks
L. Hébert-Dufresne, G. St-Onge, J. Meluso, J. P. Bagrow and A. Allard
arXiv

The network epidemiology of an Ebola epidemic
L. Hébert-Dufresne, J.-G. Young, J. Bedson, L. A. Skrip, D. Pedi, M. F. Jalloh, B. Raulier, O. Lapointe-Gagné, A. Jambai, A. Allard and B. M. Althouse
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

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

— 2023 —

Dimension matters when modeling network communities in hyperbolic spaces
B. Désy, P. Desrosiers and A. Allard
To appear in PNAS Nexus
arXiv

Effects of global change on bird and beetle populations in boreal forest landscape: an assemblage dissimilarity analysis
I. Bouderbala, G. Labadie, J.-M. Leblanc, Y. Boulanger, C. Hébert, P. Desrosiers, A. Allard and D. Fortin
To appear in Diversity and Distributions
bioRxiv

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
To appear in SIAM Review
arXiv

Long-term effect of forest harvesting on boreal species assemblages under climate change
I. Bouderbala, G. Labadie, J.-M. Leblanc, J. A. Tremblay, Y. Boulanger, C. Hébert, P. Desrosiers, A. Allard and D. Fortin
PLOS Climate 2, e0000179 (2023)
Full text | bioRxiv

— 2022 —

Limits of Individual Consent and Models of Distributed Consent in Online Social Networks
J. Lovato, A. Allard, J. Onaolapo, R. Harp and L. Hébert-Dufresne
FAccT'22: 2022 ACM Conference on Fairness, Accountability, and Transparency 2251–2262 (2022)
Full text | arXiv | code

Predicting the diversity of early epidemic spread on networks
A. J. Allen, M. C. Boudreau, N. J. Roberts, A. Allard and L. Hébert-Dufresne
Physical Review Research 4, 013123 (2022)
Full text | arXiv

Influential groups for seeding and sustaining nonlinear contagion in heterogeneous hypergraphs
G. St-Onge, I. Iacopini, V. Latora, A. Barrat, G. Petri, A. Allard and L. Hébert-Dufresne
Communications Physics 5, 25 (2022)
Full text | 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
Physical Review Letters 127, 158301 (2021)
Full text | 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 | code

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 | code

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 | code

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 | code

— 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 | code

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