Projects

Under construction…

Physical Networks

Physical networks are networks of tangible objects, in which nodes and edges are embedded in physical space and subject to constraints such as volume exclusion [(Dehmamy, Milanlouei, and Barabási 2018)]. Examples include biological neural networks, vascular systems, porous media, and granular materials. Advances in imaging technologies and accelerated reconstruction by ML/AI have recently made it possible to obtain detailed three-dimensional maps of such complex systems, providing new opportunities for studying physical networks.

In recent years, the physical embedding of networks has been shown to give rise to emergent phenomena, including entanglement [(Liu, Dehmamy, and Barabási 2021), (Glover and Barabási 2024)], bundling (Bonamassa et al. 2024), jamming (Pósfai et al. 2024), and correlations between node degree and node volume (Pete et al. 2024).

For my PhD thesis, I am exploring the spectral and topological properties of physical networks, as well as the dynamical processes that unfold on them.

NoteLocalization

Coming soon…

TipSynchronization

Coming soon…

ImportantMagnetization

Coming soon…

WarningEntanglement

Coming soon…

Higher-Order Networks

Triadic interactions are higher-order, three-body interactions in which a node modulates the edge between two other nodes. Such interactions are ubiquitous in real-world systems, such as glia cells in the brain regulate synaptic connectivity between neurons.

NoteDiffusion dynamics on networks with triadic interactions

To investigate how triadic interactions affect dynamics, we studied diffusion dynamics on networks incorporating triadic interactions under Gaussian noise. Our results show that these interactions generate conditional correlations and conditional mutual information among the three participating nodes, which in turn reveal both the strength and direction of the triadic interactions.

We further applied this framework as a null model to identify potential triadic interactions in gene regulatory networks.

For details, see (Baptista et al. 2024).

Fractal Scale-Free Networks

A network is fractal (with respect to shortest-path lengths) if the minimum number of subgraphs (boxes) of diameter l_{\textup{B}} required to cover the network scales as \begin{equation} N_{\textup{B}}(l_{\textup{B}}) \sim l_{\textup{B}}^{-D_{\textup{f}}} \end{equation} where D_{\textup{f}} is the fractal dimension of the network (Song, Havlin, and Makse 2005). In fractal networks, the average path lengths also scales as the power of the network size, \begin{equation} \langle l \rangle \sim N^{1/D_{\textup{f}}}. \end{equation} While many empirical networks exhibit the small-world property, where the average path lengths scales logarithmically with the number of nodes (corresponding to the absence of characteristic scales, i.e., D_{\textup{f}} \to \infty), the fractal property can still hold at length scales shorter than the network’s characteristic size. Detecting this scaling through shortest paths, however, is often challenging because most real networks lack a sufficiently large diameter.

Fractal networks are of particular interest because their structure gives rise to distinctive features, such as long-range degree correlations manifested in hub repulsion (Rozenfeld et al. 2008).

NoteBifractality

When scale-free and fractal properties coexist, a broad class of networks exhibits bifractality, characterized by two distinct local fractal dimensions, d_{\textup{f}}^{\min} and d_{\textup{f}}^{\max} that depend on position within the network (Yamamoto and Yakubo 2023). In particular, consider a fractal scale-free network in which, under renormalization, the number of nodes \nu_{\textup{B}} in a supernode (subgraph) of diameter l_{\textup{B}} is proportional to the degree k_{\textup{B}} of that supernode (i.e., the number of adjacent subgraphs): \begin{equation} \nu_{\textup{B}} \propto k_{\textup{B}}. \end{equation} Under this condition, the network exhibits two local fractal dimensions (equivalently, Hölder exponents): \begin{equation} d_{\textup{f}}^{\max} = D_{\textup{f}}, \quad d_{\textup{f}}^{\min} = D_{\textup{f}} \left(\frac{\gamma-2}{\gamma-1}\right), \end{equation} where \gamma is the exponent of the degree distribution and D_{\textup{f}} is the global fractal dimension of the network.

Extensive analytical and numerical calculations for both deterministic and stochastic models suggest that this proportionality condition holds broadly across fractal scale-free networks. We therefore conjecture that bifractality is a general property of fractal scale-free networks.

For details, see (Yamamoto and Yakubo 2023).

TipRandom walks on bifractal networks

Building on the bifractality conjecture, we studied the walk and spectral dimensions of random walks on fractal scale-free networks. We found that the walk dimension d_{\textup{w}}, which characterizes how the mean topological displacement of random walkers scales, remains constant across the network and does not depend on position.

In contrast, the spectral dimension, which governs the scaling of the return probability of a random walker, splits into two distinct values, d_{\textup{s}}^{\min} and d_{\textup{s}}^{\max}. This positional dependence arises directly from the network’s bifractal structure.

For details, see (Yakubo, Shimojo, and Yamamoto 2024).

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References

Baptista, Anthony, Marta Niedostatek, Jun Yamamoto, Ben MacArthur, Jürgen Kurths, Ruben Sanchez-Garcia, and Ginestra Bianconi. 2024. “Mining Higher-Order Triadic Interactions.” arXiv Preprint arXiv:2404.14997 [Nlin.AO].
Bonamassa, I, B Ráth, M Pósfai, M Abért, D Keliger, B Szegedy, J Kertész, L Lovász, and A-L Barabási. 2024. “Logarithmic Kinetics and Bundling in Physical Networks.” arXiv e-Prints, arXiv–2401.
Dehmamy, Nima, Soodabeh Milanlouei, and Albert-László Barabási. 2018. “A Structural Transition in Physical Networks.” Nature 563 (7733): 676–80.
Glover, Cory, and Albert-László Barabási. 2024. “Measuring Entanglement in Physical Networks.” Physical Review Letters 133 (7): 077401.
Liu, Yanchen, Nima Dehmamy, and Albert-László Barabási. 2021. “Isotopy and Energy of Physical Networks.” Nature Physics 17 (2): 216–22.
Pete, Gábor, Ádám Timár, Sigurdur Örn Stefánsson, Ivan Bonamassa, and Márton Pósfai. 2024. “Physical Networks as Network-of-Networks.” Nature Communications 15 (1): 4882.
Pósfai, Márton, Balázs Szegedy, Iva Bačić, Luka Blagojević, Miklós Abért, János Kertész, László Lovász, and Albert-László Barabási. 2024. “Impact of Physicality on Network Structure.” Nature Physics 20 (1): 142–49.
Rozenfeld, Hernán D, Lazaros K Gallos, Chaoming Song, and Hernán A Makse. 2008. “Fractal and Transfractal Scale-Free Networks.” arXiv Preprint arXiv:0808.2206.
Song, Chaoming, Shlomo Havlin, and Hernan A Makse. 2005. “Self-Similarity of Complex Networks.” Nature 433 (7024): 392–95.
Yakubo, Kousuke, Gentaro Shimojo, and Jun Yamamoto. 2024. “Random Walks on Bifractal Networks.” Phys. Rev. E 110 (December): 064318. https://doi.org/10.1103/PhysRevE.110.064318.
Yamamoto, Jun, and Kousuke Yakubo. 2023. “Bifractality of Fractal Scale-Free Networks.” Phys. Rev. E 108: 024302. https://doi.org/10.1103/PhysRevE.108.024302.