Neuroscience Needs Network Science.

The brain is a complex system comprising a myriad of interacting neurons, posing significant challenges in understanding its structure, function, and dynamics. Network science has emerged as a powerful tool for studying such interconnected systems, offering a framework for integrating multiscale data and complexity. To date, network methods have significantly advanced functional imaging studies of the human brain and have facilitated the development of control theory-based applications for directing brain activity. Here, we discuss emerging frontiers for network neuroscience in the brain atlas era, addressing the challenges and opportunities in integrating multiple data streams for understanding the neural transitions from development to healthy function to disease. We underscore the importance of fostering interdisciplinary opportunities through workshops, conferences, and funding initiatives, such as supporting students and postdoctoral fellows with interests in both disciplines. By bringing together the network science and neuroscience communities, we can develop novel network-based methods tailored to neural circuits, paving the way toward a deeper understanding of the brain and its functions, as well as offering new challenges for network science.

Global Topological Synchronization on Simplicial and Cell Complexes.

Topological signals, i.e., dynamical variables defined on nodes, links, triangles, etc. of higher-order networks, are attracting increasing attention. However, the investigation of their collective phenomena is only at its infancy. Here we combine topology and nonlinear dynamics to determine the conditions for global synchronization of topological signals defined on simplicial or cell complexes. On simplicial complexes we show that topological obstruction impedes odd dimensional signals to globally synchronize. On the other hand, we show that cell complexes can overcome topological obstruction and in some structures signals of any dimension can achieve global synchronization.

Local Dirac Synchronization on networks.

We propose Local Dirac Synchronization that uses the Dirac operator to capture the dynamics of coupled nodes and link signals on an arbitrary network. In Local Dirac Synchronization, the harmonic modes of the dynamics oscillate freely while the other modes are interacting non-linearly, leading to a collectively synchronized state when the coupling constant of the model is increased. Local Dirac Synchronization is characterized by discontinuous transitions and the emergence of a rhythmic coherent phase. In this rhythmic phase, one of the two complex order parameters oscillates in the complex plane at a slow frequency (called emergent frequency) in the frame in which the intrinsic frequencies have zero average. Our theoretical results obtained within the annealed approximation are validated by extensive numerical results on fully connected networks and sparse Poisson and scale-free networks. Local Dirac Synchronization on both random and real networks, such as the connectome of Caenorhabditis Elegans, reveals the interplay between topology (Betti numbers and harmonic modes) and non-linear dynamics. This unveils how topology might play a role in the onset of brain rhythms.

Grand Canonical Ensembles of Sparse Networks and Bayesian Inference.

Maximum entropy network ensembles have been very successful in modelling sparse network topologies and in solving challenging inference problems. However the sparse maximum entropy network models proposed so far have fixed number of nodes and are typically not exchangeable. Here we consider hierarchical models for exchangeable networks in the sparse limit, i.e., with the total number of links scaling linearly with the total number of nodes. The approach is grand canonical, i.e., the number of nodes of the network is not fixed a priori: it is finite but can be arbitrarily large. In this way the grand canonical network ensembles circumvent the difficulties in treating infinite sparse exchangeable networks which according to the Aldous-Hoover theorem must vanish. The approach can treat networks with given degree distribution or networks with given distribution of latent variables. When only a subgraph induced by a subset of nodes is known, this model allows a Bayesian estimation of the network size and the degree sequence (or the sequence of latent variables) of the entire network which can be used for network reconstruction.

Universal Nonlinear Infection Kernel from Heterogeneous Exposure on Higher-Order Networks.

The collocation 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 that typically occur through environments like workplaces, restaurants, and households, and (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, superexponential spread, and hysteresis.

Explosive Higher-Order Kuramoto Dynamics on Simplicial Complexes.

The higher-order interactions of complex systems, such as the brain, are captured by their simplicial complex structure and have a significant effect on dynamics. However, the existing dynamical models defined on simplicial complexes make the strong assumption that the dynamics resides exclusively on the nodes. Here we formulate the higher-order Kuramoto model which describes the interactions between oscillators placed not only on nodes but also on links, triangles, and so on. We show that higher-order Kuramoto dynamics can lead to an explosive synchronization transition by using an adaptive coupling dependent on the solenoidal and the irrotational component of the dynamics.

Sparse Power-Law Network Model for Reliable Statistical Predictions Based on Sampled Data.

A projective network model is a model that enables predictions to be made based on a subsample of the network data, with the predictions remaining unchanged if a larger sample is taken into consideration. An exchangeable model is a model that does not depend on the order in which nodes are sampled. Despite a large variety of non-equilibrium (growing) and equilibrium (static) sparse complex network models that are widely used in network science, how to reconcile sparseness (constant average degree) with the desired statistical properties of projectivity and exchangeability is currently an outstanding scientific problem. Here we propose a network process with hidden variables which is projective and can generate sparse power-law networks. Despite the model not being exchangeable, it can be closely related to exchangeable uncorrelated networks as indicated by its information theory characterization and its network entropy. The use of the proposed network process as a null model is here tested on real data, indicating that the model offers a promising avenue for statistical network modelling.

Extracting information from multiplex networks.

Multiplex networks are generalized network structures that are able to describe networks in which the same set of nodes are connected by links that have different connotations. Multiplex networks are ubiquitous since they describe social, financial, engineering, and biological networks as well. Extending our ability to analyze complex networks to multiplex network structures increases greatly the level of information that is possible to extract from big data. For these reasons, characterizing the centrality of nodes in multiplex networks and finding new ways to solve challenging inference problems defined on multiplex networks are fundamental questions of network science. In this paper, we discuss the relevance of the Multiplex PageRank algorithm for measuring the centrality of nodes in multilayer networks and we characterize the utility of the recently introduced indicator function Θ̃(S) for describing their mesoscale organization and community structure. As working examples for studying these measures, we consider three multiplex network datasets coming for social science.

Network controllability is determined by the density of low in-degree and out-degree nodes.

The problem of controllability of the dynamical state of a network is central in network theory and has wide applications ranging from network medicine to financial markets. The driver nodes of the network are the nodes that can bring the network to the desired dynamical state if an external signal is applied to them. Using the framework of structural controllability, here, we show that the density of nodes with in degree and out degree equal to one and two determines the number of driver nodes in the network. Moreover, we show that random networks with minimum in degree and out degree greater than two, are always fully controllable by an infinitesimal fraction of driver nodes, regardless of the other properties of the degree distribution. Finally, based on these results, we propose an algorithm to improve the controllability of networks.

Selection for replicases in protocells.

We consider a world of nucleotide sequences and protocells. The sequences have the property of spontaneous self-replication. Some sequences - so-called replicases - have enzymatic activity in the sense of enhancing the replication rate of all (or almost all) sequences. In a well-mixed medium, natural selection would not favor such replicases because their presence equally benefits sequences with or without replicase activity. Here we show that protocells can select for replicases. We assume that sequences replicate within protocells and that protocells undergo spontaneous division. This leads to particular population structures which can augment the abundance of replicases. We explore various assumptions regarding replicase activity and protocell division. We calculate the error threshold that is compatible with selecting for replicases.

Nature of hypergraph k-core percolation problems.

Hypergraphs are higher-order networks that capture the interactions between two or more nodes. Hypergraphs can always be represented by factor graphs, i.e., bipartite networks between nodes and factor nodes (representing groups of nodes). Despite this universal representation, here we reveal that k-core percolation on hypergraphs can be significantly distinct from k-core percolation on factor graphs. We formulate the theory of hypergraph k-core percolation based on the assumption that a hyperedge can be intact only if all its nodes are intact. This scenario applies, for instance, to supply chains where the production of a product requires all raw materials and all processing steps; in biology it applies to protein-interaction networks where protein complexes can function only if all the proteins are present; and it applies as well to chemical reaction networks where a chemical reaction can take place only when all the reactants are present. Formulating a message-passing theory for hypergraph k-core percolation, and combining it with the theory of critical phenomena on networks, we demonstrate sharp differences with previously studied factor graph k-core percolation processes where it is allowed for hyperedges to have one or more damaged nodes and still be intact. To solve the dichotomy between k-core percolation on hypegraphs and on factor graphs, we define a set of pruning processes that act either exclusively on nodes or exclusively on hyperedges and depend on their second-neighborhood connectivity. We show that the resulting second-neighbor k-core percolation problems are significantly distinct from each other. Moreover we reveal that although these processes remain distinct from factor graphs k-core processes, when the pruning process acts exclusively on hyperedges the phase diagram is reduced to the one of factor graph k-cores.

Theory of percolation on hypergraphs.

Hypergraphs capture the higher-order interactions in complex systems and always admit a factor graph representation, consisting of a bipartite network of nodes and hyperedges. As hypegraphs are ubiquitous, investigating hypergraph robustness is a problem of major research interest. In the literature the robustness of hypergraphs so far only has been treated adopting factor-graph percolation, which describes well higher-order interactions which remain functional even after the removal of one of more of their nodes. This approach, however, fall short to describe situations in which higher-order interactions fail when any one of their nodes is removed, this latter scenario applying, for instance, to supply chains, catalytic networks, protein-interaction networks, networks of chemical reactions, etc. Here we show that in these cases the correct process to investigate is hypergraph percolation, with is distinct from factor graph percolation. We build a message-passing theory of hypergraph percolation, and we investigate its critical behavior using generating function formalism supported by Monte Carlo simulations on random graph and real data. Notably, we show that the node percolation threshold on hypergraphs exceeds node percolation threshold on factor graphs. Furthermore we show that differently from what happens in ordinary graphs, on hypergraphs the node percolation threshold and hyperedge percolation threshold do not coincide, with the node percolation threshold exceeding the hyperedge percolation threshold. These results demonstrate that any fat-tailed cardinality distribution of hyperedges cannot lead to the hyper-resilience phenomenon in hypergraphs in contrast to their factor graphs, where the divergent second moment of a cardinality distribution guarantees zero percolation threshold.

Global topological synchronization of weighted simplicial complexes.

Higher-order networks are able to capture the many-body interactions present in complex systems and to unveil fundamental phenomena revealing the rich interplay between topology, geometry, and dynamics. Simplicial complexes are higher-order networks that encode higher-order topology and dynamics of complex systems. Specifically, simplicial complexes can sustain topological signals, i.e., dynamical variables not only defined on nodes of the network but also on their edges, triangles, and so on. Topological signals can undergo collective phenomena such as synchronization, however, only some higher-order network topologies can sustain global synchronization of topological signals. Here we consider global topological synchronization of topological signals on weighted simplicial complexes. We demonstrate that topological signals can globally synchronize on weighted simplicial complexes, even if they are odd-dimensional, e.g., edge signals, thus overcoming a limitation of the unweighted case. These results thus demonstrate that weighted simplicial complexes are more advantageous for observing these collective phenomena than their unweighted counterpart. In particular, we present two weighted simplicial complexes: the weighted triangulated torus and the weighted waffle. We completely characterize their higher-order spectral properties and demonstrate that, under suitable conditions on their weights, they can sustain global synchronization of edge signals. Our results are interpreted geometrically by showing, among the other results, that in some cases edge weights can be associated with the lengths of the sides of curved simplices.

Triadic percolation induces dynamical topological patterns in higher-order networks.

Triadic interactions are higher-order interactions which occur when a set of nodes affects the interaction between two other nodes. Examples of triadic interactions are present in the brain when glia modulate the synaptic signals among neuron pairs or when interneuron axo-axonic synapses enable presynaptic inhibition and facilitation, and in ecosystems when one or more species can affect the interaction among two other species. On random graphs, triadic percolation has been recently shown to turn percolation into a fully fledged dynamical process in which the size of the giant component undergoes a route to chaos. However, in many real cases, triadic interactions are local and occur on spatially embedded networks. Here, we show that triadic interactions in spatial networks induce a very complex spatio-temporal modulation of the giant component which gives rise to triadic percolation patterns with significantly different topology. We classify the observed patterns (stripes, octopus, and small clusters) with topological data analysis and we assess their information content (entropy and complexity). Moreover, we illustrate the multistability of the dynamics of the triadic percolation patterns, and we provide a comprehensive phase diagram of the model. These results open new perspectives in percolation as they demonstrate that in presence of spatial triadic interactions, the giant component can acquire a time-varying topology. Hence, this work provides a theoretical framework that can be applied to model realistic scenarios in which the giant component is time dependent as in neuroscience.

Network science: Ising states of matter.

Network science provides very powerful tools for extracting information from interacting data. Although recently the unsupervised detection of phases of matter using machine learning has raised significant interest, the full prediction power of network science has not yet been systematically explored in this context. Here we fill this gap by providing an in-depth statistical, combinatorial, geometrical, and topological characterization of 2D Ising snapshot networks (IsingNets) extracted from Monte Carlo simulations of the 2D Ising model at different temperatures, going across the phase transition. Our analysis reveals the complex organization properties of IsingNets in both the ferromagnetic and paramagnetic phases and demonstrates the significant deviations of the IsingNets with respect to randomized null models. In particular percolation properties of the IsingNets reflect the existence of the symmetry between configurations with opposite magnetization below the critical temperature and the very compact nature of the two emerging giant clusters revealed by our persistent homology analysis of the IsingNets. Moreover, the IsingNets display a very broad degree distribution and significant degree-degree correlations and weight-degree correlations demonstrating that they encode relevant information present in the configuration space of the 2D Ising model. The geometrical organization of the critical IsingNets is reflected in their spectral properties deviating from the one of the null model. This work reveals the important insights that network science can bring to the characterization of phases of matter. The set of tools described hereby can be applied as well to numerical and experimental data.

Persistent Dirac for molecular representation.

Molecular representations are of fundamental importance for the modeling and analysing molecular systems. The successes in drug design and materials discovery have been greatly contributed by molecular representation models. In this paper, we present a computational framework for molecular representation that is mathematically rigorous and based on the persistent Dirac operator. The properties of the discrete weighted and unweighted Dirac matrix are systematically discussed, and the biological meanings of both homological and non-homological eigenvectors are studied. We also evaluate the impact of various weighting schemes on the weighted Dirac matrix. Additionally, a set of physical persistent attributes that characterize the persistence and variation of spectrum properties of Dirac matrices during a filtration process is proposed to be molecular fingerprints. Our persistent attributes are used to classify molecular configurations of nine different types of organic-inorganic halide perovskites. The combination of persistent attributes with gradient boosting tree model has achieved great success in molecular solvation free energy prediction. The results show that our model is effective in characterizing the molecular structures, demonstrating the power of our molecular representation and featurization approach.

The dynamic nature of percolation on networks with triadic interactions.

Percolation establishes the connectivity of complex networks and is one of the most fundamental critical phenomena for the study of complex systems. On simple networks, percolation displays a second-order phase transition; on multiplex networks, the percolation transition can become discontinuous. However, little is known about percolation in networks with higher-order interactions. Here, we show that percolation can be turned into a fully fledged dynamical process when higher-order interactions are taken into account. By introducing signed triadic interactions, in which a node can regulate the interactions between two other nodes, we define triadic percolation. We uncover that in this paradigmatic model the connectivity of the network changes in time and that the order parameter undergoes a period doubling and a route to chaos. We provide a general theory for triadic percolation which accurately predicts the full phase diagram on random graphs as confirmed by extensive numerical simulations. We find that triadic percolation on real network topologies reveals a similar phenomenology. These results radically change our understanding of percolation and may be used to study complex systems in which the functional connectivity is changing in time dynamically and in a non-trivial way, such as in neural and climate networks.

Neuroscience needs Network Science.

The brain is a complex system comprising a myriad of interacting elements, posing significant challenges in understanding its structure, function, and dynamics. Network science has emerged as a powerful tool for studying such intricate systems, offering a framework for integrating multiscale data and complexity. Here, we discuss the application of network science in the study of the brain, addressing topics such as network models and metrics, the connectome, and the role of dynamics in neural networks. We explore the challenges and opportunities in integrating multiple data streams for understanding the neural transitions from development to healthy function to disease, and discuss the potential for collaboration between network science and neuroscience communities. We underscore the importance of fostering interdisciplinary opportunities through funding initiatives, workshops, and conferences, as well as supporting students and postdoctoral fellows with interests in both disciplines. By uniting the network science and neuroscience communities, we can develop novel network-based methods tailored to neural circuits, paving the way towards a deeper understanding of the brain and its functions.

Evolution and control of oxygen order in a cuprate superconductor.

The disposition of defects in metal oxides is a key attribute exploited for applications from fuel cells and catalysts to superconducting devices and memristors. The most typical defects are mobile excess oxygens and oxygen vacancies, which can be manipulated by a variety of thermal protocols as well as optical and d.c. electric fields. Here we report the X-ray writing of high-quality superconducting regions, derived from defect ordering, in the superoxygenated layered cuprate, La2CuO(4+y). Irradiation of a poor superconductor prepared by rapid thermal quenching results first in the growth of ordered regions, with an enhancement of superconductivity becoming visible only after a waiting time, as is characteristic of other systems such as ferroelectrics, where strain must be accommodated for order to become extended. However, in La2CuO(4+y), we are able to resolve all aspects of the growth of (oxygen) intercalant order, including an extraordinary excursion from low to high and back to low anisotropy of the ordered regions. We can also clearly associate the onset of high-quality superconductivity with defect ordering in two dimensions. Additional experiments with small beams demonstrate a photoresist-free, single-step strategy for writing functional materials.

Dynamics of ranking processes in complex systems.

The world is addicted to ranking: everything, from the reputation of scientists, journals, and universities to purchasing decisions is driven by measured or perceived differences between them. Here, we analyze empirical data capturing real time ranking in a number of systems, helping to identify the universal characteristics of ranking dynamics. We develop a continuum theory that not only predicts the stability of the ranking process, but shows that a noise-induced phase transition is at the heart of the observed differences in ranking regimes. The key parameters of the continuum theory can be explicitly measured from data, allowing us to predict and experimentally document the existence of three phases that govern ranking stability.