arXiv subjects

Ginestra Bianconi

Publications and source records attributed to Ginestra Bianconi.

At least 55 records · Page 3Linked to original sources

arXiv2023

Zoo Guide to Network Embedding

Networks have provided extremely successful models of data and complex systems. Yet, as combinatorial objects, networks do not have in general intrinsic coordinates and do not typically lie in an ambient space. The process of assigning an embedding space to a network has attracted lots of interest in the past few decades, and has been efficiently applied to fundamental problems in network inference, such as link prediction, node classification, and community detection. In this review, we provide a user-friendly guide to the network embedding literature and current trends in this field which will allow the reader to navigate through the complex landscape of methods and approaches emerging from the vibrant research activity on these subjects.

cs.SI↗

arXiv2023

Learning from data with structured missingness

Missing data are an unavoidable complication in many machine learning tasks. When data are `missing at random' there exist a range of tools and techniques to deal with the issue. However, as machine learning studies become more ambitious, and seek to learn from ever-larger volumes of heterogeneous data, an increasingly encountered problem arises in which missing values exhibit an association or structure, either explicitly or implicitly. Such `structured missingness' raises a range of challenges that have not yet been systematically addressed, and presents a fundamental hindrance to machine learning at scale. Here, we outline the current literature and propose a set of grand challenges in learning from data with structured missingness.

stat.ML↗

arXiv2023

Diffusion-driven instability of topological signals coupled by the Dirac operator

The study of reaction-diffusion systems on networks is of paramount relevance for the understanding of nonlinear processes in systems where the topology is intrinsically discrete, such as the brain. Until now reaction-diffusion systems have been studied only when species are defined on the nodes of a network. However, in a number of real systems including, e.g., the brain and the climate, dynamical variables are not only defined on nodes but also on links, faces and higher-dimensional cells of simplicial or cell complexes, leading to topological signals. In this work we study reaction-diffusion processes of topological signals coupled through the Dirac operator. The Dirac operator allows topological signals of different dimension to interact or cross-diffuse as it projects the topological signals defined on simplices or cells of a given dimension to simplices or cells of one dimension up or one dimension down. By focusing on the framework involving nodes and links we establish the conditions for the emergence of Turing patterns and we show that the latter are never localized only on nodes or only on links of the network. Moreover when the topological signals display Turing pattern their projection does as well. We validate the theory hereby developed on a benchmark network model and on square lattices with periodic boundary conditions.

nlin.PS↗

arXiv2023

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.

nlin.AO↗

arXiv2023

Higher-order signal processing with the Dirac operator

The processing of signals on simplicial and cellular complexes defined by nodes, edges, and higher-order cells has recently emerged as a principled extension of graph signal processing for signals supported on more general topological spaces. However, most works so far have considered signal processing problems for signals associated to only a single type of cell such as the processing of node signals, or edge signals, by considering an appropriately defined shift operator, like the graph Laplacian or the Hodge Laplacian. Here we introduce the Dirac operator as a novel kind of shift operator for signal processing on complexes. We discuss how the Dirac operator has close relations but is distinct from the Hodge-Laplacian and examine its spectral properties. Importantly, the Dirac operator couples signals defined on cells of neighboring dimensions in a principled fashion. We demonstrate how this enables us, e.g., to leverage node signals for the processing of edge flows.

cs.SI↗

arXiv2023

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.

cond-mat.stat-mech↗

arXiv2023

Persistent Dirac for molecular representation

Molecular representations are of fundamental importance for the modeling and analysis of molecular systems. Representation models and in general approaches based on topological data analysis (TDA) have demonstrated great success in various steps of drug design and materials discovery. Here we develop a mathematically rigorous computational framework for molecular representation based on the persistent Dirac operator. The properties of the spectrum of the discrete weighted and unweighted Dirac matrices are systemically discussed and used to demonstrate the geometric and topological properties of both non-homology and homology eigenvectors of real molecular structures. This allows us to asses the influence of weighting schemes on the information encoded in the Dirac eigenspectrum. A series of physical persistent attributes, which characterize the spectrum of the Dirac matrices across a filtration, are proposed and used as efficient molecular fingerprints. Finally, our persistent Dirac-based model is used for clustering molecular configurations from nine types of organic-inorganic halide perovskites. We found that our model can cluster the structures very well, demonstrating the representation and featurization power of the current approach.

q-bio.BM↗

arXiv2023

Local Dirac Synchronization on Networks

We propose Local Dirac Synchronization which 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.

cond-mat.dis-nn↗

arXiv2022

Weighted simplicial complexes and their representation power of higher-order network data and topology

Hypergraphs and simplical complexes both capture the higher-order interactions of complex systems, ranging from higher-order collaboration networks to brain networks. One open problem in the field is what should drive the choice of the adopted mathematical framework to describe higher-order networks starting from data of higher-order interactions. Unweighted simplicial complexes typically involve a loss of information of the data, though having the benefit to capture the higher-order topology of the data. In this work we show that weighted simplicial complexes allow to circumvent all the limitations of unweighted simplicial complexes to represent higher-order interactions. In particular, weighted simplicial complexes can represent higher-order networks without loss of information, allowing at the same time to capture the weighted topology of the data. The higher-order topology is probed by studying the spectral properties of suitably defined weighted Hodge Laplacians displaying a normalized spectrum. The higher-order spectrum of (weighted) normalized Hodge Laplacians is here studied combining cohomology theory with information theory. In the proposed framework, we quantify and compare the information content of higher-order spectra of different dimension using higher-order spectral entropies and spectral relative entropies. The proposed methodology is tested on real higher-order collaboration networks and on the weighted version of the simplicial complex model "Network Geometry with Flavor".

physics.soc-ph↗

arXiv2022

Dirac synchronization is rhythmic and explosive

Topological signals defined on nodes, links and higher dimensional simplices define the dynamical state of a network or of a simplicial complex. As such, topological signals are attracting increasing attention in network theory, dynamical systems, signal processing and machine learning. Topological signals defined on the nodes are typically studied in network dynamics, while topological signals defined on links are much less explored. Here we investigate Dirac synchronization, describing locally coupled topological signals defined on the nodes and on the links of a network, and treated using the topological Dirac operator. The dynamics of signals defined on the nodes is affected by a phase lag depending on the dynamical state of nearby links and vice versa. We show that Dirac synchronization on a fully connected network is explosive with a hysteresis loop characterized by a discontinuous forward transition and a continuous backward transition. The analytical investigation of the phase diagram provides a theoretical understanding of this topological explosive synchronization. The model also displays an exotic coherent synchronized phase, also called rhythmic phase, characterized by non-stationary order parameters which can shed light on topological mechanisms for the emergence of brain rhythms.

cond-mat.dis-nn↗

arXiv2022

Hyper-diffusion on multiplex networks

Multiplex networks describe systems whose interactions can be of different nature, and are fundamental to understand complexity of networks beyond the framework of simple graphs. Recently it has been pointed out that restricting the attention to pairwise interactions is also a limitation, as the vast majority of complex systems include higher-order interactions that strongly affect their dynamics. Here, we propose hyper-diffusion on multiplex networks, a dynamical process in which diffusion on each single layer is coupled with the diffusion in other layers thanks to the presence of higher-order interactions occurring when there exists link overlap. We show that hyper-diffusion on a duplex network can be described by the Hyper-Laplacian in which the strength of four-body interactions among every set of four replica nodes connected by a multilink $(1,1)$ can be tuned by a parameter $δ_{11}\ge 0$. The Hyper-Laplacian reduces to the standard lower Laplacian, capturing pairwise interactions at the two layers, when $δ_{11}=0$. By combining tools of spectral graph theory, applied topology and network science we provide a general understanding of hyper-diffusion on duplex networks when $δ_{11}>0$, including theoretical bounds on the Fiedler and the largest eigenvalue of Hyper-Laplacians and the asymptotic expansion of their spectrum for $δ_{11}\ll1$ and $δ_{11}\gg1$. Although hyper-diffusion on multiplex networks does not imply a direct ``transfer of mass" among the layers (i.e. the average state of replica nodes in each layer is a conserved quantity of the dynamics), we find that the dynamics of the two layers is coupled as the relaxation to the steady state becomes synchronous when higher-order interactions are taken into account and the Fiedler eigenvalue of the Hyper-Laplacian is not localized in a single layer of the duplex network.

physics.soc-ph↗

arXiv2022

Information theory of spatial network ensembles

This chapter provides a comprehensive and self-contained discussion of the most recent developments of information theory of networks. Maximum entropy models of networks are the least biased ensembles enforcing a set of constraints and are used in a number of application to produce null model of networks. Here maximum entropy ensembles of networks are introduced by distinguishing between microcanonical and canonical ensembles revealing the the non-equivalence of these two classes of ensembles in the case in which an extensive number of constraints is imposed. It is very common that network data includes also meta-data describing feature of the nodes such as their position in a real or in an abstract space. The features of the nodes can be treated as latent variables that determine the cost associated to each link. Maximum entropy network ensembles with latent variables include spatial networks and their generalisation. In this chapter we cover the case of transportation networks including airport and rail networks. Maximum entropy network ensemble satisfy a given set of constraints. However traditional approaches do not provide any insight on the origin of such constraints. We use information theory principles to find the optimal distribution of latent variables in the framework of the classical information theory of networks. This theory explains the "blessing of non-uniformity" of data guaranteeing the efficiency of inference algorithms.

cond-mat.dis-nn↗

arXiv2022

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.

cond-mat.dis-nn↗

arXiv2022

Critical time-dependent branching process modelling epidemic spreading with containment measures

During the COVID pandemic, periods of exponential growth of the disease have been mitigated by containment measures that in different occasions have resulted in a power-law growth of the number of cases. The first observation of such behaviour has been obtained from 2020 late spring data coming from China by Ziff and Ziff in Ref. [1]. After this important observation the power-law scaling (albeit with different exponents) has also been observed in other countries during periods of containment of the spread. Early interpretations of these results suggest that this phenomenon might be due to spatial effects of the spread. Here we show that temporal modulations of infectivity of individuals due to containment measures can also cause power-law growth of the number of cases over time. To this end we propose a stochastic well-mixed Susceptible-Infected-Removed (SIR) model of epidemic spreading in presence of containment measures resulting in time-dependent infectivity and we explore the statistical properties of the resulting branching process at criticality. We show that at criticality it is possible to observe power-law growth of the number of cases with exponents ranging between one and two. Our asymptotic analytical results are confirmed by extensive Monte Carlo simulations. Although these results do not exclude that spatial effects might be important in modulating the power-law growth of the number of cases at criticality, this work shows that even well-mixed populations may already feature non-trivial power-law exponents at criticality.

physics.soc-ph↗

arXiv2022

Statistical physics of exchangeable sparse simple networks, multiplex networks and simplicial complexes

Exchangeability is a desired statistical property of network ensembles requiring their invariance upon relabelling of the nodes. However combining sparsity of network ensembles with exchangeability is challenging. Here we propose a statistical physics framework and a Metropolis-Hastings algorithm defining exchangeable sparse network ensembles. The model generates networks with heterogeneous degree distributions by enforcing only global constraints while existing (non exchangeable) exponential random graphs enforce an extensive number of local constraints. This very general theoretical framework to describe exchangeable networks is here first formulated for uncorrelated simple networks and then it is extended to treat simple networks with degree correlations, directed networks, bipartite networks and generalized network structures including multiplex networks and simplicial complexes. In particular here we formulate and treat both uncorrelated and correlated exchangeable ensembles of simplicial complexes using statistical mechanics approaches.

cond-mat.dis-nn↗

arXiv2022

Geometry, Topology and Simplicial Synchronization

Simplicial synchronization reveals the role that topology and geometry have in determining the dynamical properties of simplicial complexes. Simplicial network geometry and topology are naturally encoded in the spectral properties of the graph Laplacian and of the higher-order Laplacians of simplicial complexes. Here we show how the geometry of simplicial complexes induces spectral dimensions of the simplicial complex Laplacians that are responsible for changing the phase diagram of the Kuramoto model. In particular, simplicial complexes displaying a non-trivial simplicial network geometry cannot sustain a synchronized state in the infinite network limit if their spectral dimension is smaller or equal to four. This theoretical result is here verified on the Network Geometry with Flavor simplicial complex generative model displaying emergent hyperbolic geometry. On its turn simplicial topology is shown to determine the dynamical properties of the higher-order Kuramoto model. The higher-orderKuramoto model describes synchronization of topological signals, i.e. phases not only associated to the nodes of a simplicial complexes but associated also to higher-order simplices, including links, triangles and so on. This model displays discontinuous synchronization transitions when topological signals of different dimension and/or their solenoidal and irrotational projections are coupled in an adaptive way.

cond-mat.dis-nn↗

arXiv2022

Spectral Detection of Simplicial Communities via Hodge Laplacians

Despite being a source of rich information, graphs are limited to pairwise interactions. However, several real-world networks such as social networks, neuronal networks, etc., involve interactions between more than two nodes. Simplicial complexes provide a powerful mathematical framework to model such higher-order interactions. It is well known that the spectrum of the graph Laplacian is indicative of community structure, and this relation is exploited by spectral clustering algorithms. Here we propose that the spectrum of the Hodge Laplacian, a higher-order Laplacian defined on simplicial complexes, encodes simplicial communities. We formulate an algorithm to extract simplicial communities (of arbitrary dimension). We apply this algorithm to simplicial complex benchmarks and to real higher-order network data including social networks and networks extracted using language or text processing tools. However, datasets of simplicial complexes are scarce, and for the vast majority of datasets that may involve higher-order interactions, only the set of pairwise interactions are available. Hence, we use known properties of the data to infer the most likely higher-order interactions. In other words, we introduce an inference method to predict the most likely simplicial complex given the community structure of its network skeleton. This method identifies as most likely the higher-order interactions inducing simplicial communities that maximize the adjusted mutual information measured with respect to ground-truth community structure. Finally, we consider higher-order networks constructed through thresholding the edge weights of collaboration networks (encoding only pairwise interactions) and provide an example of persistent simplicial communities that are sustained over a wide range of the threshold.

physics.data-an↗

arXiv2021

The physics of higher-order interactions in complex systems

Complex networks have become the main paradigm for modelling the dynamics of interacting systems. However, networks are intrinsically limited to describing pairwise interactions, whereas real-world systems are often characterized by higher-order interactions involving groups of three or more units. Higher-order structures, such as hypergraphs and simplicial complexes, are therefore a better tool to map the real organization of many social, biological and man-made systems. Here, we highlight recent evidence of collective behaviours induced by higher-order interactions, and we outline three key challenges for the physics of higher-order systems.

physics.soc-ph↗