Framework to generate hypergraphs with community structure.

In recent years hypergraphs have emerged as a powerful tool to study systems with multibody interactions which cannot be trivially reduced to pairs. While highly structured methods to generate synthetic data have proved fundamental for the standardized evaluation of algorithms and the statistical study of real-world networked data, these are scarcely available in the context of hypergraphs. Here we propose a flexible and efficient framework for the generation of hypergraphs with many nodes and large hyperedges, which allows specifying general community structures and tune different local statistics. We illustrate how to use our model to sample synthetic data with desired features (assortative or disassortative communities, mixed or hard community assignments, etc.), analyze community detection algorithms, and generate hypergraphs structurally similar to real-world data. Overcoming previous limitations on the generation of synthetic hypergraphs, our work constitutes a substantial advancement in the statistical modeling of higher-order systems.

Community detection in large hypergraphs.

Hypergraphs, describing networks where interactions take place among any number of units, are a natural tool to model many real-world social and biological systems. Here, we propose a principled framework to model the organization of higher-order data. Our approach recovers community structure with accuracy exceeding that of currently available state-of-the-art algorithms, as tested in synthetic benchmarks with both hard and overlapping ground-truth partitions. Our model is flexible and allows capturing both assortative and disassortative community structures. Moreover, our method scales orders of magnitude faster than competing algorithms, making it suitable for the analysis of very large hypergraphs, containing millions of nodes and interactions among thousands of nodes. Our work constitutes a practical and general tool for hypergraph analysis, broadening our understanding of the organization of real-world higher-order systems.

Infrastructure adaptation and emergence of loops in network routing with time-dependent loads.

Network routing approaches are widely used to study the evolution in time of self-adapting systems. However, few advances have been made for problems where adaptation is governed by time-dependent inputs. In this work we study a dynamical systems where the edge conductivities of a network are regulated by time-varying mass loads injected on nodes. Motivated by empirical observations, we assume that conductivities adapt slowly with respect to the characteristic time of the loads. Furthermore, assuming the loads to be periodic, we derive a dynamics where the evolution of the system is controlled by a matrix obtained with the Fourier coefficients of the input loads. Remarkably, we find a sufficient condition on these coefficients that determines when the resulting network topologies are trees. We show an example of this on the Bordeaux bus network where we tune the input loads to interpolate between loopy and tree topologies. We validate our model on several synthetic networks and provide an expression for long-time solutions of the original conductivities.

Bilevel Optimization for Traffic Mitigation in Optimal Transport Networks.

Global infrastructure robustness and local transport efficiency are critical requirements for transportation networks. However, since passengers often travel greedily to maximize their own benefit and trigger traffic jams, overall transportation performance can be heavily disrupted. We develop adaptation rules that leverage optimal transport theory to effectively route passengers along their shortest paths while also strategically tuning edge weights to optimize traffic. As a result, we enforce both global and local optimality of transport. We prove the efficacy of our approach on synthetic networks and on real data. Our findings on the international European highways suggest that thoughtfully devised routing schemes might help to lower car-produced carbon emissions.

Inference of hyperedges and overlapping communities in hypergraphs.

Hypergraphs, encoding structured interactions among any number of system units, have recently proven a successful tool to describe many real-world biological and social networks. Here we propose a framework based on statistical inference to characterize the structural organization of hypergraphs. The method allows to infer missing hyperedges of any size in a principled way, and to jointly detect overlapping communities in presence of higher-order interactions. Furthermore, our model has an efficient numerical implementation, and it runs faster than dyadic algorithms on pairwise records projected from higher-order data. We apply our method to a variety of real-world systems, showing strong performance in hyperedge prediction tasks, detecting communities well aligned with the information carried by interactions, and robustness against addition of noisy hyperedges. Our approach illustrates the fundamental advantages of a hypergraph probabilistic model when modeling relational systems with higher-order interactions.

Community detection in networks by dynamical optimal transport formulation.

Detecting communities in networks is important in various domains of applications. While a variety of methods exist to perform this task, recent efforts propose Optimal Transport (OT) principles combined with the geometric notion of Ollivier-Ricci curvature to classify nodes into groups by rigorously comparing the information encoded into nodes' neighborhoods. We present an OT-based approach that exploits recent advances in OT theory to allow tuning between different transportation regimes. This allows for better control of the information shared between nodes' neighborhoods. As a result, our model can flexibly capture different types of network structures and thus increase performance accuracy in recovering communities, compared to standard OT-based formulations. We test the performance of our algorithm on both synthetic and real networks, achieving a comparable or better performance than other OT-based methods in the former case, while finding communities that better represent node metadata in real data. This pushes further our understanding of geometric approaches in their ability to capture patterns in complex networks.

Sustainable optimal transport in multilayer networks.

Traffic congestion is one of the major challenges faced by the transportation industry. While this problem carries a high economic and environmental cost, the need for an efficient design of optimal paths for passengers in multilayer network infrastructures is imperative. We consider an approach based on optimal transport theory to route passengers preferably along layers that are more carbon-efficient than the road, e.g., rails. By analyzing the impact of this choice on performance, we find that this approach reduces carbon emissions considerably compared to shortest-path minimization. Similarly, we find that this approach distributes traffic more homogeneously, thus alleviating the risk of traffic congestion. Our results shed light on the impact of distributing traffic flexibly across layers guided by optimal transport theory.

Multicommodity routing optimization for engineering networks.

Optimizing passengers routes is crucial to design efficient transportation networks. Recent results show that optimal transport provides an efficient alternative to standard optimization methods. However, it is not yet clear if this formalism has empirical validity on engineering networks. We address this issue by considering different response functions-quantities determining the interaction between passengers-in the dynamics implementing the optimal transport formulation. Particularly, we couple passengers' fluxes by taking their sum or the sum of their squares. The first choice naturally reflects edges occupancy in transportation networks, however the second guarantees convergence to an optimal configuration of flows. Both modeling choices are applied to the Paris metro. We measure the extent of traffic bottlenecks and infrastructure resilience to node removal, showing that the two settings are equivalent in the congested transport regime, but different in the branched one. In the latter, the two formulations differ on how fluxes are distributed, with one function favoring routes consolidation, thus potentially being prone to generate traffic overload. Additionally, we compare our method to Dijkstra's algorithm to show its capacity to efficiently recover shortest-path-like graphs. Finally, we observe that optimal transport networks lie in the Pareto front drawn by the energy dissipated by passengers, and the cost to build the infrastructure.

The interplay between ranking and communities in networks.

Community detection and hierarchy extraction are usually thought of as separate inference tasks on networks. Considering only one of the two when studying real-world data can be an oversimplification. In this work, we present a generative model based on an interplay between community and hierarchical structures. It assumes that each node has a preference in the interaction mechanism and nodes with the same preference are more likely to interact, while heterogeneous interactions are still allowed. The sparsity of the network is exploited for implementing a more efficient algorithm. We demonstrate our method on synthetic and real-world data and compare performance with two standard approaches for community detection and ranking extraction. We find that the algorithm accurately retrieves the overall node's preference in different scenarios, and we show that it can distinguish small subsets of nodes that behave differently than the majority. As a consequence, the model can recognize whether a network has an overall preferred interaction mechanism. This is relevant in situations where there is no clear "a priori" information about what structure explains the observed network datasets well. Our model allows practitioners to learn this automatically from the data.

Principled network extraction from images.

Images of natural systems may represent patterns of network-like structure, which could reveal important information about the topological properties of the underlying subject. However, the image itself does not automatically provide a formal definition of a network in terms of sets of nodes and edges. Instead, this information should be suitably extracted from the raw image data. Motivated by this, we present a principled model to extract network topologies from images that is scalable and efficient. We map this goal into solving a routing optimization problem where the solution is a network that minimizes an energy function which can be interpreted in terms of an operational and infrastructural cost. Our method relies on recent results from optimal transport theory and is a principled alternative to standard image-processing techniques that are based on heuristics. We test our model on real images of the retinal vascular system, slime mould and river networks and compare with routines combining image-processing techniques. Results are tested in terms of a similarity measure related to the amount of information preserved in the extraction. We find that our model finds networks from retina vascular network images that are more similar to hand-labelled ones, while also giving high performance in extracting networks from images of rivers and slime mould for which there is no ground truth available. While there is no unique method that fits all the images the best, our approach performs consistently across datasets, its algorithmic implementation is efficient and can be fully automatized to be run on several datasets with little supervision.

Network extraction by routing optimization.

Routing optimization is a relevant problem in many contexts. Solving directly this type of optimization problem is often computationally intractable. Recent studies suggest that one can instead turn this problem into one of solving a dynamical system of equations, which can instead be solved efficiently using numerical methods. This results in enabling the acquisition of optimal network topologies from a variety of routing problems. However, the actual extraction of the solution in terms of a final network topology relies on numerical details which can prevent an accurate investigation of their topological properties. In fact, in this context, theoretical results are fully accessible only to an expert audience and ready-to-use implementations for non-experts are rarely available or insufficiently documented. In particular, in this framework, final graph acquisition is a challenging problem in-and-of-itself. Here we introduce a method to extract network topologies from dynamical equations related to routing optimization under various parameters' settings. Our method is made of three steps: first, it extracts an optimal trajectory by solving a dynamical system, then it pre-extracts a network, and finally, it filters out potential redundancies. Remarkably, we propose a principled model to address the filtering in the last step, and give a quantitative interpretation in terms of a transport-related cost function. This principled filtering can be applied to more general problems such as network extraction from images, thus going beyond the scenarios envisioned in the first step. Overall, this novel algorithm allows practitioners to easily extract optimal network topologies by combining basic tools from numerical methods, optimization and network theory. Thus, we provide an alternative to manual graph extraction which allows a grounded extraction from a large variety of optimal topologies. The analysis of these may open up the possibility to gain new insights into the structure and function of optimal networks. We provide an open source implementation of the code online.

Community detection with node attributes in multilayer networks.

Community detection in networks is commonly performed using information about interactions between nodes. Recent advances have been made to incorporate multiple types of interactions, thus generalizing standard methods to multilayer networks. Often, though, one can access additional information regarding individual nodes, attributes, or covariates. A relevant question is thus how to properly incorporate this extra information in such frameworks. Here we develop a method that incorporates both the topology of interactions and node attributes to extract communities in multilayer networks. We propose a principled probabilistic method that does not assume any a priori correlation structure between attributes and communities but rather infers this from data. This leads to an efficient algorithmic implementation that exploits the sparsity of the dataset and can be used to perform several inference tasks; we provide an open-source implementation of the code online. We demonstrate our method on both synthetic and real-world data and compare performance with methods that do not use any attribute information. We find that including node information helps in predicting missing links or attributes. It also leads to more interpretable community structures and allows the quantification of the impact of the node attributes given in input.

A physical model for efficient ranking in networks.

We present a physically inspired model and an efficient algorithm to infer hierarchical rankings of nodes in directed networks. It assigns real-valued ranks to nodes rather than simply ordinal ranks, and it formalizes the assumption that interactions are more likely to occur between individuals with similar ranks. It provides a natural statistical significance test for the inferred hierarchy, and it can be used to perform inference tasks such as predicting the existence or direction of edges. The ranking is obtained by solving a linear system of equations, which is sparse if the network is; thus, the resulting algorithm is extremely efficient and scalable. We illustrate these findings by analyzing real and synthetic data, including data sets from animal behavior, faculty hiring, social support networks, and sports tournaments. We show that our method often outperforms a variety of others, in both speed and accuracy, in recovering the underlying ranks and predicting edge directions.

Matrix product algorithm for stochastic dynamics on networks applied to nonequilibrium Glauber dynamics.

We introduce and apply an efficient method for the precise simulation of stochastic dynamical processes on locally treelike graphs. Networks with cycles are treated in the framework of the cavity method. Such models correspond, for example, to spin-glass systems, Boolean networks, neural networks, or other technological, biological, and social networks. Building upon ideas from quantum many-body theory, our approach is based on a matrix product approximation of the so-called edge messages-conditional probabilities of vertex variable trajectories. Computation costs and accuracy can be tuned by controlling the matrix dimensions of the matrix product edge messages (MPEM) in truncations. In contrast to Monte Carlo simulations, the algorithm has a better error scaling and works for both single instances as well as the thermodynamic limit. We employ it to examine prototypical nonequilibrium Glauber dynamics in the kinetic Ising model. Because of the absence of cancellation effects, observables with small expectation values can be evaluated accurately, allowing for the study of decay processes and temporal correlations.

Community detection, link prediction, and layer interdependence in multilayer networks.

Complex systems are often characterized by distinct types of interactions between the same entities. These can be described as a multilayer network where each layer represents one type of interaction. These layers may be interdependent in complicated ways, revealing different kinds of structure in the network. In this work we present a generative model, and an efficient expectation-maximization algorithm, which allows us to perform inference tasks such as community detection and link prediction in this setting. Our model assumes overlapping communities that are common between the layers, while allowing these communities to affect each layer in a different way, including arbitrary mixtures of assortative, disassortative, or directed structure. It also gives us a mathematically principled way to define the interdependence between layers, by measuring how much information about one layer helps us predict links in another layer. In particular, this allows us to bundle layers together to compress redundant information and identify small groups of layers which suffice to predict the remaining layers accurately. We illustrate these findings by analyzing synthetic data and two real multilayer networks, one representing social support relationships among villagers in South India and the other representing shared genetic substring material between genes of the malaria parasite.

The Edge-Disjoint Path Problem on Random Graphs by Message-Passing.

We present a message-passing algorithm to solve a series of edge-disjoint path problems on graphs based on the zero-temperature cavity equations. Edge-disjoint paths problems are important in the general context of routing, that can be defined by incorporating under a unique framework both traffic optimization and total path length minimization. The computation of the cavity equations can be performed efficiently by exploiting a mapping of a generalized edge-disjoint path problem on a star graph onto a weighted maximum matching problem. We perform extensive numerical simulations on random graphs of various types to test the performance both in terms of path length minimization and maximization of the number of accommodated paths. In addition, we test the performance on benchmark instances on various graphs by comparison with state-of-the-art algorithms and results found in the literature. Our message-passing algorithm always outperforms the others in terms of the number of accommodated paths when considering non trivial instances (otherwise it gives the same trivial results). Remarkably, the largest improvement in performance with respect to the other methods employed is found in the case of benchmarks with meshes, where the validity hypothesis behind message-passing is expected to worsen. In these cases, even though the exact message-passing equations do not converge, by introducing a reinforcement parameter to force convergence towards a sub optimal solution, we were able to always outperform the other algorithms with a peak of 27% performance improvement in terms of accommodated paths. On random graphs, we numerically observe two separated regimes: one in which all paths can be accommodated and one in which this is not possible. We also investigate the behavior of both the number of paths to be accommodated and their minimum total length.

Nonequilibrium statistical mechanics of the heat bath for two Brownian particles.

We propose a new look at the heat bath for two Brownian particles, in which the heat bath as a "system" is both perturbed and sensed by the Brownian particles. Nonlocal thermal fluctuations give rise to bath-mediated static forces between the particles. Based on the general sum rule of the linear response theory, we derive an explicit relation linking these forces to the friction kernel describing the particles' dynamics. The relation is analytically confirmed in the case of two solvable models and could be experimentally challenged. Our results point out that the inclusion of the environment as a part of the whole system is important for micron- or nanoscale physics.