arXiv subjects

Tiago P. Peixoto

Publications and source records attributed to Tiago P. Peixoto.

At least 19 recordsLinked to original sources

arXiv2026

Graphs are maximally expressive for higher-order interactions

We demonstrate that graph-based models are fully capable of representing higher-order interactions, and have a long history of being used for precisely this purpose. This stands in contrast to a common claim in the recent literature on "higher-order networks" that graph-based representations are fundamentally limited to "pairwise" interactions, requiring hypergraph formulations to capture richer dependencies. We clarify this issue by emphasizing two frequently overlooked facts. First, graph-based models are not restricted to pairwise interactions, as they easily accommodate interactions that depend simultaneously on multiple adjacent nodes. Second, hypergraph formulations are strict special cases of more general graph-based representations, as they impose additional constraints on the allowable interactions between adjacent elements rather than expanding the space of possibilities. We show that key phenomenology commonly attributed to hypergraphs -- such as abrupt transitions -- can, in general, be recovered exactly using graph models, even locally tree-like ones, and thus do not constitute a class of phenomena that is inherently contingent on hypergraphs models. Finally, we argue that the broad relevance of hypergraphs for applications that is sometimes claimed in the literature is not supported by evidence. Instead it is likely grounded in misconceptions that network models cannot accommodate multibody interactions or that certain phenomena can only be captured with hypergraphs. We argue that clearly distinguishing between multivariate interactions, parametrized by graphs, and the functions that define them enables a more unified and flexible foundation for modeling interacting systems.

physics.soc-ph↗

arXiv2026

Statistical inference of dynamical processes on networks

Mechanisms of interaction in spreading models are central to our quantitative understanding of networked contagion processes, from disease transmission to opinion dynamics. Yet, while empirical data can reveal who interacts with whom, they rarely provide direct information about how interactions drive spreading, leaving the underlying mechanism to be inferred from observed dynamics, and selected among competing hypotheses. We propose a general framework for model selection in binary-state spreading processes on networks and show that asymptotic approximations in the thermodynamic limit can accurately predict inference outcomes in finite systems. By systematically exploring a broad parameter space, we characterize the detectability of six archetypal spreading mechanisms commonly used in the literature and find that accuracy generally increases in sparse networks, which are prevalent in real-world systems, and near phase transitions, such as the epidemic threshold of simple contagion processes. We further assess the prevalence of these mechanisms across a diverse set of empirical datasets, highlighting the impact of data preprocessing on model recovery. Our results show that statistical model selection can fail under common conditions and suggest new directions for overcoming these limitations.

physics.soc-ph↗

arXiv2025

Meso-scale structures in signed networks

Meso-scale structures in signed networks have been studied under the limiting assumption of the validity of social balance theory, which predicts positive connections within groups and negative connections between groups. Here, we propose and apply a methodology that overcomes this limitation and is able to find and characterize also the different possible unbalanced structures in signed networks. Applying our methodology to 24 empirical networks, from social-political, financial, and biological domains, we find that unbalanced meso-scale structures are prevalent in real-world networks, including cases with substantial balance at the micro-scale of triangles. In particular, we find that assortativity often prevails regardless of the interaction sign and that core-periphery structures are typical in online social networks. Our findings highlight the complexity of meso-scale relational structures, the importance of using computational methods that are a priori agnostic to specific patterns, and the importance of independently evaluating micro- and meso-scale predictions of social balance theory.

cs.SI↗

arXiv2025

Multiscale patterns of migration flows in Austria: regionalization, administrative barriers, and urban-rural divides

Migration is central in various societal problems related to socioeconomic development. While much of the existing research has focused on international migration, migration patterns within a single country remain relatively unexplored. In this work we study internal migration patterns in Austria for a period of over 20 years, obtained from open and high-granularity administrative records. We employ inferential network methods to characterize the flows between municipalities and extract their clustering according to similar target and destination rates. Our methodology reveals significant deviations from commonly assumed relocation patterns modeled by the gravity law. At the same time, we observe unexpected biases of internal migrations that leads to less frequent movements across boundaries at both district and state levels than predictions suggest. This leads to significant regionalization of migration at multiple geographical scales and augmented division between urban and rural areas. These patterns appear to be remarkably persistent across decades of migration data, demonstrating systematic limitations of conventionally used gravity models in migration studies. Our approach presents a robust methodology that can be used to improve such evaluations, and can reveal new phenomena in migration networks.

physics.soc-ph↗

arXiv2025

Network reconstruction via the minimum description length principle

A fundamental problem associated with the task of network reconstruction from dynamical or behavioral data consists in determining the most appropriate model complexity in a manner that prevents overfitting, and produces an inferred network with a statistically justifiable number of edges. The status quo in this context is based on $L_{1}$ regularization combined with cross-validation. However, besides its high computational cost, this commonplace approach unnecessarily ties the promotion of sparsity with weight "shrinkage". This combination forces a trade-off between the bias introduced by shrinkage and the network sparsity, which often results in substantial overfitting even after cross-validation. In this work, we propose an alternative nonparametric regularization scheme based on hierarchical Bayesian inference and weight quantization, which does not rely on weight shrinkage to promote sparsity. Our approach follows the minimum description length (MDL) principle, and uncovers the weight distribution that allows for the most compression of the data, thus avoiding overfitting without requiring cross-validation. The latter property renders our approach substantially faster to employ, as it requires a single fit to the complete data. As a result, we have a principled and efficient inference scheme that can be used with a large variety of generative models, without requiring the number of edges to be known in advance. We also demonstrate that our scheme yields systematically increased accuracy in the reconstruction of both artificial and empirical networks. We highlight the use of our method with the reconstruction of interaction networks between microbial communities from large-scale abundance samples involving in the order of $10^{4}$ to $10^{5}$ species, and demonstrate how the inferred model can be used to predict the outcome of interventions in the system.

stat.ML↗

arXiv2025

Uncertainty quantification and posterior sampling for network reconstruction

Network reconstruction is the task of inferring the unseen interactions between elements of a system, based only on their behavior or dynamics. This inverse problem is in general ill-posed, and admits many solutions for the same observation. Nevertheless, the vast majority of statistical methods proposed for this task -- formulated as the inference of a graphical generative model -- can only produce a ``point estimate,'' i.e. a single network considered the most likely. In general, this can give only a limited characterization of the reconstruction, since uncertainties and competing answers cannot be conveyed, even if their probabilities are comparable, while being structurally different. In this work we present an efficient MCMC algorithm for sampling from posterior distributions of reconstructed networks, which is able to reveal the full population of answers for a given reconstruction problem, weighted according to their plausibilities. Our algorithm is general, since it does not rely on specific properties of particular generative models, and is specially suited for the inference of large and sparse networks, since in this case an iteration can be performed in time $O(N\log^2 N)$ for a network of $N$ nodes, instead of $O(N^2)$, as would be the case for a more naive approach. We demonstrate the suitability of our method in providing uncertainties and consensus of solutions (which provably increases the reconstruction accuracy) in a variety of synthetic and empirical cases.

stat.ML↗

arXiv2024

Scalable network reconstruction in subquadratic time

Network reconstruction consists in determining the unobserved pairwise couplings between $N$ nodes given only observational data on the resulting behavior that is conditioned on those couplings -- typically a time-series or independent samples from a graphical model. A major obstacle to the scalability of algorithms proposed for this problem is a seemingly unavoidable quadratic complexity of $Ω(N^2)$, corresponding to the requirement of each possible pairwise coupling being contemplated at least once, despite the fact that most networks of interest are sparse, with a number of non-zero couplings that is only $O(N)$. Here we present a general algorithm applicable to a broad range of reconstruction problems that significantly outperforms this quadratic baseline. Our algorithm relies on a stochastic second neighbor search (Dong et al., 2011) that produces the best edge candidates with high probability, thus bypassing an exhaustive quadratic search. If we rely on the conjecture that the second-neighbor search finishes in log-linear time (Baron & Darling, 2020; 2022), we demonstrate theoretically that our algorithm finishes in subquadratic time, with a data-dependent complexity loosely upper bounded by $O(N^{3/2}\log N)$, but with a more typical log-linear complexity of $O(N\log^2N)$. In practice, we show that our algorithm achieves a performance that is many orders of magnitude faster than the quadratic baseline -- in a manner consistent with our theoretical analysis -- allows for easy parallelization, and thus enables the reconstruction of networks with hundreds of thousands and even millions of nodes and edges.

cs.DS↗

arXiv2023

Implicit models, latent compression, intrinsic biases, and cheap lunches in community detection

The task of community detection, which aims to partition a network into clusters of nodes to summarize its large-scale structure, has spawned the development of many competing algorithms with varying objectives. Some community detection methods are inferential, explicitly deriving the clustering objective through a probabilistic generative model, while other methods are descriptive, dividing a network according to an objective motivated by a particular application, making it challenging to compare these methods on the same scale. Here we present a solution to this problem that associates any community detection objective, inferential or descriptive, with its corresponding implicit network generative model. This allows us to compute the description length of a network and its partition under arbitrary objectives, providing a principled measure to compare the performance of different algorithms without the need for "ground truth" labels. Our approach also gives access to instances of the community detection problem that are optimal to any given algorithm, and in this way reveals intrinsic biases in popular descriptive methods, explaining their tendency to overfit. Using our framework, we compare a number of community detection methods on artificial networks, and on a corpus of over 500 structurally diverse empirical networks. We find that more expressive community detection methods exhibit consistently superior compression performance on structured data instances, without having degraded performance on a minority of situations where more specialized algorithms perform optimally. Our results undermine the implications of the "no free lunch" theorem for community detection, both conceptually and in practice, since it is confined to unstructured data instances, unlike relevant community detection problems which are structured by requirement.

cs.SI↗

arXiv2023

Descriptive vs. inferential community detection in networks: pitfalls, myths, and half-truths

Community detection is one of the most important methodological fields of network science, and one which has attracted a significant amount of attention over the past decades. This area deals with the automated division of a network into fundamental building blocks, with the objective of providing a summary of its large-scale structure. Despite its importance and widespread adoption, there is a noticeable gap between what is arguably the state-of-the-art and the methods that are actually used in practice in a variety of fields. Here we attempt to address this discrepancy by dividing existing methods according to whether they have a "descriptive" or an "inferential" goal. While descriptive methods find patterns in networks based on context-dependent notions of community structure, inferential methods articulate generative models, and attempt to fit them to data. In this way, they are able to provide insights into the mechanisms of network formation, and separate structure from randomness in a manner supported by statistical evidence. We review how employing descriptive methods with inferential aims is riddled with pitfalls and misleading answers, and thus should be in general avoided. We argue that inferential methods are more typically aligned with clearer scientific questions, yield more robust results, and should be in many cases preferred. We attempt to dispel some myths and half-truths often believed when community detection is employed in practice, in an effort to improve both the use of such methods as well as the interpretation of their results.

physics.soc-ph↗

arXiv2023

Bayesian stochastic blockmodeling

This chapter provides a self-contained introduction to the use of Bayesian inference to extract large-scale modular structures from network data, based on the stochastic blockmodel (SBM), as well as its degree-corrected and overlapping generalizations. We focus on nonparametric formulations that allow their inference in a manner that prevents overfitting, and enables model selection. We discuss aspects of the choice of priors, in particular how to avoid underfitting via increased Bayesian hierarchies, and we contrast the task of sampling network partitions from the posterior distribution with finding the single point estimate that maximizes it, while describing efficient algorithms to perform either one. We also show how inferring the SBM can be used to predict missing and spurious links, and shed light on the fundamental limitations of the detectability of modular structures in networks.

stat.ML↗

arXiv2022

Ordered community detection in directed networks

We develop a method to infer community structure in directed networks where the groups are ordered in a latent one-dimensional hierarchy that determines the preferred edge direction. Our nonparametric Bayesian approach is based on a modification of the stochastic block model (SBM), which can take advantage of rank alignment and coherence to produce parsimonious descriptions of networks that combine ordered hierarchies with arbitrary mixing patterns between groups. Since our model also includes directed degree correction, we can use it to distinguish non-local hierarchical structure from local in- and out-degree imbalance -- thus removing a source of conflation present in most ranking methods. We also demonstrate how we can reliably compare with the results obtained with the unordered SBM variant to determine whether a hierarchical ordering is statistically warranted in the first place. We illustrate the application of our method on a wide variety of empirical networks across several domains.

cs.SI↗

arXiv2022

Hypergraph reconstruction from network data

Networks can describe the structure of a wide variety of complex systems by specifying which pairs of entities in the system are connected. While such pairwise representations are flexible, they are not necessarily appropriate when the fundamental interactions involve more than two entities at the same time. Pairwise representations nonetheless remain ubiquitous, because higher-order interactions are often not recorded explicitly in network data. Here, we introduce a Bayesian approach to reconstruct latent higher-order interactions from ordinary pairwise network data. Our method is based on the principle of parsimony and only includes higher-order structures when there is sufficient statistical evidence for them. We demonstrate its applicability to a wide range of datasets, both synthetic and empirical.

cs.SI↗

arXiv2022

Disentangling homophily, community structure and triadic closure in networks

Network homophily, the tendency of similar nodes to be connected, and transitivity, the tendency of two nodes being connected if they share a common neighbor, are conflated properties in network analysis, since one mechanism can drive the other. Here we present a generative model and corresponding inference procedure that are capable of distinguishing between both mechanisms. Our approach is based on a variation of the stochastic block model (SBM) with the addition of triadic closure edges, and its inference can identify the most plausible mechanism responsible for the existence of every edge in the network, in addition to the underlying community structure itself. We show how the method can evade the detection of spurious communities caused solely by the formation of triangles in the network, and how it can improve the performance of edge prediction when compared to the pure version of the SBM without triadic closure.

cs.SI↗

arXiv2022

Systematic assessment of the quality of fit of the stochastic block model for empirical networks

We perform a systematic analysis of the quality of fit of the stochastic block model (SBM) for 275 empirical networks spanning a wide range of domains and orders of size magnitude. We employ posterior predictive model checking as a criterion to assess the quality of fit, which involves comparing networks generated by the inferred model with the empirical network, according to a set of network descriptors. We observe that the SBM is capable of providing an accurate description for the majority of networks considered, but falls short of saturating all modeling requirements. In particular, networks possessing a large diameter and slow-mixing random walks tend to be badly described by the SBM. However, contrary to what is often assumed, networks with a high abundance of triangles can be well described by the SBM in many cases. We demonstrate that simple network descriptors can be used to evaluate whether or not the SBM can provide a sufficiently accurate representation, potentially pointing to possible model extensions that can systematically improve the expressiveness of this class of models.

physics.soc-ph↗

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↗

arXiv2021

Multilayer Networks for Text Analysis with Multiple Data Types

We are interested in the widespread problem of clustering documents and finding topics in large collections of written documents in the presence of metadata and hyperlinks. To tackle the challenge of accounting for these different types of datasets, we propose a novel framework based on Multilayer Networks and Stochastic Block Models. The main innovation of our approach over other techniques is that it applies the same non-parametric probabilistic framework to the different sources of datasets simultaneously. The key difference to other multilayer complex networks is the strong unbalance between the layers, with the average degree of different node types scaling differently with system size. We show that the latter observation is due to generic properties of text, such as Heaps' law, and strongly affects the inference of communities. We present and discuss the performance of our method in different datasets (hundreds of Wikipedia documents, thousands of scientific papers, and thousands of E-mails) showing that taking into account multiple types of information provides a more nuanced view on topic- and document-clusters and increases the ability to predict missing links.

cs.SI↗

arXiv2021

Revealing consensus and dissensus between network partitions

Community detection methods attempt to divide a network into groups of nodes that share similar properties, thus revealing its large-scale structure. A major challenge when employing such methods is that they are often degenerate, typically yielding a complex landscape of competing answers. As an attempt to extract understanding from a population of alternative solutions, many methods exist to establish a consensus among them in the form of a single partition "point estimate" that summarizes the whole distribution. Here we show that it is in general not possible to obtain a consistent answer from such point estimates when the underlying distribution is too heterogeneous. As an alternative, we provide a comprehensive set of methods designed to characterize and summarize complex populations of partitions in a manner that captures not only the existing consensus, but also the dissensus between elements of the population. Our approach is able to model mixed populations of partitions where multiple consensuses can coexist, representing different competing hypotheses for the network structure. We also show how our methods can be used to compare pairs of partitions, how they can be generalized to hierarchical divisions, and be used to perform statistical model selection between competing hypotheses.

physics.soc-ph↗

arXiv2020

Latent Poisson models for networks with heterogeneous density

Empirical networks are often globally sparse, with a small average number of connections per node, when compared to the total size of the network. However, this sparsity tends not to be homogeneous, and networks can also be locally dense, for example with a few nodes connecting to a large fraction of the rest of the network, or with small groups of nodes with a large probability of connections between them. Here we show how latent Poisson models which generate hidden multigraphs can be effective at capturing this density heterogeneity, while being more tractable mathematically than some of the alternatives that model simple graphs directly. We show how these latent multigraphs can be reconstructed from data on simple graphs, and how this allows us to disentangle disassortative degree-degree correlations from the constraints of imposed degree sequences, and to improve the identification of community structure in empirically relevant scenarios.

physics.soc-ph↗