arXiv subjects

M. E. J. Newman

Publications and source records attributed to M. E. J. Newman.

At least 19 recordsLinked to original sources

arXiv2026

Strongly-connected percolation on directed lattices

We study percolation on lattices with directed bonds, focusing on the behavior of strongly-connected percolation clusters -- clusters in which every site is reachable from every other along a directed path. We consider the two-dimensional square lattice and various globally isotropic arrangements of the directions of the bonds. Performing simulations using a range of algorithmic approaches, we calculate high-precision values for critical exponents, fractal dimensions, crossing probabilities, and percolation thresholds for bond percolation with each bond arrangement. We find that the critical behavior is in a distinctly different universality class from that of traditional undirected percolation, but that all bond arrangements appear to fall in the same universality class.

cond-mat.stat-mech↗

arXiv2026

Component structure and percolation in block models

The stochastic block model is a widely studied model of community structure in networks. Here we study the component structure and percolation properties of networks generated from this model and its variants, using exact methods based on probability generating functions. In particular, we derive expressions for the size of the giant component and the distribution of small components in such networks and for the size of the percolating cluster and position of the percolation threshold for both node and edge percolation, for the original stochastic block model and for its degree-corrected versions. In passing, we also develop a mapping between generating functions for microcanonical and canonical block models that allows us to generalize results for the former to the latter with minimal effort.

cs.SI↗

arXiv2025

Normalized mutual information is a biased measure for classification and community detection

Normalized mutual information is widely used as a similarity measure for evaluating the performance of clustering and classification algorithms. In this paper, we argue that results returned by the normalized mutual information are biased for two reasons: first, because they ignore the information content of the contingency table and, second, because their symmetric normalization introduces spurious dependence on algorithm output. We introduce a modified version of the mutual information that remedies both of these shortcomings. As a practical demonstration of the importance of using an unbiased measure, we perform extensive numerical tests on a basket of popular algorithms for network community detection and show that one's conclusions about which algorithm is best are significantly affected by the biases in the traditional mutual information.

cs.SI↗

arXiv2025

Fast sampling and model selection for Bayesian mixture models

We study Bayesian estimation of mixture models and argue in favor of fitting the marginal posterior distribution over component assignments directly, rather than Gibbs sampling from the joint posterior on components and parameters as is commonly done. Some previous authors have found the former approach to have slow mixing, but we show that, implemented correctly, it can achieve excellent performance. In particular, we describe a new Monte Carlo algorithm for sampling from the marginal posterior of a general integrable mixture that makes use of rejection-free sampling from the prior over component assignments to achieve excellent mixing times in typical applications, outperforming standard Gibbs sampling, in some cases by a wide margin. We demonstrate the approach with a selection of applications to Gaussian, Poisson, and categorical models.

stat.CO↗

arXiv2025

Drug-disease networks and drug repurposing

Repurposing existing drugs to treat new diseases is a cost-effective alternative to de novo drug development, but there are millions of potential drug-disease combinations to be considered with only a small fraction being viable. In silico predictions of drug-disease associations can be invaluable for reducing the size of the search space. In this work we present a novel network of drugs and the diseases they treat, compiled using a combination of existing textual and machine-readable databases, natural-language processing tools, and hand curation, and analyze it using network-based link prediction methods to identify potential drug-disease combinations. We measure the efficacy of these methods using cross-validation tests and find that several methods, particularly those based on graph embedding and network model fitting, achieve impressive prediction performance, significantly better than previous approaches, with area under the ROC curve above 0.95 and average precision almost a thousand times better than chance.

q-bio.QM↗

arXiv2025

Mixture models for data with unknown distributions

We describe and analyze a broad class of mixture models for real-valued multivariate data in which the probability density of observations within each component of the model is represented as an arbitrary combination of basis functions. Fits to these models give us a way to cluster data with distributions of unknown form, including strongly non-Gaussian or multimodal distributions, and return both a division of the data and an estimate of the distributions, effectively performing clustering and density estimation within each cluster at the same time. We describe two fitting methods, one using an expectation-maximization (EM) algorithm and the other a Bayesian non-parametric method using a collapsed Gibbs sampler. The former is numerically efficient, but gives only point estimates of the probability densities. The latter is more computationally demanding but returns a full Bayesian posterior and also an estimate of the number of components. We demonstrate our methods with a selection of illustrative applications and give code implementing both algorithms.

stat.ME↗

arXiv2024

Mutual information and the encoding of contingency tables

Mutual information is commonly used as a measure of similarity between competing labelings of a given set of objects, for example to quantify performance in classification and community detection tasks. As argued recently, however, the mutual information as conventionally defined can return biased results because it neglects the information cost of the so-called contingency table, a crucial component of the similarity calculation. In principle the bias can be rectified by subtracting the appropriate information cost, leading to the modified measure known as the reduced mutual information, but in practice one can only ever compute an upper bound on this information cost, and the value of the reduced mutual information depends crucially on how good a bound is established. In this paper we describe an improved method for encoding contingency tables that gives a substantially better bound in typical use cases, and approaches the ideal value in the common case where the labelings are closely similar, as we demonstrate with extensive numerical results.

cs.SI↗

arXiv2023

Luck, skill, and depth of competition in games and social hierarchies

Patterns of wins and losses in pairwise contests, such as occur in sports and games, consumer research and paired comparison studies, and human and animal social hierarchies, are commonly analyzed using probabilistic models that allow one to quantify the strength of competitors or predict the outcome of future contests. Here we generalize this approach to incorporate two additional features: an element of randomness or luck that leads to upset wins, and a "depth of competition" variable that measures the complexity of a game or hierarchy. Fitting the resulting model to a large collection of data sets we estimate depth and luck in a range of games, sports, and social situations. In general, we find that social competition tends to be "deep," meaning it has a pronounced hierarchy with many distinct levels, but also that there is often a nonzero chance of an upset victory, meaning that dominance challenges can be won even by significant underdogs. Competition in sports and games, by contrast, tends to be shallow and in most cases there is little evidence of upset wins, beyond those already implied by the shallowness of the hierarchy.

physics.soc-ph↗

arXiv2023

Efficient computation of rankings from pairwise comparisons

We study the ranking of individuals, teams, or objects, based on pairwise comparisons between them, using the Bradley-Terry model. Estimates of rankings within this model are commonly made using a simple iterative algorithm first introduced by Zermelo almost a century ago. Here we describe an alternative and similarly simple iteration that provably returns identical results but does so much faster -- over a hundred times faster in some cases. We demonstrate this algorithm with applications to a range of example data sets and derive a number of results regarding its convergence.

stat.ML↗

arXiv2023

Hierarchical core-periphery structure in networks

We study core-periphery structure in networks using inference methods based on a flexible network model that allows for traditional onion-like cores within cores, but also for hierarchical tree-like structures and more general non-nested types of structure. We propose an efficient Monte Carlo scheme for fitting the model to observed networks and report results for a selection of real-world data sets. Among other things, we observe an empirical distinction between networks showing traditional core-periphery structure with a dense core weakly connected to a sparse periphery, and an alternative structure in which the core is strongly connected both within itself and to the periphery. Networks vary in whether they are better represented by one type of structure or the other. We also observe structures that are a hybrid between core-periphery structure and community structure, in which networks have a set of non-overlapping cores that correspond roughly to communities, surrounded by a single undifferentiated periphery. Computer code implementing our methods is available.

cs.SI↗

arXiv2022

Message passing methods on complex networks

Networks and network computations have become a primary mathematical tool for analyzing the structure of many kinds of complex systems, ranging from the Internet and transportation networks to biochemical interactions and social networks. A common task in network analysis is the calculation of quantities that reside on the nodes of a network, such as centrality measures, probabilities, or model states. In this review article we discuss message passing methods, a family of techniques for performing such calculations, based on the propagation of information between the nodes of a network. We introduce the message passing approach with a series of examples, give some illustrative applications and results, and discuss the deep connections between message passing and phase transitions in networks. We also point out some limitations of the message passing approach and describe some recently-introduced methods that address these limitations.

cs.SI↗

arXiv2022

Ranking with multiple types of pairwise comparisons

The task of ranking individuals or teams, based on a set of comparisons between pairs, arises in various contexts, including sporting competitions and the analysis of dominance hierarchies among animals and humans. Given data on which competitors beat which others, the challenge is to rank the competitors from best to worst. Here we study the problem of computing rankings when there are multiple, potentially conflicting modes of comparison, such as multiple types of dominance behaviors among animals. We assume that we do not know a priori what information each behavior conveys about the ranking, or even whether they convey any information at all. Nonetheless we show that it is possible to compute a ranking in this situation and present a fast method for doing so, based on a combination of an expectation-maximization algorithm and a modified Bradley-Terry model. We give a selection of example applications to both animal and human competition.

stat.ML↗

arXiv2022

Improved estimates for the number of non-negative integer matrices with given row and column sums

The number of non-negative integer matrices with given row and column sums appears in a variety of problems in mathematics and statistics but no closed-form expression for it is known, so we rely on approximations of various kinds. Here we describe a new such approximation, motivated by consideration of the statistics of matrices with non-integer numbers of columns. This estimate can be evaluated in time linear in the size of the matrix and returns results of accuracy as good as or better than existing linear-time approximations across a wide range of settings. We also use this new estimate as the starting point for an improved numerical method for either counting or sampling matrices using sequential importance sampling. Code implementing our methods is provided.

stat.CO↗

arXiv2022

20 years of network community detection

A fundamental technical challenge in the analysis of network data is the automated discovery of communities - groups of nodes that are strongly connected or that share similar features or roles. In this commentary we review progress in the field over the last 20 years.

physics.soc-ph↗

arXiv2022

Representative community divisions of networks

Methods for detecting community structure in networks typically aim to identify a single best partition of network nodes into communities, often by optimizing some objective function, but in real-world applications there may be many competitive partitions with objective scores close to the global optimum and one can obtain a more informative picture of the community structure by examining a representative set of such high-scoring partitions than by looking at just the single optimum. However, such a set can be difficult to interpret since its size can easily run to hundreds or thousands of partitions. In this paper we present a method for analyzing large partition sets by dividing them into groups of similar partitions and then identifying an archetypal partition as a representative of each group. The resulting set of archetypal partitions provides a succinct, interpretable summary of the form and variety of community structure in any network. We demonstrate the method on a range of example networks.

cs.SI↗

arXiv2022

Clustering of heterogeneous populations of networks

Statistical methods for reconstructing networks from repeated measurements typically assume that all measurements are generated from the same underlying network structure. This need not be the case, however. People's social networks might be different on weekdays and weekends, for instance. Brain networks may differ between healthy patients and those with dementia or other conditions. Here we describe a Bayesian analysis framework for such data that allows for the fact that network measurements may be reflective of multiple possible structures. We define a finite mixture model of the measurement process and derive a fast Gibbs sampling procedure that samples exactly from the full posterior distribution of model parameters. The end result is a clustering of the measured networks into groups with similar structure. We demonstrate the method on both real and synthetic network populations.

cs.SI↗

arXiv2022

Cutting Through the Noise to Infer Autonomous System Topology

The Border Gateway Protocol (BGP) is a distributed protocol that manages interdomain routing without requiring a centralized record of which autonomous systems (ASes) connect to which others. Many methods have been devised to infer the AS topology from publicly available BGP data, but none provide a general way to handle the fact that the data are notoriously incomplete and subject to error. This paper describes a method for reliably inferring AS-level connectivity in the presence of measurement error using Bayesian statistical inference acting on BGP routing tables from multiple vantage points. We employ a novel approach for counting AS adjacency observations in the AS-PATH attribute data from public route collectors, along with a Bayesian algorithm to generate a statistical estimate of the AS-level network. Our approach also gives us a way to evaluate the accuracy of existing reconstruction methods and to identify advantageous locations for new route collectors or vantage points.

cs.NI↗

arXiv2021

Belief propagation for networks with loops

Belief propagation is a widely used message passing method for the solution of probabilistic models on networks such as epidemic models, spin models, and Bayesian graphical models, but it suffers from the serious shortcoming that it works poorly in the common case of networks that contain short loops. Here we provide a solution to this long-standing problem, deriving a belief propagation method that allows for fast calculation of probability distributions in systems with short loops, potentially with high density, as well as giving expressions for the entropy and partition function, which are notoriously difficult quantities to compute. Using the Ising model as an example, we show that our approach gives excellent results on both real and synthetic networks, improving significantly on standard message passing methods. We also discuss potential applications of our method to a variety of other problems.

cond-mat.stat-mech↗