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1. Community detection in the human connectome: Method types, differences and their impact on inference

   https://doi.org/10.1002/hbm.26669  

   Brooks, Skylar J.; Jones, Victoria O.; Wang, Haotian; Deng, Chengyuan; Golding, Staunton G. H.; Lim, Jethro; Gao, Jie; Daoutidis, Prodromos; Stamoulis, Catherine (March 2024, Human Brain Mapping)

   Abstract Community structure is a fundamental topological characteristic of optimally organized brain networks. Currently, there is no clear standard or systematic approach for selecting the most appropriate community detection method. Furthermore, the impact of method choice on the accuracy and robustness of estimated communities (and network modularity), as well as method‐dependent relationships between network communities and cognitive and other individual measures, are not well understood. This study analyzed large datasets of real brain networks (estimated from resting‐state fMRI from = 5251 pre/early adolescents in the adolescent brain cognitive development [ABCD] study), and = 5338 synthetic networks with heterogeneous, data‐inspired topologies, with the goal to investigate and compare three classes of community detection methods: (i) modularity maximization‐based (Newman and Louvain), (ii) probabilistic (Bayesian inference within the framework of stochastic block modeling (SBM)), and (iii) geometric (based on graph Ricci flow). Extensive comparisons between methods and their individual accuracy (relative to the ground truth in synthetic networks), and reliability (when applied to multiple fMRI runs from the same brains) suggest that the underlying brain network topology plays a critical role in the accuracy, reliability and agreement of community detection methods. Consistent method (dis)similarities, and their correlations with topological properties, were estimated across fMRI runs. Based on synthetic graphs, most methods performed similarly and had comparable high accuracy only in some topological regimes, specifically those corresponding to developed connectomes with at least quasi‐optimal community organization. In contrast, in densely and/or weakly connected networks with difficult to detect communities, the methods yielded highly dissimilar results, with Bayesian inference within SBM having significantly higher accuracy compared to all others. Associations between method‐specific modularity and demographic, anthropometric, physiological and cognitive parameters showed mostly method invariance but some method dependence as well. Although method sensitivity to different levels of community structure may in part explain method‐dependent associations between modularity estimates and parameters of interest, method dependence also highlights potential issues of reliability and reproducibility. These findings suggest that a probabilistic approach, such as Bayesian inference in the framework of SBM, may provide consistently reliable estimates of community structure across network topologies. In addition, to maximize robustness of biological inferences, identified network communities and their cognitive, behavioral and other correlates should be confirmed with multiple reliable detection methods. 

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2. Tensor Network Contraction For Network Reliability Estimates

   Shepherd, K.; Dueñas-Osorio, L. (September 2022, The 13th International Conference on Structural Safety and Reliability (ICOSSAR 2021-2022))

   Li, J.; Spanos, P. D.; Chen, J.-B.; Peng, Y.-B. (Ed.)

   Quantifying network reliability is a hard problem, proven to be #P-complete [1]. For real-world network planning and decision making, approximations for the network reliability problem are necessary. This study shows that tensor network contraction (TNC) methods can quickly estimate an upper bound of All Terminal Reliability, RelATR(G), by solving a superset of the network reliability problem: the edge cover problem, EC(G). In addition, these tensor contraction methods can exactly solve source-terminal (S-T) reliability for the class of directed acyclic networks, RelS−T (G). The computational complexity of TNC methods is parameterized by treewidth, significantly benefitting from recent advancements in approximate tree decomposition algorithms [2]. This parameterization does not rely on the reliability of the graph, which means these tensor contraction methods can determine reliability faster than Monte Carlo methods on highly reliable networks, while also providing exact answers or guaranteed upper bound estimates. These tensor contraction methods are applied to grid graphs, random cubic graphs, and a selection of 58 power transmission networks [3], demonstrating computational efficiency and effective approximation using EC(G). 

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3. The Multivariate Community Hawkes model for dependent relational events in continuous-time networks

   Soliman, Hadeel; Zhao, Lingfei; Huang, Zhipeng; Paul, Subhadeep; Xu, Kevin S. (January 2022, Proceedings of Machine Learning Research)

   The stochastic block model (SBM) is one of the most widely used generative models for network data. Many continuous-time dynamic network models are built upon the same assumption as the SBM: edges or events between all pairs of nodes are conditionally independent given the block or community memberships, which prevents them from reproducing higher-order motifs such as triangles that are commonly observed in real networks. We propose the multivariate community Hawkes (MULCH) model, an extremely flexible community-based model for continuous-time networks that introduces dependence between node pairs using structured multivariate Hawkes processes. We fit the model using a spectral clustering and likelihood-based local refinement procedure. We find that our proposed MULCH model is far more accurate than existing models both for predictive and generative tasks. 

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4. Stochastic EM algorithm for partially observed stochastic epidemics with individual heterogeneity

   https://doi.org/10.1093/biostatistics/kxae018  

   Bu, Fan; Aiello, Allison E; Volfovsky, Alexander; Xu, Jason (December 2024, Biostatistics)

   Summary We develop a stochastic epidemic model progressing over dynamic networks, where infection rates are heterogeneous and may vary with individual-level covariates. The joint dynamics are modeled as a continuous-time Markov chain such that disease transmission is constrained by the contact network structure, and network evolution is in turn influenced by individual disease statuses. To accommodate partial epidemic observations commonly seen in real-world data, we propose a stochastic EM algorithm for inference, introducing key innovations that include efficient conditional samplers for imputing missing infection and recovery times which respect the dynamic contact network. Experiments on both synthetic and real datasets demonstrate that our inference method can accurately and efficiently recover model parameters and provide valuable insight at the presence of unobserved disease episodes in epidemic data. 

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5. The Small-World Effect for Interferometer Networks

   https://doi.org/10.1088/2632-072X/ad4c45  

   Krawciw, Benjamin; Carr, Lincoln D.; Diniz Behn, Cecilia (May 2024, Journal of Physics: Complexity)

   Abstract Complex network theory has focused on properties of networks with real-valued edge weights. However, in signal transfer networks, such as those representing the transfer of light across an interferometer, complex-valued edge weights are needed to represent the manipulation of the signal in both magnitude and phase. These complex-valued edge weights introduce interference into the signal transfer, but it is unknown how such interference affects network properties such as small-worldness. To address this gap, we have introduced a small-world interferometer network model with complex-valued edge weights and generalized existing network measures to define the interferometric clustering coefficient, the apparent path length, and the interferometric small-world coefficient. Using high-performance computing resources, we generated a large set of small-world interferometers over a wide range of parameters in system size, nearest-neighbor count, and edge-weight phase and computed their interferometric network measures. We found that the interferometric small-world coefficient depends significantly on the amount of phase on complex-valued edge weights: for small edge- weight phases, constructive interference led to a higher interferometric small-world coefficient; while larger edge-weight phases induced destructive interference which led to a lower interferometric small-world coefficient. Thus, for the small-world interferometer model, interferometric measures are necessary to capture the effect of interference on signal transfer. This model is an example of the type of problem that necessitates interferometric measures, and applies to any wave-based network including quantum networks. 

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