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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. Detecting Dynamic States of Temporal Networks Using Connection Series Tensors

   https://doi.org/10.1155/2020/9649310  

   Cao, Shun; Sayama, Hiroki (December 2020, Complexity)

   De Lellis, Pietro (Ed.)

   Many temporal networks exhibit multiple system states, such as weekday and weekend patterns in social contact networks. The detection of such distinct states in temporal network data has recently been studied as it helps reveal underlying dynamical processes. A commonly used method is network aggregation over a time window, which aggregates a subsequence of multiple network snapshots into one static network. This method, however, necessarily discards temporal dynamics within the time window. Here we propose a new method for detecting dynamic states in temporal networks using connection series (i.e., time series of connection status) between nodes. Our method consists of the construction of connection series tensors over nonoverlapping time windows, similarity measurement between these tensors, and community detection in the similarity network of those time windows. Experiments with empirical temporal network data demonstrated that our method outperformed the conventional approach using simple network aggregation in revealing interpretable system states. In addition, our method allows users to analyze hierarchical temporal structures and to uncover dynamic states at different spatial/temporal resolutions. 

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3. GAEN: Graph Attention Evolving Networks

   https://doi.org/10.24963/ijcai.2021/213  

   Shi, Min; Huang, Yu; Zhu, Xingquan; Tang, Yufei; Zhuang, Yuan; Liu, Jianxun (August 2021, Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence (IJCAI))

   Real-world networked systems often show dynamic properties with continuously evolving network nodes and topology over time. When learning from dynamic networks, it is beneficial to correlate all temporal networks to fully capture the similarity/relevance between nodes. Recent work for dynamic network representation learning typically trains each single network independently and imposes relevance regularization on the network learning at different time steps. Such a snapshot scheme fails to leverage topology similarity between temporal networks for progressive training. In addition to the static node relationships within each network, nodes could show similar variation patterns (e.g., change of local structures) within the temporal network sequence. Both static node structures and temporal variation patterns can be combined to better characterize node affinities for unified embedding learning. In this paper, we propose Graph Attention Evolving Networks (GAEN) for dynamic network embedding with preserved similarities between nodes derived from their temporal variation patterns. Instead of training graph attention weights for each network independently, we allow model weights to share and evolve across all temporal networks based on their respective topology discrepancies. Experiments and validations, on four real-world dynamic graphs, demonstrate that GAEN outperforms the state-of-the-art in both link prediction and node classification tasks. 

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4. Cocaine diminishes functional network robustness and destabilizes the energy landscape of neuronal activity in the medial prefrontal cortex

   https://doi.org/10.1093/pnasnexus/pgae092  

   Borzou, Ahmad; Miller, Sierra_N; Hommel, Jonathan_D; Schwarz, J_M; Bahar, ed., Ivet (March 2024, PNAS Nexus)

   Abstract We present analysis of neuronal activity recordings from a subset of neurons in the medial prefrontal cortex of rats before and after the administration of cocaine. Using an underlying modern Hopfield model as a description for the neuronal network, combined with a machine learning approach, we compute the underlying functional connectivity of the neuronal network. We find that the functional connectivity changes after the administration of cocaine with both functional-excitatory and functional-inhibitory neurons being affected. Using conventional network analysis, we find that the diameter of the graph, or the shortest length between the two most distant nodes, increases with cocaine, suggesting that the neuronal network is less robust. We also find that the betweenness centrality scores for several of the functional-excitatory and functional-inhibitory neurons decrease significantly, while other scores remain essentially unchanged, to also suggest that the neuronal network is less robust. Finally, we study the distribution of neuronal activity and relate it to energy to find that cocaine drives the neuronal network towards destabilization in the energy landscape of neuronal activation. While this destabilization is presumably temporary given one administration of cocaine, perhaps this initial destabilization indicates a transition towards a new stable state with repeated cocaine administration. However, such analyses are useful more generally to understand how neuronal networks respond to perturbations. 

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5. A Unified Spectral Clustering Approach for Detecting Community Structure in Multilayer Networks

   https://doi.org/10.3390/sym15071368  

   Al-sharoa, Esraa; Aviyente, Selin (July 2023, Symmetry)

   Networks offer a compact representation of complex systems such as social, communication, and biological systems. Traditional network models are often inadequate to capture the diverse nature of contemporary networks, which may exhibit temporal variation and multiple types of interactions between entities. Multilayer networks (MLNs) provide a more comprehensive representation by allowing interactions between nodes to be represented by different types of links, each reflecting a distinct type of interaction. Community detection reveals meaningful structure and provides a better understanding of the overall functioning of networks. Current approaches to multilayer community detection are either limited to community detection over the aggregated network or are extensions of single-layer community detection methods with simplifying assumptions such as a common community structure across layers. Moreover, most of the existing methods are limited to multiplex networks with no inter-layer edges. In this paper, we introduce a spectral-clustering-based community detection method for two-layer MLNs. The problem of detecting the community structure is formulated as an optimization problem where the normalized cut for each layer is minimized simultaneously with the normalized cut for the bipartite network along with regularization terms that ensure the consistency of the within- and across-layer community structures. The proposed method is evaluated on both synthetic and real networks and compared to state-of-the-art methods. MLNs. The problem of detecting the community structure is formulated as an optimization problem where the normalized cut for each layer is minimized simultaneously with the normalized cut for the bipartite network along with regularization terms that ensure the consistency of the intra- and inter-layer community structures. The proposed method is evaluated on both synthetic and real networks and compared to state-of-the-art methods. 

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