Community detection algorithms: a comparative analysis

Changes in topological properties of brain structural covariance networks and alertness in temporal lobe epilepsy with and without focal to bilateral tonic-clonic seizures

This study investigated brain structural covariance network (SCN) topological changes and alertness in temporal lobe epilepsy (TLE) with and without focal to bilateral tonic-clonic seizures (FBTCS). Seventy-eight subjects, including 32 TLE patients with FBTCS (TLE-FBTCS), 46 TLE patients without FBTCS (TLE-FS), and 42 healthy controls (HCs), underwent the Attention Network Test to assess alertness and volumetric MRI scans. SCNs were constructed and analyzed using graph theory. Results showed that TLE-FS patients had lower total cerebral volume than HCs, and the lowest volume was observed in the TLE-FBTCS group. Compared to HCs and TLE-FBTCS patients, TLE-FS patients exhibited increased small-worldness, normalized clustering coefficient, global efficiency, and modularity, but decreased normalized characteristic shortest path length and assortativity. Specific brain regions, such as the hippocampus, thalamus, and superior temporal sulcus, showed changes in nodal clustering coefficients and efficiency in TLE-FS patients. Further analysis revealed decreased intrinsic/phasic alertness in TLE-FBTCS patients. Correlation analysis indicated that SCN topological properties were associated with alertness in TLE-FS patients but not in TLE-FBTCS patients. These findings suggest that TLE-FS and TLE-FBTCS patients show different changes in SCN integration and segregation, with TLE-FS alertness linked to SCN topological properties, providing insights into TLE's neuropathological mechanisms.

Intrinsic brain mapping of cognitive abilities: A multiple-dataset study on intelligence and its components

This study investigates how functional brain network features contribute to general intelligence and its cognitive components by analyzing three independent cohorts of healthy participants. Cognitive scores were derived from 1) the Wechsler Adult Intelligence Scale (WAIS-IV), 2) the Raven Standard Progressive Matrices (RPM), and 3) the NIH and Penn cognitive batteries from the Human Connectome Project. Factor analysis on the NIH and Penn cognitive batteries yielded latent variables that closely resembled the content of the WAIS-IV indices and RPM. We employed graph theory and a multi-resolution network analysis by varying the modularity parameter (γ) to investigate hierarchical brain-behavior relationships across different scales of brain organization. Brain-behavior associations were quantified using multi-level robust regression analyses to accommodate variability and confounds at the subject-level, node-level, and resolution-level. Our findings reveal consistent brain-behavior relationships across the datasets. Nodal efficiency in fronto-parietal sensorimotor regions consistently played a pivotal role in fluid reasoning, whereas efficiency in visual networks was linked to executive functions and memory. A broad, low-resolution 'task-positive' network emerged as predictive of full-scale IQ scores, indicating a hierarchical brain-behavior coding. Conversely, increased cross-network connections involving default mode and subcortical-limbic networks were associated with reductions in both general and specific cognitive performance. These outcomes highlight the relevance of network efficiency and integration, as well as of the hierarchical organization in supporting specific aspects of intelligence, while recognizing the inherent complexity of these relationships. Our multi-resolution network approach offers new insights into the interplay between multilayer network properties and the structure of cognitive abilities, advancing the understanding of the neural substrates of the intelligence construct.

Measuring productivity in the healthcare sector: a bibliometric and content analysis

BACKGROUND

Productivity in the healthcare sector has evolved as an appealing research topic in the last few years. Despite the growing interest, the extant scientific literature mostly concentrates on methodologies rather than theoretical and practical insights. Although diverse methodologies provide valuable quantitative wisdom, their application is often misaligned with broader economic theories or healthcare purposes, limiting their contribution to advancing theoretical and practical understanding of efficiency and productivity in healthcare systems. In this respect, the current study endeavors to bridge the research gap concerning the lack of a comprehensive overview of productivity measurements in the healthcare sector.

METHODS

We investigate this concern through a bibliometric and content analysis of articles published on healthcare productivity measurement techniques in the Web of Science database between 2003 and 2023. We provide a quantitative and critical analysis of conceptualization, methods, findings, and implications of the selected published articles concerning productivity measurements in the healthcare sector.

RESULTS

Our research discovered that the sanitary crisis generated by COVID-19 boosted the publication of scientific papers on productivity measurements in healthcare, with Europe emerging as a leading region in publication output. Although Data Envelopment Analysis and the Malmquist Index monopolize the range of measurement techniques used to quantify productivity, current research highlights the requirement for alternative methodologies to grasp the multidimensionality of healthcare productivity, including its interaction with quality and technological progress.

CONCLUSIONS

We raise awareness that future efforts should prioritize multidimensional and context-sensitive approaches to measuring healthcare productivity, balancing efficiency, technological progress, and quality of care. Policymakers should focus on designing context-specific policies tailored to regional challenges and promoting targeted research funding to explore underrepresented areas of healthcare services.

Neural network embedding of functional microconnectome

Our brains operate as a complex network of interconnected neurons. To gain a deeper understanding of this network architecture, it is essential to extract simple rules from its intricate structure. This study aimed to compress and simplify the architecture, with a particular focus on interpreting patterns of functional connectivity in 2.5 hr of electrical activity from a vast number of neurons in acutely sliced mouse brains. Here, we combined two distinct methods together: automatic compression and network analysis. Firstly, for automatic compression, we trained an artificial neural network named NNE (neural network embedding). This allowed us to reduce the connectivity to features, be represented only by 13% of the original neuron count. Secondly, to decipher the topology, we concentrated on the variability among the compressed features and compared them with 15 distinct network metrics. Specifically, we introduced new metrics that had not previously existed, termed as indirect-adjacent degree and neighbor hub ratio. Our results conclusively demonstrated that these new metrics could better explain approximately 40%-45% of the features. This finding highlighted the critical role of NNE in facilitating the development of innovative metrics, because some of the features extracted by NNE were not captured by the currently existed network metrics.

Unraveling Multimorbidity Patterns of Psoriasis Using Network Analysis

BACKGROUND

Psoriasis is a chronic disease with a prevalence of 3% in the general population. The high prevalence of psoriasis has prompted the study of its comorbidities in recent decades. However, no studies have ever analyzed comorbidity patterns including all chronic diseases in psoriatic patients.

OBJECTIVES

To identify comorbidity patterns in psoriatic patients using network analysis and describe them from a clinical point of view.

METHODS

We conducted an observational and retrospective study with individuals of the EpiChron Cohort (Aragón, Spain) diagnosed with psoriasis from January 1st, 2010 through December 31st, 2019. The population was stratified by sex and age intervals (0-11, 12-17, 18-44, 45-64, ≥65). We built a network for each stratum (i.e., 5 for each sex), calculating the tetrachoric correlations of each pair of diseases. We used a cut-off threshold for statistical significance of p-value <0.01. We applied the Louvain community detection algorithm to identify clusters of diseases.

RESULTS

The prevalence of psoriasis in Aragón was found to be 2.84%. We identified a total of 31,178 psoriatic patients (54% men, 61% from metropolitan areas). The most common comorbidities were respiratory diseases, cardiometabolic conditions (such as hypertension and dyslipidemia), and mental health disorders (including anxiety and mood disorders). A total of 21 comorbidity patterns were identified, varying by sex and age group.

CONCLUSIONS

This is the first study ever conducted with a comprehensive analysis of the disease patterns of psoriatic patients. Our results are a comprehensive map of possible psoriasis-related comorbidities. Further studies should confirm these associations and their pathophysiological relationship with psoriasis, which could help to detect and prevent comorbidities and modifiable risk factors.

From attributes to communities: a novel approach in social network generation

Generating networks with attributes would be useful in computer game development by enabling dynamic social interactions, adaptive storylines, realistic economic systems, ecosystem modelling, urban development, strategic planning, and adaptive learning systems. To this end, we propose the Attribute-based Realistic Community and Associate NEtwork (ARCANE) algorithm to generate node-attributed networks with functional communities. We have designed a numerical node attribute-edge relationship computation system to handle the edge generation phase of our network generator, which is a different method from our predecessors. We combine this system with the proximity between nodes to create more life-like communities. Our method is compared against other node-attributed social network generators in the area with using both different evaluation metrics and a real-world dataset. The model properties evaluation identified ARCANE as the leading generator, with another generator ranking in a tie for first place. As a more favorable outcome for our approach, the community detection evaluation indicated that ARCANE exhibited superior performance compared to other competing generators within this domain. This thorough evaluation of the resulting graphs show that the proposed method can be an alternate approach to social network generators with node attributes and communities.

Pharmacologic LDH inhibition redirects intratumoral glucose uptake and improves antitumor immunity in solid tumor models

Tumor reliance on glycolysis is a hallmark of cancer. Immunotherapy is more effective in controlling glycolysis-low tumors lacking lactate dehydrogenase (LDH) due to reduced tumor lactate efflux and enhanced glucose availability within the tumor microenvironment (TME). LDH inhibitors (LDHi) reduce glucose uptake and tumor growth in preclinical models, but their impact on tumor-infiltrating T cells is not fully elucidated. Tumor cells have higher basal LDH expression and glycolysis levels compared with infiltrating T cells, creating a therapeutic opportunity for tumor-specific targeting of glycolysis. We demonstrate that LDHi treatment (a) decreases tumor cell glucose uptake, expression of the glucose transporter GLUT1, and tumor cell proliferation while (b) increasing glucose uptake, GLUT1 expression, and proliferation of tumor-infiltrating T cells. Accordingly, increasing glucose availability in the microenvironment via LDH inhibition leads to improved tumor-killing T cell function and impaired Treg immunosuppressive activity in vitro. Moreover, combining LDH inhibition with immune checkpoint blockade therapy effectively controls murine melanoma and colon cancer progression by promoting effector T cell infiltration and activation while destabilizing Tregs. Our results establish LDH inhibition as an effective strategy for rebalancing glucose availability for T cells within the TME, which can enhance T cell function and antitumor immunity.

Brain Network Interconnectivity Dynamics Explain Metacognitive Differences in Listening Behavior

Complex auditory scenes pose a challenge to attentive listening, rendering listeners slower and more uncertain in their perceptual decisions. How can we explain such behaviors from the dynamics of cortical networks that pertain to the control of listening behavior? We here follow up on the hypothesis that human adaptive perception in challenging listening situations is supported by modular reconfiguration of auditory-control networks in a sample of N = 40 participants (13 males) who underwent resting-state and task functional magnetic resonance imaging (fMRI). Individual titration of a spatial selective auditory attention task maintained an average accuracy of ∼70% but yielded considerable interindividual differences in listeners' response speed and reported confidence in their own perceptual decisions. Whole-brain network modularity increased from rest to task by reconfiguring auditory, cinguloopercular, and dorsal attention networks. Specifically, interconnectivity between the auditory network and cinguloopercular network decreased during the task relative to the resting state. Additionally, interconnectivity between the dorsal attention network and cinguloopercular network increased. These interconnectivity dynamics were predictive of individual differences in response confidence, the degree of which was more pronounced after incorrect judgments. Our findings uncover the behavioral relevance of functional cross talk between auditory and attentional-control networks during metacognitive assessment of one's own perception in challenging listening situations and suggest two functionally dissociable cortical networked systems that shape the considerable metacognitive differences between individuals in adaptive listening behavior.

Oxytocin homogenizes horse group organization

The oxytocinergic system has been suggested to make up an important part of the endocrine basis of group cohesion. However, controlled studies in open-group settings have not been performed. We here investigated the impact of exogenous intranasal oxytocin on the group-level social organization of 5 groups of horses (N = 58; 12 mares and 46 geldings) through GPS tracking and social network analysis. We find oxytocin flattened social differentiation across levels. Most strikingly, oxytocin did not simply reinforce existing bonds but selectively shifted social preferences toward homogenization - individuals and pairs who otherwise rarely associated spent more time close together, while individuals and pairs with the highest baseline association instead spent more time further apart. This resulted in a more distributed structure and lower clustering coefficient at the network level. These effects reinforce and extend oxytocin's role in collective behavior, social organization, and the evolution of group-based sociality across taxa.

Advancing skeletal health and disease research with single-cell RNA sequencing

Orthopedic conditions have emerged as global health concerns, impacting approximately 1.7 billion individuals worldwide. However, the limited understanding of the underlying pathological processes at the cellular and molecular level has hindered the development of comprehensive treatment options for these disorders. The advent of single-cell RNA sequencing (scRNA-seq) technology has revolutionized biomedical research by enabling detailed examination of cellular and molecular diversity. Nevertheless, investigating mechanisms at the single-cell level in highly mineralized skeletal tissue poses technical challenges. In this comprehensive review, we present a streamlined approach to obtaining high-quality single cells from skeletal tissue and provide an overview of existing scRNA-seq technologies employed in skeletal studies along with practical bioinformatic analysis pipelines. By utilizing these methodologies, crucial insights into the developmental dynamics, maintenance of homeostasis, and pathological processes involved in spine, joint, bone, muscle, and tendon disorders have been uncovered. Specifically focusing on the joint diseases of degenerative disc disease, osteoarthritis, and rheumatoid arthritis using scRNA-seq has provided novel insights and a more nuanced comprehension. These findings have paved the way for discovering novel therapeutic targets that offer potential benefits to patients suffering from diverse skeletal disorders.

Encoding Manual Dexterity through Modulation of Intrinsic α Band Connectivity

The human hand possesses both consolidated motor skills and remarkable flexibility in adapting to ongoing task demands. However, the underlying mechanisms by which the brain balances stability and flexibility remain unknown. In the absence of external input or behavior, spontaneous (intrinsic) brain connectivity is thought to represent a prior of stored memories. In this study, we investigated how manual dexterity modulates spontaneous functional connectivity in the motor cortex during hand movement. Using magnetoencephalography, in 47 human participants (both sexes), we examined connectivity modulations in the α and β frequency bands at rest and during two motor tasks (i.e., finger tapping or toe squeezing). The flexibility and stability of such modulations allowed us to identify two groups of participants with different levels of performance (high and low performers) on the nine-hole peg test, a test of manual dexterity. In the α band, participants with higher manual dexterity showed distributed decreases of connectivity, specifically in the motor cortex, increased segregation, and reduced nodal centrality. Participants with lower manual dexterity showed an opposite pattern. Notably, these patterns from the brain to behavior are mirrored by results from behavior to the brain. Indeed, when participants were divided using the median split of the dexterity score, we found the same connectivity patterns. In summary, this experiment shows that a long-term motor skill-manual dexterity-influences the way the motor systems respond during movements.

Towards personalized precision functional mapping in infancy

The precise network topology of functional brain systems is highly specific to individuals and undergoes dramatic changes during critical periods of development. Large amounts of high-quality resting state data are required to investigate these individual differences, but are difficult to obtain in early infancy. Using the template matching method, we generated a set of infant network templates to use as priors for individualized functional resting-state network mapping in two independent neonatal datasets with extended acquisition of resting-state functional MRI (fMRI) data. We show that template matching detects all major adult resting-state networks in individual infants and that the topology of these resting-state network maps is individual-specific. Interestingly, there was no plateau in within-subject network map similarity with up to 25 minutes of resting-state data, suggesting that the amount and/or quality of infant data required to achieve stable or high-precision network maps is higher than adults. These findings are a critical step towards personalized precision functional brain mapping in infants, which opens new avenues for clinical applicability of resting-state fMRI and potential for robust prediction of how early functional connectivity patterns relate to subsequent behavioral phenotypes and health outcomes.

A protein network refinement method based on module discovery and biological information

BACKGROUND

The identification of essential proteins can help in understanding the minimum requirements for cell survival and development to discover drug targets and prevent disease. Nowadays, node ranking methods are a common way to identify essential proteins, but the poor data quality of the underlying PIN has somewhat hindered the identification accuracy of essential proteins for these methods in the PIN. Therefore, researchers constructed refinement networks by considering certain biological properties of interacting protein pairs to improve the performance of node ranking methods in the PIN. Studies show that proteins in a complex are more likely to be essential than proteins not present in the complex. However, the modularity is usually ignored for the refinement methods of the PINs.

METHODS

Based on this, we proposed a network refinement method based on module discovery and biological information. The idea is, first, to extract the maximal connected subgraph in the PIN, and to divide it into different modules by using Fast-unfolding algorithm; then, to detect critical modules according to the orthologous information, subcellular localization information and topology information within each module; finally, to construct a more refined network (CM-PIN) by using the identified critical modules.

RESULTS

To evaluate the effectiveness of the proposed method, we used 12 typical node ranking methods (LAC, DC, DMNC, NC, TP, LID, CC, BC, PR, LR, PeC, WDC) to compare the overall performance of the CM-PIN with those on the S-PIN, D-PIN and RD-PIN. The experimental results showed that the CM-PIN was optimal in terms of the identification number of essential proteins, precision-recall curve, Jackknifing method and other criteria, and can help to identify essential proteins more accurately.

Data-driven dimensionality reduction and causal inference for spatiotemporal climate fields

We propose a data-driven framework to describe spatiotemporal climate variability in terms of a few entities and their causal linkages. Given a high-dimensional climate field, the methodology first reduces its dimensionality into a set of regionally constrained patterns. Causal relations among such patterns are then inferred in the interventional sense through the fluctuation-response formalism. To distinguish between true and spurious responses, we propose an analytical null model for the fluctuation-dissipation relation, therefore allowing us for uncertainty estimation at a given confidence level. We showcase the methodology on the sea surface temperature field from a state-of-the-art climate model. The usefulness of the proposed framework for spatiotemporal climate data is demonstrated in several ways. First, we focus on the correct identification of known causal relations across tropical basins. Second, we show how the methodology allows us to visualize the cumulative response of the whole system to climate variability in a few selected regions. Finally, each pattern is ranked in terms of its causal strength, quantifying its relative ability to influence the system's dynamics. We argue that the methodology allows us to explore and characterize causal relations in spatiotemporal fields in a rigorous and interpretable way.

Uncovering Flat and Hierarchical Topics by Community Discovery on Word Co-occurrence Network

Topic modeling aims to discover latent themes in collections of text documents. It has various applications across fields such as sociology, opinion analysis, and media studies. In such areas, it is essential to have easily interpretable, diverse, and coherent topics. An efficient topic modeling technique should accurately identify flat and hierarchical topics, especially useful in disciplines where topics can be logically arranged into a tree format. In this paper, we propose Community Topic, a novel algorithm that exploits word co-occurrence networks to mine communities and produces topics. We also evaluate the proposed approach using several metrics and compare it with usual baselines, confirming its good performances. Community Topic enables quick identification of flat topics and topic hierarchy, facilitating the on-demand exploration of sub- and super-topics. It also obtains good results on datasets in different languages.

Comparing community detection algorithms in psychometric networks: A Monte Carlo simulation

Identifying the correct number of factors in multivariate data is fundamental to psychological measurement. Factor analysis has a long tradition in the field, but it has been challenged recently by exploratory graph analysis (EGA), an approach based on network psychometrics. EGA first estimates a network and then applies the Walktrap community detection algorithm. Simulation studies have demonstrated that EGA has comparable or better accuracy for recovering the same number of communities as there are factors in the simulated data than factor analytic methods. Despite EGA's effectiveness, there has yet to be an investigation into whether other sparsity induction methods or community detection algorithms could achieve equivalent or better performance. Furthermore, unidimensional structures are fundamental to psychological measurement yet they have been sparsely studied in simulations using community detection algorithms. In the present study, we performed a Monte Carlo simulation using the zero-order correlation matrix, GLASSO, and two variants of a non-regularized partial correlation sparsity induction methods with several community detection algorithms. We examined the performance of these method-algorithm combinations in both continuous and polytomous data across a variety of conditions. The results indicate that the Fast-greedy, Louvain, and Walktrap algorithms paired with the GLASSO method were consistently among the most accurate and least-biased overall.

Transdiagnostic clustering and network analysis for questionnaire-based symptom profiling and drug recommendation in the UK Biobank and a Korean cohort

Clinical decision support systems (CDSSs) play a critical role in enhancing the efficiency of mental health care delivery and promoting patient engagement. Transdiagnostic approaches that utilize raw psychological and biological data enable personalized patient profiling and treatment. This study introduces a CDSS incorporating symptom profiling and drug recommendation for mental health care. Among the UK Biobank cohort, we analyzed 157,348 participants for symptom profiling and 14,358 participants with a drug prescription history for drug recommendation. Among the 1307 patients in the Samsung Medical Center cohort, 842 were eligible for analysis. Symptom profiling utilized demographic and questionnaire data, employing conventional clustering and community detection methods. Identified clusters were explored using diagnostic mapping, feature importance, and scoring. For drug recommendation, we employed cluster- and network-based approaches. The analysis identified nine clusters using k-means clustering and ten clusters with the Louvain method. Clusters were annotated for distinct features related to depression, anxiety, psychosis, drug addiction, and self-harm. For drug recommendation, drug prescription probabilities were retrieved for each cluster. A recommended list of drugs, including antidepressants, antipsychotics, mood stabilizers, and sedative-hypnotics, was provided to individual patients. This CDSS holds promise for efficient personalized mental health care and requires further validation and refinement with larger datasets, serving as a valuable tool for mental healthcare providers.

Pathway analysis through mutual information

MOTIVATION

In pathway analysis, we aim to establish a connection between the activity of a particular biological pathway and a difference in phenotype. There are many available methods to perform pathway analysis, many of them rely on an upstream differential expression analysis, and many model the relations between the abundances of the analytes in a pathway as linear relationships.

RESULTS

Here, we propose a new method for pathway analysis, MIPath, that relies on information theoretical principles and, therefore, does not model the association between pathway activity and phenotype, resulting in relatively few assumptions. For this, we construct a graph of the data points for each pathway using a nearest-neighbor approach and score the association between the structure of this graph and the phenotype of these same samples using Mutual Information while adjusting for the effects of random chance in each score. The initial nearest neighbor approach evades individual gene-level comparisons, hence making the method scalable and less vulnerable to missing values. These properties make our method particularly useful for single-cell data. We benchmarked our method on several single-cell datasets, comparing it to established and new methods, and found that it produces robust, reproducible, and meaningful scores.

AVAILABILITY AND IMPLEMENTATION

Source code is available at https://github.com/statisticalbiotechnology/mipath, or through Python Package Index as "mipathway."

Guiding prevention initiatives by applying network analysis to systems maps of adverse childhood experiences and adolescent suicide

Suicide is a leading cause of death in the United States, particularly among adolescents. In recent years, suicidal ideation, attempts, and fatalities have increased. Systems maps can effectively represent complex issues such as suicide, thus providing decision-support tools for policymakers to identify and evaluate interventions. While network science has served to examine systems maps in fields such as obesity, there is limited research at the intersection of suicidology and network science. In this paper, we apply network science to a large causal map of adverse childhood experiences (ACEs) and suicide to address this gap. The National Center for Injury Prevention and Control (NCIPC) within the Centers for Disease Control and Prevention recently created a causal map that encapsulates ACEs and adolescent suicide in 361 concept nodes and 946 directed relationships. In this study, we examine this map and three similar models through three related questions: (Q1) how do existing network-based models of suicide differ in terms of node- and network-level characteristics? (Q2) Using the NCIPC model as a unifying framework, how do current suicide intervention strategies align with prevailing theories of suicide? (Q3) How can the use of network science on the NCIPC model guide suicide interventions?

Embedding-based link predictions to explore latent comorbidity of chronic diseases

Purpose

Comorbidity is a term used to describe when a patient simultaneously has more than one chronic disease. Comorbidity is a significant health issue that affects people worldwide. This study aims to use machine learning and graph theory to predict the comorbidity of chronic diseases.

Methods

A patient-disease bipartite graph is constructed based on the administrative claim data. The bipartite graph projection approach was used to create the comorbidity network. For the link prediction task, three graph machine learning embedding-based models (node2vec, graph neural networks and hand-crafted approach) with different variants were used on the comorbidity network to compare their performance. This study also considered three commonly used similarity-based link prediction approaches (Jaccard coefficient, Adamic-Adar index and Resource allocation index) for performance comparison.

Results

The results showed that the embedding-based hand-crafted features technique achieved outstanding performance compared with the remaining similarity-based and embedding-based models. Especially, the hand-crafted technique with the extreme gradient boosting classifier achieved the highest accuracy (91.67%), followed by the same technique with the Logistic regression classifier (90.26%). For this shallow embedding method, the Jaccard coefficient and the degree centrality of the original chronic disease were the most important features for comorbidity prediction.

Conclusion

The proposed framework can be used to predict the comorbidity of chronic disease at an early stage of hospital admission. Thus, the prediction outcome could be valuable for medical practice, giving healthcare providers more control over their services and lowering expenses.

A network community structure similarity index for weighted networks

Identification of communities in complex systems is an essential part of network analysis. Accordingly, measuring similarities between communities is a fundamental part of analysing community structure in different, yet related, networks. Commonly used methods for quantifying network community similarity fail to consider the effects of edge weights. Existing methods remain limited when the two networks being compared have different numbers of nodes. In this study, we address these issues by proposing a novel network community structure similarity index (NCSSI) based on the edit distance concept. NCSSI is proposed as a similarity index for comparing network communities. The NCSSI incorporates both community labels and edge weights. The NCSSI can also be employed to assess the similarity between two communities with varying numbers of nodes. We test the proposed method using simulated data and case-study analysis of New York Yellow Taxi flows and compare the results with that of other commonly used methods (i.e., mutual information and the Jaccard index). Our results highlight how NCSSI effectively captures the impact of both label and edge weight changes and their impacts on community structure, which are not captured in existing approaches. In conclusion, NCSSI offers a new approach that incorporates both label and weight variations for community similarity measurement in complex networks.

Aesthetic emotions are affected by context: a psychometric network analysis

Aesthetic emotions are defined as emotions arising when a person evaluates a stimulus for its aesthetic appeal. Whether these emotions are unique to aesthetic activities is debated. We address this debate by examining if recollections of different types of engaging activities entail different emotional profiles. A large sample of participants were asked to recall engaging aesthetic (N = 167), non-aesthetic (N = 160), or consumer (N = 172) activities. They rated the extent to which 75 candidate aesthetic emotions were evoked by these activities. We applied a computational psychometric network approach to represent and compare the space of these emotions across the three conditions. At the behavioral level, recalled aesthetic activities were rated as the least vivid but most intense compared to the two other conditions. At the network level, we found several quantitative differences across the three conditions, related to the typology, community (clusters) and core nodes (emotions) of these networks. Our results suggest that aesthetic and non-aesthetic activities evoke emotional spaces differently. Thus, we propose that aesthetic emotions are distributed differently in a multidimensional aesthetic space than for other engaging activities. Our results highlight the context-specificity of aesthetic emotions.

Inflammatory bowel disease biomarkers revealed by the human gut microbiome network

Inflammatory bowel diseases (IBDs) are complex medical conditions in which the gut microbiota is attacked by the immune system of genetically predisposed subjects when exposed to yet unclear environmental factors. The complexity of this class of diseases makes them suitable to be represented and studied with network science. In this paper, the metagenomic data of control, Crohn's disease, and ulcerative colitis subjects' gut microbiota were investigated by representing this data as correlation networks and co-expression networks. We obtained correlation networks by calculating Pearson's correlation between gene expression across subjects. A percolation-based procedure was used to threshold and binarize the adjacency matrices. In contrast, co-expression networks involved the construction of the bipartite subjects-genes networks and the monopartite genes-genes projection after binarization of the biadjacency matrix. Centrality measures and community detection were used on the so-built networks to mine data complexity and highlight possible biomarkers of the diseases. The main results were about the modules of Bacteroides, which were connected in the control subjects' correlation network, Faecalibacterium prausnitzii, where co-enzyme A became central in IBD correlation networks and Escherichia coli, whose module has different patterns of integration within the whole network in the different diagnoses.

A community partitioning algorithm for cyberspace

Community partitioning is an effective technique for cyberspace mapping. However, existing community partitioning algorithm only uses the topological structure of the network to divide the community and disregards factors such as real hierarchy, overlap, and directionality of information transmission between communities in cyberspace. Consequently, the traditional community division algorithm is not suitable for dividing cyberspace resources effectively. Based on cyberspace community structure characteristics, this study introduces an algorithm that combines an improved local fitness maximization (LFM) algorithm with the PageRank (PR) algorithm for community partitioning on cyberspace resources, called PR-LFM. First, seed nodes are determined using degree centrality, followed by local community expansion. Nodes belonging to multiple communities undergo further partitioning so that they are retained in the community where they are most important, thus preserving the community's original structure. The experimental data demonstrate good results in the resource division of cyberspace.

Robustness of community structure under edge addition

Communities often represent key structural and functional clusters in networks. To preserve such communities, it is important to understand their robustness under network perturbations. Previous work in community robustness analysis has focused on studying changes in the community structure as a response of edge rewiring and node or edge removal. However, the impact of increasing connectivity on the robustness of communities in networked systems is relatively unexplored. Studying the limits of community robustness under edge addition is crucial to better understanding the cases in which density expands or false edges erroneously appear. In this paper, we analyze the effect of edge addition on community robustness in synthetic and empirical temporal networks. We study two scenarios of edge addition: random and targeted. We use four community detection algorithms, Infomap, Label Propagation, Leiden, and Louvain, and demonstrate the results in community similarity metrics. The experiments on synthetic networks show that communities are more robust when the initial partition is stronger or the edge addition is random, and the experiments on empirical data also indicate that robustness performance can be affected by the community similarity metric. Overall, our results suggest that the communities identified by the different types of community detection algorithms exhibit different levels of robustness, and so the robustness of communities depends strongly on the choice of detection method.

HB-DSBM: Modeling the Dynamic Complex Networks From Community Level to Node Level

A variety of methods have been proposed for modeling and mining dynamic complex networks, in which the topological structure varies with time. As the most popular and successful network model, the stochastic block model (SBM) has been extended and applied to community detection, link prediction, anomaly detection, and evolution analysis of dynamic networks. However, all current models based on the SBM for modeling dynamic networks are designed at the community level, assuming that nodes in each community have the same dynamic behavior, which usually results in poor performance on temporal community detection and loses the modeling of node abnormal behavior. To solve the above-mentioned problem, this article proposes a hierarchical Bayesian dynamic SBM (HB-DSBM) for modeling the node-level and community-level dynamic behavior in a dynamic network synchronously. Based on the SBM, we introduce a hierarchical Dirichlet generative mechanism to associate the global community evolution with the microscopic transition behavior of nodes near-perfectly and generate the observed links across the dynamic networks. Meanwhile, an effective variational inference algorithm is developed and we can easy to infer the communities and dynamic behaviors of the nodes. Furthermore, with the two-level evolution behaviors, it can identify nodes or communities with abnormal behavior. Experiments on simulated and real-world networks demonstrate that HB-DSBM has achieved state-of-the-art performance on community detection and evolution. In addition, abnormal evolutionary behavior and events on dynamic networks can be effectively identified by our model.

Generative models for two-ground-truth partitions in networks

A myriad of approaches have been proposed to characterize the mesoscale structure of networks most often as a partition based on patterns variously called communities, blocks, or clusters. Clearly, distinct methods designed to detect different types of patterns may provide a variety of answers' to the networks mesoscale structure. Yet even multiple runs of a given method can sometimes yield diverse and conflicting results, producing entire landscapes of partitions which potentially include multiple (locally optimal) mesoscale explanations of the network. Such ambiguity motivates a closer look at the ability of these methods to find multiple qualitatively different "ground truth" partitions in a network. Here we propose the stochastic cross-block model (SCBM), a generative model which allows for two distinct partitions to be built into the mesoscale structure of a single benchmark network. We demonstrate a use case of the benchmark model by appraising the power of stochastic block models (SBMs) to detect implicitly planted coexisting bicommunity and core-periphery structures of different strengths. Given our model design and experimental setup, we find that the ability to detect the two partitions individually varies by SBM variant and that coexistence of both partitions is recovered only in a very limited number of cases. Our findings suggest that in most instances only one-in some way dominating-structure can be detected, even in the presence of other partitions. They underline the need for considering entire landscapes of partitions when different competing explanations exist and motivate future research to advance partition coexistence detection methods. Our model also contributes to the field of benchmark networks more generally by enabling further exploration of the ability of new and existing methods to detect ambiguity in the mesoscale structure of networks.

A unified approach of detecting phase transition in time-varying complex networks

Deciphering the non-trivial interactions and mechanisms driving the evolution of time-varying complex networks (TVCNs) plays a crucial role in designing optimal control strategies for such networks or enhancing their causal predictive capabilities. In this paper, we advance the science of TVCNs by providing a mathematical framework through which we can gauge how local changes within a complex weighted network affect its global properties. More precisely, we focus on unraveling unknown geometric properties of a network and determine its implications on detecting phase transitions within the dynamics of a TVCN. In this vein, we aim at elaborating a novel and unified approach that can be used to depict the relationship between local interactions in a complex network and its global kinetics. We propose a geometric-inspired framework to characterize the network's state and detect a phase transition between different states, to infer the TVCN's dynamics. A phase of a TVCN is determined by its Forman-Ricci curvature property. Numerical experiments show the usefulness of the proposed curvature formalism to detect the transition between phases within artificially generated networks. Furthermore, we demonstrate the effectiveness of the proposed framework in identifying the phase transition phenomena governing the training and learning processes of artificial neural networks. Moreover, we exploit this approach to investigate the phase transition phenomena in cellular re-programming by interpreting the dynamics of Hi-C matrices as TVCNs and observing singularity trends in the curvature network entropy. Finally, we demonstrate that this curvature formalism can detect a political change. Specifically, our framework can be applied to the US Senate data to detect a political change in the United States of America after the 1994 election, as discussed by political scientists.

Heterogeneous changes in mobility in response to the SARS-CoV-2 Omicron BA.2 outbreak in Shanghai

The coronavirus disease 2019 (COVID-19) pandemic and the measures taken by authorities to control its spread have altered human behavior and mobility patterns in an unprecedented way. However, it remains unclear whether the population response to a COVID-19 outbreak varies within a city or among demographic groups. Here, we utilized passively recorded cellular signaling data at a spatial resolution of 1 km × 1 km for over 5 million users and epidemiological surveillance data collected during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.2 outbreak from February to June 2022 in Shanghai, China, to investigate the heterogeneous response of different segments of the population at the within-city level and examine its relationship with the actual risk of infection. Changes in behavior were spatially heterogenous within the city and population groups and associated with both the infection incidence and adopted interventions. We also found that males and individuals aged 30 to 59 y old traveled more frequently, traveled longer distances, and their communities were more connected; the same groups were also associated with the highest SARS-CoV-2 incidence. Our results highlight the heterogeneous behavioral change of the Shanghai population to the SARS-CoV-2 Omicron BA.2 outbreak and the effect of heterogenous behavior on the spread of COVID-19, both spatially and demographically. These findings could be instrumental for the design of targeted interventions for the control and mitigation of future outbreaks of COVID-19, and, more broadly, of respiratory pathogens.

An analysis of the spatio-temporal behavior of COVID-19 patients using activity trajectory data

During the global pandemic, COVID-19 patients' activity trajectories and actions emerge as revelatory conduits elucidating their spatiotemporal behavior and transmission dynamics. This study analyzes COVID-19 patients' behavior in Nanjing and Yangzhou, China, by using patient activity trajectory data in conjunction with complex network theory. The main findings are as follows: (1) The evaluation of the activity network structure of patients revealed that "residential areas" and "vegetable markets" had the highest betweenness centrality, indicating that these are the primary nodes of COVID-19 transmission. (2) The power-law distribution of the degree distribution of nodes for different facility types revealed that residential areas, vegetable markets, and shopping malls had the most scale-free characteristics, indicating that a large number of patients visited these three facility types at a few access points. (3) Community detection showed that patient visitation sites in Nanjing and Yangzhou were divided into five or six communities, with the largest community containing the outbreak origin and several residential areas surrounding it. (4) Patients had fewer activities across administrative regions but more activities across the life circle when the pandemic broke out in the suburbs, and more activities across administrative regions but fewer activities across the life circle when the pandemic broke out in the central city. Based on these findings, this paper makes recommendations for future pandemic preparedness in an effort to achieve effective pandemic control and reduce the damage caused by pandemics. Overall, this study provides insights into understanding the transmission patterns of COVID-19 and may inform future pandemic control strategies.

Is ecology different when studied with citizen scientists? A bibliometric analysis

Ecology is broad and relies on several complementary approaches to study the mechanisms driving the distribution and abundance of organisms and their interactions. One of them is citizen science (CitSci), the co-production of scientific data and knowledge by nonprofessional scientists, in collaboration with, or under the direction of, professional scientists. CitSci has bloomed in the scientific literature over the last decade and its popularity continues to increase, but its qualitative contribution to the development of academic knowledge remains understudied. We used a bibliometric analysis to study whether the epistemic content of CitSci-based articles is different from traditional, non-CitSci ones within the field of ecology. We analyzed keywords and abstracts of articles published in ecology over the last decade, disentangling CitSci articles (those explicitly referring to citizen science) and non-CitSci articles. Keyword co-occurrence and thematic map analyses first revealed that CitSci and non-CitSci articles broadly focused on biodiversity, conservation, and climate change. However, CitSci articles did so in a more descriptive way than non-CitSci articles, which were more likely to address mechanisms. Conservation biology and its links with socio-ecosystems and ecosystem services was a central theme in the CitSci corpus, much less in the non-CitSci corpus. The situation was opposite for climate change and its consequences on species distribution and adaptation, which was a central theme in the non-CitSci corpus only. We only revealed subtle differences in the relative importance of particular themes and in the way these themes are tackled in CitSci and non-CitSci articles, thus indicating that citizen science is well integrated in the main, classical research themes of ecology.

Efficiency of Heterogenous Functional Connectomes Explains Variance in Callous-Unemotional Traits After Computational Lesioning of Cortical Midline and Salience Regions

Introduction: Callous-unemotional (CU) traits are a youth antisocial phenotype hypothesized to be a result of differences in the integration of multiple brain systems. However, mechanistic insights into these brain systems are a continued challenge. Where prior work describes activation and connectivity, new mechanistic insights into the brain's functional connectome can be derived by removing nodes and quantifying changes in network properties (hereafter referred to as computational lesioning) to characterize connectome resilience and vulnerability. Methods: Here, we study the resilience of connectome integration in CU traits by estimating changes in efficiency after computationally lesioning individual-level connectomes. From resting-state data of 86 participants (48% female, age 14.52 ± 1.31) drawn from the Nathan Kline institute's Rockland study, individual-level connectomes were estimated using graphical lasso. Computational lesioning was conducted both sequentially and by targeting global and local hubs. Elastic net regression was applied to determine how these changes explained variance in CU traits. Follow-up analyses characterized modeled node hubs, examined moderation, determined impact of targeting, and decoded the brain mask by comparing regions to meta-analytic maps. Results: Elastic net regression revealed that computational lesioning of 23 nodes, network modularity, and Tanner stage explained variance in CU traits. Hub assignment of selected hubs differed at higher CU traits. No evidence for moderation between simulated lesioning and CU traits was found. Targeting global hubs increased efficiency and targeting local hubs had no effect at higher CU traits. Identified brain mask meta-analytically associated with more emotion and cognitive terms. Although reliable patterns were found across participants, adolescent brains were heterogeneous even for those with a similar CU traits score. Conclusion: Adolescent brain response to simulated lesioning revealed a pattern of connectome resiliency and vulnerability that explains variance in CU traits, which can aid prediction of youth at greater risk for higher CU traits.

Unraveling the key drivers of community composition in the agri-food trade network

In the complex global food system, the dynamics associated with international food trade have become crucial determinants of food security. In this paper, we employ a community detection approach along with a supervised learning technique to explore the evolution of communities in the agri-food trade network and to identify key factors influencing their composition. By leveraging a large dataset that includes both volume and monetary value of trades, we identify similarities between countries and uncover the primary drivers that shape trade dynamics over time. The analysis also takes into account the impact of evolving climate conditions on food production and trading. The results highlight how the network's topological structure is continuously evolving, influencing the composition of communities over time. Alongside geographical proximity and geo-political relations, our analysis identifies sustainability, climate and food nutrition aspects as emerging factors that contribute to explaining trade relationships. These findings shed light on the intricate interactions within the global food trade system and provide valuable insights into the factors affecting its stability.

Students' Learning Behaviour in Programming Education Analysis: Insights from Entropy and Community Detection

The high dropout rates in programming courses emphasise the need for monitoring and understanding student engagement, enabling early interventions. This activity can be supported by insights into students' learning behaviours and their relationship with academic performance, derived from student learning log data in learning management systems. However, the high dimensionality of such data, along with their numerous features, pose challenges to their analysis and interpretability. In this study, we introduce entropy-based metrics as a novel manner to represent students' learning behaviours. Employing these metrics, in conjunction with a proven community detection method, we undertake an analysis of learning behaviours across higher- and lower-performing student communities. Furthermore, we examine the impact of the COVID-19 pandemic on these behaviours. The study is grounded in the analysis of empirical data from 391 Software Engineering students over three academic years. Our findings reveal that students in higher-performing communities typically tend to have lower volatility in entropy values and reach stable learning states earlier than their lower-performing counterparts. Importantly, this study provides evidence of the use of entropy as a simple yet insightful metric for educators to monitor study progress, enhance understanding of student engagement, and enable timely interventions.

Low-frequency repetitive transcranial magnetic stimulation alters the individual functional dynamical landscape

Repetitive transcranial magnetic stimulation (rTMS) is a noninvasive approach to modulate brain activity and behavior in humans. Still, how individual resting-state brain dynamics after rTMS evolves across different functional configurations is rarely studied. Here, using resting state fMRI data from healthy subjects, we aimed to examine the effects of rTMS to individual large-scale brain dynamics. Using Topological Data Analysis based Mapper approach, we construct the precise dynamic mapping (PDM) for each participant. To reveal the relationship between PDM and canonical functional representation of the resting brain, we annotated the graph using relative activation proportion of a set of large-scale resting-state networks (RSNs) and assigned the single brain volume to corresponding RSN-dominant or a hub state (not any RSN was dominant). Our results show that (i) low-frequency rTMS could induce changed temporal evolution of brain states; (ii) rTMS didn't alter the hub-periphery configurations underlined resting-state brain dynamics; and (iii) the rTMS effects on brain dynamics differ across the left frontal and occipital lobe. In conclusion, low-frequency rTMS significantly alters the individual temporo-spatial dynamics, and our finding further suggested a potential target-dependent alteration of brain dynamics. This work provides a new perspective to comprehend the heterogeneous effect of rTMS.

Reliable Identification and Interpretation of Single-Cell Molecular Heterogeneity and Transcriptional Regulation using Dynamic Ensemble Pruning

Unsupervised clustering is an essential step in identifying cell types from single-cell RNA sequencing (scRNA-seq) data. However, a common issue with unsupervised clustering models is that the optimization direction of the objective function and the final generated clustering labels in the absence of supervised information may be inconsistent or even arbitrary. To address this challenge, a dynamic ensemble pruning framework (DEPF) is proposed to identify and interpret single-cell molecular heterogeneity. In particular, a silhouette coefficient-based indicator is developed to determine the optimization direction of the bi-objective function. In addition, a hierarchical autoencoder is employed to project the high-dimensional data onto multiple low-dimensional latent space sets, and then a clustering ensemble is produced in the latent space by the basic clustering algorithm. Following that, a bi-objective fruit fly optimization algorithm is designed to prune dynamically the low-quality basic clustering in the ensemble. Multiple experiments are conducted on 28 real scRNA-seq datasets and one large real scRNA-seq dataset from diverse platforms and species to validate the effectiveness of the DEPF. In addition, biological interpretability and transcriptional and post-transcriptional regulatory are conducted to explore biological patterns from the cell types identified, which could provide novel insights into characterizing the mechanisms.

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.

The evolution of scientific literature as metastable knowledge states

The problem of identifying common concepts in the sciences and deciding when new ideas have emerged is an open one. Metascience researchers have sought to formalize principles underlying stages in the life cycle of scientific research, understand how knowledge is transferred between scientists and stakeholders, and explain how new ideas are generated and take hold. Here, we model the state of scientific knowledge immediately preceding new directions of research as a metastable state and the creation of new concepts as combinatorial innovation. Through a novel approach combining natural language clustering and citation graph analysis, we predict the evolution of ideas over time and thus connect a single scientific article to past and future concepts in a way that goes beyond traditional citation and reference connections.

Clinical subtyping using community detection: Limited utility?

OBJECTIVES

To discover psychiatric subtypes, researchers are adopting a method called community detection. This method was not subjected to the same scrutiny in the psychiatric literature as traditional clustering methods. Furthermore, many community detection algorithms have been developed without psychiatric sample sizes and variable numbers in mind. We aim to provide clarity to researchers on the utility of this method.

METHODS

We provide an introduction to community detection algorithms, specifically describing the crucial differences between correlation-based and distance-based community detection. We compare community detection results to results of traditional methods in a simulation study representing typical psychiatry settings, using three conceptualizations of how subtypes might differ.

RESULTS

We discovered that the number of recovered subgroups was often incorrect with several community detection algorithms. Correlation-based community detection fared better than distance-based community detection, and performed relatively well with smaller sample sizes. Latent profile analysis was more consistent in recovering subtypes. Whether methods were successful depended on how differences were introduced.

CONCLUSIONS

Traditional methods like latent profile analysis remain reasonable choices. Furthermore, results depend on assumptions and theoretical choices underlying subtyping analyses, which researchers need to consider before drawing conclusions on subtypes. Employing multiple subtyping methods to establish method dependency is recommended.

Modules in connectomes of phase-synchronization comprise anatomically contiguous, functionally related regions

Modules in brain functional connectomes are essential to balancing segregation and integration of neuronal activity. Connectomes are the complete set of pairwise connections between brain regions. Non-invasive Electroencephalography (EEG) and Magnetoencephalography (MEG) have been used to identify modules in connectomes of phase-synchronization. However, their resolution is suboptimal because of spurious phase-synchronization due to EEG volume conduction or MEG field spread. Here, we used invasive, intracerebral recordings from stereo-electroencephalography (SEEG, N = 67), to identify modules in connectomes of phase-synchronization. To generate SEEG-based group-level connectomes affected only minimally by volume conduction, we used submillimeter accurate localization of SEEG contacts and referenced electrode contacts in cortical gray matter to their closest contacts in white matter. Combining community detection methods with consensus clustering, we found that the connectomes of phase-synchronization were characterized by distinct and stable modules at multiple spatial scales, across frequencies from 3 to 320 Hz. These modules were highly similar within canonical frequency bands. Unlike the distributed brain systems identified with functional Magnetic Resonance Imaging (fMRI), modules up to the high-gamma frequency band comprised only anatomically contiguous regions. Notably, the identified modules comprised cortical regions involved in shared repertoires of sensorimotor and cognitive functions including memory, language and attention. These results suggest that the identified modules represent functionally specialised brain systems, which only partially overlap with the brain systems reported with fMRI. Hence, these modules might regulate the balance between functional segregation and functional integration through phase-synchronization.

LazyFox: fast and parallelized overlapping community detection in large graphs

The detection of communities in graph datasets provides insight about a graph's underlying structure and is an important tool for various domains such as social sciences, marketing, traffic forecast, and drug discovery. While most existing algorithms provide fast approaches for community detection, their results usually contain strictly separated communities. However, most datasets would semantically allow for or even require overlapping communities that can only be determined at much higher computational cost. We build on an efficient algorithm, Fox, that detects such overlapping communities. Fox measures the closeness of a node to a community by approximating the count of triangles which that node forms with that community. We propose LazyFox, a multi-threaded adaptation of the Fox algorithm, which provides even faster detection without an impact on community quality. This allows for the analyses of significantly larger and more complex datasets. LazyFox enables overlapping community detection on complex graph datasets with millions of nodes and billions of edges in days instead of weeks. As part of this work, LazyFox's implementation was published and is available as a tool under an MIT licence at https://github.com/TimGarrels/LazyFox.

Brain and behavioral contributions to individual choices in response to affective-cognitive persuasion

Affective and cognitive information conveyed by persuasive stimuli is evaluated and integrated by individuals according to their behavioral predispositions. However, the neurocognitive structure that supports persuasion based on either affective or cognitive content is poorly understood. Here, we examine the neural and behavioral processes supporting choices based on affective and cognitive persuasion by integrating 4 information processing features: intrinsic brain connectivity, stimulus-evoked brain activity, intrinsic affective-cognitive orientation, and explicit target evaluations. We found that the intrinsic cross-network connections of a multimodal fronto-parietal network are associated with individual affective-cognitive orientation. Moreover, using a cross-validated classifier, we found that individuals' intrinsic brain-behavioral dimensions, such as affective-cognitive orientation and intrinsic brain connectivity, can predict individual choices between affective and cognitive targets. Our findings show that affective- and cognitive-based choices rely on multiple sources, including behavioral orientation, stimulus evaluation, and intrinsic functional brain architecture.

A fast and intuitive method for calculating dynamic network reconfiguration and node flexibility

Dynamic interactions between brain regions, either during rest or performance of cognitive tasks, have been studied extensively using a wide variance of methods. Although some of these methods allow elegant mathematical interpretations of the data, they can easily become computationally expensive or difficult to interpret and compare between subjects or groups. Here, we propose an intuitive and computationally efficient method to measure dynamic reconfiguration of brain regions, also termed flexibility. Our flexibility measure is defined in relation to an a-priori set of biologically plausible brain modules (or networks) and does not rely on a stochastic data-driven module estimation, which, in turn, minimizes computational burden. The change of affiliation of brain regions over time with respect to these a-priori template modules is used as an indicator of brain network flexibility. We demonstrate that our proposed method yields highly similar patterns of whole-brain network reconfiguration (i.e., flexibility) during a working memory task as compared to a previous study that uses a data-driven, but computationally more expensive method. This result illustrates that the use of a fixed modular framework allows for valid, yet more efficient estimation of whole-brain flexibility, while the method additionally supports more fine-grained (e.g. node and group of nodes scale) flexibility analyses restricted to biologically plausible brain networks.

Modularity maximization to design contiguous policy zones for pandemic response

The health and economic devastation caused by the COVID-19 pandemic has created a significant global humanitarian disaster. Pandemic response policies guided by geospatial approaches are appropriate additions to traditional epidemiological responses when addressing this disaster. However, little is known about finding the optimal set of locations or jurisdictions to create policy coordination zones. In this study, we propose optimization models and algorithms to identify coordination communities based on the natural movement of people. To do so, we develop a mixed-integer quadratic-programming model to maximize the modularity of detected communities while ensuring that the jurisdictions within each community are contiguous. To solve the problem, we present a heuristic and a column-generation algorithm. Our computational experiments highlight the effectiveness of the models and algorithms in various instances. We also apply the proposed optimization-based solutions to identify coordination zones within North Carolina and South Carolina, two highly interconnected states in the U.S. Results of our case study show that the proposed model detects communities that are significantly better for coordinating pandemic related policies than the existing geopolitical boundaries.

Towards explainable community finding

The detection of communities of nodes is an important task in understanding the structure of networks. Multiple approaches have been developed to tackle this problem, many of which are in common usage in real-world applications, such as in public health networks. However, clear insight into the reasoning behind the community labels produced by these algorithms is rarely provided. Drawing inspiration from the machine learning literature, we aim to provide post-hoc explanations for the outputs of these algorithms using interpretable features of the network. In this paper, we propose a model-agnostic methodology that identifies a set of informative features to help explain the output of a community finding algorithm. We apply it to three well-known algorithms, though the methodology is designed to generalise to new approaches. As well as identifying important features for a post-hoc explanation system, we report on the common features found made by the different algorithms and the differences between the approaches.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s41109-022-00515-6.

Who polarizes Twitter? Ideological polarization, partisan groups and strategic networked campaigning on Twitter during the 2017 and 2021 German Federal elections 'Bundestagswahlen'

Political campaign activities are increasingly digital. A crucial part of digital campaigning is communication efforts on social media platforms. As a forum for political discourse and political communication, parties and candidates on Twitter share public messages and aim to attract media attention and persuade voters. Party or prominent candidate hashtags are a central element of the campaign communication strategy since journalists and citizens search for these hashtags to follow the current debate concerning the hashed party or political candidate. Political elites and partisans use social media strategically, e.g., to link their messages to a broader debate, increase the visibility of messages, criticize other parties, or take over their hashtags (hashjacking). This study investigates the cases of the most recent 2017 and 2021 German federal elections called 'Bundestagswahlen'. The investigation (1) identifies communities of partisans in retweet networks in order to analyze the polarization of the most prominent hashtags of parties, 2) assesses the political behavior by partisan groups that amplify messages by political elites in these party networks, and 3) examines the polarization and strategic behavior of the identified partisan groups in the broader election hashtag debates using #BTW17 and #BTW21 as the prominent hashtags of the 2017 and 2021 elections. While in 2017, the far-right party 'Alternative für Deutschland' (AfD) and its partisans are in an isolated community, in 2021, they are part of the same community as the official party accounts of established conservative and liberal parties. This broader polarization may indicate changes in the political ideology of these actors. While the overall activity of political elites and partisans increased between 2017 and 2021, AfD politicians and partisans are more likely to use other party hashtags, which resulted in the polarization of the observed parts of the German political twitter sphere. While in 2017, the AfD polarized German Twitter, 2021 shows a broader division along the classical left–right divide.

Using Community Detection Techniques to Identify Themes in COVID-19-Related Patient Safety Event Reports

OBJECTIVES

The COVID-19 pandemic has transformed how healthcare is delivered to patients. As the pandemic progresses and healthcare systems continue to adapt, it is important to understand how these changes in care have changed patient care. This study aims to use community detection techniques to identify and facilitate analysis of themes in patient safety event (PSE) reports to better understand COVID-19 pandemic's impact on patient safety. With this approach, we also seek to understand how community detection techniques can be used to better identify themes and extract information from PSE reports.

METHODS

We used community detection techniques to group 2082 PSE reports from January 1, 2020, to January 31, 2021, that mentioned COVID-19 into 65 communities. We then grouped these communities into 8 clinically relevant themes for analysis.

RESULTS

We found the COVID-19 pandemic is associated with the following clinically relevant themes: (1) errors due to new and unknown COVID-19 protocols/workflows; (2) COVID-19 patients developing pressure ulcers; (3) unsuccessful/incomplete COVID-19 testing; (4) inadequate isolation of COVID-19 patients; (5) inappropriate/inadequate care for COVID-19 patients; (6) COVID-19 patient falls; (7) delays or errors communicating COVID-19 test results; and (8) COVID-19 patients developing venous thromboembolism.

CONCLUSIONS

Our study begins the long process of understanding new challenges created by the pandemic and highlights how machine learning methods can be used to understand these and similar challenges. Using community detection techniques to analyze PSE reports and identify themes within them can help give healthcare systems the necessary information to improve patient safety and the quality of care they deliver.

Cognitive control training enhances the integration of intrinsic functional networks in adolescents

Introduction

We have demonstrated that intensive cognitive training can produce sustained improvements in cognitive performance in adolescents. Few studies, however, have investigated the neural basis of these training effects, leaving the underlying mechanism of cognitive plasticity during this period unexplained.

Methods

In this study, we trained 51 typically developing adolescents on cognitive control tasks and examined how their intrinsic brain networks changed by applying graph theoretical analysis. We hypothesized that the training would accelerate the process of network integration, which is a key feature of network development throughout adolescence.

Results

We found that the cognitive control training enhanced the integration of functional networks, particularly the cross-network integration of the cingulo-opercular network. Moreover, the analysis of additional data from older adolescents revealed that the cingulo-opercular network was more integrated with other networks in older adolescents than in young adolescents.

Discussion

These findings are consistent with the hypothesis that cognitive control training may speed up network development, such that brain networks exhibit more mature patterns after training.

Detecting hierarchical organization of pervasive communities by modular decomposition of Markov chain

Connecting nodes that contingently co-appear, which is a common process of networking in social and biological systems, normally leads to modular structure characterized by the absence of definite boundaries. This study seeks to find and evaluate methods to detect such modules, which will be called 'pervasive' communities. We propose a mathematical formulation to decompose a random walk spreading over the entire network into localized random walks as a proxy for pervasive communities. We applied this formulation to biological and social as well as synthetic networks to demonstrate that it can properly detect communities as pervasively structured objects. We further addressed a question that is fundamental but has been little discussed so far: What is the hierarchical organization of pervasive communities and how can it be extracted? Here we show that hierarchical organization of pervasive communities is unveiled from finer to coarser layers through discrete phase transitions that intermittently occur as the value for a resolution-controlling parameter is quasi-statically increased. To our knowledge, this is the first elucidation of how the pervasiveness and hierarchy, both hallmarks of community structure of real-world networks, are unified.