Community detection algorithms: a comparative analysis

AmbiguityVis: Visualization of Ambiguity in Graph Layouts

Node-link diagrams provide an intuitive way to explore networks and have inspired a large number of automated graph layout strategies that optimize aesthetic criteria. However, any particular drawing approach cannot fully satisfy all these criteria simultaneously, producing drawings with visual ambiguities that can impede the understanding of network structure. To bring attention to these potentially problematic areas present in the drawing, this paper presents a technique that highlights common types of visual ambiguities: ambiguous spatial relationships between nodes and edges, visual overlap between community structures, and ambiguity in edge bundling and metanodes. Metrics, including newly proposed metrics for abnormal edge lengths, visual overlap in community structures and node/edge aggregation, are proposed to quantify areas of ambiguity in the drawing. These metrics and others are then displayed using a heatmap-based visualization that provides visual feedback to developers of graph drawing and visualization approaches, allowing them to quickly identify misleading areas. The novel metrics and the heatmap-based visualization allow a user to explore ambiguities in graph layouts from multiple perspectives in order to make reasonable graph layout choices. The effectiveness of the technique is demonstrated through case studies and expert reviews.

The Contribution of Network Organization and Integration to the Development of Cognitive Control

Cognitive control, which continues to mature throughout adolescence, is supported by the ability for well-defined organized brain networks to flexibly integrate information. However, the development of intrinsic brain network organization and its relationship to observed improvements in cognitive control are not well understood. In the present study, we used resting state functional magnetic resonance imaging (RS-fMRI), graph theory, the antisaccade task, and rigorous head motion control to characterize and relate developmental changes in network organization, connectivity strength, and integration to inhibitory control development. Subjects were 192 10–26-y-olds who were imaged during 5 min of rest. In contrast to initial studies, our results indicate that network organization is stable throughout adolescence. However, cross-network integration, predominantly of the cingulo-opercular/salience network, increased with age. Importantly, this increased integration of the cingulo-opercular/salience network significantly moderated the robust effect of age on the latency to initiate a correct inhibitory control response. These results provide compelling evidence that the transition to adult-level inhibitory control is dependent upon the refinement and strengthening of integration between specialized networks. Our findings support a novel, two-stage model of neural development, in which networks stabilize prior to adolescence and subsequently increase their integration to support the cross-domain incorporation of information processing critical for mature cognitive control.

This study reveals that although the organization of functional brain networks remains stable during adolescence, between-network integration continues to increase, underlying maturation in cognitive control.

Adolescence is a unique period of brain development, with major changes occurring across the brain at many different levels of brain functioning. At the macroscopic level, the brain is composed of individual regions that collaborate in networks to perform diverse cognitive functions. Some networks of brain regions perform lower-level sensorimotor processing, while other networks orchestrate more complex functions, such as cognitive control. The affiliation of each region to a network is referred to as network organization. Brain regions not only can communicate with other regions belonging to their own network but also with regions in other networks. Brain regions that communicate with regions belonging to other networks display a high level of integration since they link their network with another network. We found that during adolescence, network organization does not change. However, integration continues to increase, underscoring the notion that brain function becomes more distributed and collaborative during this unique period of development. Furthermore, this increased network integration underlies improvements in cognitive control. Thus, we provide a network-based account for improvements in cognitive functioning during adolescence.

Maximal Neighbor Similarity Reveals Real Communities in Networks

An important problem in the analysis of network data is the detection of groups of densely interconnected nodes also called modules or communities. Community structure reveals functions and organizations of networks. Currently used algorithms for community detection in large-scale real-world networks are computationally expensive or require a priori information such as the number or sizes of communities or are not able to give the same resulting partition in multiple runs. In this paper we investigate a simple and fast algorithm that uses the network structure alone and requires neither optimization of pre-defined objective function nor information about number of communities. We propose a bottom up community detection algorithm in which starting from communities consisting of adjacent pairs of nodes and their maximal similar neighbors we find real communities. We show that the overall advantage of the proposed algorithm compared to the other community detection algorithms is its simple nature, low computational cost and its very high accuracy in detection communities of different sizes also in networks with blurred modularity structure consisting of poorly separated communities. All communities identified by the proposed method for facebook network and E-Coli transcriptional regulatory network have strong structural and functional coherence.

Hierarchical block matrices as efficient representations of chromosome topologies and their application for 3C data integration

MOTIVATION

Recent advancements in molecular methods have made it possible to capture physical contacts between multiple chromatin fragments. The resulting association matrices provide a noisy estimate for average spatial proximity that can be used to gain insights into the genome organization inside the nucleus. However, extracting topological information from these data is challenging and their integration across resolutions is still poorly addressed. Recent findings suggest that a hierarchical approach could be advantageous for addressing these challenges.

RESULTS

We present an algorithmic framework, which is based on hierarchical block matrices (HBMs), for topological analysis and integration of chromosome conformation capture (3C) data. We first describe chromoHBM, an algorithm that compresses high-throughput 3C (HiT-3C) data into topological features that are efficiently summarized with an HBM representation. We suggest that instead of directly combining HiT-3C datasets across resolutions, which is a difficult task, we can integrate their HBM representations, and describe chromoHBM-3C, an algorithm which merges HBMs. Since three-dimensional (3D) reconstruction can also benefit from topological information, we further present chromoHBM-3D, an algorithm which exploits the HBM representation in order to gradually introduce topological constraints to the reconstruction process. We evaluate our approach in light of previous image microscopy findings and epigenetic data, and show that it can relate multiple spatial scales and provide a more complete view of the 3D genome architecture.

AVAILABILITY AND IMPLEMENTATION

The presented algorithms are available from: https://github.com/yolish/hbm

CONTACT

ys388@cam.ac.uk or pl219@cam.ac.uk

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

DeFiNe: an optimisation-based method for robust disentangling of filamentous networks

Thread-like structures are pervasive across scales, from polymeric proteins to root systems to galaxy filaments, and their characteristics can be readily investigated in the network formalism. Yet, network links usually represent only parts of filaments, which, when neglected, may lead to erroneous conclusions from network-based analyses. The existing alternatives to detect filaments in network representations require tuning of parameters over a large range of values and treat all filaments equally, thus, precluding automated analysis of diverse filamentous systems. Here, we propose a fully automated and robust optimisation-based approach to detect filaments of consistent intensities and angles in a given network. We test and demonstrate the accuracy of our solution with contrived, biological, and cosmic filamentous structures. In particular, we show that the proposed approach provides powerful automated means to study properties of individual actin filaments in their network context. Our solution is made publicly available as an open-source tool, "DeFiNe", facilitating decomposition of any given network into individual filaments.

The modular and integrative functional architecture of the human brain

Network-based analyses of brain imaging data consistently reveal distinct modules and connector nodes with diverse global connectivity across the modules. How discrete the functions of modules are, how dependent the computational load of each module is to the other modules' processing, and what the precise role of connector nodes is for between-module communication remains underspecified. Here, we use a network model of the brain derived from resting-state functional MRI (rs-fMRI) data and investigate the modular functional architecture of the human brain by analyzing activity at different types of nodes in the network across 9,208 experiments of 77 cognitive tasks in the BrainMap database. Using an author-topic model of cognitive functions, we find a strong spatial correspondence between the cognitive functions and the network's modules, suggesting that each module performs a discrete cognitive function. Crucially, activity at local nodes within the modules does not increase in tasks that require more cognitive functions, demonstrating the autonomy of modules' functions. However, connector nodes do exhibit increased activity when more cognitive functions are engaged in a task. Moreover, connector nodes are located where brain activity is associated with many different cognitive functions. Connector nodes potentially play a role in between-module communication that maintains the modular function of the brain. Together, these findings provide a network account of the brain's modular yet integrated implementation of cognitive functions.

Hierarchical mutual information for the comparison of hierarchical community structures in complex networks

The quest for a quantitative characterization of community and modular structure of complex networks produced a variety of methods and algorithms to classify different networks. However, it is not clear if such methods provide consistent, robust, and meaningful results when considering hierarchies as a whole. Part of the problem is the lack of a similarity measure for the comparison of hierarchical community structures. In this work we give a contribution by introducing the hierarchical mutual information, which is a generalization of the traditional mutual information and makes it possible to compare hierarchical partitions and hierarchical community structures. The normalized version of the hierarchical mutual information should behave analogously to the traditional normalized mutual information. Here the correct behavior of the hierarchical mutual information is corroborated on an extensive battery of numerical experiments. The experiments are performed on artificial hierarchies and on the hierarchical community structure of artificial and empirical networks. Furthermore, the experiments illustrate some of the practical applications of the hierarchical mutual information, namely the comparison of different community detection methods and the study of the consistency, robustness, and temporal evolution of the hierarchical modular structure of networks.

Finding New Order in Biological Functions from the Network Structure of Gene Annotations

The Gene Ontology (GO) provides biologists with a controlled terminology that describes how genes are associated with functions and how functional terms are related to one another. These term-term relationships encode how scientists conceive the organization of biological functions, and they take the form of a directed acyclic graph (DAG). Here, we propose that the network structure of gene-term annotations made using GO can be employed to establish an alternative approach for grouping functional terms that captures intrinsic functional relationships that are not evident in the hierarchical structure established in the GO DAG. Instead of relying on an externally defined organization for biological functions, our approach connects biological functions together if they are performed by the same genes, as indicated in a compendium of gene annotation data from numerous different sources. We show that grouping terms by this alternate scheme provides a new framework with which to describe and predict the functions of experimentally identified sets of genes.

Metagenome Analysis Exploiting High-Throughput Chromosome Conformation Capture (3C) Data

Microbial communities are complex and constitute important parts of our environment. Genomic analysis of these populations is a dynamic research area but remains limited by the difficulty in assembling full genomes of individual species. Recently, a new method for metagenome assembly/analysis based on chromosome conformation capture has emerged (meta3C). This approach quantifies the collisions experienced by DNA molecules to identify those sharing the same cellular compartments, allowing the characterization of genomes present within complex mixes of species. The exploitation of these chromosome 3D signatures holds promising perspectives for genome sequencing of discrete species in complex populations. It also has the potential to assign correctly extra-chromosomal elements, such as plasmids, mobile elements and phages, to their host cells.

Identifying robust communities and multi-community nodes by combining top-down and bottom-up approaches to clustering

Biological functions are carried out by groups of interacting molecules, cells or tissues, known as communities. Membership in these communities may overlap when biological components are involved in multiple functions. However, traditional clustering methods detect non-overlapping communities. These detected communities may also be unstable and difficult to replicate, because traditional methods are sensitive to noise and parameter settings. These aspects of traditional clustering methods limit our ability to detect biological communities, and therefore our ability to understand biological functions. To address these limitations and detect robust overlapping biological communities, we propose an unorthodox clustering method called SpeakEasy which identifies communities using top-down and bottom-up approaches simultaneously. Specifically, nodes join communities based on their local connections, as well as global information about the network structure. This method can quantify the stability of each community, automatically identify the number of communities, and quickly cluster networks with hundreds of thousands of nodes. SpeakEasy shows top performance on synthetic clustering benchmarks and accurately identifies meaningful biological communities in a range of datasets, including: gene microarrays, protein interactions, sorted cell populations, electrophysiology and fMRI brain imaging.

Social network analysis identified central outcomes for core outcome sets using systematic reviews of HIV/AIDS

OBJECTIVES

Methods to develop core outcome sets, the minimum outcomes that should be measured in research in a topic area, vary. We applied social network analysis methods to understand outcome co-occurrence patterns in human immunodeficiency virus (HIV)/AIDS systematic reviews and identify outcomes central to the network of outcomes in HIV/AIDS.

STUDY DESIGN AND SETTING

We examined all Cochrane reviews of HIV/AIDS as of June 2013. We defined a tie as two outcomes (nodes) co-occurring in ≥2 reviews. To identify central outcomes, we used normalized node betweenness centrality (nNBC) (the extent to which connections between other outcomes in a network rely on that outcome as an intermediary). We conducted a subgroup analysis by HIV/AIDS intervention type (i.e., clinical management, biomedical prevention, behavioral prevention, and health services).

RESULTS

The 140 included reviews examined 1,140 outcomes, 294 of which were unique. The most central outcome overall was all-cause mortality (nNBC = 23.9). The most central and most frequent outcomes differed overall and within subgroups. For example, "adverse events (specified)" was among the most central but not among the most frequent outcomes, overall.

CONCLUSION

Social network analysis methods are a novel application to identify central outcomes, which provides additional information potentially useful for developing core outcome sets.

Community Detection in Signed Networks: the Role of Negative ties in Different Scales

Extracting community structure of complex network systems has many applications from engineering to biology and social sciences. There exist many algorithms to discover community structure of networks. However, it has been significantly under-explored for networks with positive and negative links as compared to unsigned ones. Trying to fill this gap, we measured the quality of partitions by introducing a Map Equation for signed networks. It is based on the assumption that negative relations weaken positive flow from a node towards a community, and thus, external (internal) negative ties increase the probability of staying inside (escaping from) a community. We further extended the Constant Potts Model, providing a map spectrum for signed networks. Accordingly, a partition is selected through balancing between abridgment and expatiation of a signed network. Most importantly, multi-scale spectrum of signed networks revealed how informative are negative ties in different scales, and quantified the topological placement of negative ties between dense positive ones. Moreover, an inconsistency was found in the signed Modularity: as the number of negative ties increases, the density of positive ties is neglected more. These results shed lights on the community structure of signed networks.

Modular Brain Networks

The development of new technologies for mapping structural and functional brain connectivity has led to the creation of comprehensive network maps of neuronal circuits and systems. The architecture of these brain networks can be examined and analyzed with a large variety of graph theory tools. Methods for detecting modules, or network communities, are of particular interest because they uncover major building blocks or subnetworks that are particularly densely connected, often corresponding to specialized functional components. A large number of methods for community detection have become available and are now widely applied in network neuroscience. This article first surveys a number of these methods, with an emphasis on their advantages and shortcomings; then it summarizes major findings on the existence of modules in both structural and functional brain networks and briefly considers their potential functional roles in brain evolution, wiring minimization, and the emergence of functional specialization and complex dynamics.

Netgram: Visualizing Communities in Evolving Networks

Real-world complex networks are dynamic in nature and change over time. The change is usually observed in the interactions within the network over time. Complex networks exhibit community like structures. A key feature of the dynamics of complex networks is the evolution of communities over time. Several methods have been proposed to detect and track the evolution of these groups over time. However, there is no generic tool which visualizes all the aspects of group evolution in dynamic networks including birth, death, splitting, merging, expansion, shrinkage and continuation of groups. In this paper, we propose Netgram: a tool for visualizing evolution of communities in time-evolving graphs. Netgram maintains evolution of communities over 2 consecutive time-stamps in tables which are used to create a query database using the sql outer-join operation. It uses a line-based visualization technique which adheres to certain design principles and aesthetic guidelines. Netgram uses a greedy solution to order the initial community information provided by the evolutionary clustering technique such that we have fewer line cross-overs in the visualization. This makes it easier to track the progress of individual communities in time evolving graphs. Netgram is a generic toolkit which can be used with any evolutionary community detection algorithm as illustrated in our experiments. We use Netgram for visualization of topic evolution in the NIPS conference over a period of 11 years and observe the emergence and merging of several disciplines in the field of information processing systems.

Faster unfolding of communities: speeding up the Louvain algorithm

Many complex networks exhibit a modular structure of densely connected groups of nodes. Usually, such a modular structure is uncovered by the optimization of some quality function. Although flawed, modularity remains one of the most popular quality functions. The Louvain algorithm was originally developed for optimizing modularity, but has been applied to a variety of methods. As such, speeding up the Louvain algorithm enables the analysis of larger graphs in a shorter time for various methods. We here suggest to consider moving nodes to a random neighbor community, instead of the best neighbor community. Although incredibly simple, it reduces the theoretical runtime complexity from O(m) to O(nlog〈k〉) in networks with a clear community structure. In benchmark networks, it speeds up the algorithm roughly 2-3 times, while in some real networks it even reaches 10 times faster runtimes. This improvement is due to two factors: (1) a random neighbor is likely to be in a "good" community and (2) random neighbors are likely to be hubs, helping the convergence. Finally, the performance gain only slightly diminishes the quality, especially for modularity, thus providing a good quality-performance ratio. However, these gains are less pronounced, or even disappear, for some other measures such as significance or surprise.

Detecting communities using asymptotical surprise

Nodes in real-world networks are repeatedly observed to form dense clusters, often referred to as communities. Methods to detect these groups of nodes usually maximize an objective function, which implicitly contains the definition of a community. We here analyze a recently proposed measure called surprise, which assesses the quality of the partition of a network into communities. In its current form, the formulation of surprise is rather difficult to analyze. We here therefore develop an accurate asymptotic approximation. This allows for the development of an efficient algorithm for optimizing surprise. Incidentally, this leads to a straightforward extension of surprise to weighted graphs. Additionally, the approximation makes it possible to analyze surprise more closely and compare it to other methods, especially modularity. We show that surprise is (nearly) unaffected by the well-known resolution limit, a particular problem for modularity. However, surprise may tend to overestimate the number of communities, whereas they may be underestimated by modularity. In short, surprise works well in the limit of many small communities, whereas modularity works better in the limit of few large communities. In this sense, surprise is more discriminative than modularity and may find communities where modularity fails to discern any structure.

Hologenome theory supported by cooccurrence networks of species-specific bacterial communities in siphonous algae (Caulerpa)

The siphonous algae of the Caulerpa genus harbor internal microbial communities hypothesized to play important roles in development, defense and metabolic activities of the host. Here, we characterize the endophytic bacterial community of four Caulerpa taxa in the Mediterranean Sea, through 16S rRNA amplicon sequencing. Results reveal a striking alpha diversity of the bacterial communities, similar to levels found in sponges and coral holobionts. These comprise (1) a very small core community shared across all hosts (< 1% of the total community), (2) a variable portion (ca. 25%) shared by some Caulerpa taxa but not by all, which might represent environmentally acquired bacteria and (3) a large (>70%) species-specific fraction of the community, forming very specific clusters revealed by modularity in networks of cooccurrence, even in areas where distinct Caulerpa taxa occurred in sympatry. Indirect inferences based on sequence homology suggest that these communities may play an important role in the metabolism of their host, in particular on their ability to grow on anoxic sediment. These findings support the hologenome theory and the need for a holistic framework in ecological and evolutionary studies of these holobionts that frequently become invasive.

Limitations in the spectral method for graph partitioning: Detectability threshold and localization of eigenvectors

Investigating the performance of different methods is a fundamental problem in graph partitioning. In this paper, we estimate the so-called detectability threshold for the spectral method with both un-normalized and normalized Laplacians in sparse graphs. The detectability threshold is the critical point at which the result of the spectral method is completely uncorrelated to the planted partition. We also analyze whether the localization of eigenvectors affects the partitioning performance in the detectable region. We use the replica method, which is often used in the field of spin-glass theory, and focus on the case of bisection. We show that the gap between the estimated threshold for the spectral method and the threshold obtained from Bayesian inference is considerable in sparse graphs, even without eigenvector localization. This gap closes in a dense limit.

Generating attributed networks with communities

In many modern applications data is represented in the form of nodes and their relationships, forming an information network. When nodes are described with a set of attributes we have an attributed network. Nodes and their relationships tend to naturally form into communities or clusters, and discovering these communities is paramount to many applications. Evaluating algorithms or comparing algorithms for automatic discovery of communities requires networks with known structures. Synthetic generators of networks have been proposed for this task but most solely focus on connectivity and their properties and overlook attribute values and the network properties vis-à-vis these attributes. In this paper, we propose a new generator for attributed networks with community structure that dependably follows the properties of real world networks.

Edge Weight Method for Community Detection on Mixed Scale-Free Networks

In this paper, we proposed an edge weight method for performing a community detection on mixed scale-free networks.We use the phrase “mixed scale-free networks” for networks where some communities have node degree that follows a power law similar to scale-free networks, while some have node degree that follows normal distribution. In this type of network, community detection algorithms that are designed for scale-free networks will have reduced accuracy because some communities do not have scale-free properties. On the other hand, algorithms that are not designed for scale-free networks will also have reduced accuracy because some communities have scale-free properties. To solve this problem, our algorithm consists of two community detection steps; one is aimed at extracting communities whose node degree follows power law distribution (scale-free), while the other one is aimed at extracting communities whose node degree follows normal distribution (non scale-free). To evaluate our method, we use NMI — Normalized Mutual Information — to measure our results on both synthetic and real-world datasets comparing with both scale-free and non scale-free community detection methods. The results show that our method outperforms all other based line methods on mixed scale-free networks.

Mining the modular structure of protein interaction networks

BACKGROUND

Cluster-based descriptions of biological networks have received much attention in recent years fostered by accumulated evidence of the existence of meaningful correlations between topological network clusters and biological functional modules. Several well-performing clustering algorithms exist to infer topological network partitions. However, due to respective technical idiosyncrasies they might produce dissimilar modular decompositions of a given network. In this contribution, we aimed to analyze how alternative modular descriptions could condition the outcome of follow-up network biology analysis.

METHODOLOGY

We considered a human protein interaction network and two paradigmatic cluster recognition algorithms, namely: the Clauset-Newman-Moore and the infomap procedures. We analyzed to what extent both methodologies yielded different results in terms of granularity and biological congruency. In addition, taking into account Guimera's cartographic role characterization of network nodes, we explored how the adoption of a given clustering methodology impinged on the ability to highlight relevant network meso-scale connectivity patterns.

RESULTS

As a case study we considered a set of aging related proteins and showed that only the high-resolution modular description provided by infomap, could unveil statistically significant associations between them and inter/intra modular cartographic features. Besides reporting novel biological insights that could be gained from the discovered associations, our contribution warns against possible technical concerns that might affect the tools used to mine for interaction patterns in network biology studies. In particular our results suggested that sub-optimal partitions from the strict point of view of their modularity levels might still be worth being analyzed when meso-scale features were to be explored in connection with external source of biological knowledge.

A DIseAse MOdule Detection (DIAMOnD) algorithm derived from a systematic analysis of connectivity patterns of disease proteins in the human interactome

The observation that disease associated proteins often interact with each other has fueled the development of network-based approaches to elucidate the molecular mechanisms of human disease. Such approaches build on the assumption that protein interaction networks can be viewed as maps in which diseases can be identified with localized perturbation within a certain neighborhood. The identification of these neighborhoods, or disease modules, is therefore a prerequisite of a detailed investigation of a particular pathophenotype. While numerous heuristic methods exist that successfully pinpoint disease associated modules, the basic underlying connectivity patterns remain largely unexplored. In this work we aim to fill this gap by analyzing the network properties of a comprehensive corpus of 70 complex diseases. We find that disease associated proteins do not reside within locally dense communities and instead identify connectivity significance as the most predictive quantity. This quantity inspires the design of a novel Disease Module Detection (DIAMOnD) algorithm to identify the full disease module around a set of known disease proteins. We study the performance of the algorithm using well-controlled synthetic data and systematically validate the identified neighborhoods for a large corpus of diseases.

Diseases are rarely the result of an abnormality in a single gene, but involve a whole cascade of interactions between several cellular processes. To disentangle these complex interactions it is necessary to study genotype-phenotype relationships in the context of protein-protein interaction networks. Our analysis of 70 diseases shows that disease proteins are not randomly scattered within these networks, but agglomerate in specific regions, suggesting the existence of specific disease modules for each disease. The identification of these modules is the first step towards elucidating the biological mechanisms of a disease or for a targeted search of drug targets. We present a systematic analysis of the connectivity patterns of disease proteins and determine the most predictive topological property for their identification. This allows us to rationally design a reliable and efficient Disease Module Detection algorithm (DIAMOnD).

The painful tweet: text, sentiment, and community structure analyses of tweets pertaining to pain

Background

Despite the widespread popularity of social media, little is known about the extent or context of pain-related posts by users of those media.

Objective

The aim was to examine the type, context, and dissemination of pain-related tweets.

Methods

We used content analysis of pain-related tweets from 50 cities to unobtrusively explore the meanings and patterns of communications about pain. Content was examined by location and time of day, as well as within the context of online social networks.

Results

The most common terms published in conjunction with the term “pain” included feel (n=1504), don’t (n=702), and love (n=649). The proportion of tweets with positive sentiment ranged from 13% in Manila to 56% in Los Angeles, CA, with a median of 29% across cities. Temporally, the proportion of tweets with positive sentiment ranged from 24% at 1600 to 38% at 2400, with a median of 32%. The Twitter-based social networks pertaining to pain exhibited greater sparsity and lower connectedness than did those social networks pertaining to common terms such as apple, Manchester United, and Obama. The number of word clusters in proportion to node count was greater for emotion terms such as tired (0.45), happy (0.43), and sad (0.4) when compared with objective terms such as apple (0.26), Manchester United (0.14), and Obama (0.25).

Conclusions

Taken together, our results suggest that pain-related tweets carry special characteristics reflecting unique content and their communication among tweeters. Further work will explore how geopolitical events and seasonal changes affect tweeters’ perceptions of pain and how such perceptions may affect therapies for pain.

Identification of hybrid node and link communities in complex networks

Identifying communities in complex networks is an effective means for analyzing complex systems, with applications in diverse areas such as social science, engineering, biology and medicine. Finding communities of nodes and finding communities of links are two popular schemes for network analysis. These schemes, however, have inherent drawbacks and are inadequate to capture complex organizational structures in real networks. We introduce a new scheme and an effective approach for identifying complex mixture structures of node and link communities, called hybrid node-link communities. A central piece of our approach is a probabilistic model that accommodates node, link and hybrid node-link communities. Our extensive experiments on various real-world networks, including a large protein-protein interaction network and a large network of semantically associated words, illustrated that the scheme for hybrid communities is superior in revealing network characteristics. Moreover, the new approach outperformed the existing methods for finding node or link communities separately.

Flow networks: a characterization of geophysical fluid transport

We represent transport between different regions of a fluid domain by flow networks, constructed from the discrete representation of the Perron-Frobenius or transfer operator associated to the fluid advection dynamics. The procedure is useful to analyze fluid dynamics in geophysical contexts, as illustrated by the construction of a flow network associated to the surface circulation in the Mediterranean sea. We use network-theory tools to analyze the flow network and gain insights into transport processes. In particular, we quantitatively relate dispersion and mixing characteristics, classically quantified by Lyapunov exponents, to the degree of the network nodes. A family of network entropies is defined from the network adjacency matrix and related to the statistics of stretching in the fluid, in particular, to the Lyapunov exponent field. Finally, we use a network community detection algorithm, Infomap, to partition the Mediterranean network into coherent regions, i.e., areas internally well mixed, but with little fluid interchange between them.

Identification of gene co-expression clusters in liver tissues from multiple porcine populations with high and low backfat androstenone phenotype

Background

Boar taint is principally caused by accumulation of androstenone and skatole in adipose tissues. Studies have shown high heritability estimates for androstenone whereas skatole production is mainly dependent on nutritional factors. Androstenone is a lipophilic steroid mainly metabolized in liver. Majority of the studies on hepatic androstenone metabolism focus only on a single breed and very few studies account for population similarities/differences in gene expression patterns. In this work, we concentrated on population similarities in gene expression to identify the common genes involved in hepatic androstenone metabolism of multiple pig populations. Based on androstenone measurements, publicly available gene expression datasets from three porcine populations were compiled into either low or high androstenone dataset. Gene expression correlation coefficients from these datasets were converted to rank ratios and joint probabilities of these rank ratios were used to generate dataset specific co-expression clusters. Finally, these networks were clustered using a graph clustering technique.

Results

Cluster analysis identified a number of statistically significant co-expression clusters in the dataset. Further enrichment analysis of these clusters showed that one of the clusters from low androstenone dataset was highly enriched for xenobiotic, drug, cholesterol and lipid metabolism and cytochrome P450 associated metabolism of drugs and xenobiotics. Literature references revealed that a number of genes in this cluster were involved in phase I and phase II metabolism. Physical and functional similarity assessment showed that the members of this cluster were dispersed across multiple clusters in high androstenone dataset, possibly indicating a weak co-expression of these genes in high androstenone dataset.

Conclusions

Based on these results we hypothesize that majority of the genes in this cluster forms a signature co-expression cluster in low androstenone dataset in our experiment and that majority of the members of this cluster might be responsible for hepatic androstenone metabolism across all the three populations used in our study. We propose these results as a background work towards understanding breed similarities in hepatic androstenone metabolism. Additional large scale experiments using data from multiple porcine breeds are necessary to validate these findings.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-014-0158-8) contains supplementary material, which is available to authorized users.

Bridging topological and functional information in protein interaction networks by short loops profiling

Protein-protein interaction networks (PPINs) have been employed to identify potential novel interconnections between proteins as well as crucial cellular functions. In this study we identify fundamental principles of PPIN topologies by analysing network motifs of short loops, which are small cyclic interactions of between 3 and 6 proteins. We compared 30 PPINs with corresponding randomised null models and examined the occurrence of common biological functions in loops extracted from a cross-validated high-confidence dataset of 622 human protein complexes. We demonstrate that loops are an intrinsic feature of PPINs and that specific cell functions are predominantly performed by loops of different lengths. Topologically, we find that loops are strongly related to the accuracy of PPINs and define a core of interactions with high resilience. The identification of this core and the analysis of loop composition are promising tools to assess PPIN quality and to uncover possible biases from experimental detection methods. More than 96% of loops share at least one biological function, with enrichment of cellular functions related to mRNA metabolic processing and the cell cycle. Our analyses suggest that these motifs can be used in the design of targeted experiments for functional phenotype detection.

Exploring the Far Side of Mobile Health: Information Security and Privacy of Mobile Health Apps on iOS and Android

Background

Mobile health (mHealth) apps aim at providing seamless access to tailored health information technology and have the potential to alleviate global health burdens. Yet, they bear risks to information security and privacy because users need to reveal private, sensitive medical information to redeem certain benefits. Due to the plethora and diversity of available mHealth apps, implications for information security and privacy are unclear and complex.

Objective

The objective of this study was to establish an overview of mHealth apps offered on iOS and Android with a special focus on potential damage to users through information security and privacy infringements.

Methods

We assessed apps available in English and offered in the categories “Medical” and “Health & Fitness” in the iOS and Android App Stores. Based on the information retrievable from the app stores, we established an overview of available mHealth apps, tagged apps to make offered information machine-readable, and clustered the discovered apps to identify and group similar apps. Subsequently, information security and privacy implications were assessed based on health specificity of information available to apps, potential damage through information leaks, potential damage through information manipulation, potential damage through information loss, and potential value of information to third parties.

Results

We discovered 24,405 health-related apps (iOS; 21,953; Android; 2452). Absence or scarceness of ratings for 81.36% (17,860/21,953) of iOS and 76.14% (1867/2452) of Android apps indicates that less than a quarter of mHealth apps are in more or less widespread use. Clustering resulted in 245 distinct clusters, which were consolidated into 12 app archetypes grouping clusters with similar assessments of potential damage through information security and privacy infringements. There were 6426 apps that were excluded during clustering. The majority of apps (95.63%, 17,193/17,979; of apps) pose at least some potential damage through information security and privacy infringements. There were 11.67% (2098/17,979) of apps that scored the highest assessments of potential damages.

Conclusions

Various kinds of mHealth apps collect and offer critical, sensitive, private medical information, calling for a special focus on information security and privacy of mHealth apps. In order to foster user acceptance and trust, appropriate security measures and processes need to be devised and employed so that users can benefit from seamlessly accessible, tailored mHealth apps without exposing themselves to the serious repercussions of information security and privacy infringements.

Think locally, act locally: detection of small, medium-sized, and large communities in large networks

It is common in the study of networks to investigate intermediate-sized (or "meso-scale") features to try to gain an understanding of network structure and function. For example, numerous algorithms have been developed to try to identify "communities," which are typically construed as sets of nodes with denser connections internally than with the remainder of a network. In this paper, we adopt a complementary perspective that communities are associated with bottlenecks of locally biased dynamical processes that begin at seed sets of nodes, and we employ several different community-identification procedures (using diffusion-based and geodesic-based dynamics) to investigate community quality as a function of community size. Using several empirical and synthetic networks, we identify several distinct scenarios for "size-resolved community structure" that can arise in real (and realistic) networks: (1) the best small groups of nodes can be better than the best large groups (for a given formulation of the idea of a good community); (2) the best small groups can have a quality that is comparable to the best medium-sized and large groups; and (3) the best small groups of nodes can be worse than the best large groups. As we discuss in detail, which of these three cases holds for a given network can make an enormous difference when investigating and making claims about network community structure, and it is important to take this into account to obtain reliable downstream conclusions. Depending on which scenario holds, one may or may not be able to successfully identify "good" communities in a given network (and good communities might not even exist for a given community quality measure), the manner in which different small communities fit together to form meso-scale network structures can be very different, and processes such as viral propagation and information diffusion can exhibit very different dynamics. In addition, our results suggest that, for many large realistic networks, the output of locally biased methods that focus on communities that are centered around a given seed node (or set of seed nodes) might have better conceptual grounding and greater practical utility than the output of global community-detection methods. They also illustrate structural properties that are important to consider in the development of better benchmark networks to test methods for community detection.

Estimating the resolution limit of the map equation in community detection

A community detection algorithm is considered to have a resolution limit if the scale of the smallest modules that can be resolved depends on the size of the analyzed subnetwork. The resolution limit is known to prevent some community detection algorithms from accurately identifying the modular structure of a network. In fact, any global objective function for measuring the quality of a two-level assignment of nodes into modules must have some sort of resolution limit or an external resolution parameter. However, it is yet unknown how the resolution limit affects the so-called map equation, which is known to be an efficient objective function for community detection. We derive an analytical estimate and conclude that the resolution limit of the map equation is set by the total number of links between modules instead of the total number of links in the full network as for modularity. This mechanism makes the resolution limit much less restrictive for the map equation than for modularity; in practice, it is orders of magnitudes smaller. Furthermore, we argue that the effect of the resolution limit often results from shoehorning multilevel modular structures into two-level descriptions. As we show, the hierarchical map equation effectively eliminates the resolution limit for networks with nested multilevel modular structures.

CellNet: network biology applied to stem cell engineering

Somatic cell reprogramming, directed differentiation of pluripotent stem cells, and direct conversions between differentiated cell lineages represent powerful approaches to engineer cells for research and regenerative medicine. We have developed CellNet, a network biology platform that more accurately assesses the fidelity of cellular engineering than existing methodologies and generates hypotheses for improving cell derivations. Analyzing expression data from 56 published reports, we found that cells derived via directed differentiation more closely resemble their in vivo counterparts than products of direct conversion, as reflected by the establishment of target cell-type gene regulatory networks (GRNs). Furthermore, we discovered that directly converted cells fail to adequately silence expression programs of the starting population and that the establishment of unintended GRNs is common to virtually every cellular engineering paradigm. CellNet provides a platform for quantifying how closely engineered cell populations resemble their target cell type and a rational strategy to guide enhanced cellular engineering.

A multiobjective evolutionary algorithm based on similarity for community detection from signed social networks

Various types of social relationships, such as friends and foes, can be represented as signed social networks (SNs) that contain both positive and negative links. Although many community detection (CD) algorithms have been proposed, most of them were designed primarily for networks containing only positive links. Thus, it is important to design CD algorithms which can handle large-scale SNs. To this purpose, we first extend the original similarity to the signed similarity based on the social balance theory. Then, based on the signed similarity and the natural contradiction between positive and negative links, two objective functions are designed to model the problem of detecting communities in SNs as a multiobjective problem. Afterward, we propose a multiobjective evolutionary algorithm, called MEAs-SN. In MEAs-SN, to overcome the defects of direct and indirect representations for communities, a direct and indirect combined representation is designed. Attributing to this representation, MEAs-SN can switch between different representations during the evolutionary process. As a result, MEAs-SN can benefit from both representations. Moreover, owing to this representation, MEAs-SN can also detect overlapping communities directly. In the experiments, both benchmark problems and large-scale synthetic networks generated by various parameter settings are used to validate the performance of MEAs-SN. The experimental results show the effectiveness and efficacy of MEAs-SN on networks with 1000, 5000, and 10,000 nodes and also in various noisy situations. A thorough comparison is also made between MEAs-SN and three existing algorithms, and the results show that MEAs-SN outperforms other algorithms.

Time development in the early history of social networks: link stabilization, group dynamics, and segregation

Studies of the time development of empirical networks usually investigate late stages where lasting connections have already stabilized. Empirical data on early network history are rare but needed for a better understanding of how social network topology develops in real life. Studying students who are beginning their studies at a university with no or few prior connections to each other offers a unique opportunity to investigate the formation and early development of link patterns and community structure in social networks. During a nine week introductory physics course, first year physics students were asked to identify those with whom they communicated about problem solving in physics during the preceding week. We use these students' self reports to produce time dependent student interaction networks. We investigate these networks to elucidate possible effects of different student attributes in early network formation. Changes in the weekly number of links show that while roughly half of all links change from week to week, students also reestablish a growing number of links as they progress through their first weeks of study. Using the Infomap community detection algorithm, we show that the networks exhibit community structure, and we use non-network student attributes, such as gender and end-of-course grade to characterize communities during their formation. Specifically, we develop a segregation measure and show that students structure themselves according to gender and pre-organized sections (in which students engage in problem solving and laboratory work), but not according to end-of-coure grade. Alluvial diagrams of consecutive weeks' communities show that while student movement between groups are erratic in the beginnning of their studies, they stabilize somewhat towards the end of the course. Taken together, the analyses imply that student interaction networks stabilize quickly and that students establish collaborations based on who is immediately available to them and on observable personal characteristics.

Network structure and community evolution on Twitter: human behavior change in response to the 2011 Japanese earthquake and tsunami

To investigate the dynamics of social networks and the formation and evolution of online communities in response to extreme events, we collected three datasets from Twitter shortly before and after the 2011 earthquake and tsunami in Japan. We find that while almost all users increased their online activity after the earthquake, Japanese speakers, who are assumed to be more directly affected by the event, expanded the network of people they interact with to a much higher degree than English speakers or the global average. By investigating the evolution of communities, we find that the behavior of joining or quitting a community is far from random: users tend to stay in their current status and are less likely to join new communities from solitary or shift to other communities from their current community. While non-Japanese speakers did not change their conversation topics significantly after the earthquake, nearly all Japanese users changed their conversations to earthquake-related content. This study builds a systematic framework for investigating human behaviors under extreme events with online social network data and our findings on the dynamics of networks and communities may provide useful insight for understanding how patterns of social interaction are influenced by extreme events.