Assessing diversity in multiplex networks

Prediction of inhibitor development in previously untreated and minimally treated children with severe and moderately severe hemophilia A using a machine-learning network

BACKGROUND

Prediction of inhibitor development in patients with hemophilia A (HA) remains a challenge.

OBJECTIVES

To construct a predictive model for inhibitor development in HA using a network of clinical variables and biomarkers based on the individual similarity network.

METHODS

Previously untreated and minimally treated children with severe/moderately severe HA, participants of the HEMFIL Cohort Study, were followed up until reaching 75 exposure days (EDs) without inhibitor (INH-) or upon inhibitor development (INH+). Clinical data and biological samples were collected before the start of factor (F)VIII replacement (T0). A predictive model (HemfilNET) was built to compare the networks and potential global topological differences between INH- and INH+ at T0, considering the network robustness. For validation, the "leave-one-out" cross-validation technique was employed. Accuracy, precision, recall, and F1-score were used as evaluation metrics for the machine-learning model.

RESULTS

We included 95 children with HA (CHA), of whom 31 (33%) developed inhibitors. The algorithm, featuring 37 variables, identified distinct patterns of networks at T0 for INH+ and INH-. The accuracy of the model was 74.2% for CHA INH+ and 98.4% for INH-. By focusing the analysis on CHA with high-risk F8 mutations for inhibitor development, the accuracy in identifying CHA INH+ increased to 82.1%.

CONCLUSION

Our machine-learning algorithm demonstrated an overall accuracy of 90.5% for predicting inhibitor development in CHA, which further improved when restricting the analysis to CHA with a high-risk F8 genotype. However, our model requires validation in other cohorts. Yet, missing data for some variables hindered more precise predictions.

The time-evolving epileptic brain network: concepts, definitions, accomplishments, perspectives

Epilepsy is now considered a network disease that affects the brain across multiple levels of spatial and temporal scales. The paradigm shift from an epileptic focus-a discrete cortical area from which seizures originate-to a widespread epileptic network-spanning lobes and hemispheres-considerably advanced our understanding of epilepsy and continues to influence both research and clinical treatment of this multi-faceted high-impact neurological disorder. The epileptic network, however, is not static but evolves in time which requires novel approaches for an in-depth characterization. In this review, we discuss conceptual basics of network theory and critically examine state-of-the-art recording techniques and analysis tools used to assess and characterize a time-evolving human epileptic brain network. We give an account on current shortcomings and highlight potential developments towards an improved clinical management of epilepsy.

Assessing cohesion and diversity in the collaboration network of the SALURBAL project

The SALURBAL (Urban Health in Latin America) Project is an interdisciplinary multinational network aimed at generating and disseminating actionable evidence on the drivers of health in cities of Latin America. We conducted a temporal multilayer network analysis where we measured cohesion over time using network structural properties and assessed diversity within and between different project activities according to participant attributes. Between 2017 and 2020 the SALURBAL network comprised 395 participants across 26 countries, 23 disciplines, and 181 institutions. While the cohesion of the SALURBAL network fluctuated over time, overall, an increase was observed from the first to the last time point of our analysis (clustering coefficient increased [0.83-0.91] and shortest path decreased [1.70-1.68]). SALURBAL also exhibited balanced overall diversity within project activities (0.5-0.6) by designing activities for different purposes such as capacity building, team-building, research, and dissemination. The network's growth was facilitated by the creation of new diverse collaborations across a range of activities over time, while maintaining the diversity of existing collaborations (0.69-0.75 between activity diversity depending on the attribute). The SALURBAL experience can serve as an example for multinational research projects aiming to build cohesive networks while leveraging heterogeneity in countries, disciplines, career stage, and across sectors.

Models of similarity in complex networks

The analysis of networks describing many social, economic, technological, biological and other systems has attracted a lot of attention last decades. Since most of these complex systems evolve over time, there is a need to investigate the changes, which appear in the system, in order to assess the sustainability of the network and to identify stable periods. In the literature, there have been developed a large number of models that measure the similarity among the networks. There also exist some surveys, which consider a limited number of similarity measures and then perform their correlation analysis, discuss their properties or assess their performances on synthetic benchmarks or real networks. The aim of the article is to extend these studies. The article considers 39 graph distance measures and compares them on simple graphs, random graph models and real networks. The author also evaluates the performance of the models in order to identify which of them can be applied to large networks. The results of the study reveal some important aspects of existing similarity models and provide a better understanding of their advantages and disadvantages. The major finding of the work is that many graph similarity measures of different nature are well correlated and that some comprehensive methods are well agreed with simple models. Such information can be used for the choice of appropriate similarity measure as well as for further development of new models for similarity assessment in network structures.

Diffusion capacity of single and interconnected networks

Understanding diffusive processes in networks is a significant challenge in complexity science. Networks possess a diffusive potential that depends on their topological configuration, but diffusion also relies on the process and initial conditions. This article presents Diffusion Capacity, a concept that measures a node's potential to diffuse information based on a distance distribution that considers both geodesic and weighted shortest paths and dynamical features of the diffusion process. Diffusion Capacity thoroughly describes the role of individual nodes during a diffusion process and can identify structural modifications that may improve diffusion mechanisms. The article defines Diffusion Capacity for interconnected networks and introduces Relative Gain, which compares the performance of a node in a single structure versus an interconnected one. The method applies to a global climate network constructed from surface air temperature data, revealing a significant change in diffusion capacity around the year 2000, suggesting a loss of the planet's diffusion capacity that could contribute to the emergence of more frequent climatic events.

Netpro2vec: A Graph Embedding Framework for Biomedical Applications

The ever-increasing importance of structured data in different applications, especially in the biomedical field, has driven the need for reducing its complexity through projections into a more manageable space. The latest methods for learning features on graphs focus mainly on the neighborhood of nodes and edges. Methods capable of providing a representation that looks beyond the single node neighborhood are kernel graphs. However, they produce handcrafted features unaccustomed with a generalized model. To reduce this gap, in this work we propose a neural embedding framework, based on probability distribution representations of graphs, named Netpro2vec. The goal is to look at basic node descriptions other than the degree, such as those induced by the Transition Matrix and Node Distance Distribution. Netpro2vec provides embeddings completely independent from the task and nature of the data. The framework is evaluated on synthetic and various real biomedical network datasets through a comprehensive experimental classification phase and is compared to well-known competitors.

A Path-Based Distribution Measure for Network Comparison

As network data increases, it is more common than ever for researchers to analyze a set of networks rather than a single network and measure the difference between networks by developing a number of network comparison methods. Network comparison is able to quantify dissimilarity between networks by comparing the structural topological difference of networks. Here, we propose a kind of measures for network comparison based on the shortest path distribution combined with node centrality, capturing the global topological difference with local features. Based on the characterized path distributions, we define and compare network distance between networks to measure how dissimilar the two networks are, and the network entropy to characterize a typical network system. We find that the network distance is able to discriminate networks generated by different models. Combining more information on end nodes along a path can further amplify the dissimilarity of networks. The network entropy is able to detect tipping points in the evolution of synthetic networks. Extensive numerical simulations reveal the effectivity of the proposed measure in network reduction of multilayer networks, and identification of typical system states in temporal networks as well.

Clustering analysis of tumor metabolic networks

BACKGROUND

Biological networks are representative of the diverse molecular interactions that occur within cells. Some of the commonly studied biological networks are modeled through protein-protein interactions, gene regulatory, and metabolic pathways. Among these, metabolic networks are probably the most studied, as they directly influence all physiological processes. Exploration of biochemical pathways using multigraph representation is important in understanding complex regulatory mechanisms. Feature extraction and clustering of these networks enable grouping of samples obtained from different biological specimens. Clustering techniques separate networks depending on their mutual similarity.

RESULTS

We present a clustering analysis on tissue-specific metabolic networks for single samples from three primary tumor sites: breast, lung, and kidney cancer. The metabolic networks were obtained by integrating genome scale metabolic models with gene expression data. We performed network simplification to reduce the computational time needed for the computation of network distances. We empirically proved that networks clustering can characterize groups of patients in multiple conditions.

CONCLUSIONS

We provide a computational methodology to explore and characterize the metabolic landscape of tumors, thus providing a general methodology to integrate analytic metabolic models with gene expression data. This method represents a first attempt in clustering large scale metabolic networks. Moreover, this approach gives the possibility to get valuable information on what are the effects of different conditions on the overall metabolism.

The Multiplex Efficiency Index: unveiling the Brazilian air transportation multiplex network-BATMN

Modern society is increasingly massively connected, reflecting an omnipresent tendency to organize social, economic, and technological structures in complex networks. Recently, with the advent of the so-called multiplex networks, new concepts and tools were necessary to better understand the characteristics of this type of system, as well as to analyze and quantify its performance and efficiency. The concept of diversity in multiplex networks is a striking example of this intrinsically interdisciplinary effort to better understand the nature of complex networks. In this work, we introduce the Multiplex Efficiency Index, which allows quantifying the temporal evolution of connectivity diversity, particularly when the number of layers of the multiplex network varies over time. Using data related to air passenger transportation in Brazil we investigate, through the new index, how the Brazilian air transportation network has being changing over the years due to the privatization processes of airports and mergers of airlines in Brazil. Besides that, we show how the Multiplex Efficiency Index is able to quantify fluctuations in network efficiency in a non-biased way, limiting its values between 0 and 1, taking into account the number of layers in the multiplex structure. We believe that the proposed index is of great value for the evaluation of the performance of any multiplex network, and to analyze, in a quantitative way, its temporal evolution independently of the variation in the number of layers.

Analysis of the Level of Service of Unloading Zones Using Diversity Measures in a Multiplex Network

Unloading zones are a fundamental part of the infrastructure of urban freight transport. The location and accessibility of unloading zones to commercial establishments reduce the operating time and, consequently, the transportation costs. In general, unloading zones are located on-street and allocated by local authorities. In this context, this paper aims to evaluate the level of service of unloading zones. The research approach uses the diversity measures in a multiplex network to identify the level of service and cargo accessibility of unloading zones. An analysis is developed for the central area of Belo Horizonte (Brazil). The results indicate that unloading zones located up to 25 m from the establishments have a high accessibility and low level of service. In contrast, unloading zones located up to 100 m from the establishments have a low accessibility and high level of service. These results allow us to conclude that the planning process of the location of unloading zones in Belo Horizonte is flawed. In addition, the maximum distance from unloading zones to establishments must be 75 m, so that there is a balance between the accessibility and level of service.

Characterizing network topology using first-passage analysis

Understanding the topological characteristics of complex networks and how they affect navigability is one of the most important goals in science today, as it plays a central role in various economic, biological, ecological, and social systems. Here we apply first-passage analysis tools to investigate the properties and characteristics of random walkers in networks with different topology. Starting with the simplest two-dimensional square lattice, we modify its topology incrementally by randomly reconnecting links between sites. We characterize these networks by first-passage time from a significant number of random walkers without interaction, varying the departure and arrival locations. We also apply the concept of first-passage simultaneity, which measures the likelihood of two walkers reaching their destination together. These measures, together with the site occupancy statistics during the processes, allowed us to differentiate the studied networks, especially the random networks from the scale-free networks, by their navigability. We also show that small-world features can also be highlighted with the proposed technique.

Interdependent Networks: A Data Science Perspective

Traditionally, networks have been studied in an independent fashion. With the emergence of novel smart city technologies, coupling among networks has been strengthened. To capture the ever-increasing coupling, we explain the notion of interdependent networks, i.e., multi-layered networks with shared decision-making entities, and shared sensing infrastructures with interdisciplinary applications. The main challenge is how to develop data analytics solutions that are capable of enabling interdependent decision making. One of the emerging solutions is agent-based distributed decision making among heterogeneous agents and entities when their decisions are affected by multiple networks. We first provide a big picture of real-world interdependent networks in the context of smart city infrastructures. We then provide an outline of potential challenges and solutions from a data science perspective. We discuss potential hindrances to ensure reliable communication among intelligent agents from different networks. We explore future research directions at the intersection of network science and data science.

This article provides a holistic overview of interdependent cyber-physical-societal networks. We envision the subsequent research directions that require contribution of the data science community as well as interdisciplinary collaboration with network scientists, social scientists, computer scientists, and engineers to tackle the emerging problems raised by the notion of interdependent networks: (1) developing novel algorithms for data analytics and enabling interdependent decision making, (2) proposing holistic models that are capable of capturing the interdependence among human-centered multi-layer critical infrastructures, and (3) developing efficient solutions that are capable of finding globally optimum solutions using information from each network as well as modeling the interdependent information exchange. In addition to these directions, we outline policy and access-control issues, including conflict of interest among stakeholders and operators of each network. Successful implementation and development of an interdependent data analytics framework and its required algorithms will improve the quality of life of citizens by enabling globally optimum decision making, increasing efficiency, preserving privacy of intelligent agents, and reducing operational cost of interdependent networks. Further reading: Sustainable Interdependent Networks book series (interdependentnetworks.com) and Optimization, Learning, and Control for Interdependent Complex Networks (edited by M.H. Amini).