scholarly journals GLIDE: combining local methods and diffusion state embeddings to predict missing interactions in biological networks

2020 ◽  
Vol 36 (Supplement_1) ◽  
pp. i464-i473
Author(s):  
Kapil Devkota ◽  
James M Murphy ◽  
Lenore J Cowen
Keyword(s):  
Network Structure ◽  
Biological Networks ◽  
Link Prediction ◽  
Prediction Method ◽  
Global Network ◽  
Local Network ◽  
Supplementary Information ◽  
Network Data ◽  
Ppi Network ◽  
Diffusion State

Abstract Motivation One of the core problems in the analysis of biological networks is the link prediction problem. In particular, existing interactions networks are noisy and incomplete snapshots of the true network, with many true links missing because those interactions have not yet been experimentally observed. Methods to predict missing links have been more extensively studied for social than for biological networks; it was recently argued that there is some special structure in protein–protein interaction (PPI) network data that might mean that alternate methods may outperform the best methods for social networks. Based on a generalization of the diffusion state distance, we design a new embedding-based link prediction method called global and local integrated diffusion embedding (GLIDE). GLIDE is designed to effectively capture global network structure, combined with alternative network type-specific customized measures that capture local network structure. We test GLIDE on a collection of three recently curated human biological networks derived from the 2016 DREAM disease module identification challenge as well as a classical version of the yeast PPI network in rigorous cross validation experiments. Results We indeed find that different local network structure is dominant in different types of biological networks. We find that the simple local network measures are dominant in the highly connected network core between hub genes, but that GLIDE’s global embedding measure adds value in the rest of the network. For example, we make GLIDE-based link predictions from genes known to be involved in Crohn’s disease, to genes that are not known to have an association, and make some new predictions, finding support in other network data and the literature. Availability and implementation GLIDE can be downloaded at https://bitbucket.org/kap_devkota/glide. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Research on Distributed Data Sharing System based on Internet of Things and Blockchain

2021 ◽  
Vol 9 (3) ◽  
pp. 239-254
Author(s):  
Enchang Sun ◽  
Kang Meng ◽  
Ruizhe Yang ◽  
Yanhua Zhang ◽  
Meng Li
Keyword(s):  
Internet Of Things ◽  
Data Sharing ◽  
Data Storage ◽  
Network Architecture ◽  
Data Privacy ◽  
Distributed Storage ◽  
Global Network ◽  
Local Network ◽  
Network Data ◽  
Distributed Data

Abstract Aiming at the problems of the traditional centralized data sharing platform, such as poor data privacy protection ability, insufficient scalability of the system and poor interaction ability, this paper proposes a distributed data sharing system architecture based on the Internet of Things and blockchain technology. In this system, the distributed consensus mechanism of blockchain and the distributed storage technology are employed to manage the access and storage of Internet of Things data in a secure manner. Up to the physical topology of the network, a hierarchical blockchain network architecture is proposed for local network data storage and global network data sharing, which reduces networking complexity and improves the scalability of the system. In addition, smart contract and distributed machine learning are adopted to design automatic processing functions for different types of data (public or private) and supervise the data sharing process, improving both the security and interactive ability of the system.

Network statistics and measurement error

2018 ◽  
Author(s):  
Mark Newman
Keyword(s):  
Measurement Error ◽  
Em Algorithm ◽  
Error Correction ◽  
Network Structure ◽  
Expectation Maximization ◽  
Link Prediction ◽  
Network Data ◽  
Types Of Error

This chapter introduces the mathematics of network statistics, the quantification of errors in network data, and the estimation of network structure in the presence of error. The discussion starts with a summary of the types of error that can occur in network data and the empirical sources of those errors. The remainder of the chapter is given over to a discussion of the theory of network statistics, beginning with a review of the theory for ordinary real-valued (non-network) data, then developing the expectation-maximization (EM) algorithm for estimating network structure and error levels in the presence of error, with example applications. The chapter ends with a discussion of error correction methods such as link prediction and node disambiguation.

scholarly journals Bridging global and local topology in whole-brain networks using the network statistic jackknife

2020 ◽  
Vol 4 (1) ◽  
pp. 70-88 ◽  
Author(s):  
Teague R. Henry ◽  
Kelly A. Duffy ◽  
Marc D. Rudolph ◽  
Mary Beth Nebel ◽  
Stewart H. Mostofsky ◽  
...  
Keyword(s):  
Network Analysis ◽  
Network Structure ◽  
R Package ◽  
Brain Network ◽  
Global Network ◽  
Local Network ◽  
Network Organization ◽  
Whole Brain ◽  
Global Efficiency ◽  
Global Topology

Whole-brain network analysis is commonly used to investigate the topology of the brain using a variety of neuroimaging modalities. This approach is notable for its applicability to a large number of domains, such as understanding how brain network organization relates to cognition and behavior and examining disrupted brain network organization in disease. A benefit to this approach is the ability to summarize overall brain network organization with a single metric (e.g., global efficiency). However, important local differences in network structure might exist without any corresponding observable differences in global topology, making a whole-brain analysis strategy unlikely to detect relevant local findings. Conversely, using local network metrics can identify local differences, but are not directly informative of differences in global topology. Here, we propose the network statistic (NS) jackknife framework, a simulated lesioning method that combines the utility of global network analysis strategies with the ability to detect relevant local differences in network structure. We evaluate the NS jackknife framework with a simulation study and an empirical example comparing global efficiency in children with attention-deficit/hyperactivity disorder (ADHD) and typically developing (TD) children. The NS jackknife framework has been implemented in a public, open-source R package, netjack, available at https://cran.r-project.org/package=netjack .

Longitudinal symptom network structure in first-episode psychosis: a possible marker for remission

2021 ◽  
pp. 1-9
Author(s):  
Yan Hong Piao ◽  
Je-Yeon Yun ◽  
Thong Ba Nguyen ◽  
Woo-Sung Kim ◽  
Jing Sui ◽  
...  
Keyword(s):  
Network Structure ◽  
Graphical Model ◽  
First Episode Psychosis ◽  
Global Network ◽  
Local Network ◽  
First Episode ◽  
Syndrome Scale ◽  
Episode Psychosis ◽  
Network Metrics ◽  
Over Time

Abstract Background Network approach has been applied to a wide variety of psychiatric disorders. The aim of the present study was to identify network structures of remitters and non-remitters in patients with first-episode psychosis (FEP) at baseline and the 6-month follow-up. Methods Participants (n = 252) from the Korean Early Psychosis Study (KEPS) were enrolled. They were classified as remitters or non-remitters using Andreasen's criteria. We estimated network structure with 10 symptoms (three symptoms from the Positive and Negative Syndrome Scale, one depressive symptom, and six symptoms related to schema and rumination) as nodes using a Gaussian graphical model. Global and local network metrics were compared within and between the networks over time. Results Global network metrics did not differ between the remitters and non-remitters at baseline or 6 months. However, the network structure and nodal strengths associated with positive-self and positive-others scores changed significantly in the remitters over time. Unique central symptoms for remitters and non-remitters were cognitive brooding and negative-self, respectively. The correlation stability coefficients for nodal strength were within the acceptable range. Conclusion Our findings indicate that network structure and some nodal strengths were more flexible in remitters. Negative-self could be an important target for therapeutic intervention.

scholarly journals A Link Prediction Method Based on Neural Networks

2021 ◽  
Vol 11 (11) ◽  
pp. 5186
Author(s):  
Keping Li ◽  
Shuang Gu ◽  
Dongyang Yan
Keyword(s):  
Neural Network ◽  
Link Prediction ◽  
Prediction Models ◽  
Prediction Method ◽  
Network Evolution ◽  
Global Network ◽  
Network Efficiency ◽  
Structure Reliability ◽  
The Neural Network ◽  
Network Method

Link prediction to optimize network performance is of great significance in network evolution. Because of the complexity of network systems and the uncertainty of network evolution, it faces many challenges. This paper proposes a new link prediction method based on neural networks trained on scale-free networks as input data, and optimized networks trained by link prediction models as output data. In order to solve the influence of the generalization of the neural network on the experiments, a greedy link pruning strategy is applied. We consider network efficiency and the proposed global network structure reliability as objectives to comprehensively evaluate link prediction performance and the advantages of the neural network method. The experimental results demonstrate that the neural network method generates the optimized networks with better network efficiency and global network structure reliability than the traditional link prediction models.

scholarly journals Probabilistic graphlets capture biological function in probabilistic molecular networks

2020 ◽  
Vol 36 (Supplement_2) ◽  
pp. i804-i812
Author(s):  
Sergio Doria-Belenguer ◽  
Markus K. Youssef ◽  
René Böttcher ◽  
Noël Malod-Dognin ◽  
Nataša Pržulj
Keyword(s):  
Network Structure ◽  
Real World ◽  
Random Network ◽  
Probability Distributions ◽  
Network Models ◽  
Biological Information ◽  
Molecular Networks ◽  
Local Network ◽  
Supplementary Information ◽  
Probabilistic Networks

Abstract Motivation Molecular interactions have been successfully modeled and analyzed as networks, where nodes represent molecules and edges represent the interactions between them. These networks revealed that molecules with similar local network structure also have similar biological functions. The most sensitive measures of network structure are based on graphlets. However, graphlet-based methods thus far are only applicable to unweighted networks, whereas real-world molecular networks may have weighted edges that can represent the probability of an interaction occurring in the cell. This information is commonly discarded when applying thresholds to generate unweighted networks, which may lead to information loss. Results We introduce probabilistic graphlets as a tool for analyzing the local wiring patterns of probabilistic networks. To assess their performance compared to unweighted graphlets, we generate synthetic networks based on different well-known random network models and edge probability distributions and demonstrate that probabilistic graphlets outperform their unweighted counterparts in distinguishing network structures. Then we model different real-world molecular interaction networks as weighted graphs with probabilities as weights on edges and we analyze them with our new weighted graphlets-based methods. We show that due to their probabilistic nature, probabilistic graphlet-based methods more robustly capture biological information in these data, while simultaneously showing a higher sensitivity to identify condition-specific functions compared to their unweighted graphlet-based method counterparts. Availabilityand implementation Our implementation of probabilistic graphlets is available at https://github.com/Serdobe/Probabilistic_Graphlets. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Mechanisms generating asymmetric core-cohesive blockmodels

2019 ◽  
Vol 16 (1) ◽  
Author(s):  
Marjan Cugmas ◽  
Aleš Žiberna ◽  
Anuška Ferligoj
Keyword(s):  
Preschool Children ◽  
Network Structure ◽  
Research Question ◽  
Global Network ◽  
Local Network ◽  
Network Structures ◽  
Core Group ◽  
Main Research ◽  
Group Of Units ◽  
The Relationship

The paper addresses the relationship between different local network mechanisms and different global network structures, described by blockmodels. The research question is narrowed to the context of preschool children networks. Based on the studies regarding friendship, liking and interactional networks among preschool children, the popularity, transitivity, mutuality and assortativity mechanisms are assumed to be important for the evolution of such networks. It is assumed that the global network structure is defined by an asymmetric core-cohesive blockmodel consisting of one core group of units and two or more cohesive groups of units. Therefore, the main research question is whether the emergence of an asymmetric core-cohesive blockmodel can be a result of the influence of the listed mechanisms. Different initial global network structures are considered. Monte Carlo simulations were used. The relative fit measure is proposed and used to compare different blockmodel types on generated networks. The results show that the listed mechanisms indeed lead to the assumed global network structure.

scholarly journals Global structures and local network mechanisms of knowledge-flow networks

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0246660
Author(s):  
Marjan Cugmas ◽  
Anuška Ferligoj ◽  
Miha Škerlavaj ◽  
Aleš Žiberna
Keyword(s):  
Network Structure ◽  
Work Performance ◽  
Global Network ◽  
Local Network ◽  
Knowledge Flow ◽  
Flow Networks ◽  
Agent Based ◽  
Network Properties ◽  
Underlying Mechanisms ◽  
The Relationship

Understanding the patterns and underlying mechanisms that come into play when employees exchange their knowledge is crucial for their work performance and professional development. Although much is known about the relationship between certain global network properties of knowledge-flow networks and work performance, less is known about the emergence of specific global network structures of knowledge flow. The paper therefore aims to identify a global network structure in blockmodel terms within an empirical knowledge-flow network and discuss whether the selected local network mechanisms are able to drive the network towards the chosen global network structure. Existing studies of knowledge-flow networks are relied on to determine the local network mechanisms. Agent-based modelling shows the selected local network mechanisms are able to drive the network towards the assumed hierarchical global structure.

Analysis of Link Prediction Method for Link Recovery in Mobile Ad-hoc Network

2017 ◽  
Vol 7 (5) ◽  
pp. 849-854
Author(s):  
◽  
Jatinder Kaur ◽  
Danvir Mandal ◽  
Rajneesh Talwar ◽  
◽  
...  
Keyword(s):  
Ad Hoc Network ◽  
Link Prediction ◽  
Ad Hoc ◽  
Mobile Ad Hoc Network ◽  
Prediction Method ◽  
Mobile Ad Hoc

A Mobile User Preference Prediction Method Based on Trust and Link Prediction

2014 ◽  
Vol 35 (12) ◽  
pp. 2972-2977
Author(s):  
Hua Geng ◽  
Xiang-wu Meng ◽  
Yan-cui Shi
Keyword(s):  
Link Prediction ◽  
Prediction Method ◽  
Mobile User ◽  
User Preference
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