Dataset Information

Weg2vec: Event embedding for temporal networks.

ABSTRACT: Network embedding techniques are powerful to capture structural regularities in networks and to identify similarities between their local fabrics. However, conventional network embedding models are developed for static structures, commonly consider nodes only and they are seriously challenged when the network is varying in time. Temporal networks may provide an advantage in the description of real systems, but they code more complex information, which could be effectively represented only by a handful of methods so far. Here, we propose a new method of event embedding of temporal networks, called weg2vec, which builds on temporal and structural similarities of events to learn a low dimensional representation of a temporal network. This projection successfully captures latent structures and similarities between events involving different nodes at different times and provides ways to predict the final outcome of spreading processes unfolding on the temporal structure.

SUBMITTER: Torricelli M

PROVIDER: S-EPMC7189270 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature

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weg2vec: Event embedding for temporal networks.

Torricelli Maddalena M Karsai Márton M Gauvin Laetitia L

Scientific reports 20200428 1

Network embedding techniques are powerful to capture structural regularities in networks and to identify similarities between their local fabrics. However, conventional network embedding models are developed for static structures, commonly consider nodes only and they are seriously challenged when the network is varying in time. Temporal networks may provide an advantage in the description of real systems, but they code more complex information, which could be effectively represented only by a h ...[more]

PMID: 32346033

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Project description:Motivation: Graph embedding learning that aims to automatically learn low-dimensional node representations, has drawn increasing attention in recent years. To date, most recent graph embedding methods are evaluated on social and information networks and are not comprehensively studied on biomedical networks under systematic experiments and analyses. On the other hand, for a variety of biomedical network analysis tasks, traditional techniques such as matrix factorization (which can be seen as a type of graph embedding methods) have shown promising results, and hence there is a need to systematically evaluate the more recent graph embedding methods (e.g. random walk-based and neural network-based) in terms of their usability and potential to further the state-of-the-art.Results: We select 11 representative graph embedding methods and conduct a systematic comparison on 3 important biomedical link prediction tasks: drug-disease association (DDA) prediction, drug-drug interaction (DDI) prediction, protein-protein interaction (PPI) prediction; and 2 node classification tasks: medical term semantic type classification, protein function prediction. Our experimental results demonstrate that the recent graph embedding methods achieve promising results and deserve more attention in the future biomedical graph analysis. Compared with three state-of-the-art methods for DDAs, DDIs and protein function predictions, the recent graph embedding methods achieve competitive performance without using any biological features and the learned embeddings can be treated as complementary representations for the biological features. By summarizing the experimental results, we provide general guidelines for properly selecting graph embedding methods and setting their hyper-parameters for different biomedical tasks.Availability and implementation: As part of our contributions in the paper, we develop an easy-to-use Python package with detailed instructions, BioNEV, available at: https://github.com/xiangyue9607/BioNEV, including all source code and datasets, to facilitate studying various graph embedding methods on biomedical tasks.Supplementary information: Supplementary data are available at Bioinformatics online.

Dataset Information

Weg2vec: Event embedding for temporal networks.

Publications

weg2vec: Event embedding for temporal networks.

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