Abstract 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.
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Representation Learning in Heterogeneous Professional Social Networks with Ambiguous Social Connections.
Network representations have been shown to improve performance within a variety of tasks, including classification, clustering, and link prediction. However, most models either focus on moderate-sized, homogeneous networks or require a significant amount of auxiliary input to be provided by the user. Moreover, few works have studied network representations in real-world heterogeneous social networks with ambiguous social connections and are often incomplete. In the present work, we investigate the problem of learning low-dimensional node representations in heterogeneous professional social networks (HPSNs), which are incomplete and have ambiguous social connections. We present a general heterogeneous network representation learning model called Star2Vec that learns entity and person embeddings jointly using a social connection strength-aware biased random walk combined with a node-structure expansion function. Experiments on LinkedIn's Economic Graph and publicly available snapshots of Facebook's network show that Star2Vec outperforms existing methods on members' industry and social circle classification, skill and title clustering, and member-entity link predictions. We also conducted large-scale case studies to demonstrate practical applications of the Star2Vec embeddings trained on LinkedIn's Economic Graph such as next career move, alternative career suggestions, and general entity similarity searches.
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- Award ID(s):
- 1652492
- NSF-PAR ID:
- 10136391
- Date Published:
- Journal Name:
- IEEE Conference on Big Data
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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