Abstract We investigate the statistical learning of nodal attribute functionals in homophily networks using random walks. Attributes can be discrete or continuous. A generalization of various existing canonical models, based on preferential attachment is studied (model class $$\mathscr {P}$$ P ), where new nodes form connections dependent on both their attribute values and popularity as measured by degree. An associated model class $$\mathscr {U}$$ U is described, which is amenable to theoretical analysis and gives access to asymptotics of a host of functionals of interest. Settings where asymptotics for model class $$\mathscr {U}$$ U transfer over to model class $$\mathscr {P}$$ P through the phenomenon of resolvability are analyzed. For the statistical learning, we consider several canonical attribute agnostic sampling schemes such as Metropolis-Hasting random walk, versions of node2vec (Grover and Leskovec, 2016) that incorporate both classical random walk and non-backtracking propensities and propose new variants which use attribute information in addition to topological information to explore the network. Estimators for learning the attribute distribution, degree distribution for an attribute type and homophily measures are proposed. The performance of such statistical learning framework is studied on both synthetic networks (model class $$\mathscr {P}$$ P ) and real world systems, and its dependence on the network topology, degree of homophily or absence thereof, (un)balanced attributes, is assessed.
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Learning Attribute Distributions Through Random Walks
We investigate the statistical learning of nodal attribute distributions in homophily networks using random walks. Attributes can be discrete or continuous. A generalization of various existing canonical models, based on preferential attachment is studied, where new nodes form connections dependent on both their attribute values and popularity as measured by degree. We consider several canonical attribute agnostic sampling schemes such as Metropolis-Hasting random walk, versions of node2vec (Grover and Leskovec 2016) that incorporate both classical random walk and non-backtracking propensities and propose new variants which use attribute information in addition to topological information to explore the network. The performance of such algorithms is studied on both synthetic networks and real world systems, and its dependence on the degree of homophily, or absence thereof, is assessed.
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- Award ID(s):
- 2113662
- NSF-PAR ID:
- 10433605
- Editor(s):
- Cherifi, H.; Mantegna, R.N.; Rocha, L.M.; Cherifi, C.; Micciche, S.
- Date Published:
- Journal Name:
- Complex Networks and Their Applications XI
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract Motivation Accurately representing biological networks in a low-dimensional space, also known as network embedding, is a critical step in network-based machine learning and is carried out widely using node2vec, an unsupervised method based on biased random walks. However, while many networks, including functional gene interaction networks, are dense, weighted graphs, node2vec is fundamentally limited in its ability to use edge weights during the biased random walk generation process, thus under-using all the information in the network.
Results Here, we present node2vec+, a natural extension of node2vec that accounts for edge weights when calculating walk biases and reduces to node2vec in the cases of unweighted graphs or unbiased walks. Using two synthetic datasets, we empirically show that node2vec+ is more robust to additive noise than node2vec in weighted graphs. Then, using genome-scale functional gene networks to solve a wide range of gene function and disease prediction tasks, we demonstrate the superior performance of node2vec+ over node2vec in the case of weighted graphs. Notably, due to the limited amount of training data in the gene classification tasks, graph neural networks such as GCN and GraphSAGE are outperformed by both node2vec and node2vec+.
Availability and implementation The data and code are available on GitHub at https://github.com/krishnanlab/node2vecplus_benchmarks. All additional data underlying this article are available on Zenodo at https://doi.org/10.5281/zenodo.7007164.
Supplementary information Supplementary data are available at Bioinformatics online.
- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Conference Paper:
- https://doi.org/10.1007/978-3-031-21131-7_2
