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Semantic substrates are spatial templates for networks, where nodes are grouped into regions and laid out within each region according to one or more node attributes. Analysts’ ability to design their own substrates leads to a different approach than other more automatic approaches to layout nodes (force-directed, circular, etc.). While the semantic substrate approach provides more interpretable node locations, sometimes a set of nodes is compressed into a small space on the display, leading to node overlap. In this paper, we significantly improve this situation by introducing the node aggregation mechanism in the context of semantic substrates. We illustrate this functionality in a document citation network and provide pros and cons of the approach. We conclude with guidelines and future directions for this research. Throughout the paper, examples are illustrated with NVSS 3.0, the network visualization tool developed to explore the semantic substrate idea.