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I am trying to visualize graph nodes using node2vec embedding. The node2vec embeddings has lengths of 50~100 dimensions.

I have two plans:

  1. use umap to project node2vec embeddings to 2D space
  2. use PCA to project node2vec embeddings to a slightly lower-D space (~30-50 dimensions), and then use umap for 2D space outputs.

Which plan is better?

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The PCA step will remove redundancies: this is a solid first step. Then as you say it can be followed up with the 2D embedding. Option 2.

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