I looked at the repo and demo canvas. Nice work. Especially liked the 3 semantic zoom tiers and the weave/condense features. If you're enabling for less-technical users consider leading with weave and condense vs. edge deletion. Edge deletion is where the model is powerful but my Mom would get stuck there for instance. The idea that removing a wire changes what the model actually sees might not be obvious.

Consider when someone clicks a node, show a sidebar listing (node references)with remove buttons to reframe as 'what does this answer know about me" vs. "edit of the graph".

Love the graph for power users but listing can be the explanation layer.