I have no idea what your app does besides flashcards because your landing page doesn't give much information
Maybe this explanation is helpful: There is an old, tried-and-tested learning algorithm called SR (Spaced Repetition) (The algorithm used to determine when to show cards in flashcard programs) The problem is that SR is a tool that only fits 1:1 structures, and this structure does not match the structure of knowledge What fits this structure is as simple as country–capital pairs or word–meaning pairs, but not general…
One thing stood out to me in your explanation — you say “tree structure” is a natural way to organize knowledge.
Why is that the case? I generally use one of the modern “tools of thought” (first Roam and now mem.ai) and in these tools, you just dump notes and add tags and and links among notes, so you have a general graph structure (from the links) overlayed with tags.