So I have a set of 3000 features from which I would like to generate clusters. I passed my features through the T-SNE algorithm to reduce dimensionality to 2 features, and clusters are really visible in this reduced space. How would I go about figuring out a deterministic way to create this same T-SNE output to use for clustering?
Do not use tSNE visualizations for clustering. The results are misleading.
See this great answer: https://stats.stackexchange.com/a/264647/7828
Apart from that, you just need to fix the initial positions. For examples by fixing the random generator seed. But the fact thar it does not work every time should already warn you that it is not too reliable...