UMAP

[haesleinhuepf]

Hi @stefanhahmann et al,

as discussed today, it would be cool to have a way for computing the UMAP of extracted features, to allow dimensionality reduction and viewing complex measurements / data points in 2D. There is a potential Java library for this:

• https://github.com/tag-bio/umap-java

It would be interesting to know if the library can deal with big data. If it does not, I would post-pone developing a big-data version to a later point. For now, it might be most important to have a UMAP implementation we can work with to explore possibilities. A potential alternative could also be a python-wrapper using cuML, which contains a GPU-accelerated UMAP implementation.

Optionally, we could also think of t-SNE and PCA as alternatives, if not too complicated.

• https://github.com/lejon/T-SNE-Java
• https://spark.apache.org/docs/2.1.0/mllib-dimensionality-reduction.html#principal-component-analysis-pca

Let me know what you think!

Best, Robert

[stefanhahmann]

As a reference, I add a screenshot of the UI in Napari