MolSubspace For Mac

MolSubspace is an easy to use application that allows you to visualize and analyze the structural diversity of a molecule.

An obvious alternative to PCA is multidimensional scaling (MDS).  MDS is a non-linear dimensionality reduction technique that can be effective at revealing the “natural” manifold of the underlying dataset.

An interesting aspect of data embedding with MDS is that only pairwise proximity (e.g., distances) values are required (and moreover, the proximity metric used doesn’t have to strictly adhere to the standard definition of metric space).

This is quite convenient in that now we don’t have to construct an explicitly encoding of the molecular graph for embedding.