Combining a bisector tree with the Tanimoto distance for similarity searches and beyond

Abstract

A bisector tree is a data structure from computational geometry to do static spatial indexing of points. It allows to do fast and exact nearest neighbor searches (and other queries) in an N-dimensional space, provided a metric to measure the distance between any two points in that space exists.We have made an open source implementation of a bisector tree (https://github.com/UnixJunkie/bisec-tree). It is bucketized, such that several nearby molecules can be put into the same bucket. The (maximum) bucket size is a user-chosen parameter. Our implementation proposes two heuristics, in order to find good vantage points during tree construction, to accelerate subsequent queries.In this presentation, we report on the indexing and querying of millions of molecules and the associated challenges.