Dataset similarity #122
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Dataset similarity #122
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- Add new class that performs k-nearest neighbor searches using
Tanimoto similarity. The implementation uses sparse dot product
making the algorithm 2-3x faster than RDKit's BulkTanimotoSimilarity
- Add notebook illustrating NearestNeighborsRetrieverTanimoto for
dataset similarity analysis, like train/test set comaparison.
c-w-feldmann
requested changes
Feb 13, 2025
| else: | ||
| self.k = k | ||
| self.batch_size = batch_size | ||
| if n_jobs == -1: |
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Maybe use this function instead?
https://github.com/basf/MolPipeline/blob/main/molpipeline/utils/multi_proc.py#L9
|
In addition to the dot-product Tanimoto, we could also check out if its possible to add an implementation of iSim https://github.com/mqcomplab/bitbirch/blob/main/bitbirch.py |
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Tanimoto similarity. The implementation uses sparse dot product
making the algorithm 2-3x faster than RDKit's BulkTanimotoSimilarity
dataset similarity analysis, like train/test set comaparison.
Also addresses #117