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PaulWAyers avatar PaulWAyers commented on August 23, 2024

As explained on Wikipedia there is a Tanimoto similarity and a Tanimoto distance. So both exist.

The easiest test is to compare an object to itself. Its similarity is greater than zero (often one) and the distance is zero.

I feel like it is better to add AIMSim as a dependence. Implementing 30+ methods is a lot of work.

We may wish to have a few basic methods implemented; the most common distance metrics and similarity measures are already there in scikit-learn
(distances) sklearn.metrics.DistanceMetric
(similarities and divergences) sklearn.metrics.pairwise

I'd lead with interfacing to scikit-learn (I think we already did this in large part?) and then considering interfacing to AIMSim a follow-up task.

I guess it is important to distinguish between similarities/affinities and distances/divergences. I'd suggest making sure that we have these distinguished, plus the "converter" between them.

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FanwangM avatar FanwangM commented on August 23, 2024

Yes, we should make them differentiable and be obvious as much as we can to avoid any ambiguity.

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FarnazH avatar FarnazH commented on August 23, 2024

Update: We decided not to include any wrappers to support the functionality in other packages (reason: additional overhead and unnecessary dependency), instead, we showcase how our package works with other libraries in notebooks/tutorials.

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