Fanwang Meng

Add more similarity measurements, fixes #124

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This PR addresses https://github.com/theochem/Selector/issues/124. The `SimilarityIndex` class was moved to similarity module to make things consistent, which is mainly for calculating similarity matrix. The `smilarity.py` in method module was renamed...

[Diversity module] Problem of using `shannon_entropy` for computing diversity

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Sometimes, this function can return us an invalid value, NaN. You can reproduce the error by running the notebook as attached with the latest code in this repo. I think...

[Similarity module] Add more similarity measurements

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Implement methods listed in as similarity module https://vlachosgroup.github.io/AIMSim/implemented_metrics.html. Please add detailed documentation to show which similarity functions is corresponding to which distance functions in scikit-learn or scipy. One question I...

Add a command line tool for people to perform subset selection with one line of `bash` code

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This is good to have, but let's leave it to the last stage. An example can be found at https://github.com/theochem/B3clf.

[Docs] support of different metrics for binary fingerprints or descriptors

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Some metrics only work on binary fingerprints, such as Tanimoto. But some metrics can work for both cases and some metrics work for only for non-binary matrix, such as molecular...

[Selector module] Add the method in ` MultipleComparisons`

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Ramon's group has a clever way of doing diverse selector and we have an in-house implementation and should merge it to this repo.

[Selector module] Implementing D-optimal designs

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Information related to determinantal point processes can be found at #4. [fast greedy algorithm](https://proceedings.neurips.cc/paper/2018/file/dbbf603ff0e99629dda5d75b6f75f966-Paper.pdf) [review](https://arxiv.org/pdf/1207.6083.pdf) [code](https://dppy.readthedocs.io/en/latest/finite_dpps/exact_sampling.html#finite-dpps-exact-sampling) [two algorithms here](https://proceedings.neurips.cc/paper/2014/file/4462bf0ddbe0d0da40e1e828ebebeb11-Paper.pdf)

We will need to make it accessible with `pypi` and `conda`.

This is a method developed by Weitao's group, [J. Chem. Inf. Model. 2015, 55, 3, 529–537](https://pubs.acs.org/doi/10.1021/ci500749q), which relates to #4.

[Docs] List the application scenarios of `Selector`

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It would be beneficial for people to know how they can use our package for practical problems and I think we can make a list for people in the manuscript....