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docs/source/notebooks/cover.py

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# The `KNNCover` algorithm uses k-nearest neighbors to define the cover. The cover is created by
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# choosing a set of points in the dataset and then connecting each point to its k-nearest
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# neighbors.
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# neighbors. For this reason, each set in the cover has cardinality equal to the number of
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# neighbors specified.
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# ### Parameters
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# The key parameter in the `KNNCover` is the `neighbors`, which determines how many nearest
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# ## Conclusions
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# In this notebook, we explored three different cover algorithms: `CubicalCover`, `BallCover`, and
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# `KNNCover`. Each algorithm has its own strengths and weaknesses, and the choice of cover can
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# significantly influence the resulting Mapper graph. Here is a summary of the key differences
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# between the three cover algorithms:
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# +------------------------+------------------+-------------------------------------+-------------------------------------+
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# | Cover Algorithm | Parameters | Advantages | Disadvantages |
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# +========================+==================+=====================================+=====================================+
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# | CubicalCover | - `n_intervals` | - Widely used and well-supported | - Sensitive to parameters |
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# | | - `overlap_frac` | - Easy to interpret | - Only supports Euclidean spaces |
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# | | - `algorithm` | | |
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# +------------------------+------------------+-------------------------------------+-------------------------------------+
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# | BallCover | - `radius` | - Works with any metric space | - Struggles with varying densities |
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# | | - `metric` | - Can capture isolated clusters | - Radius tuning can be difficult |
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# +------------------------+------------------+-------------------------------------+-------------------------------------+
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# | KNNCover | - `neighbors` | - Works with any metric space | - Struggles with isolated clusters |
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# | | - `metric` | - Adapts to local densities | - Risk of over-connecting nodes |
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# +------------------------+------------------+-------------------------------------+-------------------------------------+
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# As a final remark, in the example dataset that we used, despite a significative difference in the
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# structure of the Mapper graph, the relationship between the different parts of the data are still
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# preserved. This means that even though the cover algorithms create different structures, they

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