ENH Adding callable function option to bicluster method #29196
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Could you provide some literature where other normalization are used to assess if we should include the feature or not. I think that the test would be enough. We will need an entry in the changelog file |
glemaitre
reviewed
Jun 6, 2024
| Method of normalizing and converting singular vectors into | ||
| biclusters. May be one of 'scale', 'bistochastic', or 'log'. | ||
| The authors recommend using 'log'. If the data is sparse, | ||
| however, log normalization will not work, which is why the | ||
| default is 'bistochastic'. | ||
| Callable must take a 2D array and return a 2D array. | ||
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| .. warning:: | ||
| if `method='log'`, the data must not be sparse. |
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| if `method='log'`, the data must not be sparse. | |
| if `method='log'`, the data must not be sparse. | |
| .. versionadded:: 1.6 | |
| The support for passing a callable was added. |
glemaitre
reviewed
Jun 6, 2024
| if self.method == "bistochastic": | ||
| if callable(self.method): | ||
| normalized_data = self.method(X) | ||
| n_sv += 1 |
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If someone add a log based normalization then this would be incorrect, isn't it?
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What does this implement/fix? Explain your changes.
This PR adds the option to provide your own custom callable to the SpectralBiclustering class
Any other comments?
The current implementation is constrained to a few normalizations from the original work; other normalizations could be helpful to others.