Umap: Does UMAP accept a distance matrix as custom metric?

[VisuMap]

[lmcinnes]

As of version 0.2 onward it does yes. @LGro provided the code to enable this. If you set metric='precomputed' then you can pass a distance matrix rather than a dataset to the fit or fit_transform method.

[LGro]

@VisuMap, in case you have trouble using that feature or any additional thoughts on the implementation, I'd be happy to discuss it.

[VisuMap]

Thanks for the info and kind offer. I guess I can wait till version 0.2 is officially released.

[lmcinnes]

@VisuMap, it is released -- and should be available on PyPI and conda-forge. If it isn't working for you as intended please let me know.

[bccho]

@lmcinnes Will support for precomputed metrics soon make its way into 0.3dev?

[lmcinnes]

@bccho It is already in 0.2, so yes it will continue to exist in 0.3dev.

[LGro]

@VisuMap, is this issue resolved or do you still have trouble accessing the feature?
If it is resolved, please consider closing the issue - thanks :)

[dawe]

As of version 0.2 onward it does yes. @LGro provided the code to enable this. If you set metric='precomputed' then you can pass a distance matrix rather than a dataset to the fit or fit_transform method.

And yet:

>>> U = umap.UMAP(metric='precomputed')
>>> XY = U.fit_transform(dm)
[…]
ValueError: Metric is neither callable, nor a recognised string
>>> umap.__version__
0.3.0

[LGro]

@dawe, it seems like the lines around L1457 in the current master branch might fix your issue. Could you please try to build from master?
https://github.com/lmcinnes/umap/blob/ec860e9280dcd4a80c820c73c4cd5fb77cd59278/umap/umap_.py#L1453-L1462