Error in spectral.py

Getting a TypeError in the spectral initialization in version 0.4.0rc2. No Error in 0.4.0rc1 (just a warning).

Reproducer here: https://github.com/acwooding/covid_nlp/blob/umap-bug/notebooks/999-UMAP-bug.ipynb

%%time embedding_2d = umap.UMAP(n_components=2, metric='hellinger', random_state=42).fit(umap_bug_matrix)

TypeError                                 Traceback (most recent call last)
<timed exec> in <module>

~/miniconda3/envs/covid_nlp/lib/python3.7/site-packages/umap/umap_.py in fit(self, X, y)
   1927             self.output_metric in ("euclidean", "l2"),
   1928             self.random_state is None,
-> 1929             self.verbose,
   1930         )[inverse]
   1931 

~/miniconda3/envs/covid_nlp/lib/python3.7/site-packages/umap/umap_.py in simplicial_set_embedding(data, graph, n_components, initial_alpha, a, b, gamma, negative_sample_rate, n_epochs, init, random_state, metric, metric_kwds, output_metric, output_metric_kwds, euclidean_output, parallel, verbose)
   1036             random_state,
   1037             metric=metric,
-> 1038             metric_kwds=metric_kwds,
   1039         )
   1040         expansion = 10.0 / np.abs(initialisation).max()

~/miniconda3/envs/covid_nlp/lib/python3.7/site-packages/umap/spectral.py in spectral_layout(data, graph, dim, random_state, metric, metric_kwds)
    273             random_state,
    274             metric=metric,
--> 275             metric_kwds=metric_kwds,
    276         )
    277 

~/miniconda3/envs/covid_nlp/lib/python3.7/site-packages/umap/spectral.py in multi_component_layout(data, graph, n_components, component_labels, dim, random_state, metric, metric_kwds)
    160             random_state,
    161             metric=metric,
--> 162             metric_kwds=metric_kwds,
    163         )
    164     else:

~/miniconda3/envs/covid_nlp/lib/python3.7/site-packages/umap/spectral.py in component_layout(data, n_components, component_labels, dim, random_state, metric, metric_kwds)
     89         else:
     90             distance_matrix = pairwise_distances(
---> 91                 component_centroids, metric=metric, **metric_kwds
     92             )
     93 

~/miniconda3/envs/covid_nlp/lib/python3.7/site-packages/sklearn/metrics/pairwise.py in pairwise_distances(X, Y, metric, n_jobs, **kwds)
   1586         func = partial(distance.cdist, metric=metric, **kwds)
   1587 
-> 1588     return _parallel_pairwise(X, Y, func, n_jobs, **kwds)
   1589 
   1590 

~/miniconda3/envs/covid_nlp/lib/python3.7/site-packages/sklearn/metrics/pairwise.py in _parallel_pairwise(X, Y, func, n_jobs, **kwds)
   1204 
   1205     if effective_n_jobs(n_jobs) == 1:
-> 1206         return func(X, Y, **kwds)
   1207 
   1208     # enforce a threading backend to prevent data communication overhead

~/miniconda3/envs/covid_nlp/lib/python3.7/site-packages/sklearn/metrics/pairwise.py in _pairwise_callable(X, Y, metric, **kwds)
   1231         iterator = itertools.combinations(range(X.shape[0]), 2)
   1232         for i, j in iterator:
-> 1233             out[i, j] = metric(X[i], Y[j], **kwds)
   1234 
   1235         # Make symmetric

TypeError: not enough arguments: expected 4, got 2

[lmcinnes]

I’m on it; for now you can use init='random' to work around it.

On Wed, Mar 25, 2020 at 4:16 PM Graham Clendenning [e-mail] wrote:

I’m also getting this error.

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[dhimmel]

Just got this error with 0.4.0rc3. It doesn’t look to me like https://github.com/lmcinnes/umap/commit/a62ffb3d1a35b477c2e1846007529bb1e7e9e09c is part of any releases yet (according to git tags).

I passed a scipy.sparse.csr_matrix to fit_transform.

/usr/local/lib/python3.8/site-packages/sklearn/metrics/pairwise.py in _pairwise_callable(X, Y, metric, force_all_finite, **kwds)
   1373         iterator = itertools.combinations(range(X.shape[0]), 2)
   1374         for i, j in iterator:
-> 1375             out[i, j] = metric(X[i], Y[j], **kwds)
   1376 
   1377         # Make symmetric

TypeError: not enough arguments: expected 4, got 2