openTSNE

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Thank you for your very good work, very inspiring to me, would like to ask where the macosko_2015.pkl.gz file can be downloaded, thank you!

yingweima2022

The docstring here https://github.com/pavlin-policar/openTSNE/blob/master/openTSNE/nearest_neighbors.py#L213 (about pickling Annoy objects into a separate file) seems obsolete: that's not the way this is currently done in the code.

dkobak

[Windows] saving/loading TSNEEmbedding objects to pickle, Directory error

8

##### Expected behaviour On Windows OS, when trying to save the TSNEEmbedding object, or affinities, tried to save it with `pickle.dump(embeddings,open(os.path.join(self.models_path,"tsne_global_embeddings.sav"),"wb"))` or also tried to save as array to reconstruct...

tomcsojn

Memory collapses with precomputed block matrix

17

##### Expected behaviour When I run tSNE on a symmetric 200x200 block matrix such as this one  I expect TSNE to return 4 distinct clusters (actually 4 points only)....

fsvbach

pandas DataFrames KeyError

8

Hi Pavlin, I worked with openTSNE using pandas DataFrames as input for a while and it worked fine. Suddenly I got a KeyError. It seems that for larger DataFrames openTSNE...

fsvbach

Hello, is there a way to use k-nearest neighbors data created externally? My current strategy is to create a dummy class of the form: ```python class PrecomputedKNNIndex: def __init__(self, indices,...

jlmelville

Numpy incompatibility

1

Hi guys, I'm using openTSNE for the first time. However, it seems that openTSNE is not compatible with newer versions of Numpy. I don't know if that is an issue,...

ll-portes

[Windows] save TSNEEmbedding to binary, Directory error

5

I'm reopening a previously closed issue (https://github.com/pavlin-policar/openTSNE/issues/210) In version 1.0.0, the problem still occurs. I tried running my code as administrator and the issue persists. There seems to be a...

Aurelien-Pelissier

Test failure on i386

9

Hey, thanks for working on this, @pavlin-policar. However, when building the package in i386, one of the tests fails: ``` =================================== FAILURES =================================== _________ TestTSNECorrectnessUsingPrecomputedDistanceMatrix.test_iris __________ self = def test_iris(self):...

utkarsh2102

oldest-supported-numpy depricated

2

Hi Pavlin, for packages that depend on openTSNE, it is somewhat cumbersome that openTSNE requires the oldest supported numpy version for the given python version, because this can easily lead...

sdamrich