eamid/trimap

Distance matrix as input

Vykintasj opened this issue · 3 comments

Vykintasj commented

Hi,
is it possible to use a precomputed distance matrix as input? / will it be added in the future?
Thank you for the reply.

Best regards,
Vykintas

eamid commented

Hi Vykintas,

Excellent idea! I will add this feature soon :)

Thank you,
Ehsan

eamid commented

Hi Vykintas,

You can now use a precomputed distance matrix as input. To find the embedding using the pairwise distance matrix D, pass D as input and set use_dist_matrix to True:

embedding = trimap.TRIMAP(use_dist_matrix=True).fit_transform(D)

You can also pass the precomputed k-nearest neighbors and their corresponding distances as a tuple (knn_nbrs, knn_distances). Note that in this case, the rows must be in order, starting from point 0 to n-1. This feature also requires X to compute the embedding

embedding = trimap.TRIMAP(knn_tuple=(knn_nbrs, knn_distances)).fit_transform(X)

Please let me know if you find any bugs / errors. Also let me know if you have any comments. Your feedback is highly appreciated.

Ehsan

Vykintasj commented

Hi Ehsan,

I tried only the distance matrix - it works just as intended. Thank you for the implementation!
Vykintas