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Questions tagged [umap]

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Using UMAP on text data (euclidean distance on jaccard distance matrix)

I am checking the capabilities of the UMAP dimensionality reduction algorithm, I am not sure whether the approach I am using is valid and does not violate the rules/limitations of this algorithm. ...
rkabuk's user avatar
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Is there a set of parameters in UMAP such that embedding an input dataset results in the embedding being the same input dataset itself?

That is, after embedding = umap.UMAP() embedding.fit(X) then the result should be embedding.embedding_ == X Then, ideally, any ...
Elijah Bartolome's user avatar
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1 answer
33 views

How do I interpret low dimentional embeddings of high dimentional embeddings?

I am trying to understand what I am supposed to learn about a problem when using dimensionality reduction methods. In particular, I am referring to methods like t-SNE and UMAP. For the most part I am ...
Finncent Price's user avatar
1 vote
1 answer
90 views

When visualizing graph nodes, should I use apply PCA to node2vec embedding?

I am trying to visualize graph nodes using node2vec embedding. The node2vec embeddings has lengths of 50~100 dimensions. I have two plans: use umap to project node2vec embeddings to 2D space use PCA ...
Sijie Chen's user avatar
2 votes
1 answer
98 views

How to improve the preservation of the global data structure in UMAP?

I have a dataset, where the features are comprised of points arranged in a regular grid on a simplex. Each of these points are defined as follows: A point $\mathbf{x}$ on the simplex can be ...
pmu2022's user avatar
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2 answers
3k views

Why is UMAP used in combination with other Clustering Algorithm?

I've noticed that UMAP is often used in combination with other clustering algorithms, such as K-means, DBSCAN, HDBSCAN. However, from what I've understood, UMAP can be used for clustering tasks. So ...
coelidonum's user avatar
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1 answer
366 views

MEL VS linear spectrograms for bioacoustics machine learning

I don't have background in bioacoustics but working on a data-science project in bioacoustics. I am working with animal vocalizations recorded at sampling rate of 250000. Animals are bats, which are ...
user305883's user avatar