lmcinnes / lmcinnes/umap

inverse_transform doesn't work on 1D data

Open
#408 2 comments 2 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

Dominant language
Python
Stars
8.3k
Forks
871
Avg merge
1d 13h
Merged PRs (30d)
5

Description

Is it possible to do an inverse transform on a 1D embedding? This is what I see:

from umap import UMAP
import numpy as np

x = np.random.random(size = (100,1000))
umap_1D = UMAP(n_components=1)
transformed = umap_1D.fit_transform(x)
umap_1D_max = transformed.max()
umap_1D_min = transformed.min()
to_be_inverted = np.random.random(size=(1,10))
generated = umap_1D.inverse_transform(to_be_inverted)
generated

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-45-2c8de5c09c47> in <module>()
      8 umap_1D_min = transformed.min()
      9 to_be_inverted = np.random.random(size=(1,10))
---> 10 generated = umap_1D.inverse_transform(to_be_inverted)
     11 generated

/usr/local/lib/python3.6/dist-packages/umap/umap_.py in inverse_transform(self, X)
   2202         # build Delaunay complex (Does this not assume a roughly euclidean output metric)?
   2203         deltri = scipy.spatial.Delaunay(
-> 2204             self.embedding_, incremental=True, qhull_options="QJ"
   2205         )
   2206         neighbors = deltri.simplices[deltri.find_simplex(X)]

qhull.pyx in scipy.spatial.qhull.Delaunay.__init__()

qhull.pyx in scipy.spatial.qhull._Qhull.__init__()

ValueError: Need at least 2-D data

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start at umap/umap_.py in inverse_transform, especially the scipy.spatial.Delaunay call shown in the traceback. Reproduce the supplied 1D embedding example and trace how the one-dimensional embedding reaches that entry point. Done means inverse_transform handles n_components=1 without the reported ValueError.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
machine-learning
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
32/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.