lmcinnes / lmcinnes/umap

Adding precomputed distances for Parametric UMAP

Open
#655 1 comment 1 reaction 0 assignees View on GitHub

Nobody has claimed this yet.

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

Description

I'm trying to figure out how we could enable precomputed distances for Parametric UMAP, since fit_transform only takes in `X` as either the distance matrix, _or_ the data, but Parametric UMAP would need both the distance matrix _and_ the data as input.

One option that wouldn't require modification to anything but parametric_umap.py would be to add a fit_transform method that takes in precomputed distances, and grabs the data as self._X:

```python
def fit_transform(self, X, y=None, precomputed_distances=None):

if self.metric == "precomputed":
if precomputed_distances is None:
raise ValueError(
"Precomputed distances must be supplied if metric \
is precomputed."
)
# prepare X for traning the network
self._X = X
# geneate the graph on precomputed distances
return super().fit_transform(precomputed_distances, y)
else:
return super().fit_transform(X, y)
```

then, in _fit_embed_data, grab back X.

```python
def _fit_embed_data(self, X, n_epochs, init, random_state):

if self.metric == "precomputed":
X = self._X
...

```

Does that seem reasonable? I can make a PR if so.

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 in parametric_umap.py at fit_transform and _fit_embed_data, where the issue proposes passing both training data and precomputed distances. Trace how Parametric UMAP currently prepares X and delegates to the parent implementation, then determine how both inputs should be retained without changing non-precomputed behavior. Done means Parametric UMAP accepts precomputed distances while still training on the original data.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
machine-learning
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
42/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.