lmcinnes / lmcinnes/umap

transform() for mixed dataset

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Description

Thanks lmcinnes for this great library!

I'm currently using umap on mixed data (and I've successfully used the code from issue #58 to implement mixed data fitting) and I was wondering how I could extend that to transform additional mixed data onto the fitted projection. Would the following implementation work?

Given that `umap_model_numerical` and `umap_model_categorical` are umap models respectively fitted onto the numerical and categorical (one encoded) data and that `df_numerical` and `df_categorical` are additional data to be projected onto the umap representation:

`fit1 = umap_model_numerical.transform(df_numerical.values)`
`fit2 = umap_model_categorical.transform(df_categorical.values)`
`intersection = umap.umap_.general_simplicial_set_intersection(fit1.graph_, fit2.graph_, weight=0.5)`
`intersection = umap.umap_.reset_local_connectivity(intersection)`
`embedding = umap.umap_.simplicial_set_embedding(fit1._raw_data, intersection, fit1.n_components,
fit1.learning_rate, fit1._a, fit1._b,
fit1.repulsion_strength, fit1.negative_sample_rate,
200, 'random', np.random, fit1.metric,
fit1._metric_kwds, False)`

From what I've seemed to understand, setting `'random'` for the `init` parameter for `simplicial_set_intersection` allows to not consider `fit1._raw_data` and `fit1._metric_kwds` parameters

Thanks in advance for your help and amazing work!

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 by reviewing UMAP's transform path and the mentioned entry points general_simplicial_set_intersection, reset_local_connectivity, and simplicial_set_embedding. Determine whether the proposed numerical and categorical workflow can support transforming additional mixed data, and define completion as a validated approach or a clearly scoped implementation with mixed-data examples.

Written by the indexing model from the issue text.

Assessment

Tech stack
numpy, python
Domain
machine-learning
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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