v0.2.0

UMAP v0.2.0

Diff since v0.1.11

Release Notes: UMAP.jl v0.2.0

Version 0.2 is a major redesign focused on generality, extensibility, and multi-modal data support. This release contains breaking changes.

New Features

• Multi-view UMAP: Native support for multi-modal data via NamedTuple inputs
• Configuration System: Explicit types for all algorithm parameters with full control over each stage
• Result Objects: UMAPResult and UMAPTransformResult that encapsulate configuration and intermediate results
• Flexible Input: Support for matrices, vectors of points, and multi-view data
• Extensibility: Multiple dispatch-based extension points for custom KNN search, initialization, and manifolds
• Better Transform: Automatic parameter inheritance from fit configuration

Breaking Changes

Function Names and Exports

• umap() → UMAP.fit(): Main function renamed; returns UMAPResult instead of embedding matrix

  # Old
  embedding = umap(X, 2)
  # New
  result = UMAP.fit(X, 2)
  embedding = result.embedding

• UMAP_ → UMAPResult: Result struct renamed and restructured

  # Old
  model = UMAP_(X, 2)
  # New
  result = UMAP.fit(X, 2)

• export → public: Functions now use public keyword

  • Call as UMAP.fit() or using UMAP: fit

Transform Function

• Signature change: transform(model::UMAP_, Q; kwargs...) → transform(result::UMAPResult, queries)
• Automatic parameter inheritance: No need to re-specify parameters; inherited from result.config

  # Old
  Q_embed = transform(model, Q; n_neighbors=15, n_epochs=100)
  # New
  Q_result = UMAP.transform(result, Q)  # Params inherited
  Q_embed = Q_result.embedding

Parameters

• init parameter: Changed from Symbol to typed objects

  # Old
  UMAP_(X, 2; init=:spectral)
  # New
  UMAP.fit(X, 2; init=UMAP.SpectralInitialization())

• a and b parameters removed: Now computed automatically from min_dist and spread

Result Structure

• Field changes:
  • model.knns and model.dists → result.knns_dists (tuple)
  • Added result.config field storing configuration
  • Added result.fs_sets field for fuzzy simplicial sets

Migration

Minimal changes for basic usage:

# v0.1.11
using UMAP
embedding = umap(X, 2; n_neighbors=15)

# v0.2
using UMAP: fit
result = fit(X, 2; n_neighbors=15)
embedding = result.embedding

Transform usage:

# v0.1.11
model = UMAP_(X, 2)
Q_embed = transform(model, Q; n_neighbors=15, n_epochs=100)

# v0.2
result = UMAP.fit(X, 2)
Q_result = UMAP.transform(result, Q)  # Simpler!
Q_embed = Q_result.embedding

Dependencies

• Added: Accessors.jl
• Updated: Minimum versions of existing dependencies may have changed

Documentation

• New comprehensive architecture guide in landing page
• Multi-view UMAP examples
• Mathematical documentation for loss function
• Complete API reference for all configuration types

Performance

Performance characteristics are similar to v0.1.11 with improved type stability through explicit configuration types.

Merged pull requests:

• V0.2 dev (#55) (@dillondaudert)

Closed issues:

• Seg fault upon @pyimport umap as py_umap; (#6)
• UMAP performance (#13)
• Arbitrary data support (#27)
• Example Notebook not working - Julia 1.6.1 (#43)
• julia> @time e = UMAP.umap(X, 2); ERROR: InexactError: Int64(... (#50)
• Project status? (#53)
• Tag a release? (#58)

v0.1.11

UMAP v0.1.11

Diff since v0.1.10

Merged pull requests:

• CompatHelper: bump compat for "LsqFit" to "0.14" (#56) (@github-actions[bot])
• CompatHelper: bump compat for "LsqFit" to "0.15" (#57) (@github-actions[bot])

v0.1.10

UMAP v0.1.10

Diff since v0.1.9

Closed issues:

• upgrade dependencies (#46)

v0.1.9

UMAP v0.1.9

Diff since v0.1.8

Closed issues:

• ERROR: MethodError: Cannot convert an object of type (#34)

Merged pull requests:

• CompatHelper: bump compat for "LsqFit" to "0.12" (#38) (@github-actions[bot])
• CompatHelper: bump compat for "Arpack" to "0.5" (#39) (@github-actions[bot])

v0.1.8

UMAP v0.1.8

Diff since v0.1.7

Closed issues:

• Isn't the input data row-major? (#32)

Merged pull requests:

• modified _knn_from_dists to enable very large distance matrices (#33) (@kragol)
• CompatHelper: bump compat for "Distances" to "0.10" (#35) (@github-actions[bot])

v0.1.7

UMAP v0.1.7

Diff since v0.1.6

Closed issues:

• DescentGraph not defined (#30)

Merged pull requests:

• CompatHelper: bump compat for "LsqFit" to "0.11" (#31) (@github-actions[bot])

v0.1.6

UMAP v0.1.6

Diff since v0.1.5

Merged pull requests:

• CompatHelper: bump compat for "LsqFit" to "0.9" (#23) (@github-actions[bot])
• CompatHelper: bump compat for "LsqFit" to "0.10" (#24) (@github-actions[bot])
• Install TagBot as a GitHub Action (#25) (@JuliaTagBot)
• add transform data functionality (#26) (@sanjmohan)
• CompatHelper: bump compat for "Distances" to "0.9" (#28) (@github-actions[bot])

v0.1.5

v0.1.5 (2019-12-27)

Diff since v0.1.4

Closed issues:

• Error in spectral layout on master (#16)

Merged pull requests:

• Reduce mem usage in optimize_embedding; eigs which=:SM (fix) (#22) (dillondaudert)
• Fix broadcast bug in initialize_embedding (#21) (baggepinnen)
• CompatHelper: bump compat for "Arpack" to "0.4" (#15) (github-actions[bot])
• CompatHelper: bump compat for "LsqFit" to "0.8" (#14) (github-actions[bot])
• V0.1.5dev (#12) (dillondaudert)

v0.1.4

v0.1.4 (2019-06-14)

Diff since v0.1.3

Closed issues:

• Float32 (#10)
• UMAP from distance matrix? (#8)

Merged pull requests:

• Relax type constraints; fix Float32 bug; which=:SR (#11) (dillondaudert)

v0.1.3

Bump version 0.1.3