Added new gensim node embedder and refactored similarity to support different backends

[eugeniashurko]

New features and major updates:

• Added the GensimNodeEmbedder interface allowing to wrap gensim embedding models (in particular, added the implementation of poincare embedding).

• Refactored SimilarityProcessor to support multiple backends (through dependency injection), in particular:

  • Added SimilarityIndex interface for backend-specific similarity indices
  • Added FaissSimilarityIndex interface for faiss similarity index
  • Added ScikitLearnSimilarityIndex interface for sklearn similarity index based on sklearn.neighbors.KDTree and sklearn.neighbors.BallTree
  • Added new similarity metric to ScikitLearnSimilarityIndex based on sklearn.neighbors.BallTree corresponding to Poincare distance
  • SimilarityProcessor API changed (takes on input a SimilarityIndex)

• Moved EmbeddingPipeline into blugraph.downstream.pipelines

Minor fixes and updates

• Updates in Neo4j (gds.beta.shortestPath.yens.stream becomes gds.shortestPath.yens.stream in the newer versions of the GDS plugin)
• Bugfixes in core
• Updated docs
• Added a tutorial notebook with embedding pipelines

[codecov-commenter]

Codecov Report

Merging #91 (c835e71) into master (00bb7b3) will increase coverage by 0.01%.
The diff coverage is 87.64%.

@@            Coverage Diff             @@
##           master      #91      +/-   ##
==========================================
+ Coverage   81.25%   81.26%   +0.01%     
==========================================
  Files          44       47       +3     
  Lines        3723     3886     +163     
==========================================
+ Hits         3025     3158     +133     
- Misses        698      728      +30     

Impacted Files	Coverage Δ
bluegraph/backends/neo4j/analyse/paths.py	80.55% <ø> (ø)
bluegraph/backends/neo4j/io.py	91.53% <ø> (ø)
bluegraph/downstream/data_structures.py	78.37% <ø> (-7.74%)	⬇️
bluegraph/core/io.py	64.02% <33.33%> (-0.11%)	⬇️
bluegraph/backends/gensim/embed/embedders.py	84.09% <84.09%> (ø)
bluegraph/downstream/similarity.py	87.73% <87.95%> (-4.42%)	⬇️
bluegraph/downstream/pipelines.py	88.78% <88.78%> (ø)
bluegraph/backends/gensim/__init__.py	100.00% <100.00%> (ø)
bluegraph/backends/neo4j/embed/embedders.py	90.99% <100.00%> (+0.16%)	⬆️
bluegraph/backends/params.py	100.00% <100.00%> (ø)
... and 6 more

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 00bb7b3...c835e71. Read the comment docs.