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fix(kg_emb): port kg_emb to the 2.0 dataset pipeline - #1202

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AxelNoun:fix/kg-emb-2.0-migration

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fix(kg_emb): port kg_emb to the 2.0 dataset pipeline#1202
AxelNoun wants to merge 46 commits into
sunlabuiuc:masterfrom
AxelNoun:fix/kg-emb-2.0-migration

Commits on Aug 25, 2026
- fix(kg_emb): decouple SampleKGDataset from the 2.0 streaming pipeline
  
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- fix(kg_emb): correct dataset type hints across models
  
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- fix(kg_emb): repair the module examples' dataset import
  
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- refactor(kg_emb): make split() side-effect free and reproducible
  
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- chore(kg_emb): remove dead imports of the undeclared pandarallel package
  
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- test(kg_emb): add behavioural regression tests for issue #952
  
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- docs(kg_emb): satisfy contribution-rules
  
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- style(kg_emb): tidy docstring punctuation
  
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Commits on Aug 29, 2026
- fix(kg_emb): make task_spec_param covariant in KGDatasetProtocol
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- fix(kg_emb): annotate __main__ demo samples for mypy
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Commits on Aug 31, 2026
- feat(kg_emb): rebase SampleKGDataset onto InMemorySampleDataset with the Tensor Trick
  
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- fix(kg_emb): satisfy contribution-rules CI gate (ruff + docstring example)
  
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Commits on Oct 6, 2026
Commits on Oct 7, 2026
- Merge upstream/master into fix/kg-emb-2.0-migration
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- refactor(kg_emb): rebuild BaseKGDataset on BaseDataset
  
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- feat(processors): add a kg_triple processor and keep long KG lists whole
  
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Commits on Oct 9, 2026
- feat(kg_emb): add the KGLinkPrediction task
  
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- refactor(kg_emb): make the KGE models consume a SampleDataset
  
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- fix(kg_emb): draw training negatives from training triples only
  
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- chore(kg_emb): deprecate the 1.x entry points for one release
  
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- docs(kg_emb): document the 2.0 pipeline and update the examples
  
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- fix(kg_emb): honour 1.x per-sample negative_sampling and NumPy integers
  
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- fix(kg_emb): refuse base datasets in the models and tighten the leak tests
  
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Commits on Oct 26, 2026
- Fusionner upstream/master (4a173f7) dans fix/kg-emb-2.0-migration
  
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Commits on Oct 27, 2026
- fix(kg_emb): replace np.in1d, removed in NumPy 2.4, with np.isin
  
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- docs(kg_emb): state what held-out triples do and do not shape
  
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- docs(kg_emb): document tie handling and the UMLS inverse-relation leakage
  
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- docs(kg_emb): use the default ns in the TransE and RotatE examples
  
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- fix(kg_emb): let UMLSDataset jobs prepare the same root at once
  
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- test(kg_emb): reference scores, filtered ranking by hand, all four models
  
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Commits on Oct 28, 2026
- refactor(kg_emb): remove the PyHealth 1.x compatibility layer
  
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- perf(kg_emb): keep the filtered-ranking sets once per task
  
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- test(kg_emb): pin the numeric row order of pre_filter
  
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- docs(kg_emb): make the cross-references of the API docs resolve
  
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- fix(kg_emb): read the held-out parts by index to build the filter sets
  
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- fix(kg_emb): read the first part when its processor is a subclass
  
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- fix(kg_emb): keep the task cache key of a processor instance stable
  
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- fix(kg_emb): give False for a malformed triple spec
  
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- fix(kg_emb): warn when the supplied kg_triple processor was never fitted
  
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- test(kg_emb): cover the subsampling weights in the loss and edge cases
  
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- docs(kg_emb): correct docstrings and the migration note
  
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- Merge sunlabuiuc/PyHealth master into fix/kg-emb-2.0-migration
  
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Commits

Commits on Aug 25, 2026

Commits on Aug 29, 2026

Commits on Aug 31, 2026

Commits on Oct 6, 2026

Commits on Oct 7, 2026

Commits on Oct 9, 2026

Commits on Oct 26, 2026

Commits on Oct 27, 2026

Commits on Oct 28, 2026