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[MRG] Poincare model keyedvectors #1700

Merged
merged 188 commits into from
Dec 4, 2017
Merged

[MRG] Poincare model keyedvectors #1700

merged 188 commits into from
Dec 4, 2017

Commits on Oct 26, 2017

  1. Initial classes and loading data for poincare model

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  2. Initial implementation of training using autograd

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  3. faster negative sampling, bugfix in vector updates

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  4. allows poincare dist function to be differentiable by autograd

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  5. batched gradient descent initial implementation

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  6. minor changes to batch poincare distance computation

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  7. Adds calculation of gradients for poincare model

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  8. Correct implementation of clipping of updated vectors

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  9. Fixes error in gradient computation

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  10. Better messages while training

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Commits on Oct 27, 2017

  1. Renames PoincareDistance to PoincareExample for clarity

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  2. Compares computed gradients to autograd gradients every few iterations

    @jayantj
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  3. Avoids doing some numpy computations twice

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  4. Avoids creating copies of numpy vectors

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  5. Only calls nan_to_num when gamma has at least one value equal to 1

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  6. Simply sets nan gradients to zero instead of nan_to_num

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  7. Adds batch-wise implementation of training and gradient computations

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Commits on Oct 30, 2017

  1. Minor correction in clipping

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  2. Merge branch 'poincare' into poincare_model

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  3. Fixes typo in clip_vectors

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Commits on Oct 31, 2017

  1. Prints average loss every few iterations instead of current loss

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Commits on Nov 2, 2017

  1. Adds weighted negative sampling

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  2. Ensures positive edges are not returned by negative sampling

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  3. Poincare model stores node indices in relations instead of node keys

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  4. Minor renaming; uses node indices for batch training instead of node … 

    …keys
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Commits on Nov 3, 2017

  1. Changes shapes of vectors passed to PoincareBatch

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  2. Minor bugfixes related to batch size

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  3. Corrects implementation of negative sampling for batch training

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  4. Adds option to check gradients in batchwise training

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  5. Checks gradients only every few iterations

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  6. Handles multiple occurrence of same node across and within batches

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  7. Removes unused section of code

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  8. Implements slightly different clipping method

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  9. Fixes bugs with wrong reshape in batchwise training

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  10. Example-wise training takes into account multiple occurrences of same… 

    … node in an example too
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  11. Batchwise training prints average loss over many iterations instead o… 

    …f current batch
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  12. Fixes bug in updating vector for batchwise training

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  13. Faster implementation of negative sampling

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Commits on Nov 6, 2017

  1. Negative sampling for a node follows different paths depending on fra… 

    …ction of positive relations
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  2. Uses a buffer for negative samples to reduce calls to np.random.choice

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  3. Cleans up poincare.py, removes unused code

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  4. Adds shapes to PoincareBatch, more documentation

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  5. Adds more documentation to PoincareModel

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  6. Stores indices for nodes in a batch in PoincareBatch for better encap… 

    …sulation
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  7. More documentation for poincare module

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  8. Implements burn-in for poincare model

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  9. Slightly better logging for poincare model

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Commits on Nov 7, 2017

  1. Uses np.random.random and np.searchsorted for random sampling rather … 

    …than np.random.choice
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  2. Removes duplicates in negative samples

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  3. Moves helper classes in poincare after PoincareModel

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  4. Change in PoincareModel API to allow initializing from an iterable, s… 

    …eparate class for streaming from file
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  5. Adds failing test for handling encoding in PoincareData

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  6. Fixes encoding handling in PoincareData

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  7. Adds docstrings to PoincareData, PoincareData streams tuples now

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Commits on Nov 8, 2017

  1. More unittests for PoincareModel

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  2. Changes handle_duplicates to staticmethod, adds test

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  3. Adds batch size and print_every parameters to train method

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  4. Renames print_check to should_print

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  5. Adds separate parameter for checking gradients

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  6. Minor fixes for coding style

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  7. Removes default values from docstrings, redundant

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  8. Adds example to PoincareModel init docstring

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  9. Extracts buffer for negatives out into a separate class

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  10. More detailed logging, fix to check_gradients

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  11. Minor fixes to documentation in poincare.py

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  12. Adds support for most_similar to PoincareKeyedVectors

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  13. Refactors most_similar and loss_fn to use PoincareKeyedVectors.poinca… 

    …re_dists
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  14. Adds tests for gradients checking

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  15. Raise AssertionError if gradients check fails

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  16. Adds failing tests for saving/loading PoincareModel instances

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  17. Fixes bug with saving/loading PoincareModel to disk

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  18. Adds test and fix for raising error on invalid input data

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  19. Adds test and fix for no duplicates and positives in negative sample

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  20. Bugfix with NegativesBuffer having less than items left

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  21. Uses larger data for poincare tests, adds data files

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  22. Bugfix with incorrect use of random state

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Commits on Nov 9, 2017

  1. Minor fixes in documentation style

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  2. Renames PoincareData to PoincareRelations

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  3. Change in the order of conditions checked before resampling

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  4. Merge branch 'poincare' into poincare_model

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  5. Imports datapath from test.utils instead of defining own

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  6. Adds working examples and a more detailed description in docstring

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  7. Renames term_relations to node_relations

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  8. Removes unused imports

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  9. Moves iter parameter to train instead of __init__, renames to epochs

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  10. Fixes term_relations in tests

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  11. Adds option to disable gradient check, disabled by default

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  12. Extracts gradient checking code into a separate method

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  13. Conditionally import autograd only if gradient checking is enabled

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  14. Marks private methods in poincare module with leading underscore

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  15. Adds init_range as an API parameter to PoincareModel

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  16. Marks private properties with a leading underscore

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  17. Fixes bug with burn-in happening on subsequent calls to train

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  18. Adds test for training multiple times

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  19. Adds autograd to test dependencies

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  20. Renames wv to kv in PoincareModel

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Commits on Nov 10, 2017

  1. add numpy==1.12 as test dependency

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  2. add missing quote

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Commits on Nov 11, 2017

  1. Merge branch 'poincare_model' into poincare_model_keyedvectors 

    Conflicts:
	gensim/models/poincare.py
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  2. Moves methods for evaluating poincare embeddings to poincare.py

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  3. Updates docstrings for newly added classes

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  4. Moves trie-related methods to LexicalEntailmentEvaluation

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  5. Moves code for loading PoincareEmbedding into notebook

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  6. Removes PoincareEmbedding class, adds functionality to PoincareKeyedV… 

    …ectors
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  7. Updates eval nb with code and evaluation results for gensim models

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Commits on Nov 12, 2017

  1. Minor documentation updates + bugfix in distance

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  2. Adds methods for rank and nodes_closer_than to PoincareKeyedVectors

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  3. Adds methods to return closest child, parent, and ancestor and descen… 

    …dant chain for an input node
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  4. Updates LE and reconstruction results for gensim models in eval nb

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  5. Adds notebook detailing Poincare embedding operations and report

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  6. Adds images for poincare embedding report

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  7. Updates image links in poincare report nb

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Commits on Nov 13, 2017

  1. try to run tests without autograd

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  2. fix PEP8 in poincare.py

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  3. fix PEP8 in test_poincare

    @menshikh-iv
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  4. PoincareRelations handles python2 correctly

    @jayantj
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  5. Bugfix with int division for python2

    @jayantj
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  6. Imports mock module for tests correctly in python2

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  7. Cleaner implementation of __iter__ for PoincareRelations

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  8. Adds rst file and updates apiref.rst for poincare module

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  9. Adds clarifying comment to PoincareRelations.__iter__

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  10. Adds functions for visualization to poincare_visualization.py

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  11. Suppresses certain numpy warnings while training model

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  12. Updates rst file for poincare

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  13. Updates poincare report nb with reduced code, section on training, be… 

    …tter visualization labels and titles
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  14. Renames hypernym pair to relations everywhere

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  15. Simpler way of detecting duplicates

    @jayantj
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Commits on Nov 14, 2017

  1. Minor documentation updates in poincare.py

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  2. Skips gradients test if autograd not installed, adds test for bytes i… 

    …nput data
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  3. Adds results of gensim models on link prediction to eval notebook

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  4. Adds link prediction results to report, more information about training

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  5. Adds further details to concept and motivation sections, section on f… 

    …uture work, and images
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  6. Fix flake8 (noqa + remove unused var)

    @menshikh-iv
    menshikh-iv committed Nov 14, 2017
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  7. Fix missing mock dependency for win

    @menshikh-iv
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  8. Fix links in docstrings

    @menshikh-iv
    menshikh-iv committed Nov 14, 2017
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Commits on Nov 15, 2017

  1. Refactors KeyedVectors into KeyedVectorsBase and EuclideanKeyedVectors

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  2. Changes error message for negative sampling failing

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  3. Adds option to specify dtype for PoincareModel and corresponding unit… 

    …test
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  4. Extends test for dtype to check after training, updates docstring

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  5. Merge branch 'poincare_model' into poincare_model_keyedvectors 

    Conflicts:
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  6. Adds tests for new methods in PoincareKeyedVectors

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  7. Fixes bug in closest_child implementation

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  8. Adds similarity and distance to KeyedVectorsBase interface, implement… 

    …ation and tests for similarity for PoincareKeyedVectors
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  9. Minor fixes to Poincare report notebook

    @jayantj
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Commits on Nov 16, 2017

  1. Adds method to compute all distances to KeyedVectorsBase, moves most_… 

    …similar from EuclideanKeyedVectors to KeyedVectorsBase
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  2. Allows PoincareKeyedVectors.distances to accept an optional list of w… 

    …ords
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  3. Adds implementation of PoincareKeyedVectors.similarities and tests

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  4. Adds restrict_vocab option to most_similar and tests for EuclideanKey… 

    …edVectors.most_similar
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  5. Adds docstring for tests

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    jayantj committed Nov 16, 2017
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Commits on Nov 17, 2017

  1. Adds implementation of EuclideanKeyedVectors.distances and tests, upd… 

    …ates docstrings
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  2. Moves most_similar_to_given to KeyedVectorsBase, adds tests

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  3. Moves similar_by_vector and similar_by_word to KeyedVectorsBase, adds… 

    … tests
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  4. Adds failing tests for similar_by_word and similar_by_vector to Poinc… 

    …areKeyedVector tests
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  5. Moves multiple methods out of KeyedVectorsBase back to EuclideanKeyed… 

    …Vectors, removes tests
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  6. Adds test for most_similar with vector input for EuclideanKeyedVectors

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  7. Adds failing test for vector input for most_similar for PoincareKeyed… 

    …Vectors
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  8. Allows passing in vector input to most_similar and distances methods … 

    …in PoincareKeyedVectors
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  9. Removes precompute_max_distance and uses simpler formula for similari… 

    …ty in PoincareKeyedVectors
    @jayantj
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  10. Renames PoincareKeyedVectors.poincare_dists to PoincareKeyedVectors.p… 

    …oincare_distance_batch
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  11. Fixes error with unclosed file in PoincareRelations

    @jayantj
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  12. Adds tests and method for computing poincare distance between two inp… 

    …ut vectors
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  13. Adds methods and tests for finding position and difference in hierarc… 

    …hical positions of input vectors
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Commits on Nov 20, 2017

  1. Merge branch 'poincare' into poincare_model_keyedvectors 

    Conflicts:
	gensim/models/poincare.py
	gensim/test/test_poincare.py
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Commits on Nov 21, 2017

  1. Fixes unused import, pep8 and docstring issues

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  2. More intuitive naming of arguments for methods in PoincareKeyedVectors

    @jayantj
    jayantj committed Nov 21, 2017
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  3. Uses w1 and w2 consistently across KeyedVectors methods

    @jayantj
    jayantj committed Nov 21, 2017
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  4. Removes most_similar from KeyedVectorsBase

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  5. Adds failing tests for words_closer_than and rank for EuclideanKeyedV… 

    …ectors and PoincareKeyedVectors
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Commits on Nov 22, 2017

  1. Adds distances method to KeyedVectorsBase and EuclideanKeyedVectors, … 

    …fixes tests
    @jayantj
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  2. Makes default argument for distances immutable

    @jayantj
    jayantj committed Nov 22, 2017
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  3. Uses conditional import for pygtrie in LexicalEntailmentEvaluation

    @jayantj
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  4. Renames position_in_hierarchy to norm with minor change in behaviour,… 

    … updates tests
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  5. Renames poincare_distance and poincare_distance_batch to vector_dista… 

    …nce and vector_distance_batch
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  6. Forces float division for positive_fraction in _sample_negatives

    @jayantj
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  7. Removes unused method from PoincareKeyedVectors

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  8. Updates report notebook with usage examples of new API methods

    @jayantj
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  9. Minor pep8 fix

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Commits on Nov 23, 2017

  1. Fixes pep8 issues, unused imports and typo

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  2. Adds example of saving and loading model to notebook

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  3. Updates docstrings in poincare.py

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Commits on Nov 27, 2017

  1. Moves poincare visualization methods to new gensim.viz module

    @jayantj
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  2. Updates rst files for poincare viz

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  3. Adds newline at the end of poincare.py in viz package

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Commits on Dec 2, 2017

  1. Adds link to original paper to poincare notebook

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Commits on Dec 4, 2017

  1. fix viz.poincare & update docs dependencies

    @menshikh-iv
    menshikh-iv committed Dec 4, 2017
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  2. add link to init file

    @menshikh-iv
    menshikh-iv committed Dec 4, 2017
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  3. fix PEP8

    @menshikh-iv
    menshikh-iv committed Dec 4, 2017
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  4. fixes for poincare.py

    @menshikh-iv
    menshikh-iv committed Dec 4, 2017
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