Code

NMF optimization & documentation#2361

Code

Merged

menshikh-iv merged 201 commits intopiskvorky:developpiskvorky/gensim:developfrom anotherbugmaster:nmf_speedupsanotherbugmaster/gensim:nmf_speedupsCopy head branch name to clipboardJan 31, 2019

+2,746-3,948

Commits

Commits on Mar 29, 2018

• Implement first version of the algorithm

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Commits on Mar 30, 2018

• Fix variable names

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Commits on Apr 2, 2018

• Add support for streaming corpora

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• Add benchmark

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Commits on Apr 15, 2018

• Fix bugs, introduce batches, add images to the benchmark notebook

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Commits on Apr 22, 2018

• Update notebook

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• Improve model

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• Merge remote-tracking branch 'upstream/develop' into online_nmf

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Commits on Apr 23, 2018

• Add show topics, change API

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• Add more LDA-like API

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• Fix logger name

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• Add more LDA API

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• Remove redundant method

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• Remove commented out lines

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• Fix flakes

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Commits on May 2, 2018

• Cythonize

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Commits on May 22, 2018

• Dramatically improve performance

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Commits on Jun 2, 2018

• Add parameters, improve accuracy and speed

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Commits on Jun 5, 2018

• Remove redundant W copying

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• Fix random seed again

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Commits on Jun 12, 2018

• Optimize E/M step

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Commits on Jun 13, 2018

• Add an eval_every option, use softmax for normalization

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• Fixes

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• Improve notebook examples a bit

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• Fix eval_every

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Commits on Jun 16, 2018

• Return outliers

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• Optimizations

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• Experimenting with loss

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Commits on Aug 14, 2018

• Merge remote-tracking branch 'upstream/develop' into online_nmf

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• Fix PEP8

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• Return nmf import

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Commits on Aug 20, 2018

• Revert "Return nmf import"

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Commits on Aug 27, 2018

• Fix

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• Merge remote-tracking branch 'upstream/develop' into online_nmf

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• Fix minimum_probability & info -> debug logs

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• Compute metrics

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Commits on Aug 28, 2018

• Count error on-the-fly

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• Speed optimizations, changed error functions

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• Beat LDA

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• Outperform sklearn in speed (WTF)

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• Remove redundant arg

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• Add Olivietti faces

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• Remove redundant code

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• Add Topics

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• Make it pretty

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• Fix wrapper

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Commits on Aug 30, 2018

• Save corpus & dict, minor fixes

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Commits on Aug 31, 2018

• Add RandomCorpus

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• Dense -> sparse

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• First doc2dense

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• Fix csc again

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• Fix len

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Commits on Sep 12, 2018

• Experimenting

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• Revert "Experimenting"

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• Fix evaluation

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Commits on Sep 23, 2018

• Sparse speedup

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Commits on Sep 25, 2018

• Improve performance

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• Divide A and B again

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• Fix A and B computation bug

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• Sparsify W init

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• Experimenting

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• New norm

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• Sparse threshold -> sparse coefficient

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Commits on Sep 26, 2018

• Optimize residuals computation

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• Fix residuals bug

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• W speedup

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• Experiment

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• Revert changes a bit

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• Fix corpus

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• Fix init error|

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• Merge branch 'online_nmf' of github.com:anotherbugmaster/gensim into online_nmf

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• Resolve conflict

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• Fix corpus iteration issue

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Commits on Oct 7, 2018

• Switch to numpy algos

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• Merge upstream

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• Train on wikipedia

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Commits on Oct 9, 2018

• Sparse coef -> density. More stable way to sparsify W matrix

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• Merge branch 'online_nmf' of github.com:anotherbugmaster/gensim into online_nmf

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• Return old sparse algo

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• Max

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Commits on Oct 10, 2018

• Optimizations

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• Fix A and B computation

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• Fix A and B normalization

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Commits on Oct 23, 2018

• Add random_state

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• Infer id2word

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Commits on Nov 6, 2018

• Fix tests

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Commits on Nov 14, 2018

• Document __init__

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• Document whole nmf

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• Remove unnecessary comments

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• Add tutorial notebook

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Commits on Nov 20, 2018

• Document __init__

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Commits on Nov 28, 2018

• Fix flake version

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• Fix flake warning

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• Remove comments, reverse parallelization order

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• Add NMF's cython extension to setup.py

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• Fix imports, add solve_r function

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• Remove comments

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• Add docstrings

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• Common corpus and common dictionary

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• Remove redundant test

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• Add signature flag

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• Add files to manifest

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Commits on Nov 29, 2018

• Fix flake8

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• Fix atol value

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• Implement top topics

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Commits on Dec 10, 2018

• Add rst files

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Commits on Dec 11, 2018

• Merge remote-tracking branch 'upstream/develop' into online_nmf

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• Fix appveyor issue

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• Fix cython error

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Commits on Dec 12, 2018

• Merge remote-tracking branch 'upstream/develop' into online_nmf

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• Fix fmax/fmin not being on win-python27

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• Add word transformation test

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Commits on Dec 21, 2018

• Improve readability of residuals computation

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• Merge remote-tracking branch 'upstream/develop' into online_nmf

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• Fix tests

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• A few fixes

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• Blank line at the end of each docstring

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• Add blank line

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• Add the paper reference

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• Fix long line

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Commits on Dec 30, 2018

• Add log_perplexity

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Commits on Jan 7, 2019

• Merge remote-tracking branch 'remotes/upstream/develop' into online_nmf

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Commits on Jan 9, 2019

• Add NMF and LDA comparison table

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• Change the sign of log perplexity

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• Add Sklearn NMF comparison

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• Merge sklearn and tm tables

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Commits on Jan 10, 2019

• Add F1

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• Remove _solve_r

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• Merge tutorial and benchmark

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• Identation's back

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• Optimize optimizers

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• Remove unnecessary pic

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• Optimize memory consumption

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• Add docstring

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• Optimize get_topic_words

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• Merge remote-tracking branch 'upstream/develop' into online_nmf

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• Fix tests

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• Fix flake8

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Commits on Jan 11, 2019

• Add missing test

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• Code review fixes

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• n_tokens -> num_tokens

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• [skip ci] Add explicit normalize parameter

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• [skip ci] Add explicit normalize parameter[2]

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• [skip ci] Update tutorial notebook

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• [skip ci] [WIP] Update wikipedia notebook

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• Merge remote-tracking branch 'upstream/develop' into online_nmf

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Commits on Jan 15, 2019

• Merge branch 'online_nmf' of github.com:anotherbugmaster/gensim into online_nmf

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• Merge remote-tracking branch 'upstream/develop' into online_nmf

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• Add more description and metrics

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• [skip ci] Fix log_probabiliy

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• Multiple format fixes in notebook, outputs cleared til tomorrow

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Commits on Jan 16, 2019

• Merge remote-tracking branch 'upstream/develop' into online_nmf

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• Train on full corpus

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• Merge branch 'online_nmf' of github.com:anotherbugmaster/gensim into online_nmf

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• [skip ci] Remove disclaimer

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• Add RAM usage stats

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• Native 20-newsgroups and additional text

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Commits on Jan 17, 2019

• Truncate outputs

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• Merge remote-tracking branch 'upstream/develop' into online_nmf

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• Fix last cell formatting

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• [skip ci] Change model hyperparameters back

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Commits on Jan 19, 2019

• Merge from upstream

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Commits on Jan 28, 2019

• [skip ci] Add module docstring

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• Merge remote-tracking branch 'upstream/develop' into nmf_docs

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• Merge branch 'online_nmf' of github.com:anotherbugmaster/gensim into online_nmf

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Commits on Jan 29, 2019

• [skip ci] Massive speedups

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• Merge branch 'nmf_docs' into nmf_speedups

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• Checkout nmf_wikipedia from develop

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• Fix tests

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• Fix corpus description

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• Add components permutation to coordinate descent

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• Fix tests

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• Fix dictionary highlight

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• Fix tests again

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Commits on Jan 30, 2019

• Remove r, it's not used for the time

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• Deprecate use_r

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• [skip ci] Rearrange params

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• [skip ci] Add disclaimer about r

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• Fix normalize and minimum_probability docstring

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• Remove unused params

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• Add csc support

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• Add examples to the docstring

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• Update tutorial notebook

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• [skip ci] Update tutorial again

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• [skip ci] Merge remote-tracking branch 'upstream/develop' into nmf_speedups

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• [skip ci] fix PEP

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• cast explicitly permutations to int32

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• [skip ci] Fix a typo

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• Merge remote-tracking branch 'origin/nmf_speedups' into nmf_speedups

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• [skip ci] Remove clip and fix error count in update

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• [skip ci] Fix error computation

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• [skip ci] Fix error counting again

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• [skip ci] Remove redundant imports

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• Fix grouper for csc matrices

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• Fix module docstring

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• Fix training corpus description

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• Fix pep8

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• Fix flake8 for real

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• Normalize, sparsity and dictionary fixes

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Commits on Jan 31, 2019

• Updated module docstring in the notebook

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