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[MRG+1] Reducing t-SNE memory usage#9032

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ogrisel merged 55 commits intoscikit-learn:masterscikit-learn/scikit-learn:masterfrom

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Jul 12, 2017

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Commits on Jul 11, 2017

• ENH improve memory usage of t-sne

  

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• ENH add a benchmark for t-SNE

  

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• ENH improve bench script+add params for TSNE

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• ENH add PCA preprocessing to benchmark [ci skip]

  

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• ENH improve benchmark script

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• WIP on fixing the optimization schedule and default parameters

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• Shuffle the data in the benchmark script

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• WIP more work on opt scheduling and stopping criterion

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• ENH add basic QuadTree in neighbors

  

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• ENH TSNE running with new QuadTree

  

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• FIX picklizable QuadTree + more tests

  

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• Compute first NN accuracy

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• TST independently seeded rng

  

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• Add script to plot TSNE benchmark results

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• CLN remove unsused code

  

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• TST improve parameter testing

  

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• CLN improve code readability

  

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• CLN more comments in quad_tree

  

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• CLN remove malloc when possible + trailing white-space

  

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• CLN fix pep8+add comments+rename methods quad_tree

  

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• CLN pep8+typo+remove plot

  

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• CLN remove knn extra args for TSNE

  

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• TST reduce test time

  

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• FIX flake8 unused import

  

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• TST make test_preserve_trustworthiness_approximately less strict

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• DOC adjust the perplexity range in t-SNE example

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• CLN clarify quad_tree header

  

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• CLN comment and typo+early free knn

  

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• CLN add what's new entry

  

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• TST improve test_t_sne for changed parameters

  

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• FIX what's new entry

  

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• FIX typo in test and reduce test time

  

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• Add uniform grid to perplexity example

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• TST 2D uniform grid recovery by TSNE

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• TST simpler code

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• TST fix comment in check_uniform_grid

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• ENH simplify example usage in TSNE docstring

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• CLN max_width->squared_max_width to improve code readability

  

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• FIX duplicated point in quad_tree summary

  

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• TST add summary test for quad_tree

  

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• TST fix t-SNE tests for uniform grid

  

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• CLN unified TSNE stopping criterion + comments

  

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• FIX pep8+typo/ more log for tests failures

  

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• FIX quad_tree boundary computations

  

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• ENH use dbl tsne_bh sum_Q to match exact solver

  

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• CLN param description+Add private optim controls

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• FIX TSNE set n_iter_without_progress=300 by default

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• FIX bench_tsne_mnist.py: no n_jobs for now

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• FIX various optimization schedule issues in TSNE

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• TST fix broken test in tsne

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• FIX debug code in bench script [ci skip]

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• TST compare KL error of BH approx vs exact with angle=0

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Commits on Jul 12, 2017

• CLN verbose log more informative

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• CLN left out debug print

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• FIX numerical precision in Barnes Hut error computation

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