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Add a graph learning module#57

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nperraud wants to merge 134 commits intomasterepfl-lts2/pygsp:masterfrom learngraphnewepfl-lts2/pygsp:learngraphnewCopy head branch name to clipboard

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Commits on Mar 19, 2018

• attempt to refactor nn graph building

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• update tests

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• fix typo

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• fix tests (avoiding not implemented combinations)

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• - fix missing space after colon in dictionary

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• fix (matlab) GSP url

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• throw exception when using FLANN + max_dist (produces incorrect results)

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• update test case to fit FLANN & max_dist exception

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Commits on Mar 20, 2018

• implement nn graph using pdist using radius

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• implement radius nn graph with flann

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• flann returns the squared distance when called with 'euclidean' distance -> fix

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• compute sqrt of list properly

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• use cyflann instead of pyflann (radius search not working)

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• check nn graphs building against pdist reference

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• cyflann needs the flann library to be installed on the system

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• check nn graphs building against pdist reference

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• backport stuff from cyflann branch

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• flann should (mostly) work for knn graphs

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Commits on Mar 21, 2018

• fix pdist warnings

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• implement and use scipy-ckdtree as default (faster than kdtree)

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Commits on Mar 22, 2018

• Merge remote-tracking branch 'origin-nas/nn_cyflann' into nn_refactor

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• backport README changes from master

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• Merge branch 'master' of https://github.com/epfl-lts2/pygsp into nn_refactor

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• Merge branch 'master' into nn_refactor

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Commits on Mar 26, 2018

• add nmslib

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• test flann when not on windows

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Commits on Mar 29, 2018

• use the same code to build sparse matrix for knn and radius

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• building the graph with rescale/center=False should also work

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• Merge pull request #1 from naspert/nmslib

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• update doc for nmslib

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Commits on Apr 9, 2018

• enable multithreading with ckdtree/nmslib

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Commits on Jun 20, 2018

• Merge branch 'master' into nn_refactor

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• fix _get_extra_repr

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Commits on Feb 8, 2019

• Merge branch 'nn_refactor' of https://github.com/naspert/pygsp into naspert-nn_refactor

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Commits on Feb 13, 2019

• Merge branch 'master' into naspert-nn_refactor

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Commits on Feb 14, 2019

• NNGraph: clean and doc (PR #21)

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• python 2.7 doesn't support keyword-only args

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Commits on Feb 15, 2019

• simplify test_nngraph (PR #21)

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• python 2.7 doesn't support dict unpacking

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• correct number of edges (PR #21)

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• order=3 by default (order=0 is not supported by all backends)

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• avoid deprecation warning

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• deal with empty neighborhood

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• nngraph: don't store features

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• nngraph: further cleanup

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• nngraph: standardize instead of center and rescale

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Commits on Feb 16, 2019

• nngraph: simplify default kernel_width

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• nngraph: test empty graph

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• no assertLogs in python 2.7

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• nngraph: fix symmetrization

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• nngraph: fix radius cKDTree (PR #21)

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Commits on Feb 19, 2019

• compact code

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• NNGraph: allow user to pass parameters to backends

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• fix flann distances

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• NNGraph: test consistency across backends

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• python 2.7 dict unpacking

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• pdist accepts no parameters

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Commits on Feb 20, 2019

• NNGraph: test distance on a circle

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• NNGraph pdist: don't sort twice

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• NNGraph: fuse knn and radius implementations

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• nmslib: number of thread is automatically set to max

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• order consistent with metric

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• cleaner error handling

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• nngraph: test standardization

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Commits on Feb 21, 2019

• nngraph: radius estimation

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• fix others uses of radius

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Commits on Feb 24, 2019

• nngraph: check shape of features

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• nngraph: fix definition of gaussian kernel

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• nngraph: allow users to choose the similarity kernel

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• nngraph: fix attributes

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• nngraph: fix intermittent test failure of nmslib

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Commits on Feb 25, 2019

• nngraph: width = radius / 2

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• nngraph: doc and examples

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• nngraph: update history

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• Update nngraph.py

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Commits on Mar 1, 2019

• nngraph: only warn for similarity > 1

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Commits on Mar 13, 2019

• show original exception if nmslib cannot be imported

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Commits on Jul 18, 2019

• backup commit

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• working sparse solution

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Commits on Jul 22, 2019

• add nn support

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• make test work

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• Merge branch 'naspert-nn_refactor' into learngraphnew

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• backup commit

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• fix tests

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• make k=4 to pass tests

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Commits on Jul 25, 2019

• test

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Commits on Jul 26, 2019

• making test pass -- not very clean nn function

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Commits on Aug 16, 2019

• update tests

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• Merge branch 'naspert-nn_refactor' into learngraphnew

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Commits on Aug 17, 2019

• Merge branch 'master' into naspert-nn_refactor

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• going further

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• small fix

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• fix doc

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• fix test

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• fix test

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• fix test_graphs

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Commits on Aug 19, 2019

• update reduction

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• Merge branch 'naspert-nn_refactor' into learngraphnew

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• move files

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• first version

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• update graph

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• updates

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• fix bugs

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• update doc

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• update history

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• small fix

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• update doc

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• add code to test each module separatly

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• fix doc

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• fix some doc

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• fix tests

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• fix compat python 2.7

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• fix compat python 2.7

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• fix compat python 2.7

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• fix random test

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Commits on Sep 26, 2019

• Update learngraph.py

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Commits on Nov 9, 2019

• Merge branch 'master' into naspert-nn_refactor

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Commits on Nov 10, 2019

• update test and remove useless files

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• small fix in import

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• update seed

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• update seed

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Commits on Nov 11, 2019

• minor fix in playground.ipynb

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Commits on Nov 15, 2019

• Merge remote-tracking branch 'origin/naspert-nn_refactor' into learngraphnew

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• rename

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• hack my way through renaming

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• fix import

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Commits on Nov 16, 2019

• Merge branch 'learngraphnew' of github.com:epfl-lts2/pygsp into learngraphnew

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Commits on Nov 17, 2019

• Big bug in graph learning: Z needs **squared** Euclidean distances

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Commits on Mar 29, 2020

• Allow to set manually edge_mask in LearnedFromSmoothSignals

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Commits on May 14, 2020

• fix square bug

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Commits on May 15, 2020

• Update learned.py

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Commits on Jun 21, 2020

• minor exception fix

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• solve merge conflict: kept my version that is more detailed

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• Merge branch 'master' into learngraphnew

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