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Working Workflow Example #36

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c2abc42
Initial copy from BHelfrecht repo, and a few minor adaptations
ceriottm Feb 9, 2020
8eb914d
Made sure importing works
ceriottm Feb 9, 2020
ed39595
Supplemented Oneoff selection with Iterative wo/ Orthogonalising, Ad…
Feb 10, 2020
c872f1f
Enabling custom pi_functions for CUR
Feb 10, 2020
e59b50b
Bugfix to KPCovR and SparseKPCovR: test kernel should be centered rel…
bhelfrecht Feb 10, 2020
d05152a
Bugfix to KPCovR and SparseKPCovR: test kernel should be centered rel…
bhelfrecht Feb 10, 2020
c61e38a
Edits from Felix
Feb 10, 2020
34a03e4
Edits from Felix
Feb 10, 2020
7904ad2
Y reshape error
Feb 10, 2020
96d2530
Add a script to generate chemiscope input for PCovR style data
Luthaf Feb 10, 2020
ff58b67
Add a small section on how to create a chemiscope input
Luthaf Feb 10, 2020
7e41bef
Rescale the properties before creating the chemiscope input
Luthaf Feb 10, 2020
98987a9
Doc-strings for CUR
Feb 10, 2020
12e3ea4
Removed old code from files
Feb 10, 2020
e19c4a2
W --> PXY or PTY in NB1
Feb 10, 2020
c679e93
W --> PXY or PTY in NB2
Feb 10, 2020
1891364
W --> PXY or PTY in NB4
Feb 10, 2020
fcaeb20
W --> PTY or PKY in NB3
Feb 10, 2020
cef4f44
W --> P?Y in utilities
Feb 10, 2020
6740148
Bug fix in CUR
Feb 11, 2020
21b63bf
Notation sync with manuscript
Feb 11, 2020
4e93068
Notation sync with manuscript
Feb 11, 2020
13ea3ba
f(A^TA)A^T
Feb 11, 2020
c15ef85
Properly backrolling CUR
Feb 12, 2020
5709fbd
Making plotting importable from any folder
Feb 12, 2020
ddd9e50
Small Bug/Typo in KPCovR Loss
rosecers Feb 12, 2020
2446646
Error in SKPCA
rosecers Feb 12, 2020
d389280
Plotting incompatibility
rosecers Feb 12, 2020
d93c8fb
Who reverted my edits to CUR?
rosecers Feb 13, 2020
55943c5
Made sps optional
rosecers Feb 13, 2020
a15a613
Fixed scaling bug in general, non-critical
rosecers Feb 14, 2020
ade33b2
Fixed Critical bug in CUR
rosecers Feb 14, 2020
f89ca75
Small, small edits to CUR
rosecers Feb 14, 2020
77787e0
Merge branch 'master' of https://github.com/cosmo-epfl/kernel-tutorials
bhelfrecht Feb 26, 2020
541b05a
Added ability to pass Yhat as an input to KPCovR and SparseKPCovR; au…
rosecers Feb 28, 2020
72cf6e3
Merge branch 'master' of https://github.com/cosmo-epfl/kernel-tutorials
rosecers Feb 28, 2020
d03cc77
Added ability to pass Yhat as an input to PCovR; autopep8 formatted
rosecers Feb 28, 2020
795f2bd
Added option to find eigenvalues via scipy sparse
rosecers Feb 28, 2020
4285c96
Added option to find eigenvalues via scipy sparse for CUR
rosecers Feb 28, 2020
76d73ff
Fixing an error in the order of sorted_eigs with scipy.sparse
rosecers Feb 28, 2020
1493d2e
Some small formatting fixes
rosecers Feb 28, 2020
6fab9e1
Make plotting utils nicer to work with and more properly formatted
rosecers Feb 28, 2020
baf2215
Enabled 2D colormaps for Projections
Mar 4, 2020
2c1c760
Swapped cmaps for X and Y
Mar 5, 2020
127457f
Fixing multidimensional Y coloring
Mar 5, 2020
c0cbcb9
Made CUR.py self-contained
Mar 5, 2020
a2a571f
Make plotting compatible with scalar or array Y_scale and Y_center
bhelfrecht Mar 6, 2020
a7c2213
Bug fix in plotting
Mar 10, 2020
30a25e0
Bug fix in plotting
Mar 10, 2020
fc024a1
Fixing cb_ax
Mar 12, 2020
3a5175c
Fixed bug in plotting
Mar 12, 2020
ef47491
Removing normalization of Ktilde and Ctilde in KPCovR, as phi is cent…
Mar 17, 2020
dd77c3d
125X (user, 5000 samples) speedup in kernel centering
Mar 17, 2020
97cc31b
125X (user, 5000 samples) speedup in kernel centering
Mar 18, 2020
eb0dc9e
125X (user, 5000 samples) speedup in kernel centering
Mar 18, 2020
31426a6
Merge branch 'master' of https://github.com/cosmo-epfl/kernel-tutorials
rosecers Mar 18, 2020
f2dbd07
Fixing slowdown in KRR
Mar 20, 2020
52b7cdb
Merge branch 'master' of https://github.com/cosmo-epfl/kernel-tutorials
rosecers Mar 20, 2020
6e20777
Overhaul of classes to define superclass structure and replace np.mat…
Mar 27, 2020
537ea1a
Test NB for new classes
Mar 27, 2020
e8c3062
Merge branch 'master' of https://github.com/cosmo-epfl/kernel-tutorials
rosecers Mar 27, 2020
e643f3e
Bug fix in classes.py
rosecers Mar 27, 2020
3fdcecf
Moving kpcovr_contained back to kpcovr
Mar 30, 2020
92a4874
Update formatting
Luthaf Mar 30, 2020
a2e3885
more robust sorted_eig
rosecers Apr 2, 2020
0facdf2
Merge
rosecers Apr 2, 2020
e8c4778
Speed up to CUR
rosecers Apr 7, 2020
46b8c07
Undid an error
Apr 8, 2020
01c4e30
Merge
Apr 8, 2020
3bed710
Adding scipy import
rosecers Apr 8, 2020
34a461d
Fixed two errors: PCovR inheritance, where the scaling parameters of …
Apr 9, 2020
072ca8d
nbstripout
Apr 9, 2020
c3ceae8
Removing comments
rosecers Apr 14, 2020
01f1c43
Update chemiscope input generation
Luthaf Apr 14, 2020
e18e2b7
Made X optional for Sparse methods
Apr 14, 2020
8c56084
Merge branch 'master' of https://github.com/cosmo-epfl/kernel-tutorials
Apr 14, 2020
accecf1
Fix bugs in Y scaling and PCovR transformation
bhelfrecht Apr 16, 2020
c8d1e9a
Added failsafe to CUR
rosecers Apr 17, 2020
4abb5df
Merge branch 'master' of https://github.com/cosmo-epfl/kernel-tutorials
rosecers Apr 17, 2020
3f5e6ec
Merge branch 'master' of https://github.com/cosmo-epfl/kernel-tutorials
bhelfrecht Apr 20, 2020
362033f
Add new sparse scaling scheme to utility classes
bhelfrecht Apr 20, 2020
e4f1aaf
Modify tests for new class structure
bhelfrecht Apr 20, 2020
4a5d312
Strip output of TestingNewClasses.ipynb
bhelfrecht Apr 20, 2020
4be750a
Made rasterize=True default for scatter plots
Apr 21, 2020
2d0209e
Increase rcond in sparse kernel scaling; other small fixes to optiona…
bhelfrecht Apr 21, 2020
c48d8aa
Merge branch 'master' of https://github.com/cosmo-epfl/kernel-tutorials
bhelfrecht Apr 21, 2020
30ea740
Made colorbars truncatable
Apr 22, 2020
081bdde
Adding default colorbars into matplotlib
Apr 22, 2020
006661f
Made it possible to pass additional properties not included into the …
Apr 28, 2020
d9536fa
Made gaussian kernel more robust with structure-structure kernels
Apr 29, 2020
36a0745
Made gaussian kernel more robust with structure-structure kernels
Apr 29, 2020
2030e6a
Variable name change for clarity
Apr 29, 2020
ce65c9c
Removed tqdm dependency of gaussian kernel
Apr 29, 2020
802064b
Truncating inputted properties to 2 parameters for colormaps
Apr 30, 2020
4c5d96c
Simpler eig_inv implementation
ceriottm May 26, 2020
cc7f8f8
First go at a sklearn-style feature scaler
ceriottm Jun 1, 2020
deaea11
Formatted PCovR fit functions ala sklearn
Jun 2, 2020
70821cc
WIP transformations in new PCovR class
bhelfrecht Jun 2, 2020
e725ca6
Pre-test PCovR
Jun 2, 2020
b63079f
Fixing an error in prediction
Jun 2, 2020
add4f43
Fixed bug in new PCovR, added test class
Jun 2, 2020
f5c6fb3
overriding error with 1D projections
Jun 2, 2020
93f0890
Merge branch 'master' into sklearn_adaptation
Jun 2, 2020
8eb4693
overriding error with 1D projections
Jun 2, 2020
5ecd404
Merge branch 'master' into sklearn_adaptation
Jun 2, 2020
93ee2aa
Csting eigenvalues as real
Jun 2, 2020
8c998fb
Finished pcovr test
Jun 2, 2020
775cacf
Made font sizes scalable and disabled 'Only plotting first column of …
Jun 2, 2020
ec68034
Overriding fs for kernel generation
Jun 2, 2020
d7129a6
Merge branch 'master' into sklearn_adaptation
Jun 2, 2020
ce2545c
Finished pcovr test
Jun 2, 2020
12939dd
Moved sklearn classes to separate folder
Jun 2, 2020
56ba816
Removed last wrong svd call
Jun 2, 2020
dc9bdbc
Ooops. Had forgotten to add scalers.
ceriottm Jun 3, 2020
1a757ed
Merge branch 'feat/utilities_cleanup' of github.com:cosmo-epfl/kernel…
ceriottm Jun 3, 2020
873d252
Merge branch 'sklearn_adaptation' into feat/utilities_cleanup
Jun 3, 2020
55da2a9
Regression Error --> l_regr, Representation Error --> l_proj
rosecers Jun 23, 2020
4d1e6a2
Fixed a bug in the saving of precomputed
rosecers Jun 23, 2020
66557f0
NB 1 needed minor changes for consistency with paper
rosecers Jun 23, 2020
b0135b9
Fix typo in text regarding location of precomputed.npz
bhelfrecht Jun 23, 2020
8df67a2
Change notation on unit-variance projections to be consistent with ma…
bhelfrecht Jun 23, 2020
b96ef4c
Implemented ell_kpcovr in utility classes and statistics
rosecers Jun 23, 2020
8fedca8
Bug in naming of statistics
rosecers Jun 23, 2020
195a95a
Pulling KPCovR from classes.py
rosecers Jun 23, 2020
c12636e
Scaling of kernels in notebook
rosecers Jun 23, 2020
1256e0e
Some aesthetic modifications to the NB
rosecers Jun 23, 2020
1a81038
Small pedagogic updates to NB
rosecers Jun 23, 2020
276e8fb
LKPcovR put into NB
rosecers Jun 23, 2020
c944144
Small aesthetic changes
rosecers Jun 23, 2020
8b6da0c
Merge branch 'master' of https://github.com/cosmo-epfl/kernel-tutorials
bhelfrecht Jun 24, 2020
efb3575
Merge pull request #12 from cosmo-epfl/NB_X_ImportingData
bhelfrecht Jun 24, 2020
749fa94
Change loss subscripts to be consistent with manuscript
bhelfrecht Jun 25, 2020
59738be
Import KPCovR class from the new superclass structure
bhelfrecht Jun 25, 2020
b120585
Make notation consistent with manuscript
bhelfrecht Jun 25, 2020
e653dd6
Fix sparse centering and add sparse scaling
bhelfrecht Jun 25, 2020
ffd2b7a
Code cleanup, fix a plotting bug
bhelfrecht Jun 25, 2020
76c6ae9
Import SKPCovR from the superclass structure
bhelfrecht Jun 25, 2020
173f28b
Change structure of kernel functions for consistent behavior between …
bhelfrecht Jun 25, 2020
ed3a3a3
Make Y centering/scaling consistent with manuscript and clean X cente…
bhelfrecht Jun 25, 2020
84f3414
Merge branch 'master' of https://github.com/cosmo-epfl/kernel-tutoria…
bhelfrecht Jun 25, 2020
f9c6ba2
Update 4_SparseKernelMethods.ipynb
rosecers Jun 25, 2020
b1bf146
Update notebooks/4_SparseKernelMethods.ipynb
bhelfrecht Jun 26, 2020
f91df8a
Update notebooks/4_SparseKernelMethods.ipynb
bhelfrecht Jun 26, 2020
9972107
More verbose note regarding the uncentering and unscaling of the X da…
bhelfrecht Jun 26, 2020
dc8b193
Merge branch 'tutorials_check_ben' of https://github.com/cosmo-epfl/k…
bhelfrecht Jun 26, 2020
ef6d261
Need to take absolute value of fps distances
rosecers Jun 26, 2020
4440b82
Merge branch 'master' of https://github.com/cosmo-epfl/kernel-tutorials
rosecers Jun 26, 2020
7d3d992
Merge pull request #15 from cosmo-epfl/tutorials_check_ben
rosecers Jul 2, 2020
5485b70
Merge branch 'master' into feat/utilities_cleanup
rosecers Sep 29, 2020
531d937
Merge with master
rosecers Sep 29, 2020
9e90916
Update 0_Foreword.ipynb
rosecers Jul 2, 2020
89c1e81
Edited notebooks for clarity and reformatted some chemiscope function…
hurricane642 Sep 28, 2020
9cc7c83
Add sklearn-based kernel methods
hurricane642 Oct 12, 2020
82b79a8
Fixed some mistakes and added some embedded hyperlinks
PKGuo Oct 13, 2020
3d3c946
added some hyperlinks
PKGuo Oct 13, 2020
b856b4d
Fixed a typo
PKGuo Oct 13, 2020
33891e7
Try to correct the wrong indentation caused by autopep8
PKGuo Oct 13, 2020
3bc45b5
Use a more appropriate reference
PKGuo Oct 13, 2020
b296bf7
Try to remove Python version lines
PKGuo Oct 13, 2020
ae801c0
Merge pull request #20 from PKGuo/dev
rosecers Oct 14, 2020
172a265
add tests
hurricane642 Oct 14, 2020
34fafbb
Merge pull request #19 from cosmo-epfl/sklearn_kernel_methods
rosecers Oct 20, 2020
005af5c
Added details for clarity and corrected errors.
PKGuo Oct 21, 2020
e6adcba
Refined the third notebook_Draft
PKGuo Oct 27, 2020
16f183e
Apply suggestions from code review
PKGuo Oct 30, 2020
3e197be
Romeved some unnecessary changes
PKGuo Oct 31, 2020
20a02e4
Enable nbextension to print variables in the markdown cell
PKGuo Nov 1, 2020
8781a06
Removed unnecessary cells
PKGuo Nov 3, 2020
febf0a2
Adding changes to NB4
rosecers Nov 4, 2020
0d7ea41
Adding changes to NB5
rosecers Nov 4, 2020
5d75077
Add notes to remind readers to enable nbextension
PKGuo Nov 1, 2020
e197a1b
Apply suggestions from code review
PKGuo Nov 4, 2020
c60b879
Modified notebooks as suggested by Benjamin
PKGuo Nov 4, 2020
52fedc4
Apply suggestions from code review
PKGuo Nov 5, 2020
bb4bd46
Modified notebooks as suggested by Rose
PKGuo Nov 5, 2020
9b44f51
Merge
rosecers Nov 5, 2020
ba8d838
Adding in references for RBF kernel
rosecers Nov 5, 2020
416af55
Removing old example
rosecers Nov 5, 2020
c2d0256
Merge pull request #26 from cosmo-epfl/pkg_nb4
rosecers Nov 11, 2020
f986f83
Merge pull request #25 from cosmo-epfl/pkg_nb5
rosecers Nov 11, 2020
7437702
Merge pull request #21 from PKGuo/dev
rosecers Nov 11, 2020
e9ebb40
Removed all references to the utility classes and referenced the appr…
rosecers Nov 11, 2020
8154444
sklearnified NB2
PKGuo Nov 17, 2020
bb4bc8d
Sklearnify NB3
PKGuo Nov 17, 2020
baa4291
Modified the text
PKGuo Nov 18, 2020
28b736d
sklearnify NB4
PKGuo Nov 18, 2020
97d3d60
Modified NB3 as suggested by Rose
PKGuo Nov 18, 2020
31a9173
Fixed a typo
PKGuo Nov 18, 2020
9b2674d
Modified NB4 as suggested by Rose
PKGuo Nov 18, 2020
0ba9b8e
Merge pull request #28 from PKGuo/sklearnify_NB2
rosecers Nov 20, 2020
41a8d20
Merge pull request #27 from cosmo-epfl/fixup/sklearnify_NB1
rosecers Nov 20, 2020
f2bcbae
Changed kernel functions
PKGuo Nov 20, 2020
5132180
Apply suggestions from code review
PKGuo Nov 20, 2020
fa1d99d
Replace the kernel function with that in sklearn
PKGuo Nov 20, 2020
f3cd1c9
Set kernel = 'precomputed'
PKGuo Nov 20, 2020
b67c014
Modified the text
PKGuo Nov 20, 2020
2edbe50
Set kernel = 'precomputed'
PKGuo Nov 20, 2020
f4ebbb6
Use functools to avoid gamma = 1.0
PKGuo Nov 24, 2020
40c1a7a
Use functools to avoid gamma = 1.0
PKGuo Nov 24, 2020
eb2c2bf
Merge pull request #30 from PKGuo/sklearnify_NB4
rosecers Nov 24, 2020
54662e5
Merge pull request #29 from PKGuo/sklearnify_NB3
rosecers Nov 24, 2020
908db63
Massive nb clean
rosecers Feb 1, 2021
cd06a6d
Working Workflow Example
rosecers Feb 8, 2021
a083353
Updates based upon github comments
rosecers Feb 8, 2021
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11 changes: 11 additions & 0 deletions .gitignore
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/Notes
main*
.ipynb_checkpoints
*__pycache__
*temp*
/datasets/*
/analysis/workspace/*/data_files
/analysis/workspace/*/*npz
/analysis/*signac*
/deprecated/*
*Untitled*
3 changes: 1 addition & 2 deletions README.md
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# kernel-tutorials
A set of utilities and pedagogic notebooks for the use of linear and kernel methods in atomistic modeling
# kernel_project
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