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Rewrite docs for dissertation #170

Merged
merged 260 commits into from
Sep 26, 2024
Merged

Rewrite docs for dissertation #170

merged 260 commits into from
Sep 26, 2024

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benedict-96
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This pull requests includes all the changes made to produce the docs used in the dissertation.

@benedict-96
Fixed typo re -> ref.
68d1a42
@benedict-96
Added more comments. Fixed ref -> cite.
5d287db
@benedict-96
Fixed references.
d5f5130
@benedict-96
Different outlines for html and pdf versions.
49e2260
@benedict-96
Added script to perform training of transformer once sae training has…
4b0d1f0 
… finished.
@benedict-96
Added mnist package.
b588c86
@benedict-96
Restored old convert_vector_of_tuples_to_matrix function as @views do…
ef15b8c 
…esn't work here.
@benedict-96
Deleted double occurance of file.
af952d7
@benedict-96
Added mnist package.
534c4fc 
Restored old convert_vector_of_tuples_to_matrix function as @views doesn't work here.

Deleted double occurance of file.

Took into account that StandardTransformerIntegrator has now field seq_length.
@benedict-96
Added gml venn diagram.
a5f501e 
Fixed appendix problem.

Added references.
@benedict-96
Seq length wrong default for array input before.
aad292e 
Fixed script.{
@benedict-96
Added routine for dense applied to QPT.
4097cb9
@benedict-96
Added references for rtx 4090 and github runners.
0d8340f 
Added information on publications that emerged as a result of developing gml.
@benedict-96
Changed some hyperparameters and adjusted things to the correct format.
e76ca6d
@benedict-96
slightly changed docstring and made iterate return the input if n_poi…
8eefed8 
…nts == 0.
@benedict-96
layers now work if input is QPT.
ab9de00 
Fixed iterate for the case n_points = 0.
@benedict-96
Remove first part: HOME.
5271907
@benedict-96
Expanded on the introduction.
fb068c4
@benedict-96
Finished symplectic autoencoder tutorial.
938689d
@benedict-96
Renamed latex part to optimizer framework.
622519f
@benedict-96
Fixed some typos.
e45d100
@benedict-96
Added new formatting commands.
6211045
@benedict-96
Fied julia package references.
722df5e
@benedict-96
Removed the comparing optimizers tutorial for now.
1f4e1d4
@benedict-96
Hid code snippet.
e184821
@benedict-96
Continued to write introduction.
eaeb7ee 
Fixed wrong references.
@benedict-96
Merge branch 'fix_bfgs_docs' of https://github.com/JuliaGNI/Geometric…
4803fdb 
…MachineLearning.jl into fix_bfgs_docs
@benedict-96
Changed parameters.
c786a77
@benedict-96
Slight reformatting.
175bf35
@benedict-96
Putted a copy because else we get a gpu error (for some reason).
61f95f8
@benedict-96
Started to make references only appear at the end of the chapter.
eb42a87
@benedict-96
Put references at the end of the chapter and made this dependent on w…
68ddaa5 
…hether we have html or latex.
@benedict-96
Made showing of references dependent on whether we have html or not.
31ddc78
@benedict-96
Further modified introductions and summaries (especially summaries).
ab9c959
@benedict-96
Added threads=2 for the workflow.
48201ca
@benedict-96
Added introduction and conclusion.
df07245
@benedict-96
Made non-standard authors display correctly.
3134022
@benedict-96
Fixed some typos.
500e612
@benedict-96
Further clarified the summary at the end.
c61e244
@benedict-96
Included Michael's new comments (version 3.).
dbe5475
@benedict-96
Added PSD for n=6.
7650920
@benedict-96
Not outputting all the things I shouldn't output (nothing at the end …
8509eb7 
…of example blocks.
@benedict-96
Added discussion on PSD + transformer.
a4b01ef
@benedict-96
Updated parameters.
76ce79f
@benedict-96
Fixed function parameterlength.
57da28a
@benedict-96
Added second examiner.
360778c
@benedict-96
Fix date.
371d1f1
@benedict-96
Commented out the section where we use PSD + Transformer.
00c6449
@benedict-96
Fixed typo.
8c8bdb9
@benedict-96
Merge branch 'fix_bfgs_docs' of https://github.com/JuliaGNI/Geometric…
0c8c6d1 
…MachineLearning.jl into fix_bfgs_docs
@benedict-96
Fixed typo \textit -> *.
9ce953c
@benedict-96
Fixed Hamiltonian.
ef72f99
@benedict-96
Started adding tutorial on HNNs.
c85a013
@benedict-96
Added fashion mnist script.
427a66e
@codecov Codecov
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codecov bot commented Sep 26, 2024 •
edited
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Codecov Report

Attention: Patch coverage is 64.28571% with 65 lines in your changes missing coverage. Please review.

Project coverage is 67.94%. Comparing base (20bddd6) to head (fd663b9).
Report is 261 commits behind head on main.

Files with missing lines Patch % Lines
src/architectures/volume_preserving_feedforward.jl 0.00% 17 Missing ⚠️
src/data_loader/data_loader.jl 18.18% 9 Missing ⚠️
src/arrays/poisson_tensor.jl 78.12% 7 Missing ⚠️
src/architectures/sympnet.jl 25.00% 6 Missing ⚠️
src/layers/resnet.jl 14.28% 6 Missing ⚠️
src/architectures/transformer_integrator.jl 33.33% 4 Missing ⚠️
src/layers/multi_head_attention.jl 33.33% 4 Missing ⚠️
src/architectures/autoencoder.jl 0.00% 2 Missing ⚠️
src/architectures/resnet.jl 0.00% 2 Missing ⚠️
src/optimizers/manifold_related/retractions.jl 75.00% 2 Missing ⚠️
... and 5 more
Additional details and impacted files 
@@            Coverage Diff             @@
##             main     #170      +/-   ##
==========================================
- Coverage   68.14%   67.94%   -0.20%     
==========================================
  Files         122      122              
  Lines        3667     3716      +49     
==========================================
+ Hits         2499     2525      +26     
- Misses       1168     1191      +23
Flag Coverage Δ
67.94% <64.28%> (?)

Flags with carried forward coverage won't be shown. Click here to find out more.

☔ View full report in Codecov by Sentry.
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@michakraus michakraus merged commit 8136bbd into main Sep 26, 2024
11 of 13 checks passed
@michakraus michakraus deleted the rewrite_docs_for_dissertation branch September 26, 2024 13:29
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@benedict-96 @michakraus