Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Rewrite docs for dissertation #170

Merged
merged 260 commits into from
Sep 26, 2024
Merged
Changes from 1 commit
Commits
Show all changes
260 commits
Select commit Hold shift + click to select a range
68d1a42
Fixed typo re -> ref.
benedict-96 Aug 12, 2024
5d287db
Added more comments. Fixed ref -> cite.
benedict-96 Aug 12, 2024
d5f5130
Fixed references.
benedict-96 Aug 12, 2024
49e2260
Different outlines for html and pdf versions.
benedict-96 Aug 12, 2024
4b0d1f0
Added script to perform training of transformer once sae training has…
benedict-96 Aug 13, 2024
b588c86
Added mnist package.
benedict-96 Aug 13, 2024
ef15b8c
Restored old convert_vector_of_tuples_to_matrix function as @views do…
benedict-96 Aug 13, 2024
af952d7
Deleted double occurance of file.
benedict-96 Aug 13, 2024
534c4fc
Added mnist package.
benedict-96 Aug 13, 2024
a5f501e
Added gml venn diagram.
benedict-96 Aug 13, 2024
aad292e
Seq length wrong default for array input before.
benedict-96 Aug 13, 2024
4097cb9
Added routine for dense applied to QPT.
benedict-96 Aug 13, 2024
0d8340f
Added references for rtx 4090 and github runners.
benedict-96 Aug 13, 2024
e76ca6d
Changed some hyperparameters and adjusted things to the correct format.
benedict-96 Aug 13, 2024
8eefed8
slightly changed docstring and made iterate return the input if n_poi…
benedict-96 Aug 13, 2024
ab9de00
layers now work if input is QPT.
benedict-96 Aug 13, 2024
5271907
Remove first part: HOME.
benedict-96 Aug 13, 2024
fb068c4
Expanded on the introduction.
benedict-96 Aug 14, 2024
938689d
Finished symplectic autoencoder tutorial.
benedict-96 Aug 14, 2024
622519f
Renamed latex part to optimizer framework.
benedict-96 Aug 14, 2024
e45d100
Fixed some typos.
benedict-96 Aug 14, 2024
6211045
Added new formatting commands.
benedict-96 Aug 14, 2024
722df5e
Fied julia package references.
benedict-96 Aug 14, 2024
1f4e1d4
Removed the comparing optimizers tutorial for now.
benedict-96 Aug 14, 2024
e184821
Hid code snippet.
benedict-96 Aug 14, 2024
eaeb7ee
Continued to write introduction.
benedict-96 Aug 14, 2024
4803fdb
Merge branch 'fix_bfgs_docs' of https://github.com/JuliaGNI/Geometric…
benedict-96 Aug 14, 2024
c786a77
Changed parameters.
benedict-96 Aug 14, 2024
175bf35
Slight reformatting.
benedict-96 Aug 14, 2024
61f95f8
Putted a copy because else we get a gpu error (for some reason).
benedict-96 Aug 14, 2024
e4d1a13
Added type name in first line.
benedict-96 Aug 14, 2024
9b1c0bc
Put adjusting loss function tutorial in the appendix.
benedict-96 Aug 14, 2024
9b292f3
Added Toda lattice to references.
benedict-96 Aug 14, 2024
7e01fae
Finished first iteration of introduction.
benedict-96 Aug 14, 2024
f16d700
removed @views.
benedict-96 Aug 15, 2024
2322500
Added the logo (without jl) as the title page for the latex version.
benedict-96 Aug 15, 2024
f5a96c8
Refactored the toc of the latex version.
benedict-96 Aug 15, 2024
ba56885
Made title page and changed outline of latex document.
benedict-96 Aug 15, 2024
0d127a9
fixed reference.
benedict-96 Aug 15, 2024
f1244f8
Added header for refernce section.
benedict-96 Aug 15, 2024
cea7313
Forgot code block comments before.
benedict-96 Aug 15, 2024
e4e956c
Made sphere on title page bigger.
benedict-96 Aug 15, 2024
81c983e
Added abstract.
benedict-96 Aug 17, 2024
75ce544
Added mnist tutorial results.
benedict-96 Aug 17, 2024
1740127
Adapted spacing.
benedict-96 Aug 17, 2024
0eae75a
Changed header.
benedict-96 Aug 17, 2024
96c55d8
Changed fonts.
benedict-96 Aug 17, 2024
31d6a44
Adjusted references.
benedict-96 Aug 17, 2024
6be3d22
Imported accuracy function.
benedict-96 Aug 19, 2024
b326da9
Finished preliminary version of acknowledgements.
benedict-96 Aug 19, 2024
ca730d8
Added copy to make differentiating with Zygote possible (should not b…
benedict-96 Aug 19, 2024
95b0c39
Reformatting thesis slightly so that abstract etc appear with roman l…
benedict-96 Aug 19, 2024
291e98a
Added some details (forgot to include sae tutorial in latex before).
benedict-96 Aug 19, 2024
e0ac716
Fixed typos.
benedict-96 Aug 19, 2024
75aaff5
4 -> four.
benedict-96 Aug 19, 2024
56ee1d5
Merge branch 'fix_bfgs_docs' of https://github.com/JuliaGNI/Geometric…
benedict-96 Aug 20, 2024
bc3aee3
Fixed train -> test.
benedict-96 Aug 20, 2024
881f3b1
Changed name of make command.
benedict-96 Aug 20, 2024
b31f00d
Fixed some typos.
benedict-96 Aug 20, 2024
2ee6b58
Fixed typos and added some explanation.
benedict-96 Aug 20, 2024
a15b387
using hyphenat package.
benedict-96 Aug 20, 2024
d888085
Added information and improved clarity.
benedict-96 Aug 20, 2024
a32fb98
Fixed typos.
benedict-96 Aug 21, 2024
3598dd8
Added deckblatt.
benedict-96 Aug 21, 2024
16926bb
Fixed typos and reorganized some docstrings a bit.
benedict-96 Aug 21, 2024
c6f9b74
Typos.
benedict-96 Aug 21, 2024
0d91a2c
Fixed typos and reorganized some docstrings a bit.
benedict-96 Aug 21, 2024
1977027
symplectic potential -> Poisson tesnor.
benedict-96 Aug 22, 2024
32bc7ac
Resolved conflict.
benedict-96 Aug 22, 2024
0d66316
resolved conflict.
benedict-96 Aug 22, 2024
6d947ef
Fixed typos.
benedict-96 Aug 22, 2024
f546062
Added text for application to NamedTuple.
benedict-96 Aug 22, 2024
17c69cc
Added functor for Poisson tensor applied to QPT.
benedict-96 Aug 22, 2024
891e4d6
Merge branch 'fix_bfgs_docs' of https://github.com/JuliaGNI/Geometric…
benedict-96 Aug 22, 2024
84038d5
parent 6d947efe0b30833de20f0afb74e5ac538dfc2825
benedict-96 Aug 22, 2024
8119ff2
Merge branch 'fix_bfgs_docs' of https://github.com/JuliaGNI/Geometric…
benedict-96 Aug 22, 2024
70ee514
Added figure to visualize reduced order modelig idea.
benedict-96 Aug 22, 2024
94d8b3d
Fixed path.
benedict-96 Aug 22, 2024
a6080ab
Slightly reworked proofs.
benedict-96 Aug 22, 2024
d8963a4
Implemented new constructor to deal with input & output.
benedict-96 Aug 21, 2024
2e12f47
Reworked docs on ROM and losses.
benedict-96 Aug 22, 2024
30abf72
Added Deckblatt.
benedict-96 Aug 23, 2024
7ae9813
Made unicode character work.
benedict-96 Aug 23, 2024
d577aed
natural sciences -> cit.
benedict-96 Aug 23, 2024
95e6082
Introduced definition of structure-preserving neural networks.
benedict-96 Aug 23, 2024
466681f
Clarified bits in the presentation of the general optimizer framework.
benedict-96 Aug 23, 2024
ce06e90
Added papers for unviersal approximation theorems.
benedict-96 Aug 23, 2024
d9e70b1
Avoided double use of word.
benedict-96 Aug 23, 2024
27d8201
changed to plural.
benedict-96 Aug 23, 2024
18557cd
Added author, title, supervisor etc.
benedict-96 Aug 23, 2024
a48ac24
Improved docstrings.
benedict-96 Aug 23, 2024
7512560
Got rid of classificationtransformerloss.
benedict-96 Aug 23, 2024
0783e28
Included symplectic Galerkin projection.
benedict-96 Aug 23, 2024
392138f
Using FeedForwardLoss now.
benedict-96 Aug 23, 2024
57775f4
Slight reformulation.
benedict-96 Aug 23, 2024
ed1f27f
Adapted to new interface.
benedict-96 Aug 23, 2024
1cffb27
Added backslash before underscore.
benedict-96 Aug 23, 2024
6fe7bd8
Fixed name.
benedict-96 Aug 23, 2024
bbdc061
Made arguments more generic.
benedict-96 Aug 23, 2024
c0eeaee
Fixed typos and clarified things.
benedict-96 Aug 24, 2024
dc44d52
Added index for docstrings.
benedict-96 Aug 24, 2024
141880a
Improved legibility of retractions section.
benedict-96 Aug 24, 2024
d745edf
Fixed latex compile problem.
benedict-96 Aug 24, 2024
d094668
hypertarget -> pagetarget.
benedict-96 Aug 25, 2024
e7a6863
Updated docs.
benedict-96 Aug 25, 2024
4c8957e
Updated optimizer sections, fixed typos and added references.
benedict-96 Aug 26, 2024
d84b2a7
Made acknowledgements more appropriate.
benedict-96 Aug 26, 2024
cda04d1
Improved formatting.
benedict-96 Aug 26, 2024
8de7a89
Fixed sympnet layers.
benedict-96 Aug 26, 2024
51b0f65
Improved optimizer-related docstrings.
benedict-96 Aug 26, 2024
c26f6ee
Reworked docs on attention layer(s).
benedict-96 Aug 26, 2024
e75c981
Installing cjk package.
benedict-96 Aug 27, 2024
c6ee732
Extend help -> extended help.
benedict-96 Aug 27, 2024
a37aec8
Added dark mode version of Venn diagram.
benedict-96 Aug 27, 2024
d9395e6
extend -> extended.
benedict-96 Aug 27, 2024
913a58c
Added line on Kronecker product.
benedict-96 Aug 27, 2024
86d37f1
Merge branch 'main' into fix_bfgs_docs
benedict-96 Aug 27, 2024
5a6234b
Did some reformatting.
benedict-96 Aug 27, 2024
138f5b6
Change spacing after headline.
benedict-96 Aug 27, 2024
cd6cefe
Merge branch 'main' into fix_bfgs_docs
benedict-96 Aug 28, 2024
ef6607a
Typos.
benedict-96 Aug 28, 2024
fbf7534
Changed direction of some arrows.
benedict-96 Aug 28, 2024
40061d6
Added explanation of how we use AbstractNeuralNetworks.
benedict-96 Aug 28, 2024
b8743c9
Slight reformatting.
benedict-96 Aug 28, 2024
5b17cbc
Improved inclusion of defaults in docstrings.
benedict-96 Aug 28, 2024
4ba318d
Reworked documentation for transformer integrator (and related docs).
benedict-96 Aug 28, 2024
a830fae
Finished revising autoencoder-related docs.
benedict-96 Aug 28, 2024
2832ce2
Added ResNet for comparison.
benedict-96 Aug 28, 2024
7e734ea
Added new tutorial.
benedict-96 Aug 29, 2024
d258bfb
Added references.
benedict-96 Aug 29, 2024
99b5600
Fixed script.
benedict-96 Aug 29, 2024
a4eba6b
Fixed typo and docstring.
benedict-96 Aug 29, 2024
fc40692
Fixed docstring.
benedict-96 Aug 29, 2024
30a4f7a
Fixed initialparameters (new interface).
benedict-96 Aug 29, 2024
e1367d7
Integrated defaults into docstring.
benedict-96 Aug 29, 2024
97acc15
Increased legibility.
benedict-96 Aug 29, 2024
167073b
Changed image size.
benedict-96 Aug 29, 2024
08d0c5b
Make line thicker.
benedict-96 Aug 29, 2024
c82026f
Improved docs (especially images).
benedict-96 Aug 30, 2024
2519cf5
Improved docstrings.
benedict-96 Aug 29, 2024
d53c652
assets/preamble.tex
benedict-96 Aug 29, 2024
c912533
Added picture visualizing workflow.
benedict-96 Aug 30, 2024
89a4ec8
Finished Grassmann layer docs (for now).
benedict-96 Aug 30, 2024
8a5e4f6
Added Villani references.
benedict-96 Aug 30, 2024
49d6033
Fixed colors.
benedict-96 Aug 30, 2024
52d02b4
Fixed typo.
benedict-96 Aug 30, 2024
9e37d2e
Fixed typos.:
benedict-96 Aug 30, 2024
f678537
Fixed github workflows.
benedict-96 Aug 30, 2024
dab8ddb
Added new routine for problem with one component.
benedict-96 Aug 31, 2024
c075704
Fixed data loader docs.
benedict-96 Sep 1, 2024
eefd80f
Made long urls work (mainly for references).
benedict-96 Sep 2, 2024
2d750e2
Added additional line to abstract.
benedict-96 Sep 2, 2024
cd6eb9c
Fixed array docs & docstrings.
benedict-96 Sep 2, 2024
441f6ab
Finished data loader docs.
benedict-96 Sep 2, 2024
953a202
Finished docstrings on tensor-matrix multiplications.
benedict-96 Sep 2, 2024
0e31812
Added a few custom hyphenations.
benedict-96 Sep 2, 2024
d54458e
Fixed typo 2N -> 2n
benedict-96 Sep 2, 2024
156c375
Removed a few spaces.
benedict-96 Sep 2, 2024
d6c7094
Made images slightly smaller.
benedict-96 Sep 2, 2024
b726702
Now using skew_sym = true.
benedict-96 Sep 2, 2024
d85b38a
Reworked docstrings.
benedict-96 Sep 2, 2024
f682481
Split docstrings according to chaper
benedict-96 Sep 3, 2024
56b19af
Fix problem with quotation marks in minted environment.
benedict-96 Sep 3, 2024
22c6c07
Added new hyphenations.
benedict-96 Sep 3, 2024
eb889b3
Removed comma.
benedict-96 Sep 4, 2024
9f0312f
Added page on port-Hamiltonian systems.
benedict-96 Sep 4, 2024
fc9d6e8
Finished docs on volume-preserving trasnformer.
benedict-96 Sep 4, 2024
d896c88
Fixed typo.
benedict-96 Sep 4, 2024
168283e
Hiding line that should be hidden.
benedict-96 Sep 4, 2024
6a5aa2f
Put line in footnote.
benedict-96 Sep 4, 2024
0f5e6a0
Files that don't include docstrings are no longer included.
benedict-96 Sep 4, 2024
376f759
[^2] -> [^3]
benedict-96 Sep 4, 2024
4428613
Added spaces.
benedict-96 Sep 4, 2024
5f0b536
Removed space.
benedict-96 Sep 4, 2024
02f6d1a
Changed backgroundcolor to white.
benedict-96 Sep 4, 2024
40e4a12
Changed backgroundcolor to white.
benedict-96 Sep 4, 2024
dd1c479
Fixed docstrings.
benedict-96 Sep 4, 2024
d9cdcc1
Added comments on left inverse of decoder.
benedict-96 Sep 6, 2024
312f026
Removed old autoencoder file.
benedict-96 Sep 6, 2024
724ee7e
Added tikz to illustrate lpH equivalence.
benedict-96 Sep 6, 2024
7f01f29
Added port-Hamiltonian systems.
benedict-96 Sep 7, 2024
7601448
included new proof on equivalence of systems with symplectic autoenco…
benedict-96 Sep 7, 2024
0e073aa
Made images smaller to fit on one page.
benedict-96 Sep 7, 2024
f7109ef
Mama's suggestions.
benedict-96 Sep 7, 2024
9f71083
Adjusted to new interface.
benedict-96 Sep 7, 2024
3734fa0
Fixed footnote.
benedict-96 Sep 7, 2024
d11863f
more Mama corrections.
benedict-96 Sep 8, 2024
89bc468
Fixed typos and introduced llangle product.
benedict-96 Sep 8, 2024
eb5e907
Moved legend slightly.
benedict-96 Sep 8, 2024
bb99b2a
added additional fonts (for producing llangle and rrangle).
benedict-96 Sep 9, 2024
fd8739d
Removed double inclusion of packages.
benedict-96 Sep 9, 2024
fdff09d
Added space.
benedict-96 Sep 9, 2024
0bebe60
Included concluding remark.
benedict-96 Sep 9, 2024
daf449a
added additional fonts.
benedict-96 Sep 9, 2024
507e344
Added periods at the end of captions.
benedict-96 Sep 9, 2024
d9c8fdf
Fixed typos.
benedict-96 Sep 9, 2024
0efec88
Updated docs (mainly fixed typos and clarified things).
benedict-96 Sep 9, 2024
0e569ef
Made text more visible.
benedict-96 Sep 10, 2024
92de2b6
Fixed typos.
benedict-96 Sep 11, 2024
67deb92
Adjusted plot legend so that it doesn't overlap with axis.
benedict-96 Sep 12, 2024
fb2059c
Cited Makie.
benedict-96 Sep 12, 2024
d24ed40
Added Michael's suggestions.
benedict-96 Sep 16, 2024
66b2c49
Fixed missing periods at the end of images.
benedict-96 Sep 17, 2024
2afd4e8
Added extra sentence on the particular Dirac structure.
benedict-96 Sep 17, 2024
2d07ab0
Started writing outlook.
benedict-96 Sep 17, 2024
d59f3df
Adjusted figure slightly (i.e. fixed proportions).
benedict-96 Sep 17, 2024
770e17b
Added description on GI for lpH systems.
benedict-96 Sep 17, 2024
192250e
Fixed flipped sections.
benedict-96 Sep 17, 2024
9af6bc6
Added mathbbJ to list of special symbols.
benedict-96 Sep 17, 2024
5ea4d06
add mathtools for xRightarrow.
benedict-96 Sep 17, 2024
84c87d9
title in headline smaller to get rid of overlap.
benedict-96 Sep 17, 2024
d2b73be
Continued outlook section.
benedict-96 Sep 17, 2024
b8145e2
CIT not NatSc.
benedict-96 Sep 18, 2024
8f3fc78
Grouped optimizer sections together.
benedict-96 Sep 18, 2024
2dcc599
Added article.
benedict-96 Sep 18, 2024
27f5499
Removed extra space.
benedict-96 Sep 18, 2024
caed906
Added references header.
benedict-96 Sep 18, 2024
129650b
Remove numbering for Chapter Summary.
benedict-96 Sep 18, 2024
796bf43
Removed unnecessary subsection in lpH chapter.
benedict-96 Sep 18, 2024
c20605b
multi-head -> multihead for consistency.
benedict-96 Sep 18, 2024
672f223
Added introduction and conclusion to every chapter; removed heading f…
benedict-96 Sep 18, 2024
32b268d
Made doctests optional.
benedict-96 Sep 19, 2024
e0c9e67
Improved chapter summaries slightly.
benedict-96 Sep 19, 2024
155c618
Slightly improved chapter summary.
benedict-96 Sep 19, 2024
eb42a87
Started to make references only appear at the end of the chapter.
benedict-96 Sep 19, 2024
68ddaa5
Put references at the end of the chapter and made this dependent on w…
benedict-96 Sep 19, 2024
31ddc78
Made showing of references dependent on whether we have html or not.
benedict-96 Sep 19, 2024
ab9c959
Further modified introductions and summaries (especially summaries).
benedict-96 Sep 19, 2024
48201ca
Added threads=2 for the workflow.
benedict-96 Sep 20, 2024
df07245
Added introduction and conclusion.
benedict-96 Sep 20, 2024
3134022
Made non-standard authors display correctly.
benedict-96 Sep 20, 2024
500e612
Fixed some typos.
benedict-96 Sep 22, 2024
c61e244
Further clarified the summary at the end.
benedict-96 Sep 23, 2024
dbe5475
Included Michael's new comments (version 3.).
benedict-96 Sep 23, 2024
7650920
Added PSD for n=6.
benedict-96 Sep 23, 2024
8509eb7
Not outputting all the things I shouldn't output (nothing at the end …
benedict-96 Sep 23, 2024
a4b01ef
Added discussion on PSD + transformer.
benedict-96 Sep 23, 2024
76ce79f
Updated parameters.
benedict-96 Sep 23, 2024
57da28a
Fixed function parameterlength.
benedict-96 Sep 23, 2024
360778c
Added second examiner.
benedict-96 Sep 23, 2024
371d1f1
Fix date.
benedict-96 Sep 23, 2024
00c6449
Commented out the section where we use PSD + Transformer.
benedict-96 Sep 23, 2024
8c8bdb9
Fixed typo.
benedict-96 Sep 24, 2024
0c8c6d1
Merge branch 'fix_bfgs_docs' of https://github.com/JuliaGNI/Geometric…
benedict-96 Sep 24, 2024
9ce953c
Fixed typo \textit -> *.
benedict-96 Sep 25, 2024
ef72f99
Fixed Hamiltonian.
benedict-96 Sep 25, 2024
c85a013
Started adding tutorial on HNNs.
benedict-96 Sep 25, 2024
427a66e
Added fashion mnist script.
benedict-96 Sep 26, 2024
048f93c
Fixed doctest problem.
benedict-96 Sep 26, 2024
fd663b9
Not training the HNN. This is not working for now.
benedict-96 Sep 26, 2024
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Prev Previous commit
Next Next commit
Fied julia package references.
benedict-96 committed Aug 14, 2024
commit 722df5e1f653b270450b711b7e3a856bf66a0f55
15 changes: 9 additions & 6 deletions docs/src/GeometricMachineLearning.bib
Original file line number Diff line number Diff line change
@@ -632,25 +632,28 @@ @article{greydanus2019hamiltonian
@misc{churavy2020kernel,
author = {Churavy, Valentin},
title = {KernelAbstractions.jl},
url = {https://github.com/JuliaGPU/KernelAbstractions.jl},
howpublished = {\url{https://github.com/JuliaGPU/KernelAbstractions.jl}},
version = {0.9.23},
date = {2024},
year = {2024},
note = {Used on August 14, 2024.}
}

@misc{besard2022one,
author = {Besard, Tim},
title = {oneAPI.jl},
url = {https://github.com/JuliaGPU/oneAPI.jl},
howpublished = {\url{https://github.com/JuliaGPU/oneAPI.jl}},
version = {0.3.0},
date = {2022}
year = {2022},
note = {Used on August 14, 2024.}
}

@misc{besard2022metal,
title = {Metal.jl},
author = {Besard, Tim and Hawkins, Max},
url = {https://github.com/JuliaGPU/Metal.jl},
howpublished = {\url{https://github.com/JuliaGPU/Metal.jl}},
version = {0.1.2},
date = {2022}
year = {2022},
note = {Used on August 14, 2024.}
}

@techreport{baker2019workshop,