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Nn stuff #2

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Nn stuff #2

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d9ff1b4
forked from julia_learn. removing everythign that's not GP_june
mis0butter Apr 30, 2023
2d58516
removed if det(K) == 0 from f_obj in GP_june.jl
mis0butter Apr 30, 2023
af9d01e
updated state plots to accommodate n_vars. working on differentiating…
mis0butter May 2, 2023
b453020
after talk with dfk, updated obj fn to try using trace of kernel, not…
mis0butter May 5, 2023
8e62960
starting to create more validation plots
mis0butter May 5, 2023
8c86cf6
created GaussianSINDy repo, renaming project
mis0butter May 26, 2023
5e2497e
renamed everything to GaussianSINDy
mis0butter May 26, 2023
6e530d7
moved a bunch of functions around. plots are in their own functions, …
mis0butter Jun 4, 2023
f17b4b0
init_params works in repo, plot_option is working
mis0butter Jun 4, 2023
ce3ccab
ok made a lot of changes ... moved some fns around, they're in utils …
mis0butter Jun 5, 2023
0f5d96c
following documentation for total variational derivative, testing in …
mis0butter Jun 5, 2023
8348b63
committing what I have, creating results
mis0butter Jun 5, 2023
ac33cb0
thanks very much to Jake for help with evaluating functions of vecto…
mis0butter Jun 7, 2023
a381cac
OMG able to dynamically create function of vector of functions, as we…
mis0butter Jun 7, 2023
c07af05
moved build_dx_fn to inside ode_fns.jl
mis0butter Jun 7, 2023
7d847e6
it works with predator_preygit add .
mis0butter Jun 7, 2023
bc860fe
got the dumb validate script to work for plotting
mis0butter Jun 7, 2023
b28b16a
ok validate_data works now with ode_sine, had to restart julia repl why
mis0butter Jun 7, 2023
b10f934
have results for predator_prey, plots are looking pretty good actually
mis0butter Jun 7, 2023
8cb6a59
fixed legend bug
mis0butter Jun 8, 2023
ba77d51
wtf that was so hard. got latex to show up in plot title
mis0butter Jun 8, 2023
9e89ec6
plot margin looks good now
mis0butter Jun 8, 2023
bc6df31
committing state that produced predator_prey plot
mis0butter Jun 8, 2023
702ed0f
fixed a bad typo. using dx_truth_train instead of dx_fd_train
mis0butter Jun 8, 2023
c90d37f
created metrics for performance. committing what I have now
mis0butter Jun 8, 2023
f07f666
put plot of predator_prey into function in utils.jl, starting test/ca…
mis0butter Jun 20, 2023
fa0ab0c
created some metrics (just norm) for truth vs sindy vs gpsindy coeffs
mis0butter Jun 20, 2023
440235f
building notes in readme. renamed variables to things that make sense…
mis0butter Jun 20, 2023
56faea1
updated predator prey coeffs and plot fns
mis0butter Jun 20, 2023
4d8045b
merging after pull
mis0butter Jun 20, 2023
86de7a3
updated axis ticks
mis0butter Jun 22, 2023
015910e
omg. I got the margins for plots to look good
mis0butter Jun 22, 2023
e3fa2f2
got the legend on the rightgit add src/
mis0butter Jun 23, 2023
9fbe676
switched to RGB colors for plotting
mis0butter Jun 23, 2023
7496fd5
tried to shove train_test_gpsindy into a function, but takes too long…
mis0butter Jun 23, 2023
a40ec17
committing code that can now generate metrics printout and plots
mis0butter Jun 23, 2023
83d448e
changed k_fn to k_SE
mis0butter Jun 25, 2023
422a577
added test/outputs to .gitignore
mis0butter Jun 28, 2023
aa67ab2
deleted plots (moved out test/outputs)
mis0butter Jun 28, 2023
bf31056
modified split_train_test to accommodate cross-validation
mis0butter Jun 29, 2023
dfa451d
plot xtick always includes min and max now
mis0butter Jun 29, 2023
a76ac59
got training data to plot separately if partitioned
mis0butter Jun 29, 2023
2651bcd
created plot for just test data
mis0butter Jun 29, 2023
f2ea030
made plot_predator_prey more efficient
mis0butter Jun 29, 2023
487573f
updating lasso admm plots
mis0butter Jun 29, 2023
dc557b2
updated plot_lasso_admm to use latexify
mis0butter Jun 29, 2023
0e1b977
ugh finally finished admm plot
mis0butter Jun 29, 2023
c30c29e
created k_periodic kernel
mis0butter Jun 30, 2023
6459fcd
sinusoidal kernel works for posterior test/gaussian_process_test.jl
mis0butter Jun 30, 2023
376a65a
found reason why validate_data wasn't propagating test plots - pool_d…
mis0butter Jul 5, 2023
3bf2083
gonna not use recursion fns, too confusing to change fn library. usin…
mis0butter Jul 5, 2023
415ec10
creating new predator_prey_test2 and SINDy_test to try only truth non…
mis0butter Jul 5, 2023
5c89d0c
fixed typo for reducing fn library in pool_data_test
mis0butter Jul 5, 2023
7b5966c
have batch and plots script running for different dx_noise params
mis0butter Jul 7, 2023
5244701
monte carlo outputs xi_1 and xi_2, creating plots for xi_2
mis0butter Jul 7, 2023
0032aa2
added hist to outputs of gpsindy fns, put monte_carlo_gpsindy into Ga…
mis0butter Jul 7, 2023
335cfbe
added Date, now saving results in folder with date-timestamps
mis0butter Jul 8, 2023
d71b783
created vv2m fn and plot for final fn val for each iter
mis0butter Jul 8, 2023
7331fbd
added lambda as input to sindy_gp_admm as tunable parameter
mis0butter Jul 8, 2023
6eb4000
adding rounding to gauss_sample to digits 12, machine precision leaki…
mis0butter Jul 9, 2023
2972d3b
ok, hyperparameter optimization is working for simple Gaussian proces…
mis0butter Jul 9, 2023
20c7f9e
adding lasso_admm_gp_opt which uses GaussianProcesses.jl to optimize …
mis0butter Jul 10, 2023
229746c
GP hyperparameter optimization is working in sindy_gp_admm_test.jl, b…
mis0butter Jul 10, 2023
a14af29
gp hyparameter optimization works really well ...
mis0butter Jul 10, 2023
7595a0b
ok, at this state ... sindy_gp_admm_test is working for j = 1
mis0butter Jul 10, 2023
982979a
added if det(Ky) == 0 in f_obj while loop to regularize
mis0butter Jul 10, 2023
2355905
committing before updating all fns in GaussianSINDy, oh god ... UNIT …
mis0butter Jul 10, 2023
3dc781d
start code cleanup. created opt_fns with opt_xi
mis0butter Jul 10, 2023
9c95a2a
created opt_hp
mis0butter Jul 10, 2023
bab4c74
moved shrinkage to opt_fns
mis0butter Jul 10, 2023
94c19f5
updated opt_xi inputs, simpler hyperparam args
mis0butter Jul 10, 2023
a637da6
finished admm_lasso, now testing
mis0butter Jul 11, 2023
6835674
added relaxation parameter to admm_lasso and rho, idk what rho does
mis0butter Jul 11, 2023
b63fd87
simplified hyperparameters as one vector of 3 elements as arg input, …
mis0butter Jul 11, 2023
94fd084
improved comments and var names
mis0butter Jul 11, 2023
2d80fd3
created push_hist fn
mis0butter Jul 11, 2023
541a50d
created gpsindy fn
mis0butter Jul 11, 2023
14309cb
gpsindy works with loopgit add . yay
mis0butter Jul 11, 2023
56f5cb0
created monte carlo loop for gpsindy
mis0butter Jul 11, 2023
9e9f7cb
monte_carlo_gpsindy is working
mis0butter Jul 11, 2023
fff76b3
moved gpsindy fns into gpinsdy_fns.jl, but julia is giving method ove…
mis0butter Jul 11, 2023
6c4e875
added hist_nvars_vec to monte carlo output
mis0butter Jul 11, 2023
9138398
using GP to smooth derivatives for GPSINDy is not helping ... gonna …
mis0butter Jul 13, 2023
642e81e
removed smoothing derivatives
mis0butter Jul 14, 2023
ce5451a
normalizing data makes it look worse in gpsindy
mis0butter Jul 14, 2023
47b8e92
deleting old test scripts, not needed
mis0butter Jul 14, 2023
8abe58b
trying out standardizing data before using GPSINDy. normalizing x and…
mis0butter Jul 14, 2023
6e303d2
put plotting fns inside new script, plot_fns
mis0butter Jul 14, 2023
c895901
moved Xi_true inside stand data case, standardization now looks correct
mis0butter Jul 14, 2023
43963a2
omg thank god. GPSINDy is working again. the objval += 1/2 * log( tr(…
mis0butter Jul 15, 2023
2232278
added cases for stand-data-true and stand-data-noisy
mis0butter Jul 15, 2023
3f4132f
GPSINDy looks better than SINDy for the first time
mis0butter Jul 17, 2023
6269f09
deleted old gp test scripts, changed gp_dx --> gp_test and have anima…
mis0butter Jul 17, 2023
f3d2931
for kernel SE, put argument order: l, sigma_f
mis0butter Jul 20, 2023
ffe016a
optimizing HPs in ADMM now looks like it's working, but adding too mu…
mis0butter Jul 20, 2023
d76f229
added animations and plots for fitting xi for sindy and gpsindy
mis0butter Jul 21, 2023
9e197c6
created sandbox for testing standardized vs. non-standardized data. i…
mis0butter Jul 23, 2023
63a1619
added another case to gpsindy monte carlo fn, plotting code is a bit …
mis0butter Jul 23, 2023
f5a98ff
committing before changing kernel to use t_train input datain f_obj
mis0butter Jul 24, 2023
018013f
made lots of changes ... added lots of different kernels and changed …
mis0butter Jul 24, 2023
70509df
fixed SINDy_test library so that it finds the correct coefficients fo…
mis0butter Jul 25, 2023
cc53494
FIXED BUG. parameters output is now correct and standardizing data wo…
mis0butter Jul 25, 2023
221497e
updated GP_tools GP fns to accommodate inputs of different sizes
mis0butter Jul 26, 2023
cf47235
created sandbox for testing Jake's car data. sindy alone looks super …
mis0butter Jul 26, 2023
cadfc28
giving up on gpsindy for now, trying to leverage SINDy with GP, updat…
mis0butter Jul 26, 2023
1622247
multivariate gps are amazing. smoothing x --> x_GP, then conditioning…
mis0butter Jul 27, 2023
12e5667
SINDy with GP looks very good compared to SINDy now ...
mis0butter Jul 27, 2023
855772c
ok, OG gpsindy is working (with temporal data) again. going to make c…
mis0butter Jul 27, 2023
6416642
plot for comparing sindy and gpsindy outputs every case
mis0butter Jul 27, 2023
72c18ab
I think I updated ADMM to use x as kernel input? fixed the super anno…
mis0butter Jul 27, 2023
5caa403
fixed gpsindy dimension inputs for all cases, no more index 173
mis0butter Jul 27, 2023
2ad4c03
removed sanity check println code
mis0butter Jul 27, 2023
c7c1409
implemented Yue's suggestion of tunning hyperparams in between ADMM i…
mis0butter Jul 28, 2023
f49bb36
made the quartile plot that took way too long
mis0butter Jul 28, 2023
a124770
comparing with box plots, the continuous box plot plot looks right
mis0butter Jul 28, 2023
d37f315
modified ribbon alpha in median/quartile plot
mis0butter Jul 28, 2023
af6117e
created test case 9 for gp-sindy-gp-sindy, but 2nd gp mean not new Th…
mis0butter Jul 28, 2023
30795ac
added LineSearches to packages so that it avoids the assertion error …
mis0butter Jul 28, 2023
a60e151
comitting this now (in broken state), need to implement hp opt for (y…
mis0butter Aug 2, 2023
52ccc4d
reorganized test folder, added test/old and test/data
mis0butter Aug 2, 2023
7f1ff1e
implemented pendulum, julia is dumb with the int and float stuff
mis0butter Aug 7, 2023
0f3ce57
moved fn outside of monte_carlo_gpsindy, is now arg input
mis0butter Aug 7, 2023
2f2543e
added cos to sin terms in fn library - now Xi_true looks right
mis0butter Aug 8, 2023
ca6652b
implemented posterior mean in stand_data_test
mis0butter Aug 9, 2023
55cbd48
added code from working stand_data_test to gpsindy_fns
mis0butter Aug 9, 2023
f380933
very interesting ... when lowering dt of data, gpsindy and gpsindy_gp…
mis0butter Aug 9, 2023
255f9c8
put sindy_gpsindy_gpsindygpsindy into script, can run monte carlos in…
mis0butter Aug 9, 2023
b0d8e07
renamed stand_data_test to gpsindygpsindy_test
mis0butter Aug 9, 2023
3adcc50
updated plotting script for gpsindy_gpsindy
mis0butter Aug 9, 2023
b3b5dcf
added double_pendulum to ode_fns
mis0butter Aug 9, 2023
71779d4
created new pendulum_test script, updated pendulum fns to use params …
mis0butter Aug 9, 2023
1ccb51c
double pendulum animation is working
mis0butter Aug 9, 2023
7c7264b
finished double pendulum animation
mis0butter Aug 10, 2023
eaf0cd0
updated fn name to gpsindy_x2
mis0butter Aug 10, 2023
66d18e9
added test/double-pendulum-chaotic to gitignore
mis0butter Aug 10, 2023
7908226
updated readme for double pendulum chaotic dataset
mis0butter Aug 10, 2023
e70b3ec
added src/structs.jl
mis0butter Aug 10, 2023
97f1a42
updated struct names for Xi to Xi_struct
mis0butter Aug 10, 2023
ceba9a9
gpsindy_x2 now takes xi_hist as input and output
mis0butter Aug 10, 2023
f70b345
added Xi_err_hist
mis0butter Aug 10, 2023
cddd770
updated gpsindy_x2 to use gp_post with comments
mis0butter Aug 10, 2023
22ed93f
ok found issue, standardizing data is making data prop wrong
mis0butter Aug 13, 2023
5cae276
fixing merge, stand_data_test stands again
mis0butter Aug 13, 2023
b6c3977
updated readme with research meeting notes
mis0butter Aug 13, 2023
e358ca4
updated readme formatting
mis0butter Aug 13, 2023
8972c4b
fixed validation plot problem yay!
mis0butter Aug 13, 2023
10a78b0
added test/data/double-pendulum-chaotic to gitignore
mis0butter Aug 14, 2023
db6ff44
added chatoic_double_pendulum_csv_test.jl, need to augment function l…
mis0butter Aug 14, 2023
0719f99
updated gp_post arguments
mis0butter Aug 14, 2023
0bf9fa8
committing current state, need to work on double pendulum fn library
mis0butter Aug 14, 2023
089ce8d
updated monte carlo gpsindy to use gp_post in case 9
mis0butter Aug 15, 2023
66aea14
resolved merge conflict
mis0butter Aug 15, 2023
f4e4bcd
there was remaining git conflict
mis0butter Aug 16, 2023
309a425
updated readme with Adam notes, emphasized motivating example
mis0butter Aug 16, 2023
00c1e25
added unicycle dynamics and started car_sim_test
mis0butter Aug 17, 2023
4c8e7c1
found issue with unicycle dynamics. need to compute more coupled nonl…
mis0butter Aug 17, 2023
fb8972b
updated readme with notes. going to update coefficients table for eas…
mis0butter Aug 17, 2023
d8c5db1
added nonlinear combinations of sine functions to fn library
mis0butter Aug 17, 2023
8a6475e
updated coefficients string vector, size now matches pool_table
mis0butter Aug 17, 2023
6d184d1
got pretty tables working for coefficients
mis0butter Aug 17, 2023
9b5468a
added control inputs to nonlinear terms
mis0butter Aug 17, 2023
de30ab3
updated SINDy_test for optional control input. now can just use one f…
mis0butter Aug 18, 2023
e24d682
using Jake's car data again, understand unicycle dynamics better now
mis0butter Aug 18, 2023
bb541b3
reorganized ode_fns into a folder, split across files
mis0butter Aug 21, 2023
4b96d6e
updated with note, deadline is ICRA SEPT 15git add .
mis0butter Aug 23, 2023
4fe4dd1
implemented linear and angular acceleration quadcopter dynamics, but …
mis0butter Aug 23, 2023
4262724
updated pretty_coeffs to only include nonzero rows
mis0butter Aug 24, 2023
a4ea89c
unicycle dynamics finally work with truth, needed to update control i…
mis0butter Aug 24, 2023
32788d1
added data_struct, created ode_train_test, reorganized ode fns
mis0butter Aug 24, 2023
527f4be
updated data_train push in ode_train_test
mis0butter Aug 24, 2023
5e2224c
updated structs for u, working on Jake's hardware data now. need to v…
mis0butter Aug 24, 2023
5ca1a32
dealt with data rollovers
mis0butter Aug 25, 2023
6e14669
got the x_GP and dx_GP train/test stuff working for Jake's car data
mis0butter Aug 25, 2023
f9f3eb9
created plot comparing FD vs GP training data for car
mis0butter Aug 25, 2023
ef7b103
that was so confusing ... fixed it build_dx_fn for control input
mis0butter Aug 27, 2023
d302e1c
CONFIRMED IT WORKS WITH XI_TRUE
mis0butter Aug 27, 2023
15ad4ad
pushing latest code. created test/int_control_test.jl for integrating…
mis0butter Sep 6, 2023
0032d5b
Added NN training as a baseline
Sep 7, 2023
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4 changes: 4 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
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/Manifest.toml
test/outputs/
test/double-pendulum-chaotic/
test/data/double-pendulum-chaotic/
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