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.

Sign up for GitHub

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

Jump to bottom

[ENH] improve MEM performance #25

Open
wants to merge 49 commits into
base: master
Choose a base branch
from
Open

[ENH] improve MEM performance #25

wants to merge 49 commits into from

Conversation

Edouard2laire
Copy link
Collaborator

@Edouard2laire Edouard2laire commented Oct 2, 2024 •
edited
Loading

This PR:

  • Update the definition of the covariance matrix along the cortical surface
  • Improve the performance
  • improve memory usage when using parallel computing.
  • Improve the disk usage of the output

Reference:

Edouard2laire and others added 28 commits October 2, 2024 18:10
@Edouard2laire
improve MNE solver
c153b37
@Edouard2laire
use scale 3 for nirs noise covariance
aee123a
@Edouard2laire
disable noise covariance in MNE for now
83d47f9
@Edouard2laire
keep all the power for nirs
11d434b
@Edouard2laire
Par-for optimization (#8)
87e0bf2 
* don't display progress bar for standalone

* First implementation

* clean code

* aestetic changes

* more aesthetic change

* add spaces
@Edouard2laire
MNE kernel (#9)
74767e9 
* Improve parameter choice for l-curve

* Improve kernel estimation using SVD trick to compute the norm
@Edouard2laire
small changes (#10)
fe22b41 
* Improve parameter choice for l-curve

* Improve kernel estimation using SVD trick to compute the norm

* better handle figures

* Remove be_main_wmem
@Edouard2laire
don't transpose the inversion matrix
06104bf
@Edouard2laire
oups
9a50128
@Edouard2laire
Move the normalization outside be_launch_mem
a9974ba
@Edouard2laire
Move the conversion to time-series outside be_launch_mem
6b66e33
@Edouard2laire
minor changes
495be0b
@Edouard2laire
clean up output
ee42333
@Edouard2laire
more clean-up on be_slice_obj
73ca08d
@Edouard2laire
Merge pull request #11 from Edouard2laire/be_free_energy
a1a2807 
Optimize be_free_energy and be_mem_struct
@Edouard2laire
save sigma_s under obj rather than option
654648b
@Edouard2laire
pre-compute G * active_var
b9dae0c
@Edouard2laire
some cleaning
8c470b4
@Edouard2laire
Even more optim
9db0652
@Edouard2laire
last changes
f852199
@Edouard2laire
fix call to be_fusion_of_modalities
6a8e3aa
@Edouard2laire
cleam up MNE code
ac8778e
@Edouard2laire
Save wMEM results as factor decomposition
02c634f
@Edouard2laire
fix format of obj.data
dfccf7a
@Edouard2laire
Merge pull request #15 from Edouard2laire/storage
05e4e51 
Save wMEM results as factor decomposition
@Edouard2laire
[bugfix] Fix the covariance matrix along the cortical surface (#17)
66ee9c9 
* Attempt to fix the covariance matrix

* refactor changes

* remove previous trick to be safer
@Edouard2laire
update optimization function (#16)
96240ab 
* attempt to use hessian to speed up calculation

* use hessian

* Remove Hessian for now
@Edouard2laire
Merge branch 'multifunkim:master' into wMEM-nirs2
05c4145
@Edouard2laire Edouard2laire marked this pull request as ready for review October 23, 2024 18:58
Edouard2laire and others added 9 commits October 28, 2024 14:15
@Edouard2laire
[be_fusion_of_modality] also create the normalized data/gain
14cbf86
@Edouard2laire
Some refactor on MNE
56a1a61
@Edouard2laire
continuation
d00433d
@Edouard2laire
remove progress bar
e2a295e
@Edouard2laire
several bugfixes
3321a57
@Edouard2laire
put back quasi-netwon for now
b6a1d97 
trust-region very slow for MEG
@Edouard2laire
Improve code performance (#18)
b89b868 
* pre-compute some matrix

* Improve call to be_dwsynthesis

* clean code

* Add option 7 for alpha
@Edouard2laire
Add option to use noise covariance in MNE. (default to false)
b95fa1e
@Edouard2laire
Refactor memstruct (#19)
3af7b4a 
* more refactor on memstruct

* more refactor

* more refactor

* Fix memory issue for EEG/MEG

* temporary move new implementation to be_free_energy2

* start support for custom mean / inactive variance

* add unsaved change

* remove unnecessary sum

* minor cosmetic change

* bug fix and clean code
@Edouard2laire Edouard2laire changed the title [wMEM] improve performance for fNIRS data [ENH] improve MEM performance Nov 26, 2024
Edouard2laire
Edouard2laire commented Dec 6, 2024
View reviewed changes
best/mem/be_launch_mem.m Outdated Show resolved Hide resolved
best/mem/be_launch_mem.m Outdated Show resolved Hide resolved
best/mem/be_minimize_free_energy.m Outdated Show resolved Hide resolved
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
1 participant
@Edouard2laire