From 99ba61c311614c7bf4d20a002d34fd264c1d6666 Mon Sep 17 00:00:00 2001 From: rivasd Date: Thu, 8 Nov 2018 19:42:31 -0500 Subject: [PATCH 1/3] gitginore for vscode --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index c24840b..5edaba7 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,4 @@ **/*.ipynb_checkpoints __pycache__ +/.vscode/ \ No newline at end of file From 1e86b7db8b9303bdbd93159ea34ea796d76842f1 Mon Sep 17 00:00:00 2001 From: rivasd Date: Thu, 8 Nov 2018 21:39:33 -0500 Subject: [PATCH 2/3] added clean pip reqs, python module structure and started bayesian optimization --- brainDecode/__init__.py | 0 brainDecode/towardMoabbIntegration/__init__.py | 0 brainDecode/towardMoabbIntegration/utils/bayesian.py | 3 +++ requirements.txt | 7 +++++++ 4 files changed, 10 insertions(+) create mode 100644 brainDecode/__init__.py create mode 100644 brainDecode/towardMoabbIntegration/__init__.py create mode 100644 brainDecode/towardMoabbIntegration/utils/bayesian.py create mode 100644 requirements.txt diff --git a/brainDecode/__init__.py b/brainDecode/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/brainDecode/towardMoabbIntegration/__init__.py b/brainDecode/towardMoabbIntegration/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/brainDecode/towardMoabbIntegration/utils/bayesian.py b/brainDecode/towardMoabbIntegration/utils/bayesian.py new file mode 100644 index 0000000..f99af1f --- /dev/null +++ b/brainDecode/towardMoabbIntegration/utils/bayesian.py @@ -0,0 +1,3 @@ +from skopt import BayesSearchCV +from brainDecode.towardMoabbIntegration.brainDecodeSKLearnWrapper.ShallowFBCSPNet_GeneralTrainer import ShallowFBCSPNet_GeneralTrainer + diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..34907c9 --- /dev/null +++ b/requirements.txt @@ -0,0 +1,7 @@ +mne>=0.16.1 +seaborn +pandas +scikit-learn +torch==0.4.0 +braindecode==0.4.5 +scikit-optimize==0.5.2 From 46b79e084da6db09c913de2777df1d78778d71cb Mon Sep 17 00:00:00 2001 From: rivasd Date: Thu, 22 Nov 2018 19:34:05 -0500 Subject: [PATCH 3/3] some bayesion optimization --- .../towardMoabbIntegration/utils/bayesian.py | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/brainDecode/towardMoabbIntegration/utils/bayesian.py b/brainDecode/towardMoabbIntegration/utils/bayesian.py index f99af1f..bbf7c6e 100644 --- a/brainDecode/towardMoabbIntegration/utils/bayesian.py +++ b/brainDecode/towardMoabbIntegration/utils/bayesian.py @@ -1,3 +1,21 @@ + from skopt import BayesSearchCV +from skopt.space import Categorical, Real, Integer from brainDecode.towardMoabbIntegration.brainDecodeSKLearnWrapper.ShallowFBCSPNet_GeneralTrainer import ShallowFBCSPNet_GeneralTrainer + +def bayes_optimize(classifier=None, X_train=None, Y_train=None): + classifier = ShallowFBCSPNet_GeneralTrainer(nb_epoch=25) + + searches = { # This should containt Dimension instances (Reals, Integer, or Categorical) + "n_filters_time":Integer(5, 15), + "filter_time_length":Integer(50,75), + "n_filters_spat":Integer(3,10), + "pool_time_length":Integer(50,80), + "pool_time_stride":Integer(20,40) + } + + bayes_optmizer = BayesSearchCV(classifier, searches) + + # now fit and profit + bayes_optmizer.fit(X_train, Y_train) \ No newline at end of file