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Ensemble learning on functional connectivity¶
This example shows how to compute SPD matrices from functional connectivity estimators and how to combine classification with ensemble learning [1].
# Authors: Sylvain Chevallier <sylvain.chevallier@universite-paris-saclay.fr>,
# Marie-Constance Corsi <marie.constance.corsi@gmail.com>
#
# License: BSD (3-clause)
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from mne import Epochs, pick_types, events_from_annotations
from mne.io import concatenate_raws
from mne.io.edf import read_raw_edf
from mne.datasets import eegbci
from sklearn.base import BaseEstimator, TransformerMixin
from sklearn.ensemble import StackingClassifier
from sklearn.linear_model import LogisticRegression
from sklearn.model_selection import GridSearchCV, StratifiedKFold
from sklearn.pipeline import Pipeline
from sklearn.svm import SVC
from pyriemann.classification import FgMDM
from pyriemann.estimation import Coherences, Covariances
from pyriemann.spatialfilters import CSP
from pyriemann.tangentspace import TangentSpace
from helpers.coherence_helpers import NearestSPD, get_results
Define connectivity transformer¶
This estimator computes the functional connectivity from input signal using pyriemann.estimation.Coherences
class Connectivities(TransformerMixin, BaseEstimator):
"""Getting connectivity features from epoch"""
def __init__(self, method="ordinary", fmin=8, fmax=35, fs=None):
self.method = method
self.fmin = fmin
self.fmax = fmax
self.fs = fs
def fit(self, X, y=None):
self._coh = Coherences(
coh=self.method,
fmin=self.fmin,
fmax=self.fmax,
fs=self.fs,
)
return self
def transform(self, X):
X_coh = self._coh.fit_transform(X)
X_con = np.mean(X_coh, axis=-1, keepdims=False)
return X_con
Load EEG data¶
# avoid classification of evoked responses by using epochs that start 1s after
# cue onset.
tmin, tmax = 1.0, 2.0
event_id = dict(hands=2, feet=3)
subject = 7
runs = [4, 8] # motor imagery: left vs right hand
raw_files = [
read_raw_edf(f, preload=True) for f in eegbci.load_data(subject, runs)
]
raw = concatenate_raws(raw_files)
picks = pick_types(
raw.info, meg=False, eeg=True, stim=False, eog=False, exclude="bads"
)
# subsample elecs
picks = picks[::2]
# Apply band-pass filter
raw.filter(7.0, 35.0, method="iir", picks=picks)
events, _ = events_from_annotations(raw, event_id=dict(T1=2, T2=3))
# Read epochs (train will be done only between 1 and 2s)
epochs = Epochs(
raw,
events,
event_id,
tmin,
tmax,
proj=True,
picks=picks,
baseline=None,
preload=True,
verbose=False,
)
labels = epochs.events[:, -1] - 2
fs = epochs.info["sfreq"]
X = 1e6 * epochs.get_data()
Downloading EEGBCI data
Download complete in 06s (5.0 MB)
Extracting EDF parameters from /home/docs/mne_data/MNE-eegbci-data/files/eegmmidb/1.0.0/S007/S007R04.edf...
EDF file detected
Setting channel info structure...
Creating raw.info structure...
Reading 0 ... 19999 = 0.000 ... 124.994 secs...
Extracting EDF parameters from /home/docs/mne_data/MNE-eegbci-data/files/eegmmidb/1.0.0/S007/S007R08.edf...
EDF file detected
Setting channel info structure...
Creating raw.info structure...
Reading 0 ... 19999 = 0.000 ... 124.994 secs...
Filtering a subset of channels. The highpass and lowpass values in the measurement info will not be updated.
Filtering raw data in 2 contiguous segments
Setting up band-pass filter from 7 - 35 Hz
IIR filter parameters
---------------------
Butterworth bandpass zero-phase (two-pass forward and reverse) non-causal filter:
- Filter order 16 (effective, after forward-backward)
- Cutoffs at 7.00, 35.00 Hz: -6.02, -6.02 dB
Used Annotations descriptions: ['T1', 'T2']
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/checkouts/latest/examples/motor-imagery/plot_ensemble_coherence.py:112: FutureWarning: The current default of copy=False will change to copy=True in 1.7. Set the value of copy explicitly to avoid this warning
X = 1e6 * epochs.get_data()
Defining pipelines¶
Compare CSP+SVM, FgMDM on covariance, tangent space logistic regression with covariance, lag coherence, and instantaneous coherence, along with ensemble method
ppl_baseline, ppl_fc, ppl_ens = {}, {}, {}
Baseline algorithms are CSP with optimal SVM and FgMDM based on covariances
param_svm = {"kernel": ("linear", "rbf"), "C": [0.1, 1, 10]}
step_csp = [
("cov", Covariances(estimator="lwf")),
("csp", CSP(nfilter=6)),
("optsvm", GridSearchCV(SVC(), param_svm, cv=3)),
]
ppl_baseline["CSP+optSVM"] = Pipeline(steps=step_csp)
step_mdm = [
("cov", Covariances(estimator="lwf")),
("fgmdm", FgMDM(metric="riemann", tsupdate=False)),
]
ppl_baseline["FgMDM"] = Pipeline(steps=step_mdm)
Functional connectivity pipelines use logistic regression in tangent space. They will be estimated from covariance, lagged coherence and instantaneous coherence.
spectral_met = ["cov", "lagged", "instantaneous"]
fmin, fmax = 8, 35
param_lr = {
"penalty": "elasticnet",
"l1_ratio": 0.15,
"intercept_scaling": 1000.0,
"solver": "saga",
}
param_ft = {"fmin": fmin, "fmax": fmax, "fs": fs}
step_fc = [
("spd", NearestSPD()),
("tg", TangentSpace(metric="riemann")),
("LogistReg", LogisticRegression(**param_lr)),
]
for sm in spectral_met:
pname = sm + "+elasticnet"
if sm == "cov":
ppl_fc[pname] = Pipeline(
steps=[("cov", Covariances(estimator="lwf"))] + step_fc
)
else:
ft = Connectivities(**param_ft, method=sm)
ppl_fc[pname] = Pipeline(steps=[("ft", ft)] + step_fc)
The ensemble classifier stacks a logistic regression on top of the three functional connectivity pipelines to make a global prediction
fc_estim = [(n, ppl_fc[n]) for n in ppl_fc]
cvkf = StratifiedKFold(n_splits=5, shuffle=True, random_state=42)
lr = LogisticRegression(**param_lr)
ppl_ens["ensemble"] = StackingClassifier(
estimators=fc_estim,
cv=cvkf,
n_jobs=1,
final_estimator=lr,
stack_method="predict_proba",
)
Evaluation¶
dataset_res = list()
all_ppl = {**ppl_baseline, **ppl_ens}
# Compute results
results = get_results(X, labels, all_ppl)
results = pd.DataFrame(results)
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/checkouts/latest/pyriemann/utils/mean.py:540: UserWarning: Convergence not reached
warnings.warn("Convergence not reached")
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/envs/latest/lib/python3.8/site-packages/sklearn/linear_model/_sag.py:350: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/checkouts/latest/pyriemann/utils/mean.py:540: UserWarning: Convergence not reached
warnings.warn("Convergence not reached")
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/envs/latest/lib/python3.8/site-packages/sklearn/linear_model/_sag.py:350: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/checkouts/latest/pyriemann/utils/mean.py:540: UserWarning: Convergence not reached
warnings.warn("Convergence not reached")
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/envs/latest/lib/python3.8/site-packages/sklearn/linear_model/_sag.py:350: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/checkouts/latest/pyriemann/utils/mean.py:540: UserWarning: Convergence not reached
warnings.warn("Convergence not reached")
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/envs/latest/lib/python3.8/site-packages/sklearn/linear_model/_sag.py:350: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/checkouts/latest/pyriemann/utils/mean.py:540: UserWarning: Convergence not reached
warnings.warn("Convergence not reached")
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/envs/latest/lib/python3.8/site-packages/sklearn/linear_model/_sag.py:350: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/checkouts/latest/pyriemann/utils/mean.py:540: UserWarning: Convergence not reached
warnings.warn("Convergence not reached")
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/envs/latest/lib/python3.8/site-packages/sklearn/linear_model/_sag.py:350: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/checkouts/latest/pyriemann/utils/mean.py:540: UserWarning: Convergence not reached
warnings.warn("Convergence not reached")
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/envs/latest/lib/python3.8/site-packages/sklearn/linear_model/_sag.py:350: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/checkouts/latest/pyriemann/utils/mean.py:540: UserWarning: Convergence not reached
warnings.warn("Convergence not reached")
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/envs/latest/lib/python3.8/site-packages/sklearn/linear_model/_sag.py:350: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/checkouts/latest/pyriemann/utils/mean.py:540: UserWarning: Convergence not reached
warnings.warn("Convergence not reached")
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/envs/latest/lib/python3.8/site-packages/sklearn/linear_model/_sag.py:350: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/checkouts/latest/pyriemann/utils/mean.py:540: UserWarning: Convergence not reached
warnings.warn("Convergence not reached")
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/envs/latest/lib/python3.8/site-packages/sklearn/linear_model/_sag.py:350: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/checkouts/latest/pyriemann/utils/mean.py:540: UserWarning: Convergence not reached
warnings.warn("Convergence not reached")
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/envs/latest/lib/python3.8/site-packages/sklearn/linear_model/_sag.py:350: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/checkouts/latest/pyriemann/utils/mean.py:540: UserWarning: Convergence not reached
warnings.warn("Convergence not reached")
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/envs/latest/lib/python3.8/site-packages/sklearn/linear_model/_sag.py:350: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/checkouts/latest/pyriemann/utils/mean.py:540: UserWarning: Convergence not reached
warnings.warn("Convergence not reached")
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/envs/latest/lib/python3.8/site-packages/sklearn/linear_model/_sag.py:350: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/checkouts/latest/pyriemann/utils/mean.py:540: UserWarning: Convergence not reached
warnings.warn("Convergence not reached")
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/envs/latest/lib/python3.8/site-packages/sklearn/linear_model/_sag.py:350: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/checkouts/latest/pyriemann/utils/mean.py:540: UserWarning: Convergence not reached
warnings.warn("Convergence not reached")
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/envs/latest/lib/python3.8/site-packages/sklearn/linear_model/_sag.py:350: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/checkouts/latest/pyriemann/utils/mean.py:540: UserWarning: Convergence not reached
warnings.warn("Convergence not reached")
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/envs/latest/lib/python3.8/site-packages/sklearn/linear_model/_sag.py:350: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/checkouts/latest/pyriemann/utils/mean.py:540: UserWarning: Convergence not reached
warnings.warn("Convergence not reached")
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/envs/latest/lib/python3.8/site-packages/sklearn/linear_model/_sag.py:350: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/checkouts/latest/pyriemann/utils/mean.py:540: UserWarning: Convergence not reached
warnings.warn("Convergence not reached")
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/envs/latest/lib/python3.8/site-packages/sklearn/linear_model/_sag.py:350: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/checkouts/latest/pyriemann/utils/mean.py:540: UserWarning: Convergence not reached
warnings.warn("Convergence not reached")
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/envs/latest/lib/python3.8/site-packages/sklearn/linear_model/_sag.py:350: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/checkouts/latest/pyriemann/utils/mean.py:540: UserWarning: Convergence not reached
warnings.warn("Convergence not reached")
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/envs/latest/lib/python3.8/site-packages/sklearn/linear_model/_sag.py:350: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/checkouts/latest/pyriemann/utils/mean.py:540: UserWarning: Convergence not reached
warnings.warn("Convergence not reached")
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/envs/latest/lib/python3.8/site-packages/sklearn/linear_model/_sag.py:350: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/checkouts/latest/pyriemann/utils/mean.py:540: UserWarning: Convergence not reached
warnings.warn("Convergence not reached")
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/envs/latest/lib/python3.8/site-packages/sklearn/linear_model/_sag.py:350: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/checkouts/latest/pyriemann/utils/mean.py:540: UserWarning: Convergence not reached
warnings.warn("Convergence not reached")
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/envs/latest/lib/python3.8/site-packages/sklearn/linear_model/_sag.py:350: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/checkouts/latest/pyriemann/utils/mean.py:540: UserWarning: Convergence not reached
warnings.warn("Convergence not reached")
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/envs/latest/lib/python3.8/site-packages/sklearn/linear_model/_sag.py:350: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/checkouts/latest/pyriemann/utils/mean.py:540: UserWarning: Convergence not reached
warnings.warn("Convergence not reached")
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/envs/latest/lib/python3.8/site-packages/sklearn/linear_model/_sag.py:350: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/envs/latest/lib/python3.8/site-packages/sklearn/linear_model/_sag.py:350: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/checkouts/latest/pyriemann/utils/mean.py:540: UserWarning: Convergence not reached
warnings.warn("Convergence not reached")
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/envs/latest/lib/python3.8/site-packages/sklearn/linear_model/_sag.py:350: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/checkouts/latest/pyriemann/utils/mean.py:540: UserWarning: Convergence not reached
warnings.warn("Convergence not reached")
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/envs/latest/lib/python3.8/site-packages/sklearn/linear_model/_sag.py:350: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/checkouts/latest/pyriemann/utils/mean.py:540: UserWarning: Convergence not reached
warnings.warn("Convergence not reached")
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/envs/latest/lib/python3.8/site-packages/sklearn/linear_model/_sag.py:350: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/checkouts/latest/pyriemann/utils/mean.py:540: UserWarning: Convergence not reached
warnings.warn("Convergence not reached")
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/envs/latest/lib/python3.8/site-packages/sklearn/linear_model/_sag.py:350: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
warnings.warn(
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/checkouts/latest/pyriemann/utils/mean.py:540: UserWarning: Convergence not reached
warnings.warn("Convergence not reached")
/home/docs/checkouts/readthedocs.org/user_builds/pyriemann/envs/latest/lib/python3.8/site-packages/sklearn/linear_model/_sag.py:350: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
warnings.warn(
Plot¶
list_fc_ens = ["ensemble", "CSP+optSVM", "FgMDM"] + \
[sm + "+elasticnet" for sm in spectral_met]
g = sns.catplot(
data=results,
x="pipeline",
y="score",
kind="bar",
order=list_fc_ens,
height=7,
aspect=2,
)
plt.show()
References¶
Total running time of the script: (0 minutes 40.184 seconds)