Deep-Learning-with-Jax / day_07_exercise_brain_decode

Exercise on convolutional neural networks about how use them to decode brain waves.

Exercise: Brain-Wave decoding with Convnets

In this exercise we will apply CNN to decode Brain-Wave or EEG data. The data-set was recorded at the University of Freiburg and appeared in Deep learning with convolutional neural networks for EEG decoding and visualization. The authors describe it as follows:

"Our “High-Gamma Dataset” is a 128-electrode dataset (of which we later only use 44 sensors covering the motor cortex, (see Section 2.7.1), obtained from 14 healthy subjects (6 female, 2 left-handed, age $27.2\pm3.6$ (mean $\pm$ std)) with roughly 1000 ($963.1\pm150.9$, mean $\pm$ std) four-second trials of executed movements divided into 13 runs per subject. The four classes of movements were movements of either the left hand, the right hand, both feet, and rest (no movement, but same type of visual cue as for the other classes)."

The dataset is available online. We have prepared a download script for you. To get the data run

cd data
python download.py

Be patient. The script will take approximately an hour to complete. Run nox -s test to check if the data-loading works properly. The plot below shows the first four EEG sensors of a recording.

Examine the data yourself.

Your task:

Train a CNN to recognize the four actions given only the EEG data. Preprocessing code from the paper-authors is already ready for in src/util.py. To get started have a look at src/train_brain_decoder.py and load the data via:

    from src.load_eeg import load_train_valid_test
    low_cut_hz = 0
    subject_id = 1

    train_filename = os.path.join('./data', 'train/{:d}.mat'.format(subject_id))
    test_filename = os.path.join('./data',
                            'test/{:d}.mat'.format(subject_id))

    # Create the dataset
    train_set, valid_set, test_set = load_train_valid_test(
        train_filename=train_filename, test_filename=test_filename,
        low_cut_hz=low_cut_hz)

Use as much of your code from the last two days as possible. You can re-use your image-processing code by treating the EEG signals as images with single rows and 44 "color"-channels. Implement your solution in src/train_brain_decoder.py. Follow the instructions and make sure you implement everything marked with a TODO.