knowledge_base/timeseries/eeg_signal_classification.py

"""
Title: Electroencephalogram Signal Classification for action identification
Author: [Suvaditya Mukherjee](https://github.com/suvadityamuk)
Date created: 2022/11/03
Last modified: 2022/11/05
Description: Training a Convolutional model to classify EEG signals produced by exposure to certain stimuli.
Accelerator: GPU
"""

"""
## Introduction

The following example explores how we can make a Convolution-based Neural Network to
perform classification on Electroencephalogram signals captured when subjects were
exposed to different stimuli.
We train a model from scratch since such signal-classification models are fairly scarce
in pre-trained format.
The data we use is sourced from the UC Berkeley-Biosense Lab where the data was collected
from 15 subjects at the same time.
Our process is as follows:

- Load the [UC Berkeley-Biosense Synchronized Brainwave Dataset](https://www.kaggle.com/datasets/berkeley-biosense/synchronized-brainwave-dataset)
- Visualize random samples from the data
- Pre-process, collate and scale the data to finally make a `tf.data.Dataset`
- Prepare class weights in order to tackle major imbalances
- Create a Conv1D and Dense-based model to perform classification
- Define callbacks and hyperparameters
- Train the model
- Plot metrics from History and perform evaluation

This example needs the following external dependencies (Gdown, Scikit-learn, Pandas,
Numpy, Matplotlib). You can install it via the following commands.

Gdown is an external package used to download large files from Google Drive. To know
more, you can refer to its [PyPi page here](https://pypi.org/project/gdown)
"""


"""
## Setup and Data Downloads

First, lets install our dependencies:
"""

"""shell
pip install gdown -q
pip install scikit-learn -q
pip install pandas -q
pip install numpy -q
pip install matplotlib -q
"""

"""
Next, lets download our dataset.
The gdown package makes it easy to download the data from Google Drive:
"""

"""shell
gdown 1V5B7Bt6aJm0UHbR7cRKBEK8jx7lYPVuX
# gdown will download eeg-data.csv onto the local drive for use. Total size of
# eeg-data.csv is 105.7 MB
"""

import pandas as pd
import matplotlib.pyplot as plt
import json
import numpy as np
import keras
from keras import layers
import tensorflow as tf
from sklearn import preprocessing, model_selection
import random

QUALITY_THRESHOLD = 128
BATCH_SIZE = 64
SHUFFLE_BUFFER_SIZE = BATCH_SIZE * 2

"""
## Read data from `eeg-data.csv`

We use the Pandas library to read the `eeg-data.csv` file and display the first 5 rows
using the `.head()` command
"""

eeg = pd.read_csv("eeg-data.csv")

"""
We remove unlabeled samples from our dataset as they do not contribute to the model. We
also perform a `.drop()` operation on the columns that are not required for training data
preparation
"""

unlabeled_eeg = eeg[eeg["label"] == "unlabeled"]
eeg = eeg.loc[eeg["label"] != "unlabeled"]
eeg = eeg.loc[eeg["label"] != "everyone paired"]

eeg.drop(
    [
        "indra_time",
        "Unnamed: 0",
        "browser_latency",
        "reading_time",
        "attention_esense",
        "meditation_esense",
        "updatedAt",
        "createdAt",
    ],
    axis=1,
    inplace=True,
)

eeg.reset_index(drop=True, inplace=True)
eeg.head()

"""
In the data, the samples recorded are given a score from 0 to 128 based on how
well-calibrated the sensor was (0 being best, 200 being worst). We filter the values
based on an arbitrary cutoff limit of 128.
"""


def convert_string_data_to_values(value_string):
    str_list = json.loads(value_string)
    return str_list


eeg["raw_values"] = eeg["raw_values"].apply(convert_string_data_to_values)

eeg = eeg.loc[eeg["signal_quality"] < QUALITY_THRESHOLD]
eeg.head()

"""
## Visualize one random sample from the data
"""

"""
We visualize one sample from the data to understand how the stimulus-induced signal looks
like
"""


def view_eeg_plot(idx):
    data = eeg.loc[idx, "raw_values"]
    plt.plot(data)
    plt.title(f"Sample random plot")
    plt.show()


view_eeg_plot(7)

"""
## Pre-process and collate data
"""

"""
There are a total of 67 different labels present in the data, where there are numbered
sub-labels. We collate them under a single label as per their numbering and replace them
in the data itself. Following this process, we perform simple Label encoding to get them
in an integer format.
"""

print("Before replacing labels")
print(eeg["label"].unique(), "\n")
print(len(eeg["label"].unique()), "\n")


eeg.replace(
    {
        "label": {
            "blink1": "blink",
            "blink2": "blink",
            "blink3": "blink",
            "blink4": "blink",
            "blink5": "blink",
            "math1": "math",
            "math2": "math",
            "math3": "math",
            "math4": "math",
            "math5": "math",
            "math6": "math",
            "math7": "math",
            "math8": "math",
            "math9": "math",
            "math10": "math",
            "math11": "math",
            "math12": "math",
            "thinkOfItems-ver1": "thinkOfItems",
            "thinkOfItems-ver2": "thinkOfItems",
            "video-ver1": "video",
            "video-ver2": "video",
            "thinkOfItemsInstruction-ver1": "thinkOfItemsInstruction",
            "thinkOfItemsInstruction-ver2": "thinkOfItemsInstruction",
            "colorRound1-1": "colorRound1",
            "colorRound1-2": "colorRound1",
            "colorRound1-3": "colorRound1",
            "colorRound1-4": "colorRound1",
            "colorRound1-5": "colorRound1",
            "colorRound1-6": "colorRound1",
            "colorRound2-1": "colorRound2",
            "colorRound2-2": "colorRound2",
            "colorRound2-3": "colorRound2",
            "colorRound2-4": "colorRound2",
            "colorRound2-5": "colorRound2",
            "colorRound2-6": "colorRound2",
            "colorRound3-1": "colorRound3",
            "colorRound3-2": "colorRound3",
            "colorRound3-3": "colorRound3",
            "colorRound3-4": "colorRound3",
            "colorRound3-5": "colorRound3",
            "colorRound3-6": "colorRound3",
            "colorRound4-1": "colorRound4",
            "colorRound4-2": "colorRound4",
            "colorRound4-3": "colorRound4",
            "colorRound4-4": "colorRound4",
            "colorRound4-5": "colorRound4",
            "colorRound4-6": "colorRound4",
            "colorRound5-1": "colorRound5",
            "colorRound5-2": "colorRound5",
            "colorRound5-3": "colorRound5",
            "colorRound5-4": "colorRound5",
            "colorRound5-5": "colorRound5",
            "colorRound5-6": "colorRound5",
            "colorInstruction1": "colorInstruction",
            "colorInstruction2": "colorInstruction",
            "readyRound1": "readyRound",
            "readyRound2": "readyRound",
            "readyRound3": "readyRound",
            "readyRound4": "readyRound",
            "readyRound5": "readyRound",
            "colorRound1": "colorRound",
            "colorRound2": "colorRound",
            "colorRound3": "colorRound",
            "colorRound4": "colorRound",
            "colorRound5": "colorRound",
        }
    },
    inplace=True,
)

print("After replacing labels")
print(eeg["label"].unique())
print(len(eeg["label"].unique()))

le = preprocessing.LabelEncoder()  # Generates a look-up table
le.fit(eeg["label"])
eeg["label"] = le.transform(eeg["label"])

"""
We extract the number of unique classes present in the data
"""

num_classes = len(eeg["label"].unique())
print(num_classes)

"""
We now visualize the number of samples present in each class using a Bar plot.
"""

plt.bar(range(num_classes), eeg["label"].value_counts())
plt.title("Number of samples per class")
plt.show()

"""
## Scale and split data
"""

"""
We perform a simple Min-Max scaling to bring the value-range between 0 and 1. We do not
use Standard Scaling as the data does not follow a Gaussian distribution.
"""

scaler = preprocessing.MinMaxScaler()
series_list = [
    scaler.fit_transform(np.asarray(i).reshape(-1, 1)) for i in eeg["raw_values"]
]

labels_list = [i for i in eeg["label"]]

"""
We now create a Train-test split with a 15% holdout set. Following this, we reshape the
data to create a sequence of length 512. We also convert the labels from their current
label-encoded form to a one-hot encoding to enable use of several different
`keras.metrics` functions.
"""

x_train, x_test, y_train, y_test = model_selection.train_test_split(
    series_list, labels_list, test_size=0.15, random_state=42, shuffle=True
)

print(
    f"Length of x_train : {len(x_train)}\nLength of x_test : {len(x_test)}\nLength of y_train : {len(y_train)}\nLength of y_test : {len(y_test)}"
)

x_train = np.asarray(x_train).astype(np.float32).reshape(-1, 512, 1)
y_train = np.asarray(y_train).astype(np.float32).reshape(-1, 1)
y_train = keras.utils.to_categorical(y_train)

x_test = np.asarray(x_test).astype(np.float32).reshape(-1, 512, 1)
y_test = np.asarray(y_test).astype(np.float32).reshape(-1, 1)
y_test = keras.utils.to_categorical(y_test)

"""
## Prepare `tf.data.Dataset`
"""

"""
We now create a `tf.data.Dataset` from this data to prepare it for training. We also
shuffle and batch the data for use later.
"""

train_dataset = tf.data.Dataset.from_tensor_slices((x_train, y_train))
test_dataset = tf.data.Dataset.from_tensor_slices((x_test, y_test))

train_dataset = train_dataset.shuffle(SHUFFLE_BUFFER_SIZE).batch(BATCH_SIZE)
test_dataset = test_dataset.batch(BATCH_SIZE)

"""
## Make Class Weights using Naive method
"""

"""
As we can see from the plot of number of samples per class, the dataset is imbalanced.
Hence, we **calculate weights for each class** to make sure that the model is trained in
a fair manner without preference to any specific class due to greater number of samples.

We use a naive method to calculate these weights, finding an **inverse proportion** of
each class and using that as the weight.
"""

vals_dict = {}
for i in eeg["label"]:
    if i in vals_dict.keys():
        vals_dict[i] += 1
    else:
        vals_dict[i] = 1
total = sum(vals_dict.values())

# Formula used - Naive method where
# weight = 1 - (no. of samples present / total no. of samples)
# So more the samples, lower the weight

weight_dict = {k: (1 - (v / total)) for k, v in vals_dict.items()}
print(weight_dict)

"""
## Define simple function to plot all the metrics present in a `keras.callbacks.History`
object
"""


def plot_history_metrics(history: keras.callbacks.History):
    total_plots = len(history.history)
    cols = total_plots // 2

    rows = total_plots // cols

    if total_plots % cols != 0:
        rows += 1

    pos = range(1, total_plots + 1)
    plt.figure(figsize=(15, 10))
    for i, (key, value) in enumerate(history.history.items()):
        plt.subplot(rows, cols, pos[i])
        plt.plot(range(len(value)), value)
        plt.title(str(key))
    plt.show()


"""
## Define function to generate Convolutional model
"""


def create_model():
    input_layer = keras.Input(shape=(512, 1))

    x = layers.Conv1D(
        filters=32, kernel_size=3, strides=2, activation="relu", padding="same"
    )(input_layer)
    x = layers.BatchNormalization()(x)

    x = layers.Conv1D(
        filters=64, kernel_size=3, strides=2, activation="relu", padding="same"
    )(x)
    x = layers.BatchNormalization()(x)

    x = layers.Conv1D(
        filters=128, kernel_size=5, strides=2, activation="relu", padding="same"
    )(x)
    x = layers.BatchNormalization()(x)

    x = layers.Conv1D(
        filters=256, kernel_size=5, strides=2, activation="relu", padding="same"
    )(x)
    x = layers.BatchNormalization()(x)

    x = layers.Conv1D(
        filters=512, kernel_size=7, strides=2, activation="relu", padding="same"
    )(x)
    x = layers.BatchNormalization()(x)

    x = layers.Conv1D(
        filters=1024,
        kernel_size=7,
        strides=2,
        activation="relu",
        padding="same",
    )(x)
    x = layers.BatchNormalization()(x)

    x = layers.Dropout(0.2)(x)

    x = layers.Flatten()(x)

    x = layers.Dense(4096, activation="relu")(x)
    x = layers.Dropout(0.2)(x)

    x = layers.Dense(
        2048, activation="relu", kernel_regularizer=keras.regularizers.L2()
    )(x)
    x = layers.Dropout(0.2)(x)

    x = layers.Dense(
        1024, activation="relu", kernel_regularizer=keras.regularizers.L2()
    )(x)
    x = layers.Dropout(0.2)(x)
    x = layers.Dense(
        128, activation="relu", kernel_regularizer=keras.regularizers.L2()
    )(x)
    output_layer = layers.Dense(num_classes, activation="softmax")(x)

    return keras.Model(inputs=input_layer, outputs=output_layer)


"""
## Get Model summary
"""

conv_model = create_model()
conv_model.summary()

"""
## Define callbacks, optimizer, loss and metrics
"""

"""
We set the number of epochs at 30 after performing extensive experimentation. It was seen
that this was the optimal number, after performing Early-Stopping analysis as well.
We define a Model Checkpoint callback to make sure that we only get the best model
weights.
We also define a ReduceLROnPlateau as there were several cases found during
experimentation where the loss stagnated after a certain point. On the other hand, a
direct LRScheduler was found to be too aggressive in its decay.
"""

epochs = 30

callbacks = [
    keras.callbacks.ModelCheckpoint(
        "best_model.keras", save_best_only=True, monitor="loss"
    ),
    keras.callbacks.ReduceLROnPlateau(
        monitor="val_top_k_categorical_accuracy",
        factor=0.2,
        patience=2,
        min_lr=0.000001,
    ),
]

optimizer = keras.optimizers.Adam(amsgrad=True, learning_rate=0.001)
loss = keras.losses.CategoricalCrossentropy()

"""
## Compile model and call `model.fit()`
"""

"""
We use the `Adam` optimizer since it is commonly considered the best choice for
preliminary training, and was found to be the best optimizer.
We use `CategoricalCrossentropy` as the loss as our labels are in a one-hot-encoded form.

We define the `TopKCategoricalAccuracy(k=3)`, `AUC`, `Precision` and `Recall` metrics to
further aid in understanding the model better.
"""

conv_model.compile(
    optimizer=optimizer,
    loss=loss,
    metrics=[
        keras.metrics.TopKCategoricalAccuracy(k=3),
        keras.metrics.AUC(),
        keras.metrics.Precision(),
        keras.metrics.Recall(),
    ],
)

conv_model_history = conv_model.fit(
    train_dataset,
    epochs=epochs,
    callbacks=callbacks,
    validation_data=test_dataset,
    class_weight=weight_dict,
)

"""
## Visualize model metrics during training
"""

"""
We use the function defined above to see model metrics during training.
"""

plot_history_metrics(conv_model_history)

"""
## Evaluate model on test data
"""

loss, accuracy, auc, precision, recall = conv_model.evaluate(test_dataset)
print(f"Loss : {loss}")
print(f"Top 3 Categorical Accuracy : {accuracy}")
print(f"Area under the Curve (ROC) : {auc}")
print(f"Precision : {precision}")
print(f"Recall : {recall}")


def view_evaluated_eeg_plots(model):
    start_index = random.randint(10, len(eeg))
    end_index = start_index + 11
    data = eeg.loc[start_index:end_index, "raw_values"]
    data_array = [scaler.fit_transform(np.asarray(i).reshape(-1, 1)) for i in data]
    data_array = [np.asarray(data_array).astype(np.float32).reshape(-1, 512, 1)]
    original_labels = eeg.loc[start_index:end_index, "label"]
    predicted_labels = np.argmax(model.predict(data_array, verbose=0), axis=1)
    original_labels = [
        le.inverse_transform(np.array(label).reshape(-1))[0]
        for label in original_labels
    ]
    predicted_labels = [
        le.inverse_transform(np.array(label).reshape(-1))[0]
        for label in predicted_labels
    ]
    total_plots = 12
    cols = total_plots // 3
    rows = total_plots // cols
    if total_plots % cols != 0:
        rows += 1
    pos = range(1, total_plots + 1)
    fig = plt.figure(figsize=(20, 10))
    for i, (plot_data, og_label, pred_label) in enumerate(
        zip(data, original_labels, predicted_labels)
    ):
        plt.subplot(rows, cols, pos[i])
        plt.plot(plot_data)
        plt.title(f"Actual Label : {og_label}\nPredicted Label : {pred_label}")
        fig.subplots_adjust(hspace=0.5)
    plt.show()


view_evaluated_eeg_plots(conv_model)