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Biomedicines
  • Article
  • Open Access

28 October 2022

Modified SqueezeNet Architecture for Parkinson’s Disease Detection Based on Keypress Data

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1
Department of Software Engineering, Kaunas University of Technology, 51368 Kaunas, Lithuania
2
Department of Electrical and Data Engineering, University of Technology Sydney, Sydney 2007, Australia
3
Department of Teleinformatics Engineering, Federal University of Ceará, Fortaleza 60455-970, Brazil
4
Instituto de Ciência e Inovação em Engenharia Mecânica e Engenharia Industrial, Departamento de Engenharia Mecânica, Faculdade de Engenharia, Universidade do Porto, 4200-465 Porto, Portugal
This article belongs to the Special Issue State of the Art: Prerequisites, Prevention and Treatment of Neurodegenerative Diseases

Abstract

Parkinson’s disease (PD) is the most common form of Parkinsonism, which is a group of neurological disorders with PD-like motor impairments. The disease affects over 6 million people worldwide and is characterized by motor and non-motor symptoms. The affected person has trouble in controlling movements, which may affect simple daily-life tasks, such as typing on a computer. We propose the application of a modified SqueezeNet convolutional neural network (CNN) for detecting PD based on the subject’s key-typing patterns. First, the data are pre-processed using data standardization and the Synthetic Minority Oversampling Technique (SMOTE), and then a Continuous Wavelet Transformation is applied to generate spectrograms used for training and testing a modified SqueezeNet model. The modified SqueezeNet model achieved an accuracy of 90%, representing a noticeable improvement in comparison to other approaches.

1. Introduction

Parkinson’s disease (PD) is a chronic and progressive movement disorder [1], being the second most prevalent neurodegenerative disorder in the world. It is believed that the disease affects over 1% of the world’s population, with its prevalence expected to double by 2030 [2]. The PD progression goes slowly, happening in several stages based on the affected brain region [3]. The disease’s early symptoms manifest in the disease’s middle stage, which correspond to a degeneration of 50%, or more, of the dopaminergic neuros in the Substantia Nigra part of the human brain [4].
In clinical environments, the common process of a PD diagnosis is performed based on the patient’s symptomatic history examination, where prodromal features, for instance, rapid eye movement, sleep disorder, hyposmia, and constipation; movement impairments, such as tremor, stiffness, and slowness [5]; psychological or cognitive disorders, such as, for example, anxiety, depression, and cognitive decline [6]; and family history, because 5 to 15% of the cases manifest in a family-related form [7], are taken into account.
With the progress of technology, each day more Artificial Intelligence (AI)-based solutions are allowing an automated recognition of many diseases [8,9,10], mainly a better understanding of PD [11], allowing the early diagnostics of the disease. Each year, numerous studies are published aiming to speed up the diagnosis [12] and management [13] of PD in order to allow a better patient quality of life. The motor symptoms characteristic of the disease affect simple daily activities performed by patients, such as typing on a computer’s keyboard [14,15]. In view of that, and aligned to the advances in AI-based solutions and current computational power, researchers [16,17,18] are aiming to find new approaches capable of detecting the motor impairments characteristic of PD [19].
In this study, we are focusing on the frequency aspect and how it influences the keyboard typing process by applying a convolutional neural network (CNN) on spectrograms generated from key-typing features of individuals belonging to two classes: subjects with PD and healthy (normal) individuals.
For the development of the proposed approach, the database [20] was applied as the data source. The presented database consists of 214 fields from which 202 features were extracted from 217 individuals from which 162 are PD patients and 55 are healthy individuals. Dekelly, et al. [20] divided the computer keyboard into three regions, left (L), right (R), and space (S), while measuring the pressure time on individual regions, such as the pressure on consecutive regions. From the collected values, 202 features, such as the flight time, mean pressure time, mean flight time, and others, were generated.
Due to the unbalanced nature of the dataset, a Synthetic Minority Oversampling Technique (SMOTE) was applied, increasing the volume of the data to 324. The values were then normalized using the MinMax technique and later applied to a Continuous Wavelet Transformer (CWT) in order to obtain the spectrogram of the data. The resulting images were applied to train a modified SqueezeNet model with seven fire modules and seven MaxPooling2D modules placed interleaved with each other.
The main contributions of this article are:
  • A new approach for detecting Parkinson’s disease based on modifying a SqueezeNet CNN model.
  • A new approach for detecting the symptoms of PD based on keyboard input, focusing on converting the acquired data into images by converting the input values into wavelets using a CWT in order to improve the results when detecting PD based on deep learning, which is an alternative approach to [21].
This article is organized into the following sections: Section 2, where similar works are described; Section 3, where the methods used are described; Section 4, where the obtained results and their assessment are presented; and Section 5, where the main conclusions are outlined and future work is suggested.

3. Methodology

In this section, the theoretical and methodological concepts needed to better understand the proposed solution are presented.

3.1. Workflow

The main steps for the development of this study are presented in Figure 1, which offers a visual summary of the procedures taken in this study.
Figure 1. Fluxogram of the proposed solution.
The steps are summarized below:
  • Data preparation, with features selection, data balancing with SMOTE technique, and data isolation (Section 3.2 and Section 3.3).
  • Image generation applying the Continuous Wavelet Transform (Section 3.4).
  • The modified SqueezeNet structure is presented (Section 3.7).

3.2. Dataset

Keyboard Taps Data from Kaggle and MIT is a dataset developed by [21], composed of key-pressing data collected from 227 healthy and PD-affected individuals from Canada, United States, Australia, and United Kingdom. The author divided the computer keyboard into 3 regions: the left region (L), right region (R), and space bar region (S), Figure 2.
Figure 2. Keyboard collection structure used to build the used experimental dataset.
The software developed in [21], Tappy, kept tracking the normal usage of the computer’s keyboard by the volunteers of the study, storing the input data in text files, Figure 3, which stored the individual’s identification code (ID), the date (DT) and time (TM) when the key was pressed, the pressing region (SD), the hold time (PT) in milliseconds (ms), the region change (RC), the latency time (TR1), the flight time between subsequent keys (TR2). Other features which were not considered for this study included disease manifestation side, body side which is most affected by the disease motor symptoms, and the disease stage according to the Unified Parkinson’s Disease Rating Scale (UPDRS).
Figure 3. Structure of the used dataset.
For this study, an updated version based on the base structure of the database was used, where 202 features were generated from regions L, R, and change in regions based on the descriptive statistics, such as mean, standard deviation, and kurtosis, to generate the following features:
  • Flight time mean;
  • Flight time standard deviation;
  • Flight time kurtosis;
  • Flight time skew;
  • Flight time percentile 10th;
  • Flight time percentile 20th;
  • Flight time percentile 40th;
  • Flight time percentile 60th;
  • Flight time percentile 70th;
  • Flight time percentile 80th;
  • Flight time percentile 90;
  • Hold time mean;
  • Hold time standard deviation;
  • Hold time kurtosis;
  • Hold time skew;
  • Hold time percentile 10th;
  • Hold time percentile 20th;
  • Hold time percentile 40th;
  • Hold time percentile 60th;
  • Hold time percentile 70th;
  • Hold time percentile 80th;
  • Hold time percentile 90th;
  • Latency time mean;
  • Latency time standard deviation;
  • Latency time kurtosis;
  • Latency time skew;
  • Latency time percentile 10th;
  • Latency time percentile 20th;
  • Latency time percentile 40th;
  • Latency time percentile 60th;
  • Latency time percentile 70th;
  • Latency time percentile 80th;
  • Latency time percentile 90th;
  • Total count;
  • Mean difference L/R hold time;
  • Mean difference LR/RL latency time;
  • Mean difference LL/RR latency time.
Those values were then stored as a csv file for the image generation process.

3.3. SMOTE

Unbalanced data are a recurrent issue in classification tasks, being found in numerous applications [37]. To balance the data and overcome eventual issues caused by such nature of the input set techniques, such as the Synthetic Minority Oversampling Technique (SMOTE), are applied.
SMOTE generates data for the minority class by applying a K-nearest neighbors (K-NN) approach, although, differently from other KNN-based oversampling approaches where the synthetic values are randomly generated directing to its k-nearest neighbors, the SMOTE technique consists of assigning weights to each neighbor direction, assigning smaller weights for positions that can generate over generalization [38].
Mathematically, the SMOTE technique can be expressed by a given minority class A, where for each x A the Euclidean distance between x and the other samples of A are extracted. Later, a set for samples from N are randomly chosen from its K-nearest neighbors, constructing a set A 1 .
For each x k i n A 1 , Equation (1) is applied to generate a new oversampled set.
x = x + r a n d ( 0 , 1 ) | x x k |

3.4. Continuous Wavelet Transform

Continuous Wavelet Transform (CWT) offers a straightforward approach for visualizing the signal behavior on frequency domain; CWT consists of a correlation measure between a signal and multiple wavelets deriving from the base one. It can be obtained by changing the size of the analysis window, translating it on time, multiplying it by the input signal, and integrating it across the time intervals. We can express such concept mathematically by Equation (2), where d Z ( a , b ) represents the wavelet coefficient of the continuous variable Z = { Z ( t ) , t R } for a given scale a and shift b.
d Z ( a , b ) = 1 a R ψ ( t a b ) Z ( t ) d t = < ψ λ , Z > L 2 ( R )
For discrete input signals, the discretized wavelet coefficient e Z ( a , b ) can be obtained by applying the Riemman sum. Equation (3) is obtained, in such cases, when the function ψ satisfies M e * .
R t m ψ ( t ) d t = 0 for all m { 0 , 1 , , M }
Given a signal x ( t ) , its CWT is given by Equation (4), where W λ , t is the wavelet coefficient. ψ ( t ) corresponds to the functional form of the reference wavelet and ψ * its complex conjugate, λ corresponds to the scale responsible for changing the frequency being measured by a given wavelet.
W λ , t = x ( τ ) ψ λ , t * ( τ ) d τ .
The functional form of the mother wavelet ψ can be represented by Equation (5)
ψ λ , t ( τ ) = 1 λ ψ τ t λ

3.5. Convolutional Neural Network

In a standard manner, a CNN, Figure 4, has an input layer, three convolutional layers, two max-pooling layers, and one fully connected layer. An input layer receives the image from which the pixels contribute to the output through a set of kernel filters, also known as weights or mask. Typically, the applied filter is fixed, depending on the specified network layer, the output being a result of bi-dimensional convolutional operations:
U = conv 2 d ( X , W )
where X corresponds to the input image, U the output image, and W the weight matrix or 2D filter matrix.
Figure 4. Common architecture of a Convolutional Neural Network.
A non-linear function σ is also added to the linear part of U layer, in that manner the output is obtained:
z m n = σ ( u m n + b ) , or Z = σ ( W X + B )
where σ represents the d activation function such as Sigmoid, B represents the bias for the layer, and Z represents a feature map.
For a given 2 D image (I), the convolution of the feature map (X) by the weight matrix (W) in a given point ( I ( p , q ) ) is:
U p , q = ( W X ) p , q = m = 0 r 1 n = 0 c 1 W m , n X p m , q n

3.6. SqueezeNet

Mentioned for the first time in [39], SqueezeNet consists of a network designed with an architecture 50 times smaller than AlexNet network, although equally powerful and 3 times faster. SqueezeNet is vastly used in medical field due to its performance and fast execution, as we can see in [40].
A SqueezeNet model is composed of a standalone convolutional layer, responsible for receiving the input image, followed by 8 fire modules, and ending with a convolutional layer, Figure 5. The network is characterized by a series of “squeeze”, composed by 1 × 1 filters, and “expand”, composed by a series of 1 × 1 and 3 × 3 filters, layers. The joint of both layers is named Fire module.
Figure 5. Architecture of a SqueezeNet model.

3.7. Modified SqueezeNet

During tests applying a SqueezeNet model, it was observed that such architecture outperformed other applied models; however, the resulted metrics still presented inferior values than those desired. In view of that, a set of trials was performed in changing the original SqueezeNet architecture, aiming to maximize the performance of the network. As a result of such trials, an improved architecture composed of 1 input layer, 1 batch normalization layer, 7 Fire modules, Table 2, 6 pooling layers with a pool size of 2 × 2 , 1 global pooling layer, and 1 fully connected layer was generated(see Figure 6).
Table 2. Fire modules.
Figure 6. Modified SqueezeNet structure.

3.8. Performance Evaluation

To evaluate the performance of the proposed solution, we use the confusion matrix for the binary classification problem under study, which is presented in Table 3.
Table 3. Confusion matrix built for the binary classification problem under analysis.
Many performance measures can be obtained from the confusion matrix, such as:
Sensitivity, which is the rate of data correctly classified as positive observations;
Specificity, which is the rate of data correctly classified as negative observations.
F1-Score is applied to establish the performance of a binary classifier as the harmonic mean of precision (PPV) and recall.
The validation loss (valid loss) is obtained by running the neural network forward over the inputs ( x i ), comparing the outputs ( y i ^ ) with the true values, i.e., the ground-truth values, ( y i ) by applying a loss function defined as:
J = 1 N N i = 1 L ( y i ^ , y i )
where L represents the individual loss function based on the differences in predicted and target values, and N the number of generated outputs.

4. Experiments and Results

This section will approach the computational and mathematical experiments performed for the development of this work.

4.1. Data Preparation

The dataset was stored in a csv file, with 215 columns containing information, such as the subject’s identification, and attributes, such as gender, state of Parkinson’s, tremors, and diagnosis year. Initially, those values are excluded from the set of features from the collection, once only the numerical values are relevant for this study.
The 201 data rows, each belonging to different individuals, are mapped and converted into a single matrix M ( 217 , 202 ) , and the matrix’s points distribution can be seen in Figure 7.
Figure 7. Dataset points distribution according to health status.
Due to the highly unbalanced nature of the data, the matrix M is submitted to an oversampling process where a SMOTE technique was applied with a random generation seed of 42. This process results in a matrix M ( 321 , 212 ) , from which 160 are Parkinson’s and 161 are healthy, as presented in Figure 8.
Figure 8. Oversampled dataset points distribution according to health status.

4.2. Image Dataset

The rows of matrix M are then isolated and separated into two sets of vectors, h e a l t h y and p a r k i n s o n , which are normalized with a MinMaxScale ranging the values in the interval [ 0 , 1 ] . The vectors are then applied to the image generation by applying scales in the interval A = [ 0 , 20 ] and the Morlet Wavelet following Equation (10). The sample images of the time domain and frequency domain data can be seen in Figure 9.
ψ ( t ) = e x p t 2 2 c o s ( 5 t )
Figure 9. Examples of time and frequency domain data in the dataset.
To increase the volume of the data, and thus improving the precision of the model, the newly generated images are submitted to a data augmentation process, where the morphological transformations rescale, rotation at the 0 to 40 range, horizontal flip, 0 to 0.2 height shift range, shear at 0 to 0.2 range, and zoom ranging from 0 to 0.2. Those processes increased the input data volume from 217 to 712 images in both classes. The data were then split into three datasets, train, test, and valid, used for training, testing, and validating the model.

4.3. Experimental Setting

For the development of this work, a Colab GPU, with 13 GB of RAM, running Ubuntu 18.04.3 LTS, was used. For the implementation of the proposed solution, the Python 3 programming language was used, and to assess its efficiency, metrics such as accuracy, recall, F1-Score, and the binary confusion matrix were adopted.

4.4. Training

The training process was performed applying a batch size of 8 with images of 240 × 240 × 3 , Figure 10, performing 20 steps per epoch in 35 epochs and applying the early stop by valid loss method. This measures the validation loss obtained during each epoch, stopping the process of training once the valid loss value reached a point lower than the established threshold of 0.4 , where the model reached an accuracy of 90 % with a valid loss of 0.3353, which was plotted in Figure 11, from which was possible to observe the convergence of the valid loss and train loss during the training process.
Figure 10. Batch sample of images used for model training.
Figure 11. Validation loss and model accuracy by epoch during the training process.

4.5. Results

For an easier view of the individual performance by class, the obtained metrics were placed in Table 4 and later applied for the construction of the confusion matrix, Figure 12.
Table 4. Summary of classes performance.
Figure 12. Confusion matrix for the validation process.
From the confusion matrix, it was possible to observe that from the 71 images applied to test the final trained model, 35 belonging to the healthy class were correctly classified, while 9 were wrongly classified as Parkinson’s disease. On the other hand, only 5 of the 35 images belonging to the Parkinson’s disease class were wrongly classified as healthy, while 30 were correctly detected, thus achieving, on average, 90% accuracy with a 95% confidence interval of [0.22, 0.4] and a mean of 0.3.

4.6. Comparison of Results

To compare the efficiency of our proposed model, which achieved 90% accuracy when submitted to the validation set (validation accuracy), three other CNN models were trained and validated, being SqueezeNet which achieved an accuracy of 72.53%, AlexNet with an accuracy of 76.76%, and MobileNet V3 with an accuracy of 76.56%. The results are summarized in Table 5.
Table 5. Comparison of obtained performance metrics.
To assess the influence of the SMOTE technique in the proposed solution’s result, the values with and without the SMOTE technique were compared, and the results are presented in Table 6. The results show that SMOTE has allowed to improve the performance of the classification.
Table 6. Comparison SMOTE technique.

5. Conclusions

This study showed that altering the original structure of the SqueezeNet architecture, aligned with the usage of the Continuous Wavelet Transform (CWT) for image generation, can significantly improve the process of detecting Parkinson’s disease. The results of the current study displayed that in terms of the used accuracy metrics, the intrinsic features can be observed within the input key-typing data [21] which are responsible for the good achieved performance. Therefore, a simple task such as key typing can help in the diagnosis of Parkinson’s disease which affects millions of people worldwide.

Author Contributions

Conceptualization, R.D. and S.H.L.; methodology, R.D., V.H.C.d.A. and S.H.L.; software, L.S.B.; validation, L.S.B., R.D., S.H.L. and V.H.C.d.A.; formal analysis, L.S.B., R.D. and J.M.R.S.T.; investigation, L.S.B. and R.D.; resources, R.D.; data curation, L.S.B.; writing—original draft preparation, L.S.B. and R.D.; writing—review and editing, V.H.C.d.A., S.H.L. and J.M.R.S.T.; visualization, L.S.B.; supervision, R.D.; funding acquisition, R.D. All authors have read and agreed to the published version of the manuscript.

Funding

This research received no external funding.

Institutional Review Board Statement

Not applicable.

Data Availability Statement

Data used in this investigation are available under the ODC Public Domain Dedication and License from the PhysioNet repository at https://physionet.org/physiobank/database/tappy/ (accessed on 16 June 2022).

Conflicts of Interest

The authors declare no conflict of interest.

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