scholarly journals Machine Learning Prediction of Parkinson's Disease Onset and Subtype Using Germline Variants

2021 ◽  
Author(s):  
Saya R Dennis ◽  
Tanya Simuni ◽  
Yuan Luo
Keyword(s):  
Machine Learning ◽  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Neurodegenerative Disorder ◽  
Disease Onset ◽  
The United States ◽  
Machine Learning Algorithms ◽  
Progression Rate ◽  
High Importance ◽  
Germline Variants

Parkinson's Disease is the second most common neurodegenerative disorder in the United States, and is characterized by a largely irreversible worsening of motor and non-motor symptoms as the disease progresses. A prominent characteristic of the disease is its high heterogeneity in manifestation as well as the progression rate. For sporadic Parkinson's Disease, which comprises ~90% of all diagnoses, the relationship between the patient genome and disease onset or progression subtype remains largely elusive. Machine learning algorithms are increasingly adopted to study the genomics of diseases due to their ability to capture patterns within the vast feature space of the human genome that might be contributing to the phenotype of interest. In our study, we develop two machine learning models that predict the onset as well as the progression subtype of Parkinson's Disease based on subjects' germline mutations. Our best models achieved an ROC of 0.77 and 0.61 for disease onset and subtype prediction, respectively. To the best of our knowledge, our models present state-of-the-art prediction performances of PD onset and subtype solely based on the subjects' germline variants. The genes with high importance in our best-performing models were enriched for several canonical pathways related to signaling, immune system, and protein modifications, all of which have been previously associated with PD symptoms or pathogenesis. These high-importance gene sets provide us with promising candidate genes for future biomedical and clinical research.

Machine Learning Approaches in Parkinson’s Disease

2021 ◽  
Vol 28 ◽  
Author(s):  
Annamaria Landolfi ◽  
Carlo Ricciardi ◽  
Leandro Donisi ◽  
Giuseppe Cesarelli ◽  
Jacopo Troisi ◽  
...  
Keyword(s):  
Machine Learning ◽  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Neurodegenerative Disorder ◽  
Learning Algorithms ◽  
Disease Diagnosis ◽  
Machine Learning Algorithms ◽  
Clinical Aspects ◽  
Learning Approaches

Background:: Parkinson’s disease is the second most frequent neurodegenerative disorder. Its diagnosis is challenging and mainly relies on clinical aspects. At present, no biomarker is available to obtain a diagnosis of certainty in vivo. Objective:: The present review aims at describing machine learning algorithms as they have been variably applied to different aspects of Parkinson’s disease diagnosis and characterization. Methods:: A systematic search was conducted on PubMed in December 2019, resulting in 230 publications obtained with the following search query: “Machine Learning” “AND” “Parkinson Disease”. Results:: the obtained publications were divided into 6 categories, based on different application fields: “Gait Analysis - Motor Evaluation”, “Upper Limb Motor and Tremor Evaluation”, “Handwriting and typing evaluation”, “Speech and Phonation evaluation”, “Neuroimaging and Nuclear Medicine evaluation”, “Metabolomics application”, after excluding the papers of general topic. As a result, a total of 166 articles were analyzed, after elimination of papers written in languages other than English or not directly related to the selected topics. Conclusion:: Machine learning algorithms are computer-based statistical approaches which can be trained and are able to find common patterns from big amounts of data. The machine learning approaches can help clinicians in classifying patients according to several variables at the same time.

scholarly journals Diagnosis of Parkinson’s Disorder through Speech Data using Machine Learning Algorithms

2020 ◽  
Vol 9 (3) ◽  
pp. 69-72
Keyword(s):  
Machine Learning ◽  
Parkinson’S Disease ◽  
Health Care ◽  
Decision Making ◽  
Parkinson's Disease ◽  
Neurodegenerative Disorder ◽  
Machine Learning Algorithms ◽  
Speech Data ◽  
Computer Aided ◽  
Comprehensive Comparison

Parkinson's disease is a neurodegenerative disorder that affects millions of people around the globe. Detecting Parkinson's disease at an earlier stage could help to better diagnose the disease. Machine learning provides potentially large opportunities for computer-aided identification and diagnosis that could minimize unavoidable health care errors and inherent clinical uncertainty, provide guidance, and improve decision-making. In this paper, we explore the feature extraction and prediction algorithms used to predict Parkinson's disease and provide a comprehensive comparison of these algorithms

Tremor Identification Using Machine Learning in Parkinson's Disease

2019 ◽  
pp. 128-151
Author(s):  
Angana Saikia ◽  
Vinayak Majhi ◽  
Masaraf Hussain ◽  
Sudip Paul ◽  
Amitava Datta
Keyword(s):  
Machine Learning ◽  
Parkinson’S Disease ◽  
Support Vector Machine ◽  
Parkinson's Disease ◽  
Discriminant Analysis ◽  
Learning Algorithms ◽  
The Body ◽  
Machine Learning Algorithms ◽  
Support Vector

Tremor is an involuntary quivering movement or shake. Characteristically occurring at rest, the classic slow, rhythmic tremor of Parkinson's disease (PD) typically starts in one hand, foot, or leg and can eventually affect both sides of the body. The resting tremor of PD can also occur in the jaw, chin, mouth, or tongue. Loss of dopamine leads to the symptoms of Parkinson's disease and may include a tremor. For some people, a tremor might be the first symptom of PD. Various studies have proposed measurable technologies and the analysis of the characteristics of Parkinsonian tremors using different techniques. Various machine-learning algorithms such as a support vector machine (SVM) with three kernels, a discriminant analysis, a random forest, and a kNN algorithm are also used to classify and identify various kinds of tremors. This chapter focuses on an in-depth review on identification and classification of various Parkinsonian tremors using machine learning algorithms.

scholarly journals Can Gut Microbiota Be a Good Predictor for Parkinson’s Disease? A Machine Learning Approach

2020 ◽  
Vol 10 (4) ◽  
pp. 242 ◽  
Author(s):  
Daniele Pietrucci ◽  
Adelaide Teofani ◽  
Valeria Unida ◽  
Rocco Cerroni ◽  
Silvia Biocca ◽  
...  
Keyword(s):  
Machine Learning ◽  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Random Forest ◽  
Gut Microbiota ◽  
Biological Data ◽  
Machine Learning Algorithms ◽  
Support Vector ◽  
Published Data ◽  
Promising Tool

The involvement of the gut microbiota in Parkinson’s disease (PD), investigated in several studies, identified some common alterations of the microbial community, such as a decrease in Lachnospiraceae and an increase in Verrucomicrobiaceae families in PD patients. However, the results of other bacterial families are often contradictory. Machine learning is a promising tool for building predictive models for the classification of biological data, such as those produced in metagenomic studies. We tested three different machine learning algorithms (random forest, neural networks and support vector machines), analyzing 846 metagenomic samples (472 from PD patients and 374 from healthy controls), including our published data and those downloaded from public databases. Prediction performance was evaluated by the area under curve, accuracy, precision, recall and F-score metrics. The random forest algorithm provided the best results. Bacterial families were sorted according to their importance in the classification, and a subset of 22 families has been identified for the prediction of patient status. Although the results are promising, it is necessary to train the algorithm with a larger number of samples in order to increase the accuracy of the procedure.

Tremor Identification Using Machine Learning in Parkinson's Disease

2021 ◽  
pp. 341-365
Author(s):  
Angana Saikia ◽  
Vinayak Majhi ◽  
Masaraf Hussain ◽  
Sudip Paul ◽  
Amitava Datta
Keyword(s):  
Machine Learning ◽  
Parkinson’S Disease ◽  
Support Vector Machine ◽  
Parkinson's Disease ◽  
Discriminant Analysis ◽  
Learning Algorithms ◽  
The Body ◽  
Machine Learning Algorithms ◽  
Support Vector

Tremor is an involuntary quivering movement or shake. Characteristically occurring at rest, the classic slow, rhythmic tremor of Parkinson's disease (PD) typically starts in one hand, foot, or leg and can eventually affect both sides of the body. The resting tremor of PD can also occur in the jaw, chin, mouth, or tongue. Loss of dopamine leads to the symptoms of Parkinson's disease and may include a tremor. For some people, a tremor might be the first symptom of PD. Various studies have proposed measurable technologies and the analysis of the characteristics of Parkinsonian tremors using different techniques. Various machine-learning algorithms such as a support vector machine (SVM) with three kernels, a discriminant analysis, a random forest, and a kNN algorithm are also used to classify and identify various kinds of tremors. This chapter focuses on an in-depth review on identification and classification of various Parkinsonian tremors using machine learning algorithms.

scholarly journals Engaging cognitive circuits to promote motor recovery in degenerative disorders. exercise as a learning modality

2016 ◽  
Vol 52 (1) ◽  
pp. 35-51 ◽  
Author(s):  
Michael W. Jakowec ◽  
Zhou Wang ◽  
Daniel Holschneider ◽  
Jeff Beeler ◽  
Giselle M. Petzinger
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Neurodegenerative Disorder ◽  
Wide Spectrum ◽  
Disease Onset ◽  
Short Review ◽  
Motor Recovery ◽  
Adult Brain ◽  
Brain Disorders ◽  
Dopamine Depletion

AbstractExercise and physical activity are fundamental components of a lifestyle essential in maintaining a healthy brain. This is primarily due to the fact that the adult brain maintains a high degree of plasticity and activity is essential for homeostasis throughout life. Plasticity is not lost even in the context of a neurodegenerative disorder, but could be maladaptive thus promoting disease onset and progression. A major breakthrough in treating brain disorders such as Parkinson’s disease is to drive neuroplasticity in a direction to improve motor and cognitive dysfunction. The purpose of this short review is to present the evidence from our laboratories that supports neuroplasticity as a potential therapeutic target in treating brain disorders. We consider that the enhancement of motor recovery in both animal models of dopamine depletion and in patients with Parkinson’s disease is optimized when cognitive circuits are engaged; in other words, the brain is engaged in a learning modality. Therefore, we propose that to be effective in treating Parkinson’s disease, physical therapy must employ both skill-based exercise (to drive specific circuits) and aerobic exercise (to drive the expression of molecules required to strengthen synaptic connections) components to select those neuronal circuits, such as the corticostriatal pathway, necessary to restore proper motor and cognitive behaviors. In the wide spectrum of different forms of exercise, learning as the fundamental modality likely links interventions used to treat patients with Parkinson’s disease and may be necessary to drive beneficial neuroplasticity resulting in symptomatic improvement and possible disease modification.

scholarly journals An Optimized Brain-Based Algorithm for Classifying Parkinson’s Disease

2020 ◽  
Vol 10 (5) ◽  
pp. 1827 ◽  
Author(s):  
Rodrigo Olivares ◽  
Roberto Munoz ◽  
Ricardo Soto ◽  
Broderick Crawford ◽  
Diego Cárdenas ◽  
...  
Keyword(s):  
Machine Learning ◽  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Extreme Learning Machine ◽  
Neurodegenerative Disorder ◽  
Fine Tuning ◽  
Machine Learning Techniques ◽  
Learning Approaches ◽  
Classification Problems ◽  
Learning Machine

During the last years, highly-recognized computational intelligence techniques have been proposed to treat classification problems. These automatic learning approaches lead to the most recent researches because they exhibit outstanding results. Nevertheless, to achieve this performance, artificial learning methods firstly require fine tuning of their parameters and then they need to work with the best-generated model. This process usually needs an expert user for supervising the algorithm’s performance. In this paper, we propose an optimized Extreme Learning Machine by using the Bat Algorithm, which boosts the training phase of the machine learning method to increase the accuracy, and decreasing or keeping the loss in the learning phase. To evaluate our proposal, we use the Parkinson’s Disease audio dataset taken from UCI Machine Learning Repository. Parkinson’s disease is a neurodegenerative disorder that affects over 10 million people. Although its diagnosis is through motor symptoms, it is possible to evidence the disorder through variations in the speech using machine learning techniques. Results suggest that using the bio-inspired optimization algorithm for adjusting the parameters of the Extreme Learning Machine is a real alternative for improving its performance. During the validation phase, the classification process for Parkinson’s Disease achieves a maximum accuracy of 96.74% and a minimum loss of 3.27%.

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