Dataset Information

Multi-modality machine learning predicting Parkinson's disease.

ABSTRACT: Personalized medicine promises individualized disease prediction and treatment. The convergence of machine learning (ML) and available multimodal data is key moving forward. We build upon previous work to deliver multimodal predictions of Parkinson's disease (PD) risk and systematically develop a model using GenoML, an automated ML package, to make improved multi-omic predictions of PD, validated in an external cohort. We investigated top features, constructed hypothesis-free disease-relevant networks, and investigated drug-gene interactions. We performed automated ML on multimodal data from the Parkinson's progression marker initiative (PPMI). After selecting the best performing algorithm, all PPMI data was used to tune the selected model. The model was validated in the Parkinson's Disease Biomarker Program (PDBP) dataset. Our initial model showed an area under the curve (AUC) of 89.72% for the diagnosis of PD. The tuned model was then tested for validation on external data (PDBP, AUC 85.03%). Optimizing thresholds for classification increased the diagnosis prediction accuracy and other metrics. Finally, networks were built to identify gene communities specific to PD. Combining data modalities outperforms the single biomarker paradigm. UPSIT and PRS contributed most to the predictive power of the model, but the accuracy of these are supplemented by many smaller effect transcripts and risk SNPs. Our model is best suited to identifying large groups of individuals to monitor within a health registry or biobank to prioritize for further testing. This approach allows complex predictive models to be reproducible and accessible to the community, with the package, code, and results publicly available.

SUBMITTER: Makarious MB

PROVIDER: S-EPMC8975993 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature

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Multi-modality machine learning predicting Parkinson's disease.

Makarious Mary B MB Leonard Hampton L HL Vitale Dan D Iwaki Hirotaka H Sargent Lana L Dadu Anant A Violich Ivo I Hutchins Elizabeth E Saffo David D Bandres-Ciga Sara S Kim Jonggeol Jeff JJ Song Yeajin Y Maleknia Melina M Bookman Matt M Nojopranoto Willy W Campbell Roy H RH Hashemi Sayed Hadi SH Botia Juan A JA Carter John F JF Craig David W DW Van Keuren-Jensen Kendall K Morris Huw R HR Hardy John A JA Blauwendraat Cornelis C Singleton Andrew B AB Faghri Faraz F Nalls Mike A MA

NPJ Parkinson's disease 20220401 1

Personalized medicine promises individualized disease prediction and treatment. The convergence of machine learning (ML) and available multimodal data is key moving forward. We build upon previous work to deliver multimodal predictions of Parkinson's disease (PD) risk and systematically develop a model using GenoML, an automated ML package, to make improved multi-omic predictions of PD, validated in an external cohort. We investigated top features, constructed hypothesis-free disease-relevant ne ...[more]

PMID: 35365675

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Project description:Recent studies have identified that peripheral stimulation in Parkinson's disease (PD) is effective in tremor reduction, indicating that a peripheral feedback loop plays an important role in the tremor reset mechanism. This was an open-label, quasi-experimental, pre- and post-test design, single-blind, single-group study involving 20 tremor-dominant PD patients. The objective of this study is to explore the effect of electrical muscle stimulation (EMS) as an adjunctive treatment for resting tremor during "on" period and to identify the best machine learning model to predict the suitable stimulation level that will yield the longest period of tremor reduction or tremor reset time. In this study, we used a Parkinson's glove to evaluate, stimulate, and quantify the tremors of PD patients. This adjustable glove incorporates a 3-axis gyroscope to measure tremor signals and an EMS to provide an on-demand muscle stimulation to suppress tremors. Machine learning models were applied to identify the suitable pulse amplitude (stimulation level) in five classes that led to the longest tremor reset time. The study was registered at the www.clinicaltrials.gov under the name "The Study of Rest Tremor Suppression by Using Electrical Muscle Stimulation" (NCT02370108). Twenty tremor-dominant PD patients were recruited. After applying an average pulse amplitude of 6.25 (SD 2.84) mA and stimulation period of 440.7 (SD 560.82) seconds, the total time of tremor reduction, or tremor reset time, was 329.90 (SD 340.91) seconds. A significant reduction in tremor parameters during stimulation was demonstrated by a reduction of Unified Parkinson's Disease Rating Scale (UPDRS) scores, and objectively, with a reduction of gyroscopic data (p < 0.05, each). None of the subjects reported any serious adverse events. We also compared gyroscopic data with five machine learning techniques: Logistic Regression, Random Forest, Support Vector Machine (SVM), Neural Network (NN), and Long-Short-Term-Memory (LSTM). The machine learning model that gave the highest accuracy was LSTM, which obtained: accuracy = 0.865 and macro-F1 = 0.736. This study confirms the efficacy of EMS in the reduction of resting tremors in PD. LSTM was identified as the most effective model for predicting pulse amplitude that would elicit the longest tremor reset time. Our study provides further insight on the tremor reset mechanism in PD.

Dataset Information

Multi-modality machine learning predicting Parkinson's disease.

Publications

Multi-modality machine learning predicting Parkinson's disease.

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