PDKit: A data science toolkit for the digital assessment of Parkinson’s Disease

Cosmin Stamate, Joan Saez Pons, David Weston and George Roussos

PLOS Computational Biology, 2021, vol. 17, issue 3, 1-11

Abstract: PDkit is an open source software toolkit supporting the collaborative development of novel methods of digital assessment for Parkinson’s Disease, using symptom measurements captured continuously by wearables (passive monitoring) or by high-use-frequency smartphone apps (active monitoring). The goal of the toolkit is to help address the current lack of algorithmic and model transparency in this area by facilitating open sharing of standardised methods that allow the comparison of results across multiple centres and hardware variations. PDkit adopts the information-processing pipeline abstraction incorporating stages for data ingestion, quality of information augmentation, feature extraction, biomarker estimation and finally, scoring using standard clinical scales. Additionally, a dataflow programming framework is provided to support high performance computations. The practical use of PDkit is demonstrated in the context of the CUSSP clinical trial in the UK. The toolkit is implemented in the python programming language, the de facto standard for modern data science applications, and is widely available under the MIT license.Author summary: Parkinson’s Disease is the fastest growing neurological condition affecting millions of people across the world. People with Parkinson’s suffer from a variety of symptoms that result in diminished ability to move, eat, remember or sleep. Research in new treatments are limited because the clinical tools used to assess its symptoms are subjective, require considerable time to perform and specialised skills and can only detect coarse-grain changes. To address this situation, clinicians are turning to smartphone apps and wearables to create new ways to assess symptoms that are more sensitive to change and can be applied frequently at home by patients and their carers. In this paper, we discuss PDkit, an open source toolkit that we developed to help address this current lack of algorithmic and model transparency. Adopting PDkit facilitates the open sharing of standardised methods and can accelerate the development of new methods and system to assess Parkinson’s and enables research groups to innovate. The toolkit provides funcionality that support data ingestion, quality of information augmentation, feature extraction, biomarker estimation and finally, scoring using standard clinical scales. The practical use of PDkit is demonstrated via its use by the CUSSP clinical trial conducted in the UK.

Date: 2021
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pcbi00:1008833

DOI: 10.1371/journal.pcbi.1008833

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