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pySuStaIn: A Python implementation of the Subtype and Stage Inference algorithm

Aksman, LM; Wijeratne, PA; Oxtoby, NP; Eshaghi, A; Shand, C; Altmann, A; Alexander, DC; (2021) pySuStaIn: A Python implementation of the Subtype and Stage Inference algorithm. SoftwareX , 16 , Article 100811. 10.1016/j.softx.2021.100811. Green open access

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Abstract

Progressive disorders are highly heterogeneous. Symptom-based clinical classification of these disorders may not reflect the underlying pathobiology. Data-driven subtyping and staging of patients has the potential to disentangle the complex spatiotemporal patterns of disease progression. Tools that enable this are in high demand from clinical and treatment-development communities. Here we describe the pySuStaIn software package, a Python-based implementation of the Subtype and Stage Inference (SuStaIn) algorithm. SuStaIn unravels the complexity of heterogeneous diseases by inferring multiple disease progression patterns (subtypes) and individual severity (stages) from cross-sectional data. The primary aims of pySuStaIn are to enable widespread application and translation of SuStaIn via an accessible Python package that supports simple extension and generalization to novel modeling situations within a single, consistent architecture.

Type: Article
Title: pySuStaIn: A Python implementation of the Subtype and Stage Inference algorithm
Open access status: An open access version is available from UCL Discovery
DOI: 10.1016/j.softx.2021.100811
Publisher version: https://doi.org/10.1016/j.softx.2021.100811
Language: English
Additional information: Copyright © 2021 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
Keywords: Disease progression modeling, Disease heterogeneity, Disease subtyping, Disease staging
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences > UCL Queen Square Institute of Neurology
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences > UCL Queen Square Institute of Neurology > Neuroinflammation
UCL > Provost and Vice Provost Offices > UCL BEAMS
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science > Dept of Computer Science
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science > Dept of Med Phys and Biomedical Eng
URI: https://discovery.ucl.ac.uk/id/eprint/10135908
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