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Embedding electronic health records onto a knowledge network recognizes prodromal features of multiple sclerosis and predicts diagnosis.
Nelson, Charlotte A; Bove, Riley; Butte, Atul J; Baranzini, Sergio E.
Afiliación
  • Nelson CA; Integrated Program in Quantitative Biology, University of California San Francisco, San Francisco, California, USA.
  • Bove R; Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, California, USA.
  • Butte AJ; Department of Neurology, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, California, USA.
  • Baranzini SE; Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, California, USA.
J Am Med Inform Assoc ; 29(3): 424-434, 2022 01 29.
Article en En | MEDLINE | ID: mdl-34915552
OBJECTIVE: Early identification of chronic diseases is a pillar of precision medicine as it can lead to improved outcomes, reduction of disease burden, and lower healthcare costs. Predictions of a patient's health trajectory have been improved through the application of machine learning approaches to electronic health records (EHRs). However, these methods have traditionally relied on "black box" algorithms that can process large amounts of data but are unable to incorporate domain knowledge, thus limiting their predictive and explanatory power. Here, we present a method for incorporating domain knowledge into clinical classifications by embedding individual patient data into a biomedical knowledge graph. MATERIALS AND METHODS: A modified version of the Page rank algorithm was implemented to embed millions of deidentified EHRs into a biomedical knowledge graph (SPOKE). This resulted in high-dimensional, knowledge-guided patient health signatures (ie, SPOKEsigs) that were subsequently used as features in a random forest environment to classify patients at risk of developing a chronic disease. RESULTS: Our model predicted disease status of 5752 subjects 3 years before being diagnosed with multiple sclerosis (MS) (AUC = 0.83). SPOKEsigs outperformed predictions using EHRs alone, and the biological drivers of the classifiers provided insight into the underpinnings of prodromal MS. CONCLUSION: Using data from EHR as input, SPOKEsigs describe patients at both the clinical and biological levels. We provide a clinical use case for detecting MS up to 5 years prior to their documented diagnosis in the clinic and illustrate the biological features that distinguish the prodromal MS state.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Registros Electrónicos de Salud / Esclerosis Múltiple Tipo de estudio: Diagnostic_studies / Prognostic_studies / Risk_factors_studies Límite: Humans Idioma: En Revista: J Am Med Inform Assoc Asunto de la revista: INFORMATICA MEDICA Año: 2022 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Reino Unido
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Registros Electrónicos de Salud / Esclerosis Múltiple Tipo de estudio: Diagnostic_studies / Prognostic_studies / Risk_factors_studies Límite: Humans Idioma: En Revista: J Am Med Inform Assoc Asunto de la revista: INFORMATICA MEDICA Año: 2022 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Reino Unido