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SEEDS: Data driven inference of structural model errors and unknown inputs for dynamic systems biology

: Newmiwaka, Tobias; Engelhardt, Benjamin; Wendland, Philipp; Kahl, Dominik; Fröhlich, Holger; Kschischo, Maik


Bioinformatics 37 (2021), Nr.9, S.1330-1331
ISSN: 1367-4803
ISSN: 1460-2059
ISSN: 1367-4811
Deutsche Forschungsgemeinschaft DFG
Fraunhofer SCAI ()
artificial intelligence; biomarkers; Data Science; precision medicine

Dynamic models formulated as ordinary differential equations (ODEs) can provide information about the mechanistic and causal interactions in biological systems to guide targeted interventions and to design further experiments. Inaccurate knowledge about the structure, functional form and parameters of interactions is a major obstacle to mechanistic modelling. A further challenge is the open nature of biological systems which receive unknown inputs from their environment. The R-package SEEDS implements two recently developed algorithms to infer structural model errors and unknown inputs from output measurements. This information can facilitate efficient model recalibration as well as experimental design in the case of misfits between the initial model and data.