Biomarker Selection for Adaptive Systems

Biomarker selection and real-time monitoring of cell dynamics remains an active challenge in cell biology and biomanufacturing. Here, we develop scalable adaptations of classic approaches to sensor selection for biomarker identification on several transcriptomics and biological datasets that are otherwise cannot be studied from a controls perspective. To address challenges in system identification of biological systems and provide robust biomarkers, we propose Dynamic and Structure Guided Sensors Selection (DSS and SGSS), methods by which temporal models and structural experimental data can be used to supplement traditional approaches to sensor selection. These approaches leverage temporal models and experimental data to enhance traditional sensor selection techniques. Unlike conventional methods that assume well-known, fixed dynamics, DSS and SGSS adaptively select sensors that maximize observability while accounting for the time-varying nature of biological systems. Additionally, they incorporate structural information to identify robust sensors even in cases where system dynamics are poorly understood. We validate these two approaches by performing estimation on several high dimensional systems derived from temporal gene expression data from partial observations.