133 research outputs found

    Determining Structurally Identifiable Parameter Combinations Using Subset Profiling

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    Identifiability is a necessary condition for successful parameter estimation of dynamic system models. A major component of identifiability analysis is determining the identifiable parameter combinations, the functional forms for the dependencies between unidentifiable parameters. Identifiable combinations can help in model reparameterization and also in determining which parameters may be experimentally measured to recover model identifiability. Several numerical approaches to determining identifiability of differential equation models have been developed, however the question of determining identifiable combinations remains incompletely addressed. In this paper, we present a new approach which uses parameter subset selection methods based on the Fisher Information Matrix, together with the profile likelihood, to effectively estimate identifiable combinations. We demonstrate this approach on several example models in pharmacokinetics, cellular biology, and physiology

    In Silico Synchronization of Cellular Populations Through Expression Data Deconvolution

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    Cellular populations are typically heterogenous collections of cells at different points in their respective cell cycles, each with a cell cycle time that varies from individual to individual. As a result, true single-cell behavior, particularly that which is cell-cycle--dependent, is often obscured in population-level (averaged) measurements. We have developed a simple deconvolution method that can be used to remove the effects of asynchronous variability from population-level time-series data. In this paper, we summarize some recent progress in the development and application of our approach, and provide technical updates that result in increased biological fidelity. We also explore several preliminary validation results and discuss several ongoing applications that highlight the method's usefulness for estimating parameters in differential equation models of single-cell gene regulation.Comment: accepted for the 48th ACM/IEEE Design Automation Conferenc

    Linking Decision Theory and Quantitative Microbial Risk Assessment: Tradeoffs Between Compliance and Efficacy for Waterborne Disease Interventions

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    Achieving health gains from the U.N. Sustainable Development Goals of universal coverage for water and sanitation will require interventions that can be widely adopted and maintained. Effectiveness—how an intervention performs based on actual use—as opposed to efficacy will therefore be central to evaluations of new and existing interventions. Incomplete compliance—when people do not always use the intervention and are therefore exposed to contamination—is thought to be responsible for the lower‐than‐expected risk reductions observed from water, sanitation, and hygiene interventions based on their efficacy at removing pathogens. We explicitly incorporated decision theory into a quantitative microbial risk assessment model. Specifically, we assume that the usability of household water treatment (HWT) devices (filters and chlorine) decreases as they become more efficacious due to issues such as taste or flow rates. Simulations were run to examine the tradeoff between device efficacy and usability. For most situations, HWT interventions that trade lower efficacy (i.e., remove less pathogens) for higher compliance (i.e., better usability) contribute substantial reductions in diarrheal disease risk compared to devices meeting current World Health Organization efficacy guidelines. Recommendations that take into account both the behavioral and microbiological properties of treatment devices are likely to be more effective at reducing the burden of diarrheal disease than current standards that only consider efficacy.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/151809/1/risa13381.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/151809/2/risa13381-sup-0001-Appendix.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/151809/3/risa13381_am.pd

    A Systematic Approach to Determining the Identifiability of Multistage Carcinogenesis Models

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    Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/137771/1/risa12684_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/137771/2/risa12684.pd