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MINDS Seminar Series | Boseung Choi (Korea University) - Bayesian Inference of Biochemical Reactions with Delays
| Date | 2021-10-14 ~ 2021-10-14 | Time | 17:00:00 ~ 18:00:00 |
| Speaker | Boseung Choi | Affiliation | Korea University |
| Place | Online streaming(Zoom) and Math Bldg Rm 404 | Streaming link | ID : 688 896 1076 / PW : 54321 |
| Topic | Bayesian Inference of Biochemical Reactions with Delays | ||
| Contents | Motivation: Advances in experimental and imaging techniques have allowed for unprecedented insights into the dynamical processes within individual cells. However, many facets of intracellular dynamics remain hidden, or can be measured only indirectly. This makes it challenging to recon- struct the regulatory networks that govern the biochemical processes underlying various cell func- tions. Current estimation techniques for inferring reaction rates frequently rely on marginalization over unobserved processes and states. Even in simple systems this approach can be computation- ally challenging, and can lead to large uncertainties and lack of robustness in parameter estimates. Therefore we will require alternative approaches to efficiently uncover the interactions in complex biochemical networks. Results: We propose a Bayesian inference framework based on replacing uninteresting or unob- served reactions with time delays. Although the resulting models are non-Markovian, recent results on stochastic systems with random delays allow us to rigorously obtain expressions for the likeli- hoods of model parameters. In turn, this allows us to extend MCMC methods to efficiently estimate reaction rates, and delay distribution parameters, from single-cell assays. We illustrate the advan- tages, and potential pitfalls, of the approach using a birth–death model with both synthetic and experimental data, and show that we can robustly infer model parameters using a relatively small number of measurements. We demonstrate how to do so even when only the relative molecule count within the cell is measured, as in the case of fluorescence microscopy. |
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