Parameter estimation and inference for stochastic reaction-diffusion systems: application to morphogenesis in D. melanogaster

Background: Reaction-diffusion systems are frequently used in systems biology to model developmental and signalling processes. In many applications, count numbers of the diffusing molecular species are very low, leading to the need to explicitly model the inherent variability using stochastic methods. Despite their importance and frequent use, parameter estimation for both deterministic and stochastic reaction-diffusion systems is still a challenging problem. Results: We present a Bayesian inference approach to solve both the parameter and state estimation problem for stochastic reaction-diffusion systems. This allows a determination of the full posterior distribution of the parameters (expected values and uncertainty). We benchmark the method by illustrating it on a simple synthetic experiment. We then test the method on real data about the diffusion of the morphogen Bicoid in Drosophila melanogaster. The results show how the precision with which parameters can be inferred varies dramatically, indicating that the ability to infer full posterior distributions on the parameters can have important experimental design consequences. Conclusions: The results obtained demonstrate the feasibility and potential advantages of applying a Bayesian approach to parameter estimation in stochastic reaction-diffusion systems. In particular, the ability to estimate credibility intervals associated with parameter estimates can be precious for experimental design. Further work, however, will be needed to ensure the method can scale up to larger problems

Enhanced Welding Operator Quality Performance Measurement: Work Experience-Integrated Bayesian Prior Determination

Measurement of operator quality performance has been challenging in the construction fabrication industry. Among various causes, the learning effect is a significant factor, which needs to be incorporated in achieving a reliable operator quality performance analysis. This research aims to enhance a previously developed operator quality performance measurement approach by incorporating the learning effect (i.e., work experience). To achieve this goal, the Plateau learning model is selected to quantitatively represent the relationship between quality performance and work experience through a beta-binomial regression approach. Based on this relationship, an informative prior determination approach, which incorporates operator work experience information, is developed to enhance the previous Bayesian-based operator quality performance measurement. Academically, this research provides a systematic approach to derive Bayesian informative priors through integrating multi-source information. Practically, the proposed approach reliably measures operator quality performance in fabrication quality control processes.Comment: 8 pages, 5 figures, 2 tables, i3CE 201

Dose Finding with Escalation with Overdose Control (EWOC) in Cancer Clinical Trials

Traditionally, the major objective in phase I trials is to identify a working-dose for subsequent studies, whereas the major endpoint in phase II and III trials is treatment efficacy. The dose sought is typically referred to as the maximum tolerated dose (MTD). Several statistical methodologies have been proposed to select the MTD in cancer phase I trials. In this manuscript, we focus on a Bayesian adaptive design, known as escalation with overdose control (EWOC). Several aspects of this design are discussed, including large sample properties of the sequence of doses selected in the trial, choice of prior distributions, and use of covariates. The methodology is exemplified with real-life examples of cancer phase I trials. In particular, we show in the recently completed ABR-217620 (naptumomab estafenatox) trial that omitting an important predictor of toxicity when dose assignments to cancer patients are determined results in a high percent of patients experiencing severe side effects and a significant proportion treated at sub-optimal doses.Comment: Published in at http://dx.doi.org/10.1214/10-STS333 the Statistical Science (http://www.imstat.org/sts/) by the Institute of Mathematical Statistics (http://www.imstat.org

A Bayesian-Based Approach for Public Sentiment Modeling

Public sentiment is a direct public-centric indicator for the success of effective action planning. Despite its importance, systematic modeling of public sentiment remains untapped in previous studies. This research aims to develop a Bayesian-based approach for quantitative public sentiment modeling, which is capable of incorporating uncertainty and guiding the selection of public sentiment measures. This study comprises three steps: (1) quantifying prior sentiment information and new sentiment observations with Dirichlet distribution and multinomial distribution respectively; (2) deriving the posterior distribution of sentiment probabilities through incorporating the Dirichlet distribution and multinomial distribution via Bayesian inference; and (3) measuring public sentiment through aggregating sampled sets of sentiment probabilities with an application-based measure. A case study on Hurricane Harvey is provided to demonstrate the feasibility and applicability of the proposed approach. The developed approach also has the potential to be generalized to model various types of probability-based measures

Noncommutative Bayesian Statistical Inference from a wedge of a Bifurcate Killing Horizon

Expanding a remark of my PHD-thesis the noncommutative bayesian statistical inference from one wedge of a bifurcate Killing horizon is analyzed looking at its inter-relation with the Unruh effectComment: some correction performed; to appear in "International Journal of Theoretical Physics

Bayesian Nonstationary Spatial Modeling for Very Large Datasets

With the proliferation of modern high-resolution measuring instruments mounted on satellites, planes, ground-based vehicles and monitoring stations, a need has arisen for statistical methods suitable for the analysis of large spatial datasets observed on large spatial domains. Statistical analyses of such datasets provide two main challenges: First, traditional spatial-statistical techniques are often unable to handle large numbers of observations in a computationally feasible way. Second, for large and heterogeneous spatial domains, it is often not appropriate to assume that a process of interest is stationary over the entire domain. We address the first challenge by using a model combining a low-rank component, which allows for flexible modeling of medium-to-long-range dependence via a set of spatial basis functions, with a tapered remainder component, which allows for modeling of local dependence using a compactly supported covariance function. Addressing the second challenge, we propose two extensions to this model that result in increased flexibility: First, the model is parameterized based on a nonstationary Matern covariance, where the parameters vary smoothly across space. Second, in our fully Bayesian model, all components and parameters are considered random, including the number, locations, and shapes of the basis functions used in the low-rank component. Using simulated data and a real-world dataset of high-resolution soil measurements, we show that both extensions can result in substantial improvements over the current state-of-the-art.Comment: 16 pages, 2 color figure