Predictions for physical systems often rely upon knowledge acquired from ensembles of entities, e.g., ensembles of cells in biological sciences. For qualitative and quantitative analysis, these ensembles are simulated with parametric families of mechanistic models (MM). Two classes of methodologies, based on Bayesian inference and Population of Models, currently prevail in parameter estimation for physical systems. However, in Bayesian analysis, uninformative priors for MM parameters introduce undesirable bias. Here, we propose how to infer parameters within the framework of stochastic inverse problems (SIP), also termed data-consistent inversion, wherein the prior targets only uncertainties that arise due to MM non-invertibility. To demonstrate, we introduce new methods to solve SIP based on rejection sampling, Markov chain Monte Carlo, and generative adversarial networks (GANs). In addition, to overcome limitations of SIP, we reformulate SIP based on constrained optimization and present a novel GAN to solve the constrained optimization problem.
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The study of moving particles (e.g. molecules, virus, vesicles, organelles, or whole cells) is crucial to decipher a plethora of cellular mechanisms within physiological and pathological conditions. Powerful live-imaging approaches enable life scientists to capture particle movements at different scale from cells to single molecules, that are collected in a series of frames. However, although these events can be captured, an accurate quantitative analysis of live-imaging experiments still remains a challenge. Two main approaches are currently used to study particle kinematics: kymographs, which are graphical representation of spatial motion over time, and single particle tracking (SPT) followed by linear linking. Both kymograph and SPT apply a space-time approximation in quantifying particle kinematics, considering the velocity constant either over several frames or between consecutive frames, respectively. Thus, both approaches intrinsically limit the analysis of complex motions with rapid changes in velocity. Therefore, we design, implement and validate a novel reconstruction algorithm aiming at supporting tracking particle trafficking analysis with mathematical foundations. Our method is based on polynomial reconstruction of 4D (3D+time) particle trajectories, enabling to assess particle instantaneous velocity and acceleration, at any time, over the entire trajectory. Here, the new algorithm is compared to state-of-the-art SPT followed by linear linking, demonstrating an increased accuracy in quantifying particle kinematics. Our approach is directly derived from the governing equations of motion, thus it arises from physical principles and, as such, it is a versatile and reliable numerical method for accurate particle kinematics analysis which can be applied to any live-imaging experiment where the space-time coordinates can be retrieved.
This paper considers the extension of data-enabled predictive control (DeePC) to nonlinear systems via general basis functions. Firstly, we formulate a basis functions DeePC behavioral predictor and we identify necessary and sufficient conditions for equivalence with a corresponding basis functions multi-step identified predictor. The derived conditions yield a dynamic regularization cost function that enables a well-posed (i.e., consistent) basis functions formulation of nonlinear DeePC. To optimize computational efficiency of basis functions DeePC we further develop two alternative formulations that use a simpler, sparse regularization cost function and ridge regression, respectively. Consistency implications for Koopman DeePC as well as several methods for constructing the basis functions representation are also indicated. The effectiveness of the developed consistent basis functions DeePC formulations is illustrated on a benchmark nonlinear pendulum state-space model, for both noise free and noisy data.
An iterative algorithm for high-dimensional linear models with both sparse and non-sparse structures
Numerous practical medical problems often involve data that possess a combination of both sparse and non-sparse structures. Traditional penalized regularizations techniques, primarily designed for promoting sparsity, are inadequate to capture the optimal solutions in such scenarios. To address these challenges, this paper introduces a novel algorithm named Non-sparse Iteration (NSI). The NSI algorithm allows for the existence of both sparse and non-sparse structures and estimates them simultaneously and accurately. We provide theoretical guarantees that the proposed algorithm converges to the oracle solution and achieves the optimal rate for the upper bound of the $l_2$-norm error. Through simulations and practical applications, NSI consistently exhibits superior statistical performance in terms of estimation accuracy, prediction efficacy, and variable selection compared to several existing methods. The proposed method is also applied to breast cancer data, revealing repeated selection of specific genes for in-depth analysis.
Unconstrained convex optimization problems have enormous applications in various field of science and engineering. Different iterative methods are available in literature to solve such problem, and Newton method is among the oldest and simplest one. Due to slow convergence rate of Newton's methods, many research have been carried out to modify the Newton's method for faster convergence rate. In 2019, Ghazali et al. modified Newton's method and proposed Netwon-SOR method, which is a combination of Newton method with SOR iterative method to solve a linear system. In this paper, we propose a modification of Newton-SOR method by modifying SOR method to generalized SOR method. Numerical experiments are carried out to check the efficiently of the proposed method.
We consider an unknown multivariate function representing a system-such as a complex numerical simulator-taking both deterministic and uncertain inputs. Our objective is to estimate the set of deterministic inputs leading to outputs whose probability (with respect to the distribution of the uncertain inputs) of belonging to a given set is less than a given threshold. This problem, which we call Quantile Set Inversion (QSI), occurs for instance in the context of robust (reliability-based) optimization problems, when looking for the set of solutions that satisfy the constraints with sufficiently large probability. To solve the QSI problem, we propose a Bayesian strategy based on Gaussian process modeling and the Stepwise Uncertainty Reduction (SUR) principle, to sequentially choose the points at which the function should be evaluated to efficiently approximate the set of interest. We illustrate the performance and interest of the proposed SUR strategy through several numerical experiments.
Throughout the life sciences we routinely seek to interpret measurements and observations using parameterised mechanistic mathematical models. A fundamental and often overlooked choice in this approach involves relating the solution of a mathematical model with noisy and incomplete measurement data. This is often achieved by assuming that the data are noisy measurements of the solution of a deterministic mathematical model, and that measurement errors are additive and normally distributed. While this assumption of additive Gaussian noise is extremely common and simple to implement and interpret, it is often unjustified and can lead to poor parameter estimates and non-physical predictions. One way to overcome this challenge is to implement a different measurement error model. In this review, we demonstrate how to implement a range of measurement error models in a likelihood-based framework for estimation, identifiability analysis, and prediction, called Profile-Wise Analysis. This frequentist approach to uncertainty quantification for mechanistic models leverages the profile likelihood for targeting parameters and understanding their influence on predictions. Case studies, motivated by simple caricature models routinely used in systems biology and mathematical biology literature, illustrate how the same ideas apply to different types of mathematical models. Open-source Julia code to reproduce results is available on GitHub.
FetMRQC: an open-source machine learning framework for multi-centric fetal brain MRI quality control
Fetal brain MRI is becoming an increasingly relevant complement to neurosonography for perinatal diagnosis, allowing fundamental insights into fetal brain development throughout gestation. However, uncontrolled fetal motion and heterogeneity in acquisition protocols lead to data of variable quality, potentially biasing the outcome of subsequent studies. We present FetMRQC, an open-source machine-learning framework for automated image quality assessment and quality control that is robust to domain shifts induced by the heterogeneity of clinical data. FetMRQC extracts an ensemble of quality metrics from unprocessed anatomical MRI and combines them to predict experts' ratings using random forests. We validate our framework on a pioneeringly large and diverse dataset of more than 1600 manually rated fetal brain T2-weighted images from four clinical centers and 13 different scanners. Our study shows that FetMRQC's predictions generalize well to unseen data while being interpretable. FetMRQC is a step towards more robust fetal brain neuroimaging, which has the potential to shed new insights on the developing human brain.
The optimization of open-loop shallow geothermal systems, which includes both design and operational aspects, is an important research area aimed at improving their efficiency and sustainability and the effective management of groundwater as a shallow geothermal resource. This paper investigates various approaches to address optimization problems arising from these research and implementation questions about GWHP systems. The identified optimization approaches are thoroughly analyzed based on criteria such as computational cost and applicability. Moreover, a novel classification scheme is introduced that categorizes the approaches according to the types of groundwater simulation model and the optimization algorithm used. Simulation models are divided into two types: numerical and simplified (analytical or data-driven) models, while optimization algorithms are divided into gradient-based and derivative-free algorithms. Finally, a comprehensive review of existing approaches in the literature is provided, highlighting their strengths and limitations and offering recommendations for both the use of existing approaches and the development of new, improved ones in this field.
We propose three test criteria each of which is appropriate for testing, respectively, the equivalence hypotheses of symmetry, of homogeneity, and of independence, with multivariate data. All quantities have the common feature of involving weighted--type distances between characteristic functions and are convenient from the computational point of view if the weight function is properly chosen. The asymptotic behavior of the tests under the null hypothesis is investigated, and numerical studies are conducted in order to examine the performance of the criteria in finite samples.
Shape optimization approaches to inverse design offer low-dimensional, physically-guided parameterizations of structures by representing them as combinations of shape primitives. However, on discretized rectilinear simulation grids, computing the gradient of a user objective via the adjoint variables method requires a sum reduction of the forward/adjoint field solutions and the Jacobian of the simulation material distribution with respect to the structural shape parameters. These shape parameters often perturb large or global parts of the simulation grid resulting in many non-zero Jacobian entries, which are typically computed by finite-difference in practice. Consequently, the gradient calculation can be non-trivial. In this work we propose to accelerate the gradient calculation by invoking automatic differentiation (AutoDiff) in instantiations of structural material distributions. In doing so, we develop extensible differentiable mappings from shape parameters to shape primitives and differentiable effective logic operations (denoted AutoDiffGeo). These AutoDiffGeo definitions may introduce some additional discretization error into the field solutions because they relax notions of sub-pixel smoothing along shape boundaries. However, we show that some mappings (e.g. simple cuboids) can achieve zero error with respect to volumetric averaging strategies. We demonstrate AutoDiff enhanced shape optimization using three integrated photonic examples: a multi-etch blazed grating coupler, a non-adiabatic waveguide transition taper, and a polarization-splitting grating coupler. We find accelerations of the gradient calculation by AutoDiff relative to finite-difference often exceed 50x, resulting in total wall time accelerations of 4x or more on the same hardware with little or no compromise to final device performance. Our code is available open source at //github.com/smhooten/emopt
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