Changes in climate can greatly affect the phenology of plants, which can have important feedback effects, such as altering the carbon cycle. These phenological feedback effects are often induced by a shift in the start or end dates of the growing season of plants. The normalized difference vegetation index (NDVI) serves as a straightforward indicator for assessing the presence of green vegetation and can also provide an estimation of the plants' growing season. In this study, we investigated the effect of soil temperature on the timing of the start of the season (SOS), timing of the peak of the season (POS), and the maximum annual NDVI value (PEAK) in subarctic grassland ecosystems between 2014 and 2019. We also explored the impact of other meteorological variables, including air temperature, precipitation, and irradiance, on the inter-annual variation in vegetation phenology. Using machine learning (ML) techniques and SHapley Additive exPlanations (SHAP) values, we analyzed the relative importance and contribution of each variable to the phenological predictions. Our results reveal a significant relationship between soil temperature and SOS and POS, indicating that higher soil temperatures lead to an earlier start and peak of the growing season. However, the Peak NDVI values showed just a slight increase with higher soil temperatures. The analysis of other meteorological variables demonstrated their impacts on the inter-annual variation of the vegetation phenology. Ultimately, this study contributes to our knowledge of the relationships between soil temperature, meteorological variables, and vegetation phenology, providing valuable insights for predicting vegetation phenology characteristics and managing subarctic grasslands in the face of climate change. Additionally, this work provides a solid foundation for future ML-based vegetation phenology studies.
We derive a model for the optimization of the bending and torsional rigidities of non-homogeneous elastic rods. This is achieved by studying a sharp interface shape optimization problem with perimeter penalization, that treats both rigidities as objectives. We then formulate a phase field approximation of the optimization problem and show the convergence to the aforementioned sharp interface model via $\Gamma$-convergence. In the final part of this work we numerically approximate minimizers of the phase field problem by using a steepest descent approach and relate the resulting optimal shapes to the development of the morphology of plant stems.
We introduce a method to construct a stochastic surrogate model from the results of dimensionality reduction in forward uncertainty quantification. The hypothesis is that the high-dimensional input augmented by the output of a computational model admits a low-dimensional representation. This assumption can be met by numerous uncertainty quantification applications with physics-based computational models. The proposed approach differs from a sequential application of dimensionality reduction followed by surrogate modeling, as we "extract" a surrogate model from the results of dimensionality reduction in the input-output space. This feature becomes desirable when the input space is genuinely high-dimensional. The proposed method also diverges from the Probabilistic Learning on Manifold, as a reconstruction mapping from the feature space to the input-output space is circumvented. The final product of the proposed method is a stochastic simulator that propagates a deterministic input into a stochastic output, preserving the convenience of a sequential "dimensionality reduction + Gaussian process regression" approach while overcoming some of its limitations. The proposed method is demonstrated through two uncertainty quantification problems characterized by high-dimensional input uncertainties.
Collecting large quantities of high-quality data is often prohibitively expensive or impractical, and a crucial bottleneck in machine learning. One may instead augment a small set of $n$ data points from the target distribution with data from more accessible sources like public datasets, data collected under different circumstances, or synthesized by generative models. Blurring distinctions, we refer to such data as `surrogate data'. We define a simple scheme for integrating surrogate data into training and use both theoretical models and empirical studies to explore its behavior. Our main findings are: $(i)$ Integrating surrogate data can significantly reduce the test error on the original distribution; $(ii)$ In order to reap this benefit, it is crucial to use optimally weighted empirical risk minimization; $(iii)$ The test error of models trained on mixtures of real and surrogate data is well described by a scaling law. This can be used to predict the optimal weighting and the gain from surrogate data.
Spatially distributed functional data are prevalent in many statistical applications such as meteorology, energy forecasting, census data, disease mapping, and neurological studies. Given their complex and high-dimensional nature, functional data often require dimension reduction methods to extract meaningful information. Inverse regression is one such approach that has become very popular in the past two decades. We study the inverse regression in the framework of functional data observed at irregularly positioned spatial sites. The functional predictor is the sum of a spatially dependent functional effect and a spatially independent functional nugget effect, while the relation between the scalar response and the functional predictor is modeled using the inverse regression framework. For estimation, we consider local linear smoothing with a general weighting scheme, which includes as special cases the schemes under which equal weights are assigned to each observation or to each subject. This framework enables us to present the asymptotic results for different types of sampling plans over time such as non-dense, dense, and ultra-dense. We discuss the domain-expanding infill (DEI) framework for spatial asymptotics, which is a mix of the traditional expanding domain and infill frameworks. The DEI framework overcomes the limitations of traditional spatial asymptotics in the existing literature. Under this unified framework, we develop asymptotic theory and identify conditions that are necessary for the estimated eigen-directions to achieve optimal rates of convergence. Our asymptotic results include pointwise and $L_2$ convergence rates. Simulation studies using synthetic data and an application to a real-world dataset confirm the effectiveness of our methods.
Finding suitable preconditioners to accelerate iterative solution methods, such as the conjugate gradient method, is an active area of research. In this paper, we develop a computationally efficient data-driven approach to replace the typically hand-engineered algorithms with neural networks. Optimizing the condition number of the linear system directly is computationally infeasible. Instead, our method generates an incomplete factorization of the matrix and is, therefore, referred to as neural incomplete factorization (NeuralIF). For efficient training, we utilize a stochastic approximation of the Frobenius loss which only requires matrix-vector multiplications. At the core of our method is a novel messagepassing block, inspired by sparse matrix theory, that aligns with the objective of finding a sparse factorization of the matrix. By replacing conventional preconditioners used within the conjugate gradient method by data-driven models based on graph neural networks, we accelerate the iterative solving procedure. We evaluate our proposed method on both a synthetic and a real-world problem arising from scientific computing and show its ability to reduce the solving time while remaining computationally efficient.
Experiments in engineering are typically conducted in controlled environments where parameters can be set to any desired value. This assumes that the same applies in a real-world setting -- an assumption that is often incorrect as many experiments are influenced by uncontrollable environmental conditions such as temperature, humidity and wind speed. When optimising such experiments, the focus should lie on finding optimal values conditionally on these uncontrollable variables. This article extends Bayesian optimisation to the optimisation of systems in changing environments that include controllable and uncontrollable parameters. The extension fits a global surrogate model over all controllable and environmental variables but optimises only the controllable parameters conditional on measurements of the uncontrollable variables. The method is validated on two synthetic test functions and the effects of the noise level, the number of the environmental parameters, the parameter fluctuation, the variability of the uncontrollable parameters, and the effective domain size are investigated. ENVBO, the proposed algorithm resulting from this investigation, is applied to a wind farm simulator with eight controllable and one environmental parameter. ENVBO finds solutions for the full domain of the environmental variable that outperforms results from optimisation algorithms that only focus on a fixed environmental value in all but one case while using a fraction of their evaluation budget. This makes the proposed approach very sample-efficient and cost-effective. An off-the-shelf open-source version of ENVBO is available via the NUBO Python package.
In longitudinal observational studies with a time-to-event outcome, a common objective in causal analysis is to estimate the causal survival curve under hypothetical intervention scenarios within the study cohort. The g-formula is a particularly useful tool for this analysis. To enhance the traditional parametric g-formula approach, we developed a more adaptable Bayesian g-formula estimator. This estimator facilitates both longitudinal predictive and causal inference. It incorporates Bayesian additive regression trees in the modeling of the time-evolving generative components, aiming to mitigate bias due to model misspecification. Specifically, we introduce a more general class of g-formulas for discrete survival data. These formulas can incorporate the longitudinal balancing scores, which serve as an effective method for dimension reduction and are vital when dealing with an expanding array of time-varying confounders. The minimum sufficient formulation of these longitudinal balancing scores is linked to the nature of treatment regimes, whether static or dynamic. For each type of treatment regime, we provide posterior sampling algorithms, which are grounded in the Bayesian additive regression trees framework. We have conducted simulation studies to illustrate the empirical performance of our proposed Bayesian g-formula estimators, and to compare them with existing parametric estimators. We further demonstrate the practical utility of our methods in real-world scenarios using data from the Yale New Haven Health System's electronic health records.
Building prediction models from mass-spectrometry data is challenging due to the abundance of correlated features with varying degrees of zero-inflation, leading to a common interest in reducing the features to a concise predictor set with good predictive performance. In this study, we formally established and examined regularized regression approaches, designed to address zero-inflated and correlated predictors. In particular, we describe a novel two-stage regularized regression approach (ridge-garrote) explicitly modelling zero-inflated predictors using two component variables, comprising a ridge estimator in the first stage and subsequently applying a nonnegative garrote estimator in the second stage. We contrasted ridge-garrote with one-stage methods (ridge, lasso) and other two-stage regularized regression approaches (lasso-ridge, ridge-lasso) for zero-inflated predictors. We assessed the predictive performance and predictor selection properties of these methods in a comparative simulation study and a real-data case study to predict kidney function using peptidomic features derived from mass-spectrometry. In the simulation study, the predictive performance of all assessed approaches was comparable, yet the ridge-garrote approach consistently selected more parsimonious models compared to its competitors in most scenarios. While lasso-ridge achieved higher predictive accuracy than its competitors, it exhibited high variability in the number of selected predictors. Ridge-lasso exhibited slightly superior predictive accuracy than ridge-garrote but at the expense of selecting more noise predictors. Overall, ridge emerged as a favourable option when variable selection is not a primary concern, while ridge-garrote demonstrated notable practical utility in selecting a parsimonious set of predictors, with only minimal compromise in predictive accuracy.
A rectangulation is a decomposition of a rectangle into finitely many rectangles. Via natural equivalence relations, rectangulations can be seen as combinatorial objects with a rich structure, with links to lattice congruences, flip graphs, polytopes, lattice paths, Hopf algebras, etc. In this paper, we first revisit the structure of the respective equivalence classes: weak rectangulations that preserve rectangle-segment adjacencies, and strong rectangulations that preserve rectangle-rectangle adjacencies. We thoroughly investigate posets defined by adjacency in rectangulations of both kinds, and unify and simplify known bijections between rectangulations and permutation classes. This yields a uniform treatment of mappings between permutations and rectangulations that unifies the results from earlier contributions, and emphasizes parallelism and differences between the weak and the strong cases. Then, we consider the special case of guillotine rectangulations, and prove that they can be characterized - under all known mappings between permutations and rectangulations - by avoidance of two mesh patterns that correspond to "windmills" in rectangulations. This yields new permutation classes in bijection with weak guillotine rectangulations, and the first known permutation class in bijection with strong guillotine rectangulations. Finally, we address enumerative issues and prove asymptotic bounds for several families of strong rectangulations.
Forecasts for key macroeconomic variables are almost always made simultaneously by the same organizations, presented together, and used together in policy analyses and decision-makings. It is therefore important to know whether the forecasters are skillful enough to forecast the future values of those variables. Here a method for joint evaluation of skill in directional forecasts of multiple variables is introduced. The method is simple to use and does not rely on complicated assumptions required by the conventional statistical methods for measuring accuracy of directional forecast. The data on GDP growth and inflation forecasts of three organizations from Thailand, namely, the Bank of Thailand, the Fiscal Policy Office, and the Office of the National Economic and Social Development Council as well as the actual data on GDP growth and inflation of Thailand between 2001 and 2021 are employed in order to demonstrate how the method could be used to evaluate the skills of forecasters in practice. The overall results indicate that these three organizations are somewhat skillful in forecasting the direction-of-changes of GDP growth and inflation when no band and a band of +/- 1 standard deviation of the forecasted outcome are considered. However, when a band of +/- 0.5% of the forecasted outcome is introduced, the skills in forecasting the direction-of-changes of GDP growth and inflation of these three organizations are, at best, little better than intelligent guess work.