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Building efficient, accurate and generalizable reduced order models of developed turbulence remains a major challenge. This manuscript approaches this problem by developing a hierarchy of parameterized reduced Lagrangian models for turbulent flows, and investigates the effects of enforcing physical structure through Smoothed Particle Hydrodynamics (SPH) versus relying on neural networks (NN)s as universal function approximators. Starting from Neural Network (NN) parameterizations of a Lagrangian acceleration operator, this hierarchy of models gradually incorporates a weakly compressible and parameterized SPH framework, which enforces physical symmetries, such as Galilean, rotational and translational invariances. Within this hierarchy, two new parameterized smoothing kernels are developed in order to increase the flexibility of the learn-able SPH simulators. For each model we experiment with different loss functions which are minimized using gradient based optimization, where efficient computations of gradients are obtained by using Automatic Differentiation (AD) and Sensitivity Analysis (SA). Each model within the hierarchy is trained on two data sets associated with weekly compressible Homogeneous Isotropic Turbulence (HIT): (1) a validation set using weakly compressible SPH; and (2) a high fidelity set from Direct Numerical Simulations (DNS). Numerical evidence shows that encoding more SPH structure improves generalizability to different turbulent Mach numbers and time shifts, and that including the novel parameterized smoothing kernels improves the accuracy of SPH at the resolved scales.

Language models have been shown to be very effective in predicting brain recordings of subjects experiencing complex language stimuli. For a deeper understanding of this alignment, it is important to understand the correspondence between the detailed processing of linguistic information by the human brain versus language models. We investigate this correspondence via a direct approach, in which we eliminate information related to specific linguistic properties in the language model representations and observe how this intervention affects the alignment with fMRI brain recordings obtained while participants listened to a story. We investigate a range of linguistic properties (surface, syntactic, and semantic) and find that the elimination of each one results in a significant decrease in brain alignment. Specifically, we find that syntactic properties (i.e. Top Constituents and Tree Depth) have the largest effect on the trend of brain alignment across model layers. These findings provide clear evidence for the role of specific linguistic information in the alignment between brain and language models, and open new avenues for mapping the joint information processing in both systems. We make the code publicly available [//github.com/subbareddy248/linguistic-properties-brain-alignment].

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.

In credit risk analysis, survival models with fixed and time-varying covariates are widely used to predict a borrower's time-to-event. When the time-varying drivers are endogenous, modelling jointly the evolution of the survival time and the endogenous covariates is the most appropriate approach, also known as the joint model for longitudinal and survival data. In addition to the temporal component, credit risk models can be enhanced when including borrowers' geographical information by considering spatial clustering and its variation over time. We propose the Spatio-Temporal Joint Model (STJM) to capture spatial and temporal effects and their interaction. This Bayesian hierarchical joint model reckons the survival effect of unobserved heterogeneity among borrowers located in the same region at a particular time. To estimate the STJM model for large datasets, we consider the Integrated Nested Laplace Approximation (INLA) methodology. We apply the STJM to predict the time to full prepayment on a large dataset of 57,258 US mortgage borrowers with more than 2.5 million observations. Empirical results indicate that including spatial effects consistently improves the performance of the joint model. However, the gains are less definitive when we additionally include spatio-temporal interactions.

1. Automated analysis of bioacoustic recordings using machine learning (ML) methods has the potential to greatly scale biodiversity monitoring efforts. The use of ML for high-stakes applications, such as conservation research, demands a data-centric approach with a focus on utilizing carefully annotated and curated evaluation and training data that is relevant and representative. Creating annotated datasets of sound recordings presents a number of challenges, such as managing large collections of recordings with associated metadata, developing flexible annotation tools that can accommodate the diverse range of vocalization profiles of different organisms, and addressing the scarcity of expert annotators. 2. We present Whombat a user-friendly, browser-based interface for managing audio recordings and annotation projects, with several visualization, exploration, and annotation tools. It enables users to quickly annotate, review, and share annotations, as well as visualize and evaluate a set of machine learning predictions on a dataset. The tool facilitates an iterative workflow where user annotations and machine learning predictions feedback to enhance model performance and annotation quality. 3. We demonstrate the flexibility of Whombat by showcasing two distinct use cases: an project aimed at enhancing automated UK bat call identification at the Bat Conservation Trust (BCT), and a collaborative effort among the USDA Forest Service and Oregon State University researchers exploring bioacoustic applications and extending automated avian classification models in the Pacific Northwest, USA. 4. Whombat is a flexible tool that can effectively address the challenges of annotation for bioacoustic research. It can be used for individual and collaborative work, hosted on a shared server or accessed remotely, or run on a personal computer without the need for coding skills.

Combinatorial testing is a widely adopted technique for efficiently detecting faults in software. The quality of combinatorial test generators plays a crucial role in achieving effective test coverage. Evaluating combinatorial test generators remains a challenging task that requires diverse and representative benchmarks. Having such benchmarks might help developers to test their tools, and improve their performance. For this reason, in this paper, we present BenCIGen, a highly configurable generator of benchmarks to be used by combinatorial test generators, empowering users to customize the type of benchmarks generated, including constraints and parameters, as well as their complexity. An initial version of such a tool has been used during the CT-Competition, held yearly during the International Workshop on Combinatorial Testing. This paper describes the requirements, the design, the implementation, and the validation of BenCIGen. Tests for the validation of BenCIGen are derived from its requirements by using a combinatorial interaction approach. Moreover, we demonstrate the tool's ability to generate benchmarks that reflect the characteristics of real software systems. BenCIGen not only facilitates the evaluation of existing generators but also serves as a valuable resource for researchers and practitioners seeking to enhance the quality and effectiveness of combinatorial testing methodologies.

Stress prediction in porous materials and structures is challenging due to the high computational cost associated with direct numerical simulations. Convolutional Neural Network (CNN) based architectures have recently been proposed as surrogates to approximate and extrapolate the solution of such multiscale simulations. These methodologies are usually limited to 2D problems due to the high computational cost of 3D voxel based CNNs. We propose a novel geometric learning approach based on a Graph Neural Network (GNN) that efficiently deals with three-dimensional problems by performing convolutions over 2D surfaces only. Following our previous developments using pixel-based CNN, we train the GNN to automatically add local fine-scale stress corrections to an inexpensively computed coarse stress prediction in the porous structure of interest. Our method is Bayesian and generates densities of stress fields, from which credible intervals may be extracted. As a second scientific contribution, we propose to improve the extrapolation ability of our network by deploying a strategy of online physics-based corrections. Specifically, we condition the posterior predictions of our probabilistic predictions to satisfy partial equilibrium at the microscale, at the inference stage. This is done using an Ensemble Kalman algorithm, to ensure tractability of the Bayesian conditioning operation. We show that this innovative methodology allows us to alleviate the effect of undesirable biases observed in the outputs of the uncorrected GNN, and improves the accuracy of the predictions in general.

Previous efforts to support creative problem-solving have included (a) techniques (such as brainstorming and design thinking) to stimulate creative ideas, and (b) software tools to record and share these ideas. Now, generative AI technologies can suggest new ideas that might never have occurred to the users, and users can then select from these ideas or use them to stimulate even more ideas. Here, we describe such a system, Supermind Ideator. The system uses a large language model (GPT 3.5) and adds prompting, fine tuning, and a user interface specifically designed to help people use creative problem-solving techniques. Some of these techniques can be applied to any problem; others are specifically intended to help generate innovative ideas about how to design groups of people and/or computers ("superminds"). We also describe our early experiences with using this system and suggest ways it could be extended to support additional techniques for other specific problem-solving domains.

The synthesis of information deriving from complex networks is a topic receiving increasing relevance in ecology and environmental sciences. In particular, the aggregation of multilayer networks, i.e. network structures formed by multiple interacting networks (the layers), constitutes a fast-growing field. In several environmental applications, the layers of a multilayer network are modelled as a collection of similarity matrices describing how similar pairs of biological entities are, based on different types of features (e.g. biological traits). The present paper first discusses two main techniques for combining the multi-layered information into a single network (the so-called monoplex), i.e. Similarity Network Fusion (SNF) and Similarity Matrix Average (SMA). Then, the effectiveness of the two methods is tested on a real-world dataset of the relative abundance of microbial species in the ecosystems of nine glaciers (four glaciers in the Alps and five in the Andes). A preliminary clustering analysis on the monoplexes obtained with different methods shows the emergence of a tightly connected community formed by species that are typical of cryoconite holes worldwide. Moreover, the weights assigned to different layers by the SMA algorithm suggest that two large South American glaciers (Exploradores and Perito Moreno) are structurally different from the smaller glaciers in both Europe and South America. Overall, these results highlight the importance of integration methods in the discovery of the underlying organizational structure of biological entities in multilayer ecological networks.

Individualized treatment rules (ITRs) for treatment recommendation is an important topic for precision medicine as not all beneficial treatments work well for all individuals. Interpretability is a desirable property of ITRs, as it helps practitioners make sense of treatment decisions, yet there is a need for ITRs to be flexible to effectively model complex biomedical data for treatment decision making. Many ITR approaches either focus on linear ITRs, which may perform poorly when true optimal ITRs are nonlinear, or black-box nonlinear ITRs, which may be hard to interpret and can be overly complex. This dilemma indicates a tension between interpretability and accuracy of treatment decisions. Here we propose an additive model-based nonlinear ITR learning method that balances interpretability and flexibility of the ITR. Our approach aims to strike this balance by allowing both linear and nonlinear terms of the covariates in the final ITR. Our approach is parsimonious in that the nonlinear term is included in the final ITR only when it substantially improves the ITR performance. To prevent overfitting, we combine cross-fitting and a specialized information criterion for model selection. Through extensive simulations, we show that our methods are data-adaptive to the degree of nonlinearity and can favorably balance ITR interpretability and flexibility. We further demonstrate the robust performance of our methods with an application to a cancer drug sensitive study.