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Gaussian process (GP) is a Bayesian model which provides several advantages for regression tasks in machine learning such as reliable quantitation of uncertainty and improved interpretability. Their adoption has been precluded by their excessive computational cost and by the difficulty in adapting them for analyzing sequences (e.g. amino acid and nucleotide sequences) and graphs (e.g. ones representing small molecules). In this study, we develop efficient and scalable approaches for fitting GP models as well as fast convolution kernels which scale linearly with graph or sequence size. We implement these improvements by building an open-source Python library called xGPR. We compare the performance of xGPR with the reported performance of various deep learning models on 20 benchmarks, including small molecule, protein sequence and tabular data. We show that xGRP achieves highly competitive performance with much shorter training time. Furthermore, we also develop new kernels for sequence and graph data and show that xGPR generally outperforms convolutional neural networks on predicting key properties of proteins and small molecules. Importantly, xGPR provides uncertainty information not available from typical deep learning models. Additionally, xGPR provides a representation of the input data that can be used for clustering and data visualization. These results demonstrate that xGPR provides a powerful and generic tool that can be broadly useful in protein engineering and drug discovery.

In this study, we focus on learning Hamiltonian systems, which involves predicting the coordinate (q) and momentum (p) variables generated by a symplectic mapping. Based on Chen & Tao (2021), the symplectic mapping is represented by a generating function. To extend the prediction time period, we develop a new learning scheme by splitting the time series (q_i, p_i) into several partitions. We then train a large-step neural network (LSNN) to approximate the generating function between the first partition (i.e. the initial condition) and each one of the remaining partitions. This partition approach makes our LSNN effectively suppress the accumulative error when predicting the system evolution. Then we train the LSNN to learn the motions of the 2:3 resonant Kuiper belt objects for a long time period of 25000 yr. The results show that there are two significant improvements over the neural network constructed in our previous work (Li et al. 2022): (1) the conservation of the Jacobi integral, and (2) the highly accurate predictions of the orbital evolution. Overall, we propose that the designed LSNN has the potential to considerably improve predictions of the long-term evolution of more general Hamiltonian systems.

Full waveform inversion (FWI) updates the subsurface model from an initial model by comparing observed and synthetic seismograms. Due to high nonlinearity, FWI is easy to be trapped into local minima. Extended domain FWI, including wavefield reconstruction inversion (WRI) and extended source waveform inversion (ESI) are attractive options to mitigate this issue. This paper makes an in-depth analysis for FWI in the extended domain, identifying key challenges and searching for potential remedies torwards practical applications. WRI and ESI are formulated within the same mathematical framework using Lagrangian-based adjoint-state method with a special focus on time-domain formulation using extended sources, while putting connections between classical FWI, WRI and ESI: both WRI and ESI can be viewed as weighted versions of classic FWI. Due to symmetric positive definite Hessian, the conjugate gradient is explored to efficiently solve the normal equation in a matrix free manner, while both time and frequency domain wave equation solvers are feasible. This study finds that the most significant challenge comes from the huge storage demand to store time-domain wavefields through iterations. To resolve this challenge, two possible workaround strategies can be considered, i.e., by extracting sparse frequencial wavefields or by considering time-domain data instead of wavefields for reducing such challenge. We suggest that these options should be explored more intensively for tractable workflows.

We present an artificial intelligence (AI) method for automatically computing the melting point based on coexistence simulations in the NPT ensemble. Given the interatomic interaction model, the method makes decisions regarding the number of atoms and temperature at which to conduct simulations, and based on the collected data predicts the melting point along with the uncertainty, which can be systematically improved with more data. We demonstrate how incorporating physical models of the solid-liquid coexistence evolution enhances the AI method's accuracy and enables optimal decision-making to effectively reduce predictive uncertainty. To validate our approach, we compare our results with approximately 20 melting point calculations from the literature. Remarkably, we observe significant deviations in about one-third of the cases, underscoring the need for accurate and reliable AI-based algorithms for materials property calculations.

The ultimate goal of studying the magnetopause position is to accurately determine its location. Both traditional empirical computation methods and the currently popular machine learning approaches have shown promising results. In this study, we propose a Regression-based Physics-Informed Neural Networks (Reg-PINNs) that combines physics-based numerical computation with vanilla machine learning. This new generation of Physics Informed Neural Networks overcomes the limitations of previous methods restricted to solving ordinary and partial differential equations by incorporating conventional empirical models to aid the convergence and enhance the generalization capability of the neural network. Compared to Shue et al. [1998], our model achieves a reduction of approximately 30% in root mean square error. The methodology presented in this study is not only applicable to space research but can also be referenced in studies across various fields, particularly those involving empirical models.

We present an implicit-explicit finite volume scheme for two-fluid single-temperature flow in all Mach number regimes which is based on a symmetric hyperbolic thermodynamically compatible description of the fluid flow. The scheme is stable for large time steps controlled by the interface transport and is computational efficient due to a linear implicit character. The latter is achieved by linearizing along constant reference states given by the asymptotic analysis of the single-temperature model. Thus, the use of a stiffly accurate IMEX Runge Kutta time integration and the centered treatment of pressure based quantities provably guarantee the asymptotic preserving property of the scheme for weakly compressible Euler equations with variable volume fraction. The properties of the first and second order scheme are validated by several numerical test cases.

Full waveform inversion (FWI) has the potential to provide high-resolution subsurface model estimations. However, due to limitations in observation, e.g., regional noise, limited shots or receivers, and band-limited data, it is hard to obtain the desired high-resolution model with FWI. To address this challenge, we propose a new paradigm for FWI regularized by generative diffusion models. Specifically, we pre-train a diffusion model in a fully unsupervised manner on a prior velocity model distribution that represents our expectations of the subsurface and then adapt it to the seismic observations by incorporating the FWI into the sampling process of the generative diffusion models. What makes diffusion models uniquely appropriate for such an implementation is that the generative process retains the form and dimensions of the velocity model. Numerical examples demonstrate that our method can outperform the conventional FWI with only negligible additional computational cost. Even in cases of very sparse observations or observations with strong noise, the proposed method could still reconstruct a high-quality subsurface model. Thus, we can incorporate our prior expectations of the solutions in an efficient manner. We further test this approach on field data, which demonstrates the effectiveness of the proposed method.

The operation of machine tools often demands a highly accurate knowledge of the tool center point's (TCP) position. The displacement of the TCP over time can be inferred from thermal models, which comprise a set of geometrically coupled heat equations. Each of these equations represents the temperature in part of the machine, and they are often formulated on complicated geometries. The accuracy of the TCP prediction depends highly on the accuracy of the model parameters, such as heat exchange parameters, and the initial temperature. Thus it is of utmost interest to determine the influence of these parameters on the TCP displacement prediction. In turn, the accuracy of the parameter estimate is essentially determined by the measurement accuracy and the sensor placement. Determining the accuracy of a given sensor configuration is a key prerequisite of optimal sensor placement. We develop here a thermal model for a particular machine tool. On top of this model we propose two numerical algorithms to evaluate any given thermal sensor configuration with respect to its accuracy. We compute the posterior variances from the posterior covariance matrix with respect to an uncertain initial temperature field. The full matrix is dense and potentially very large, depending on the model size. Thus, we apply a low-rank method to approximate relevant entries, i.e. the variances on its diagonal. We first present a straightforward way to compute this approximation which requires computation of the model sensitivities with with respect to the initial values. Additionally, we present a low-rank tensor method which exploits the underlying system structure. We compare the efficiency of both algorithms with respect to runtime and memory requirements and discuss their respective advantages with regard to optimal sensor placement problems.

Recently, graph neural networks have been gaining a lot of attention to simulate dynamical systems due to their inductive nature leading to zero-shot generalizability. Similarly, physics-informed inductive biases in deep-learning frameworks have been shown to give superior performance in learning the dynamics of physical systems. There is a growing volume of literature that attempts to combine these two approaches. Here, we evaluate the performance of thirteen different graph neural networks, namely, Hamiltonian and Lagrangian graph neural networks, graph neural ODE, and their variants with explicit constraints and different architectures. We briefly explain the theoretical formulation highlighting the similarities and differences in the inductive biases and graph architecture of these systems. We evaluate these models on spring, pendulum, gravitational, and 3D deformable solid systems to compare the performance in terms of rollout error, conserved quantities such as energy and momentum, and generalizability to unseen system sizes. Our study demonstrates that GNNs with additional inductive biases, such as explicit constraints and decoupling of kinetic and potential energies, exhibit significantly enhanced performance. Further, all the physics-informed GNNs exhibit zero-shot generalizability to system sizes an order of magnitude larger than the training system, thus providing a promising route to simulate large-scale realistic systems.

Graphs, which describe pairwise relations between objects, are essential representations of many real-world data such as social networks. In recent years, graph neural networks, which extend the neural network models to graph data, have attracted increasing attention. Graph neural networks have been applied to advance many different graph related tasks such as reasoning dynamics of the physical system, graph classification, and node classification. Most of the existing graph neural network models have been designed for static graphs, while many real-world graphs are inherently dynamic. For example, social networks are naturally evolving as new users joining and new relations being created. Current graph neural network models cannot utilize the dynamic information in dynamic graphs. However, the dynamic information has been proven to enhance the performance of many graph analytical tasks such as community detection and link prediction. Hence, it is necessary to design dedicated graph neural networks for dynamic graphs. In this paper, we propose DGNN, a new {\bf D}ynamic {\bf G}raph {\bf N}eural {\bf N}etwork model, which can model the dynamic information as the graph evolving. In particular, the proposed framework can keep updating node information by capturing the sequential information of edges, the time intervals between edges and information propagation coherently. Experimental results on various dynamic graphs demonstrate the effectiveness of the proposed framework.