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Sparse coding has a variety of applications, such as image denoising and data compression. Recent work has shown the how sparse coding and biologically inspired architectures can mitigate adversarial attacks on images.
The global monsoon system, encompassing the Asian-Australian, African, and American monsoons, sustains two-thirds of the world’s population by regulating water resources and agriculture. Monsoon anomalies pose severe risks, including floods and droughts. Recent research associated with the implementation of the Global Monsoons Model Intercomparison Project under the umbrella of CMIP6 has advanced our understanding of its historical variability and driving mechanisms. Observational data reveal a 20th-century shift: increased rainfall pre-1950s, followed by aridification and partial recovery post-1980s, driven by both internal variability (e.g., Atlantic Multidecadal Oscillation) and external forcings (greenhouse gases, aerosols), while ENSO drives interannual variability through ocean-atmosphere interactions. Future projections under greenhouse forcing suggest long-term monsoon intensification, though regional disparities and model uncertainties persist. Models indicate robust trends but struggle to quantify extremes, where thermodynamic effects (warming-induced moisture rise) uniformly boost heavy rainfall, while dynamical shifts (circulation changes) create spatial heterogeneity. Volcanic eruptions and proposed solar radiation modification (SRM) further complicate predictions: tropical eruptions suppress monsoons, whereas high-latitude events alter cross-equatorial flows, highlighting unresolved feedbacks. The emergent constraint approach is booming in terms of correcting future projections and reducing uncertainty with respect to the global monsoons. Critical challenges remain. Model biases and sparse 20th-century observational data hinder accurate attribution. The interplay between natural variability and anthropogenic forcings, along with nonlinear extreme precipitation risks under warming, demands deeper mechanistic insights. Additionally, SRM’s regional impacts and hemispheric monsoon interactions require systematic evaluation. Addressing these gaps necessitates enhanced observational networks, refined climate models, and interdisciplinary efforts to disentangle multiscale drivers, ultimately improving resilience strategies for monsoon-dependent regions.
The deployment of liquid chromatography-mass spectrometry-based plasma proteomics experiments in a large cohort is sparse, leading to a lack of data available for benchmarking, method development or validation. Comprised of 6,426 plasma analyses, The Environmental Determinants of Diabetes in the Young (TEDDY) proteomics validation study constitutes one of the largest targeted proteomics experiments in the literature to date. The proteomics data from this study were generated over the course of 2.5 years from over 900 study subjects, each providing up to 29 longitudinal samples. The data also includes 916 quality control samples. The targeted mass spectrometry assay was comprised of 694 peptides mapping to 167 proteins and the panel was measured in each subject and QC sample. The targeted proteomic dataset presented here can be used as a resource for new computational method development, such as for batch correction, as well as for benchmarking and comparing the performance of different methods/tools.
We consider the inverse source problem in the parabolic equation, where the unknown source possesses the semi-discrete formulation. Theoretically, we prove that the flux data from any nonempty open subset of the boundary can uniquely determine the semi-discrete source. This means the observed area can be extremely small, and that is the reason we call it sparse boundary data. For the numerical reconstruction, we formulate the problem from the Bayesian sequential prediction perspective and conduct the numerical examples which estimate the space-time-dependent source state by state. To better demonstrate the method’s performance, we solve two common multiscale problems from two models with a long source sequence. The numerical results illustrate that the inversion is accurate and efficient.
Metabolic models can estimate intrinsic product yields for microbial factories, but such frameworks struggle to predict cell performance (including product titer or rate) under suboptimal metabolism and complex bioprocess conditions. On the other hand, machine learning, complementary to metabolic modeling necessitates large amounts of data. Building such a database for metabolic engineering designs requires significant manpower and is prone to human errors and bias. We propose an approach to integrate data-driven methods with genome scale metabolic model for assessment of microbial bio-production (yield, titer and rate). Using engineered E. coli as an example, we manually extracted and curated a data set comprising about 1200 experimentally realized cell factories from ~100 papers. We furthermore augmented the key design features (e.g., genetic modifications and bioprocess variables) extracted from literature with additional features derived from running the genome-scale metabolic model iML1515 simulations with constraints that match the experimental data. Then, data augmentation and ensemble learning (e.g., support vector machines, gradient boosted trees, and neural networks in a stacked regressor model) are employed to alleviate the challenges of sparse, non-standardized, and incomplete data sets, while multiple correspondence analysis/principal component analysis are used to rank influential factors on bio-production. The hybrid framework demonstrates a reasonably high cross-validation accuracy for prediction of E.coli factory performance metrics under presumed bioprocess and pathway conditions (Pearson correlation coefficients between 0.8 and 0.93 on new data not seen by the model).
Since the point cloud data of cultural heritage artifacts obtained by the laser scanner is enormous and dense, these lead to a large quantity of network resource for storing, processing, and transmission. This paper provided a fast reconstruction method of the dense point cloud model for cultural relics based on sparse auto-encoder and compressed sensing. Firstly, the octree method based on the hash function was utilized to extract local features and remove redundant points. Secondly, the point cloud, which can be seen as the 3D geometric signal, is projected to the discrete Laplacian sparse basis via the point cloud adjacency matrix. Then, aiming at the bottleneck of slow recovery caused by tremendous scale of inverse problem based on compressed sensing theory, the sparse auto-encoder was applied to reduce the dimension and speed up the recovery. Finally, the OMP algorithm was applied to reconstruct 3D point cloud model based on the stochastic Gauss matrix. In order to test the performance of our methods, the 3D point cloud model of terracotta warriors and horses head were used. And the experimental results demonstrated that our approach can obviously accelerate the process of reconstruction of the dense point cloud model for the cultural heritage artifacts and ensure the recovery accuracy.
In this paper, we study the performance of a two-level algebraic-multigrid algorithm, with a focus on the impact of the coarse-grid solver on performance. We consider two algorithms for solving the coarse-space systems: the preconditioned conjugate gradient method and a new robust HSS-embedded low-rank sparse-factorization algorithm. Our test data comes from the SPE Comparative Solution Project for oil-reservoir simulations. We contrast the performance of our code on one 12-core socket of a Cray XC30 machine with performance on a 60-core Intel Xeon Phi coprocessor. To obtain top performance, we optimized the code to take full advantage of fine-grained parallelism and made it thread-friendly for high thread count. We also developed a bounds-and-bottlenecks performance model of the solver which we used to guide us through the optimization effort, and also carried out performance tuning in the solver’s large parameter space. Finally, as a result, significant speedups were obtained on both machines.
Real-time state estimation and forecasting are critical for the efficient operation of power grids. In this paper, a physics-informed Gaussian process regression (PhI-GPR) method is presented and used for forecasting and estimating the phase angle, angular speed, and wind mechanical power of a three-generator power grid system using sparse measurements. In standard data-driven Gaussian process regression (GPR), parameterized models for the prior statistics are fit by maximizing the marginal likelihood of observed data. In the PhI-GPR method, we propose to compute the prior statistics offline by solving stochastic differential equations (SDEs) governing the power grid dynamics. The short-term forecast of a power grid system dominated by wind generation is complicated by the stochastic nature of the wind and the resulting uncertainty in wind mechanical power. Here, we assume that the power grid dynamics are governed by swing equations, with the wind mechanical power fluctuating randomly in time. We solve these equations for the mean and covariances of the power grid states using the Monte Carlo simulation method. We demonstrate that the proposed PhI-GPR method can accurately forecast and estimate observed and unobserved states. For the considered problem, PhI-GPR has computational advantages over the ensemble Kalman filter (EnKF) method: In PhI-GPR, ensembles are computed offline and independently of the data acquisition process, whereas for EnFK, ensembles are computed online with data acquisition, rendering real-time forecast more challenging. We also demonstrate that the PhI-GPR forecast is more accurate than the EnKF forecast when the random mechanical wind power is non-Markovian. In contrast, the two methods produce similar forecasts for the Markovian mechanical wind power. For observed states, we show that PhI-GPR provides a forecast comparable to the standard data-driven GPR; both forecasts are significantly more accurate than the autoregressive integrated moving average (ARIMA) forecast. We also show that the ARIMA forecast is more sensitive to observation frequency and measurement errors than the PhI-GPR forecast.
Physics-informed neural networks (PINNs) are effective in solving inverse problems based on differential and integro-differential equations with sparse, noisy, unstructured, and multifidelity data. PINNs incorporate all available information, including governing equations (reflecting physical laws), initial-boundary conditions, and observations of quantities of interest, into a loss function to be minimized, thus recasting the original problem into an optimization problem. In this paper, we extend PINNs to parameter and function inference for integral equations such as nonlocal Poisson and nonlocal turbulence models, and we refer to them as nonlocal PINNs (nPINNs). The contribution of the paper is three-fold. First, we propose a unified nonlocal Laplace operator, which converges to the classical Laplacian as one of the operator parameters, the nonlocal interaction radius $\delta$ goes to zero, and to the fractional Laplacian as $\delta$ goes to infinity. This universal operator forms a super-set of classical Laplacian and fractional Laplacian operators and, thus, has the potential to fit a broad spectrum of data sets. We also provide theoretical convergence rates with respect to $\delta$ and verify them via numerical experiments. Second, we use nPINNs to estimate the two parameters, $\delta$ and $\alpha$, characterizing the kernel of the unified operator. The strong non-convexity of the loss function yielding multiple (good) local minima reveals the occurrence of the operator mimicking phenomenon, that is, different pairs of estimated parameters could produce multiple solutions of comparable accuracy. Third, we propose another nonlocal operator with spatially variable order $\alpha(y)$, which is more suitable for modeling turbulent Couette flow. Our results show that nPINNs can jointly infer this function as well as $\delta$. More importantly, these parameters exhibit a universal behavior with respect to the Reynolds number, a finding that contributes to our understanding of nonlocal interactions in wall-bounded turbulence.
The selection of a salt species for use in a molten salt reactor MSR is a key part of any MSR design. However, many salts have sparse or no thermophysical property data sets, especially those with higher melting points. One such salt is the eutectic mixture of (NaF)0.345(KF)0.59(MgF 2 )0.065, or FMgNaK, and is explored here through ab initio molecular dynamics (AIMD) simulation (1023-1273K) as well as experimental measurement of the liquid density using the Archimedean method (973-1223K). Predicted densities from AIMD are similar to experimentally-measured densities, though with more noise, suggesting that the small scale necessitated by AIMD simulations may be problematic for simulating FMgNaK in particular. Here the coefficient of thermal expansion is predicted from simulation, and salt structure is characterized. Mg-F-Mg chaining is observed in the salt network, though the low concentration of Mg inhibits chaining on the scale that is observed in (LiF) 0.67 (BeF 2 ) 0.33 , or FLiBe.
Southern Ocean (S. Ocean) clouds are important for climate prediction. Yet previous global climate models failed to accurately represent cloud phase distributions in this observation-sparse region. In this study, data from the Southern Ocean Clouds, Radiation, Aerosol, Transport Experimental Study (SOCRATES) experiment is compared to constrained simulations from a global climate model (the Community Atmosphere Model, CAM). Nudged versions of CAM are found to reproduce many of the features of detailed in situ observations, such as cloud location, cloud phase, and boundary layer structure. The simulation in CAM6 has improved its representation of S. Ocean clouds with adjustments to the ice nucleation and cloud microphysics schemes that permit more supercooled liquid. Comparisons between modeled and observed hydrometeor size distributions suggest that the modeled hydrometeor size distributions represent the dual peaked shape and form of observed distributions, which is remarkable given the scale difference between model and observations. Comparison to satellite observations of cloud physics is difficult due to model assumptions that do not match retrieval assumptions. Some biases in the model's representation of S. Ocean clouds and aerosols remain, but the detailed cloud physical parameterization provides a basis for process level improvement and direct comparisons to observations. This is crucial because cloud feedbacks and climate sensitivity are sensitive to the representation of S. Ocean clouds.
Decreasing reservoir storage capacity due to sedimentation poses great challenges to aging U.S. reservoirs, as it reduces the efficacy and reliability of their socio‐economic services. However, systematic assessments of reservoir sedimentation rates and associated issues remain limited because of sparse and infrequent bathymetry survey data. In this study, we use remote sensing‐driven estimates of sediment concentrations to identify regions experiencing rapid reservoir capacity loss, as observed in repeated bathymetry surveys. Our analysis focuses on Texas, where one of the most reliable state‐level reservoir capacity loss data sets is available through a unique long‐term monitoring program by the Texas Water Development Board. We find that reservoirs with large storage capacities and high sedimentation rate are concentrated in Northeast Texas. We also show that reduced forest, increased barren land, and erosive soil properties are co‐varying with high reservoir sedimentation rates. Temporal changes in the longitudinal gradient of the remotely sensed sediment flux highlight the nonlinear nature of sediment trapping processes, and can be used to estimate the reservoir storage capacity loss over time. In combination with standard bathymetry surveys, our approach shows potential for more cost‐effective and frequent assessment of reservoir storage loss.
Relative stabilities of small Ga{sub n}As{sub m} clusters, as well as their structural electronic and vibrational properties, were computed and analysed using a CCSD(T) reference method since experimental data in this area are sparse or unknown. With the aim of investigating larger clusters, we explored several DFT functionals and basis sets able to mimic the reliable CCSD(T) approach. Among them, the PBE0/SBKJC+sp,d appears as the most efficient to describe the structural and vibrational properties since average differences of about 0.042Å and 5.1cm{sup −1} were obtained for bond lengths and fundamental vibrational frequencies, respectively for the first small clusters [1] of the series found from our GSAM method [2]. As further test, this model is used in order to investigate and revisit an experimental IR spectrum of Ga{sub n}As{sub m} mixture previously published by Li et al. [3]. More complicated is the difficulty which arises in the electronic description due to the presence of numerous low lying electronic states nearly degenerated to correctly describe the electronic structure. The case of Ga{sub 2}As will be discussed and the photoelectron spectra of the Ga{sub 2}As anion reanalyzed on the ground of our calculations [4] comparatively to the experimental spectra obtained by Neumark and co-workers [5].
Here, we present a Bayesian inference framework for reconstructing anisotropic two-dimensional small-angle scattering (2D SAS) patterns from sparse, noisy, or partially missing data. The method combines a symmetry-aware angular basis with radial Gaussian process priors to enable accurate, training-free interpolation and denoising. Computational benchmarks demonstrate reliable recovery of both isotropic and high-order anisotropic features under severe data reduction. Experimental validations on stretched polymers, sheared wormlike micelles, and carbon fibers show improved fidelity and resolution compared to raw measurements, achieving comparable accuracy with up to 50-fold fewer detected neutrons. This approach enables quantitative structural analysis under low-flux, time-limited, or single-shot conditions, extending the applicability of 2D SAS techniques to compact neutron sources and mechanically driven soft matter systems undergoing transient structural changes.
The basic matrix library (bml) is a collection of various matrix data formats (in dense and sparse) and their associated algorithms for basic matrix operations.
Optimal experimental design is a classic topic in statistics, with many well-studied problems, applications, and solutions. The design problem we study is the placement of sensors to monitor spatiotemporal processes, explicitly accounting for the temporal dimension in our modeling and optimization. We observe that recent advancements in computational sciences often yield large datasets based on physics-based simulations, which are rarely leveraged in experimental design. We introduce a novel model-based sensor placement criterion, along with a highly-efficient optimization algorithm, which integrates physics-based simulations and Bayesian experimental design principles to identify sensor networks that “minimize information loss” from simulated data. Our technique relies on sparse variational inference and (separable) Gauss-Markov priors, and thus may adapt many techniques from Bayesian experimental design. We validate our method through a case study monitoring air temperature in Phoenix, Arizona, using state-of-the-art physics-based simulations. Our results show our framework to be superior to random or quasi-random sampling, particularly with a limited number of sensors. We conclude by discussing practical considerations and implications of our framework, including more complex modeling tools and real-world deployments.
Physics-informed neural networks (PINNs) are effective in solving inverse problems based on differential and integro-differential equations with sparse, noisy, unstructured, and multifidelity data. PINNs incorporate all available information, including governing equations (reflecting physical laws), initial-boundary conditions, and observations of quantities of interest, into a loss function to be minimized, thus recasting the original problem into an optimization problem. In this paper, we extend PINNs to parameter and function inference for integral equations such as nonlocal Poisson and nonlocal turbulence models, and we refer to them as nonlocal PINNs (nPINNs). The contribution of the paper is three-fold. First, we propose a unified nonlocal Laplace operator, which converges to the classical Laplacian as one of the operator parameters, the nonlocal interaction radius δ goes to zero, and to the fractional Laplacian as δ goes to infinity. This universal operator forms a super-set of classical Laplacian and fractional Laplacian operators and, thus, has the potential to fit a broad spectrum of data sets. We provide theoretical convergence rates with respect to δ and verify them via numerical experiments. Second, we use nPINNs to estimate the two parameters, δ and α, characterizing the kernel of the unified operator. The strong non-convexity of the loss function yielding multiple (good) local minima reveals the occurrence of the operator mimicking phenomenon, that is, different pairs of estimated parameters could produce multiple solutions of comparable accuracy. Third, we propose another nonlocal operator with spatially variable order α(γ), which is more suitable for modeling turbulent Couette flow. Our results show that nPINNs can jointly infer this function as well as δ. More importantly, these parameters exhibit a universal behavior with respect to the Reynolds number, a finding that contributes to our understanding of nonlocal interactions in wall-bounded turbulence.
Large Language Models (LLMs) struggle out of the box when answering factually about detailed questions, especially in domains that are sparsely represented in their training data. This causes hallucinations and reduces reliability making it difficult for them to be used in practice. This work shows that using RAG techniques can improve factual accuracy and reliability, allowing for the application of LLMs in specialized areas, even when those areas that aren’t extensively covered in their initial training.