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At least 343 records · Page 19

Variational inference of effective range parameters for 3 He− 4 He scattering

We use two different methods, Monte Carlo sampling and variational inference (VI), to perform a Bayesian calibration of the effective-range parameters in 3 He– 4 He elastic scattering. The parameters are calibrated to data from a recent set of 3 He– 4 He elastic scattering differential cross section measurements. Analysis of these data for E lab ≤ 4.3 MeV yields a unimodal posterior for which both methods obtain the same structure. However, the effective-range expansion amplitude does not account for the 7/2 − state of 7 Be so, even after calibration, the description of data at the upper end of this energy range is poor. The data up to E lab = 2.6 MeV can be well described, but calibration to this lower-energy subset of the data yields a bimodal posterior. After adapting VI to treat such a multi-modal posterior we find good agreement between the VI results and those obtained with parallel-tempered Monte Carlo sampling.

effective field theory↗

Inferring the shape of data: a probabilistic framework for analysing experiments in the natural sciences

A critical step in data analysis for many different types of experiments is the identification of features with theoretically defined shapes in N -dimensional datasets; examples of this process include finding peaks in multi-dimensional molecular spectra or emitters in fluorescence microscopy images. Identifying such features involves determining if the overall shape of the data is consistent with an expected shape; however, it is generally unclear how to quantitatively make this determination. In practice, many analysis methods employ subjective, heuristic approaches, which complicates the validation of any ensuing results—especially as the amount and dimensionality of the data increase. Here, we present a probabilistic solution to this problem by using Bayes’ rule to calculate the probability that the data have any one of several potential shapes. This probabilistic approach may be used to objectively compare how well different theories describe a dataset, identify changes between datasets and detect features within data using a corollary method called Bayesian Inference-based Template Search; several proof-of-principle examples are provided. Altogether, this mathematical framework serves as an automated ‘engine’ capable of computationally executing analysis decisions currently made by visual inspection across the sciences.

Science & Technology - Other Topics↗

The Ground Truth Program: Simulations as Test Beds for Social Science Research Methods.

Social systems are uniquely complex and difficult to study, but understanding them is vital to solving the world’s problems. The Ground Truth program developed a new way of testing the research methods that attempt to understand and leverage the Human Domain and its associated complexities. The program developed simulations of social systems as virtual world test beds. Not only were these simulations able to produce data on future states of the system under various circumstances and scenarios, but their causal ground truth was also explicitly known. Research teams studied these virtual worlds, facilitating deep validation of causal inference, prediction, and prescription methods. The Ground Truth program model provides a way to test and validate research methods to an extent previously impossible, and to study the intricacies and interactions of different components of research.

97 MATHEMATICS AND COMPUTING↗

Physics-informed regularization and structure preservation for learning stable reduced models from data with operator inference

Operator inference learns low-dimensional dynamical-system models with polynomial nonlinear terms from trajectories of high-dimensional physical systems (non-intrusive model reduction). Here, this work focuses on the large class of physical systems that can be well described by models with quadratic and cubic nonlinear terms and proposes a regularizer for operator inference that induces a stability bias onto learned models. The proposed regularizer is physics informed in the sense that it penalizes higher-order terms with large norms and so explicitly leverages the polynomial model form that is given by the underlying physics. This means that the proposed approach judiciously learns from data and physical insights combined, rather than from either data or physics alone. Additionally, a formulation of operator inference is proposed that enforces model constraints for preserving structure such as symmetry and definiteness in linear terms. Numerical results demonstrate that models learned with operator inference and the proposed regularizer and structure preservation are accurate and stable even in cases where using no regularization and Tikhonov regularization leads to models that are unstable.

97 MATHEMATICS AND COMPUTING↗

Evaluating the limitations of Bayesian metabolic control analysis

AbstractBayesian Metabolic Control Analysis (BMCA) has emerged as a promising framework for inferring metabolic control coefficients in data-limited scenarios by integrating Bayesian inference with linlog rate laws. However, its predictive accuracy and limitations remain underexplored. This study systematically evaluates BMCA’s ability to infer elasticity values, flux control coefficients (FCCs), and concentration control coefficients (CCCs) under varying data availability conditions using three synthetic metabolic network models. Our findings highlight the strengths and weaknesses of BMCA, guiding its application in metabolic engineering and emphasizing the need for methodological refinements.Author summaryUnderstanding how enzymes control metabolic pathways is crucial for optimizing biomanufacturing and synthetic biology applications. Bayesian Metabolic Control Analysis (BMCA) is a promising computational method that integrates Bayesian inference with metabolic control analysis to estimate key control parameters, even in cases with limited experimental data. However, the accuracy and limitations of BMCA remain unclear. In this study, we systematically evaluate BMCA using three synthetic metabolic networks to determine how different types of physiological data impact its predictive performance. We find that BMCA requires flux and enzyme concentration data for accurate predictions, while external metabolite concentrations contribute little. Additionally, BMCA fails to predict elasticity values beyond a magnitude of 1.5 and reliably infer allosteric regulation, even when strong regulatory interactions exist. In addition, BMCA does not accurately rank metabolic control points, which may limit its utility in identifying key enzymes in engineered pathways. Our work provides practical insights into when and how BMCA can be applied, guiding future research in metabolic modeling and control analysis.

Shin, Janis (ORCID:0000000216572455)↗

Disentangling direct from indirect relationships in association networks

Networks are vital tools for understanding and modeling interactions in complex systems in science and engineering, and direct and indirect interactions are pervasive in all types of networks. However, quantitatively disentangling direct and indirect relationships in networks remains a formidable task. Here, we present a framework, called iDIRECT (Inference of Direct and Indirect Relationships with Effective Copula-based Transitivity), for quantitatively inferring direct dependencies in association networks. Using copula-based transitivity, iDIRECT eliminates/ameliorates several challenging mathematical problems, including ill-conditioning, self-looping, and interaction strength overflow. With simulation data as benchmark examples, iDIRECT showed high prediction accuracies. Application of iDIRECT to reconstruct gene regulatory networks in Escherichia coli also revealed considerably higher prediction power than the best-performing approaches in the DREAM5 (Dialogue on Reverse Engineering Assessment and Methods project, #5) Network Inference Challenge. In addition, applying iDIRECT to highly diverse grassland soil microbial communities in response to climate warming showed that the iDIRECT-processed networks were significantly different from the original networks, with considerably fewer nodes, links, and connectivity, but higher relative modularity. Further analysis revealed that the iDIRECT-processed network was more complex under warming than the control and more robust to both random and target species removal ( P < 0.001). As a general approach, iDIRECT has great advantages for network inference, and it should be widely applicable to infer direct relationships in association networks across diverse disciplines in science and engineering.

59 BASIC BIOLOGICAL SCIENCES↗

Verification, Validation, and Calibration Through a Causal Lens

While typical validation and verification approaches focus on identifying the associations between data elements using statistical and machine learning methods, the novel methods in this paper focus instead on identifying causal relationships between data elements. Statistical and machine-learning-based approaches are strictly data-driven, meaning that they provide quantitative comparison measures between data sets without explicitly considering the hypotheses behind them. This can lead to the erroneous conclusion that, if two data sets are close enough, the models that generated them are similar. In addition, when experimental and simulated data differ to an extent that fails to meet the acceptance criteria, calibration techniques are used to tweak simulation model parameters to reduce the gap between the two types of data. This produces the false expectation that a simulation model will match reality. The methods presented in this paper move away from these strictly data-driven methods for validation and calibration toward more robust, model-driven methods based on causal inference. Causal inference aims to identify the possible mechanisms that might have generated data. Thus, this analysis targets the prediction of the effects when one (or more) of the identified mechanisms are altered. There are many approaches to identify, quantify, and illustrate causal relationships. For the scope of this paper, directed graphs are employed as causal models. If the directed graph lacks cycles, it is known as a directed acyclic graph. A node in such a graph represents an observed data element while a directed edge connecting two nodes represents a causal relationship between two variables. The developed causal methods are designed to extract causal models from simulation models and experimental data. Causal models capture the causal relationships between data elements (e.g., simulated and experimental data). In this context, validation and verification are performed by comparing causal models. The proposed approach does not only inform system analysts on how a simulation model matches real-world data, but also identifies elements of the simulation model that should be revised when discrepancies between simulation and experimental data are observed. Through these causal methods, analysts can identify the portion of the model equation(s) that are behind an edge connecting two variables. Hence, once the structural differences between causal models have been determined, model calibration can occur by changing only those model parameters that impact the identified causal relationships.

97 MATHEMATICS AND COMPUTING↗

Tracking the topology of neural manifolds across populations

Neural manifolds summarize the intrinsic structure of the information encoded by a population of neurons. Advances in experimental techniques have made simultaneous recordings from multiple brain regions increasingly commonplace, raising the possibility of studying how these manifolds relate across populations. However, when the manifolds are nonlinear and possibly code for multiple unknown variables, it is challenging to extract robust and falsifiable information about their relationships. We introduce a framework, called the method of analogous cycles, for matching topological features of neural manifolds using only observed dissimilarity matrices within and between neural populations. We demonstrate via analysis of simulations and in vivo experimental data that this method can be used to correctly identify multiple shared circular coordinate systems across both stimuli and inferred neural manifolds. Conversely, the method rejects matching features that are not intrinsic to one of the systems. Further, as this method is deterministic and does not rely on dimensionality reduction or optimization methods, it is amenable to direct mathematical investigation and interpretation in terms of the underlying neural activity. We thus propose the method of analogous cycles as a suitable foundation for a theory of cross-population analysis via neural manifolds.

97 MATHEMATICS AND COMPUTING↗

A Scalable Gaussian Process Approach to Shear Mapping with MuyGPs

Analysis of cosmic shear is an integral part of understanding structure growth across cosmic time, which in turn provides us with information about the nature of dark energy. Conventional methods generate shear maps from which we can infer the matter distribution in the universe. Current methods (e.g., Kaiser–Squires inversion) for generating these maps, however, are tricky to implement and can introduce bias. Recent alternatives construct a spatial process prior for the lensing potential, which allows for inference of the convergence and shear parameters given lensing shear measurements. Realizing these spatial processes, however, scales cubically in the number of observations—an unacceptable expense as near-term surveys expect billions of correlated measurements. Therefore, we present a linearly scaling shear map construction alternative using a scalable Gaussian process prior called MuyGPs. MuyGPs avoids cubic scaling by conditioning interpolation on only nearest neighbors and fits hyperparameters using batched leave-one-out cross-validation. This work is the first step toward a full, scalable mass mapping method. We work in a simplified regime where we validate our method by interpolating and analyzing maps given noisy point-estimate data from all three shear fields, taken from a suite of N -body ray-tracing simulations. We also show that we can perform these operations at the scale of billions of galaxies on high-performance computing platforms.

79 ASTRONOMY AND ASTROPHYSICS↗

Integration of ecosystem science into radioecology: A consensus perspective

In the Fall of 2016 a workshop was held which brought together over 50 scientists from the ecological and radiological fields to discuss feasibility and challenges of reintegrating ecosystem science into radioecology. There is a growing desire to incorporate attributes of ecosystem science into radiological risk assessment and radioecological research more generally, fueled by recent advances in quantification of emergent ecosystem attributes and the desire to accurately reflect impacts of radiological stressors upon ecosystem function. This work is a synthesis of the discussions and consensus of the workshop participant's responses to three primary questions, which were: 1) How can ecosystem science support radiological risk assessment? 2) What ecosystem level endpoints potentially could be used for radiological risk assessment? and 3) What inference strategies and associated methods would be most appropriate to assess the effects of radionuclides on ecosystem structure and function? The consensus of the participants was that ecosystem science can and should support radiological risk assessment through the incorporation of quantitative metrics that reflect ecosystem functions which are sensitive to radiological contaminants. The participants also agreed that many such endpoints exit or are thought to exit and while many are used in ecological risk assessment currently, additional data need to be collected that link the causal mechanisms of radiological exposure to these endpoints. Finally, the participants agreed that radiological risk assessments must be designed and informed by rigorous statistical frameworks capable of revealing the causal inference tying radiological exposure to the endpoints selected for measurement.

54 ENVIRONMENTAL SCIENCES↗

Dark Energy Survey Year 6 Results: Redshift Calibration of the MagLim++ Lens Sample

In this work, we derive and calibrate the redshift distribution of the MagLim++ lens galaxy sample used in the Dark Energy Survey Year 6 (DES Y6) 3x2pt cosmology analysis. The 3x2pt analysis combines galaxy clustering from the lens galaxy sample and weak gravitational lensing. The redshift distributions are inferred using the SOMPZ method - a Self-Organizing Map framework that combines deep-field multi-band photometry, wide-field data, and a synthetic source injection (Balrog) catalog. Key improvements over the DES Year 3 (Y3) calibration include a noise-weighted SOM metric, an expanded Balrog catalogue, and an improved scheme for propagating systematic uncertainties, which allows us to generate O($10^8$) redshift realizations that collectively span the dominant sources of uncertainty. These realizations are then combined with independent clustering-redshift measurements via importance sampling. The resulting calibration achieves typical uncertainties on the mean redshift of 1-2%, corresponding to a 20-30% average reduction relative to DES Y3. We compress the $n(z)$ uncertainties into a small number of orthogonal modes for use in cosmological inference. Marginalizing over these modes leads to only a minor degradation in cosmological constraints. This analysis establishes the MagLim++ sample as a robust lens sample for precision cosmology with DES Y6 and provides a scalable framework for future surveys.

Giannini, G. [Chicago U., Astron. Astrophys. Ctr.;↗

Dark Energy Survey Year 6 results: Redshift calibration of the MagLim++ lens sample

In this work, we derive and calibrate the redshift distribution of the MagLim++ lens galaxy sample used in the Dark Energy Survey Year 6 (DES Y6) 3 x 2pt cosmology analysis. The 3 x 2pt analysis combines galaxy clustering from the lens galaxy sample and weak gravitational lensing. The redshift distributions are inferred using the SOMPZ method - a Self-Organizing Map framework that combines deep-field multi-band photometry, wide-field data, and a synthetic source injection ( B alrog) catalog. Key improvements over the DES Year 3 (Y3) calibration include a noise-weighted SOM metric, an expanded Balrog catalogue, and an improved scheme for propagating systematic uncertainties, which allows us to generate O(10 8 ) redshift realizations that collectively span the dominant sources of uncertainty. These realizations are then combined with independent clustering-redshift measurements via importance sampling. The resulting calibration achieves typical uncertainties on the mean redshift of 1-2%, corresponding to a 20-30% average reduction relative to DES Y3. We compress the n(z) uncertainties into a small number of orthogonal modes for use in cosmological inference. Marginalizing over these modes leads to only a minor degradation in cosmological constraints. Here, this analysis establishes the MagLim++ sample as a robust lens sample for precision cosmology with DES Y6 and provides a scalable framework for future surveys.

dark energy↗

Analyzing line-of-sight selection biases in galaxy-scale strong lensing with external convergence and shear

The upcoming Vera Rubin Observatory Legacy Survey of Space and Time (LSST) will dramatically increase the number of strong gravitational lensing systems, requiring precise modeling of line-of-sight (LOS) effects to mitigate biases in lensing observations and cosmological inferences. We develop a method to construct joint distributions of external convergence (κ ext ) and shear (γ ext ) for strong lensing LOS by aggregating large-scale structure simulations with high-resolution halo renderings and non-linear correction. Our approach captures both smooth background matter and perturbations from halos, enabling accurate modeling of LOS effects. Here, we apply non-linear LOS corrections to κ ext and γ ext that address the non-additive lensing effects caused by objects along the LOS in strong lensing. We find that, with a minimum image separation of 1.0'', non-linear LOS correction due to the presence of a dominant deflector slightly increases the ratio of quadruple to double lenses; this non-linear LOS correction also introduces systematic biases of ∼ 0.1% for galaxy-AGN lens in the inferred Hubble constant (H 0 ) if not accounted for. We also observe a 0.66% bias for galaxy-galaxy lenses on H 0 , and even larger biases 1.02% for galaxy-AGN systems if LOS effects are not accounted for. These results highlight the importance of LOS for precision cosmology. The publicly available code and datasets provide tools for incorporating LOS effects in future analyses.

Hubble constant↗

On the use of neural networks for energy reconstruction in high-granularity calorimeters

We contrasted the performance of deep neural networks — Convolutional Neural Network (CNN) and Graph Neural Network (GNN) — to current state of the art energy regression methods in a finely 3D-segmented calorimeter simulated by GEANT4. This comparative benchmark gives us some insight to assess the particular latent signals neural network methods exploit to achieve superior resolution. A CNN trained solely on a pure sample of pions achieved substantial improvement in the energy resolution for both single pions and jets over the conventional approaches. It maintained good performance for electron and photon reconstruction. We also used the Graph Neural Network (GNN) with edge convolution to assess the importance of timing information in the shower development for improved energy reconstruction. We implement a simple simulation based correction to the energy sum derived from the fraction of energy deposited in the electromagnetic shower component. This serves as an approximate dual-readout analogue for our benchmark comparison. Although this study does not include the simulation of detector effects, such as electronic noise, the margin of improvement seems robust enough to suggest these benefits will endure in real-world application. We also find reason to infer that the CNN/GNN methods leverage latent features that concur with our current understanding of the physics of calorimeter measurement.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Intelligent resolution: Integrating Cryo-EM with AI-driven multi-resolution simulations to observe the severe acute respiratory syndrome coronavirus-2 replication-transcription machinery in action

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) replication transcription complex (RTC) is a multi-domain protein responsible for replicating and transcribing the viral mRNA inside a human cell. Attacking RTC function with pharmaceutical compounds is a pathway to treating COVID-19. Conventional tools, e.g., cryo-electron microscopy and all-atom molecular dynamics (AAMD), do not provide sufficiently high resolution or timescale to capture important dynamics of this molecular machine. Consequently, we develop an innovative workflow that bridges the gap between these resolutions, using mesoscale fluctuating finite element analysis (FFEA) continuum simulations and a hierarchy of AI-methods that continually learn and infer features for maintaining consistency between AAMD and FFEA simulations. We leverage a multi-site distributed workflow manager to orchestrate AI, FFEA, and AAMD jobs, providing optimal resource utilization across HPC centers. Our study provides unprecedented access to study the SARS-CoV-2 RTC machinery, while providing general capability for AI-enabled multi-resolution simulations at scale.

Trifan, Anda↗

Using Downwelling Far- and Thermal-Infrared Hyperspectral Radiance for Cloud Phase Classification in the Antarctic

The cloud phase is one of the most important parameters of clouds. In this paper, we propose a method for cloud phase classification that synergistically utilizes the far- and thermal-infrared bands based on the Atmospheric Emitted Radiance Interferometer (AERI) at the Atmospheric Radiation Measurement West Antarctic Radiation Experiment (AWARE) observatory in 2016. The possible features in the far- and thermal-infrared bands are analyzed based on the differences in the simulated cloud brightness temperature (BT) spectra with different cloud phases. Using the support vector machine (SVM) algorithm, four features are determined to identify the cloud phase, which include the BT at 900 cm -1 , the slope of the fitted function of BT in the 900–1000 cm -1 interval, the BT difference (BTD) between 512 cm -1 and 726 cm -1 , and the BTD between 550 cm -1 and 726 cm -1 . Here, the performance of the proposed method is evaluated with Shupe’s and Turner’s method. The monthly average accuracy of the proposed method, the method without the two far-infrared features, and Turner’s method are about 76%, 36%, and 49%, respectively, which infer the good performance of the proposed method and also indicate that the far-infrared band features can effectively enhance cloud phase classification. It is notable that, compared to Shupe’s method, the accuracy for the proposed method is only 61% during the Antarctic summer, which results from the definitions of cloud phase and radiative effect. In addition, the accuracy is only 44% for Turner’s method in seasons with a low frequency of mixed clouds due to the significant effect of water vapor.

54 ENVIRONMENTAL SCIENCES↗

Role of the likelihood for elastic scattering uncertainty quantification

In the last decade, uncertainty quantification (UQ) for optical model potentials (OMPs) has become a focal point for nuclear reaction theory, and several competing approaches for OMP UQ have recently been developed. Here, we clarify recent efforts to compare frequentist and Bayesian approaches in the context of OMP UQ [G. B. King et al., Phys. Rev. Lett. 122, 232502 (2019)]. We replicate a portion of that OMP UQ study but use independent statistical tools. Specifically, we compare two methods for OMP parameter inference from elastic scattering data: the Levenberg-Marquardt algorithm for χ 2 minimization on one hand and Markov chain Monte Carlo (MCMC) sampling on the other. Separately, we assess the common practice of using a renormalized likelihood (χ 2 /N), N being the number of data points, instead of the canonical weighted-least-squares likelihood (χ 2 ), as a way of accounting for unknown data correlations. Here, we show that for a generic linear model and for a five-parameter OMP analysis, frequentist and uniform-prior Bayesian approaches recover the same optimum and uncertainty estimates—not systematically larger uncertainties for the Bayesian approach, as was concluded in G. B. King et al., Phys. Rev. Lett. 122, 232502 (2019). Further, we show that if an additional, near-degenerate parameter is introduced into the same OMP analysis such that the parameter posterior becomes non-Gaussian, then covariance-based estimates of uncertainty become unreliable. Finally, we show that regardless of optimization approach, if χ 2 /N is used for the likelihood, the resulting parametric uncertainties increase by $\sqrt{N}$, and that this is responsible for the conclusions drawn in the revisited study. Based on our replication results, we find that a fortuitous cancellation of unreported errors and the renormalization factor can lead to improvement in empirical coverages, as was the case in the original comparative study. We emphasize that developing and applying a realistic likelihood function is an essential task in a UQ analysis, and that several recent UQ studies that employed a renormalized likelihood (i.e., including a 1/N factor) may have yielded unrealistically large uncertainties for elastic-scattering observables. If the parameter posterior deviates from multivariate-normal, a sampling-based approach like MCMC has a clear advantage over methods that assume the Laplace approximation holds. We note that empirical coverage can serve as an important internal check for the analyst whose model or data may have additional, unaccounted-for uncertainties.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Unrealized Global Temperature Increase: Implications of Current Uncertainties

Unrealized increase in global mean surface air temperature (GMST) may result from the climate system not being in steady state with forcings and/or from cessation of negative aerosol forcing that would result from decreases in emissions. An observation-constrained method is applied to infer the dependence of Earth's climate sensitivity on forcing by anthropogenic aerosols within the uncertainty on that forcing given by the Fifth (2013) Assessment Report of the Intergovernmental Panel on Climate Change. Within these uncertainty ranges the increase in GMST due to temperature lag for future forcings held constant is slight (0.09–0.19 K over 20 years; 0.12–0.26 K over 100 years). However the incremental increase in GMST that would result from a hypothetical abrupt cessation of sources of aerosols could be quite large, but is highly uncertain, 0.1–1.3 K over 20 years. Decrease in CO2 abundance and forcing following abrupt cessation of emissions would offset these increases in GMST over 100 years by as little as 0.09 K to as much as 0.8 K. The uncertainties quantified here greatly limit confidence in projections of change in GMST that would result from any strategy for future reduction of emissions.

54 ENVIRONMENTAL SCIENCES↗