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At least 433 records · Page 24

The Patterson function as auto-hologram and graph enables the direct solution to the phase problem for coherently illuminated atomistic structures

Abstract The coherent Patterson function, derived from the coherent scattering intensities from N atoms, can be described as an auto-holographic image, i.e., the superposition of N -holographic images in which each atom serves as the source of a different reference wave, and as a mathematical graph of the unknown structure. These insights indicate that the unknown structure is significantly over-determined by the inherent information content in a Patterson function by a factor of ( N − 1)/2 (for non-degenerate structures), independent of dimensionality. However, we also show that the ability to resolve the distinct features in the Patterson function depends strongly on details of the experimental design (data range, sampling frequency, and dimensionality). This re-interpretation suggests that the coherent Patterson function provides a natural context for describing the information content in coherent scattering, reveals that there is no inherent phase problem for coherently illuminated pointwise structures, and enables the design of an algorithm which retrieves the structure directly from the Patterson function, without using error metric minimization.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Do-calculus enables estimation of causal effects in partially observed biomolecular pathways

Abstract Motivation Estimating causal queries, such as changes in protein abundance in response to a perturbation, is a fundamental task in the analysis of biomolecular pathways. The estimation requires experimental measurements on the pathway components. However, in practice many pathway components are left unobserved (latent) because they are either unknown, or difficult to measure. Latent variable models (LVMs) are well-suited for such estimation. Unfortunately, LVM-based estimation of causal queries can be inaccurate when parameters of the latent variables are not uniquely identified, or when the number of latent variables is misspecified. This has limited the use of LVMs for causal inference in biomolecular pathways. Results In this article, we propose a general and practical approach for LVM-based estimation of causal queries. We prove that, despite the challenges above, LVM-based estimators of causal queries are accurate if the queries are identifiable according to Pearl’s do-calculus and describe an algorithm for its estimation. We illustrate the breadth and the practical utility of this approach for estimating causal queries in four synthetic and two experimental case studies, where structures of biomolecular pathways challenge the existing methods for causal query estimation. Availability and implementation The code and the data documenting all the case studies are available at https://github.com/srtaheri/LVMwithDoCalculus. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

Depth-resolved Laue microdiffraction with coded apertures

A rapid data acquisition and reconstruction method is introduced to image the crystalline structure of materials and the associated strain and orientations at micrometre resolution using Laue diffraction. The method relies on scanning a coded aperture across the diffracted X-ray beam from broadband illumination and a reconstruction algorithm to resolve Laue microdiffraction patterns as a function of depth along the incident illumination path. It provides rapid access to full diffraction information for sub-micrometre volume elements in bulk materials. Both the theory and the experimental validation of this imaging approach are presented in this report.

36 MATERIALS SCIENCE↗

Homomorphic Encryption for Machine Learning and Artificial Intelligence Applications

Third-party and expert analysis is a cost-effective solution for solving specialized problems or processing large datasets related to reactor structural health monitoring and nondestructive evaluation. However, when handling proprietary information, third-party and expert analysts pose a privacy risk. To address this challenge, Homomorphic Encryption (HE) permits arithmetic operations on encrypted data without exposing the underlying data. Implementations of Machine Learning (ML) and Artificial Intelligence (AI) algorithms using HE greatly enhances the capabilities of third-party analysts while maintaining a low security risk. This paper details current success in applying Principal Component Analysis (PCA) and Fully Connected Neural Networks (NN) using the Microsoft SEAL implementation of the popular CKKS Fully Homomorphic Encryption (FHE) algorithm. The MNIST Handwritten Dataset is analyzed as a proof-of-concept demonstration of the implementations.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Macromolecular phasing using diffraction from multiple crystal forms

A phasing algorithm for macromolecular crystallography is proposed that utilizes diffraction data from multiple crystal forms – crystals of the same molecule with different unit-cell packings (different unit-cell parameters or space-group symmetries). The approach is based on the method of iterated projections, starting with no initial phase information. The practicality of the method is demonstrated by simulation using known structures that exist in multiple crystal forms, assuming some information on the molecular envelope and positional relationships between the molecules in the different unit cells. With incorporation of new or existing methods for determination of these parameters, the approach has potential as a method for ab initio phasing.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

How much information on precipitation is contained in satellite infrared imagery?

Satellite infrared (IR) brightness temperature providing information on the characteristics of cloud tops is one of the primary input data used for estimating precipitation from satellites. Thus, the natural questions to ask are: Does IR imagery contain more information about precipitation in some regions more than others? What are the factors that lead to such differences? Should we expect the amount of information provided by IR imagery to change with respect to temporal or spatial aggregation? Comprehensive analysis of the accuracy of satellite-based precipitation estimates obtained from any given algorithm may provide qualitative answers to the above questions. However, such an approach only offers conclusions within the limited context of the algorithm used to obtain precipitation estimates; that is, patterns caused by the inherent information content of IR imagery are inextricable from those induced by assumptions embedded in the precipitation estimation algorithm. Here, we address the abovementioned questions from a different perspective using an information-theoretic measure, free of structural assumptions and general to a wide range of relationships, to characterize the average and seasonal dependence between IR imagery provided by satellite sensors in the spectral range (10.7–11.5 μm) and precipitation rates in the contiguous United States (CONUS) across distinct temporal and spatial scales. We analyze a total of more than 1.3 billion pairs of IR and precipitation observations over CONUS, and we observe interesting patterns. First, we show that there is a strong inverse relationship (ρ = - 0.73) between the information content of IR data and the number of no-rain observations; however, its robustness varies regionally and seasonally with less significant correlation during the warm season. Second, we demonstrate that the intuitive relationship of increasing dependence between IR and precipitation as a result of temporal or spatial aggregation exhibits a diminishing returns behavior. For instance, temporal aggregation from 1 to 3 h increases the dependence approximately 7 times as much as temporal aggregation from 12 to 24 h. Furthermore, we quantitatively examine and re-confirm several statements previously reported in the literature such as the strong association between IR and precipitation in convective storms and the low association in orographic rainfall. Finally, we conclude by illustrating the potential of the analysis in diagnosis of operational algorithms for estimating precipitation from IR brightness temperature. The findings of this study pinpoint spatial domains and time scales at which IR is not an adequate proxy for estimating precipitation. Thus, they can potentially guide the development of operational algorithms that utilize satellite Infrared imagery for estimating, downscaling and data fusion of precipitation. Finally, the analysis presented here opens up the possibility of developing new methodologies for diagnosis of satellite-based precipitation estimation algorithms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Hierarchical Analysis of Halo Center in Cosmology

Ever-increasing data size raises many challenges for scientific data analysis. Particularly in cosmological N-body simulation, finding the center of a dark matter halo suffers heavily from the large computational cost associated with the large number of particles (up to 20 million). In this work, we exploit the latent structure embed in a halo, and we propose a hierarchical approach to approximate the exact gravitational potential calculation for each particle in order to more efficiently find the halo center. Tests of our method on data from N-body simulations show that in many cases the hierarchical algorithm performs significantly faster than existing methods with a desirable accuracy.

97 MATHEMATICS AND COMPUTING↗

Multi-reward Reinforcement Learning Based Bond-Order Potential to Study Strain-Assisted Phase Transitions in Phosphorene

Here, we introduce a multi-reward reinforcement learning (RL) approach to train a flexible bond-order potential (BOP) for 2D phosphorene based on ab initio training data sets. Our approach is based on a continuous action space Monte Carlo tree search algorithm that is general and scalable and presents an efficient multiobjective optimization scheme for high-dimensional materials design problems. As a proof-of-concept, we deploy this scheme to parametrize multiple structural and dynamical properties of 2D phosphorene polymorphs. Our RL-trained BOP model adequately captures the structure, energetics, transformation barriers, equation of state, elastic constants, and phonon dispersions of various 2D P polymorphs. We use this model to probe the impact of temperature and strain rate on the phase transition from black (α-P) to blue phosphorene (β-P) through molecular dynamics simulations. A decrease in critical strain for this phase transition with increase in temperature is observed, and the underlying atomistic mechanisms are discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Performance Comparison of Machine Learning Models for Ultrasonic Nondestructive Evaluation of Alkali-Silica Reaction in Concrete

Alkali-silica reaction (ASR) causes concrete degradation, leading to cracking, rebar corrosion, and reduced structural integrity, which raises safety concerns. Ultrasonic nondestructive evaluation (NDE) effectively assesses concrete properties and monitors ASR progression. However, its deployment and analysis require specialized expertise and subjective interpretation. As computational power increases, artificial intelligence (AI) and machine learning (ML) algorithms are increasingly being used to automate NDE data analysis across various industries for AI-assisted automation. Regulatory agencies are adapting to this technological shift, prompting a need to evaluate current ML technologies’ capabilities and limitations in assessing concrete material properties and damage. This report presents a comparative analysis of four ML regression models for predicting concrete material damage induced by ASR expansion using long-term ultrasonic data monitoring. The models investigated include linear regression (LR), support vector regression (SVR), shallow neural networks (NN), and deep neural networks (DNN). LR, SVR, and shallow NN models use features extracted from ultrasonic signals, whereas the DNN model processes time-domain ultrasonic signals and frequency spectra directly. The study systematically compared the models’ performance from various perspectives, including model input, prediction performance, and generalization ability. The findings indicate significant variability in model performance, with some ML algorithms achieving very high or very low prediction accuracy depending on the preprocessing and feature engineering (extraction and selection) applied. Key insights include the observation that shallow ML models (LR, SVR, and shallow NNs) require meticulous preprocessing and feature extraction to achieve high accuracy. In contrast, the DNN model, although it bypasses the need for feature engineering, necessitates extensive preprocessing to mitigate noise and computational demands. The SVR model emerged as the top performer among the shallow models, and the DNN model exhibited superior performance on specific datasets but struggled with generalization across specimens from different batches. Additionally, the SVR model is sensitive to temperature variations, whereas the DNN model is robust in this regard. Using recurrent neural networks is recommended for future ASR expansion prediction studies. Recurrent neural networks’ inherent ability to capture temporal dependencies and long-term patterns makes them well suited for analyzing sequential ultrasonic monitoring data. Overall, the results and conclusions of this study could provide insights into the capabilities and effectiveness of ML when applied to ultrasonic NDE data and help identify best practices for using ML for ultrasonic NDE of concrete material properties.

36 MATERIALS SCIENCE↗

Reinforcement Learning-based Output Structured Feedback for Distributed Multi-Area Power System Frequency Control

Load frequency control (LFC) is a key factor to maintain the stable frequency in multi-area power systems. As the modern power systems evolve from centralized to decentralized paradigm, LFC needs to consider the decentralized scheme that considers limited information from the information-exchange graph for the generator control of each interconnected area. This paper aims to solve a data-driven constrained LQR problem with mean-variance risk constraints and output structured feedback, and applies this framework to solve the LFC problem in multi-area power systems. By reformulating the constrained optimization problem into a minimax problem, the stochastic gradient descent max-oracle (SGDmax) algorithm with zero-order policy gradient (ZOPG) is adopted to find the optimal feedback gain from the learning, while guaranteeing the convergence. In addition, to improve the adaptation of the proposed learning method to new or varying models, we construct an emulator grid that approximates the dynamics of a physical grid and performs training based on this model. Once the feedback gain is obtained from the emulator grid, it is applied to the physical grid with a robustness test to check whether the controller from the approximated emulator applies to the actual system. Numerical tests show that the obtained feedback controller can successfully control the frequency of each area, while mitigating the uncertainty from the loads, with reliable robustness that ensures the adaptability of the obtained feedback gain to the actual physical grid.

Kwon, Kyung-bin↗

Bayesian chain graph models to characterize microbe-environment dynamics

Microbiome data require statistical models that can simultaneously decode microbes' reaction to the environment and interactions among microbes. While a multiresponse linear regression model seems like a straight-forward solution, we argue that treating it as a graphical model is problematic given that the regression coefficient matrix does not encode the conditional dependence structure between response and predictor nodes. This observation is especially important in biological settings when we have prior knowledge on the edges from specific experimental interventions that can only be properly encoded under a conditional dependence model. Here, we propose a chain graph model with two sets of nodes (predictors and responses) whose solution yields a graph with edges that indeed represent conditional dependence, thus agreeing with the experimenter's intuition on the average behavior of nodes under treatment. The solution to our model is sparse via the Bayesian linear regression (LASSO). In addition, we propose an adaptive extension so that different shrinkages can be applied to different edges to incorporate edge-specific prior knowledge. Our model is computationally inexpensive through an efficient Gibbs sampling algorithm and can account for binary, counting, and compositional responses via an appropriate hierarchical structure. We test the performance of our model in a variety of simulated datasets, thereby showing superior performance to state-of-the-art approaches. We further apply our model to human gut and soil microbial compositional datasets, and we highlight that CG-LASSO can estimate biologically meaningful network structures in the data.

compositional data↗

The parallelism motifs of genomic data analysis

Genomic datasets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share these data with the research community, but some of these genomic data analysis problems require large-scale computational platforms to meet both the memory and computational requirements. These applications differ from scientific simulations that dominate the workload on high-end parallel systems today and place different requirements on programming support, software libraries and parallel architectural design. For example, they involve irregular communication patterns such as asynchronous updates to shared data structures. We consider several problems in high-performance genomics analysis, including alignment, profiling, clustering and assembly for both single genomes and metagenomes. We identify some of the common computational patterns or ‘motifs’ that help inform parallelization strategies and compare our motifs to some of the established lists, arguing that at least two key patterns, sorting and hashing, are missing. This article is part of a discussion meeting issue ‘Numerical algorithms for high-performance computational science’.

59 BASIC BIOLOGICAL SCIENCES↗

Energy landscapes from cryo-EM snapshots: a benchmarking study

Abstract Biomolecules undergo continuous conformational motions, a subset of which are functionally relevant. Understanding, and ultimately controlling biomolecular function are predicated on the ability to map continuous conformational motions, and identify the functionally relevant conformational trajectories. For equilibrium and near-equilibrium processes, function proceeds along minimum-energy pathways on one or more energy landscapes, because higher-energy conformations are only weakly occupied. With the growing interest in identifying functional trajectories, the need for reliable mapping of energy landscapes has become paramount. In response, various data-analytical tools for determining structural variability are emerging. A key question concerns the veracity with which each data-analytical tool can extract functionally relevant conformational trajectories from a collection of single-particle cryo-EM snapshots. Using synthetic data as an independently known ground truth, we benchmark the ability of four leading algorithms to determine biomolecular energy landscapes and identify the functionally relevant conformational paths on these landscapes. Such benchmarking is essential for systematic progress toward atomic-level movies of continuous biomolecular function.

59 BASIC BIOLOGICAL SCIENCES↗

Discovery of structure–property relations for molecules via hypothesis-driven active learning over the chemical space

The discovery of the molecular candidates for application in drug targets, biomolecular systems, catalysts, photovoltaics, organic electronics, and batteries necessitates the development of machine learning algorithms capable of rapid exploration of chemical spaces targeting the desired functionalities. Here, we introduce a novel approach for active learning over the chemical spaces based on hypothesis learning. We construct the hypotheses on the possible relationships between structures and functionalities of interest based on a small subset of data followed by introducing them as (probabilistic) mean functions for the Gaussian process. This approach combines the elements from the symbolic regression methods, such as SISSO and active learning, into a single framework. The primary focus of constructing this framework is to approximate physical laws in an active learning regime toward a more robust predictive performance, as traditional evaluation on hold-out sets in machine learning does not account for out-of-distribution effects which may lead to a complete failure on unseen chemical space. Here, we demonstrate it for the QM9 dataset, but it can be applied more broadly to datasets from both domains of molecular and solid-state materials sciences.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Autonomous Sensor System for Wind Turbine Blade Collision Detection

This paper presents an automated blade collision detection system for use on wind turbines, toward the goal of supporting monitoring and quantitative assessment of wind energy impacts on wildlife. A wireless, multisensor module mounted at the blade root measures surface vibrations, and a blade-mounted camera provides image capture of colliding objects. Using sensor data recorded during field testing of the system on an operational wind turbine, we present the development, training, and testing of automated detection algorithms for collision detection using machine-learning approaches. In particular, we compare the use of a new two-step, anomaly-based classification algorithm with conventional adaptive boosting and amplitude-based detection techniques, where the two-step approach improves average precision for the experimental data set. This integrated sensor and classification systems demonstrates a new approach for automated, on-blade collision detection for wind turbines, with broad utility across structural health monitoring applications.

17 WIND ENERGY↗

A Transformational Natural Gas Fueled Dynamic SOFC for Data Center in-Rack Power (Final Technical Report)

Data centers consume 250TWh or 1% of global electricity use in 2019. This electricity demand is expected to grow exponentially in the future. The current data center power supply relies on electric grids with diesel engines and batteries as backup; the latter is critically important because a sudden loss of power could erase crucial data, causing catastrophic economic loss. However, such a double protection architecture is costly, inefficient and polluting. In search for better in-rack power system, fuel-cell based generators have recently emerged as a promising alternative to diesel engines and batteries because of its potential to be more cost-effective, more efficient and less polluting. Among many types of fuel cells, solid oxide fuel cells stand out to be a front runner because of their ability to directly operate on natural gas that has an existing infrastructure. However, there are several critical challenges facing SOFC generators to meet the rigorous power requirements of data centers: high cost, poor reliability and more importantly, slow response to the datacenters’ dynamic load change. The unexpected overload conditions in data centers can cause fuel starvation; the latter can initiate microcracks in the anode structure, thus jeopardizing the lifetime of the SOFC generator. The current efforts to increase transient power capabilities of traditional SOFCs and therefore protect SOFC stacks from internal damage during transient loading, rely primarily upon mathematical algorithms. One of the challenges to these control methodologies is the physical limitations of the fuel delivery system such as slow response of mass flow controllers to fast power demand.

30 DIRECT ENERGY CONVERSION↗

Multiresolution GPC-Structured Control of a Single-Loop Cold-Flow Chemical Looping Testbed

Chemical looping is a near-zero emission process for generating power from coal. It is based on a multi-phase gas-solid flow and has extremely challenging nonlinear, multi-scale dynamics with jumps, producing large dynamic model uncertainty, which renders traditional robust control techniques, such as linear parameter varying H ∞ design, largely inapplicable. This process complexity is addressed in the present work through the temporal and the spatiotemporal multiresolution modeling along with the corresponding model-based control laws. Namely, the nonlinear autoregressive with exogenous input model structure, nonlinear in the wavelet basis, but linear in parameters, is used to identify the dominant temporal chemical looping process dynamics. The control inputs and the wavelet model parameters are calculated by optimizing a quadratic cost function using a gradient descent method. The respective identification and tracking error convergence of the proposed self-tuning identification and control schemes, the latter using the unconstrained generalized predictive control structure, is separately ascertained through the Lyapunov stability theorem. The rate constraint on the control signal in the temporal control law is then imposed and the control topology is augmented by an additional control loop with self-tuning deadbeat controller which uses the spatiotemporal wavelet riser dynamics representation. The novelty of this work is three-fold: (1) developing the self-tuning controller design methodology that consists in embedding the real-time tunable temporal highly nonlinear, but linearly parametrizable, multiresolution system representations into the classical rate-constrained generalized predictive quadratic optimal control structure, (2) augmenting the temporal multiresolution loop by a more complex spatiotemporal multiresolution self-tuning deadbeat control loop, and (3) demonstrating the effectiveness of the proposed methodology in producing fast recursive real-time algorithms for controlling highly uncertain nonlinear multiscale processes. The latter is shown through the data from the implemented temporal and augmented spatiotemporal solutions of a difficult chemical looping cold flow tracking control problem.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A massively parallel and scalable multi-CPU material point method

Harnessing the power of modern multi-GPU architectures, we present a massively parallel simulation system based on the Material Point Method (MPM) for simulating physical behaviors of materials undergoing complex topological changes, self-collision, and large deformations. Our system makes three critical contributions. First, we introduce a new particle data structure that promotes coalesced memory access patterns on the GPU and eliminates the need for complex atomic operations on the memory hierarchy when writing particle data to the grid. Second, we propose a kernel fusion approach using a new Grid-to-Particles-to-Grid (G2P2G) scheme, which efficiently reduces GPU kernel launches, improves latency, and significantly reduces the amount of global memory needed to store particle data. Finally, we introduce optimized algorithmic designs that allow for efficient sparse grids in a shared memory context, enabling us to best utilize modern multi-GPU computational platforms for hybrid Lagrangian-Eulerian computational patterns. We demonstrate the effectiveness of our method with extensive benchmarks, evaluations, and dynamic simulations with elastoplasticity, granular media, and fluid dynamics. In comparisons against an open-source and heavily optimized CPU-based MPM codebase [Fang et al. 2019] on an elastic sphere colliding scene with particle counts ranging from 5 to 40 million, our GPU MPM achieves over 100x per-time-step speedup on a workstation with an Intel 8086K CPU and a single Quadro P6000 GPU, exposing exciting possibilities for future MPM simulations in computer graphics and computational science. Moreover, compared to the state-of-the-art GPU MPM method [Hu et al. 2019a], we not only achieve 2x acceleration on a single GPU but our kernel fusion strategy and Array-of-Structs-of-Array (AoSoA) data structure design also generalizes to multi-GPU systems. Our multi-GPU MPM exhibits near-perfect weak and strong scaling with 4 GPUs, enabling performant and large-scale simulations on a 10243 grid with close to 100 million particles with less than 4 minutes per frame on a single 4-GPU workstation and 134 million particles with less than 1 minute per frame on an 8-GPU workstation.

Wang, Xinlei↗