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At least 361 records · Page 20

An finite element analysis surrogate model with boundary oriented graph embedding approach for rapid design

Abstract In this work, we present a boundary oriented graph embedding (BOGE) approach for the graph neural network to assist in rapid design and digital prototyping. The cantilever beam problem has been solved as an example to validate its potential of providing physical field results and optimized designs using only 10 ms. Providing shortcuts for both boundary elements and local neighbor elements, the BOGE approach can embed unstructured mesh elements into the graph and performs an efficient regression on large-scale triangular-mesh-based finite element analysis (FEA) results, which cannot be realized by other machine-learning-based surrogate methods. It has the potential to serve as a surrogate model for other boundary value problems. Focusing on the cantilever beam problem, the BOGE approach with 3-layer DeepGCN model achieves the regression with mean square error (MSE) of 0.011 706 (2.41% mean absolute percentage error) for stress field prediction and 0.002 735 MSE (with 1.58% elements having error larger than 0.01) for topological optimization. The overall concept of the BOGE approach paves the way for a general and efficient deep-learning-based FEA simulator that will benefit both industry and Computer Aided Design (CAD) design-related areas.

42 ENGINEERING↗

Noise Robustness and Experimental Demonstration of a Quantum Generative Adversarial Network for Continuous Distributions

Abstract The potential advantage of machine learning in quantum computers is a topic of intense discussion in the literature. Theoretical, numerical, and experimental explorations will most likely be required to understand its power. There have been different algorithms proposed to exploit the probabilistic nature of variational quantum circuits for generative modeling. In this paper, a hybrid architecture for quantum generative adversarial networks (QGANs) is employed and their robustness in the presence of noise is studied. A simple way of adding different types of noise to the quantum generator circuit is devised, and the noisy hybrid QGANs (HQGANs) are simulated numerically to learn continuous probability distributions, and to show that the performance of HQGANs remains unaffected. The effect of different parameters on the training time is also investigated to reduce the computational scaling of the algorithm and simplify its deployment on a quantum computer. The training on Rigetti's Aspen‐4‐2Q‐A quantum processing unit is then performed, and the results from the training are presented. The authors' results pave the way for experimental exploration of different quantum machine learning algorithms on noisy intermediate‐scale quantum devices.

Anand, Abhinav↗

Navigating the Noise: Bringing Clarity to ML Parameterization Design With O $\boldsymbol{\mathcal{O}}$(100) Ensembles

Abstract Machine‐learning (ML) parameterizations of subgrid processes (here of turbulence, convection, and radiation) may one day replace conventional parameterizations by emulating high‐resolution physics without the cost of explicit simulation. However, uncertainty about the relationship between offline and online performance (i.e., when integrated with a large‐scale general circulation model) hinders their development. Much of this uncertainty stems from limited sampling of the noisy, emergent effects of upstream ML design decisions on downstream online hybrid simulation. Our work rectifies the sampling issue via the construction of a semi‐automated, end‐to‐end pipeline for size ensembles of hybrid simulations, revealing important nuances in how systematic reductions in offline error manifest in changes to online error and online stability. For example, removing dropout and switching from a Mean Squared Error to a Mean Absolute Error loss both reduce offline error, but they have opposite effects on online error and online stability. Other design decisions, like incorporating memory, converting moisture input from specific humidity to relative humidity, using batch normalization, and training on multiple climates do not come with any such compromises. Finally, we show that ensemble sizes of may be necessary to reliably detect causally relevant differences online. By enabling rapid online experimentation at scale, we can empirically settle debates regarding subgrid ML parameterization design that would have otherwise remained unresolved in the noise.

Lin, Jerry [Department of Earth System Sciences Un↗

Using a physics-informed neural network and fault zone acoustic monitoring to predict lab earthquakes

Abstract Predicting failure in solids has broad applications including earthquake prediction which remains an unattainable goal. However, recent machine learning work shows that laboratory earthquakes can be predicted using micro-failure events and temporal evolution of fault zone elastic properties. Remarkably, these results come from purely data-driven models trained with large datasets. Such data are equivalent to centuries of fault motion rendering application to tectonic faulting unclear. In addition, the underlying physics of such predictions is poorly understood. Here, we address scalability using a novel Physics-Informed Neural Network (PINN). Our model encodes fault physics in the deep learning loss function using time-lapse ultrasonic data. PINN models outperform data-driven models and significantly improve transfer learning for small training datasets and conditions outside those used in training. Our work suggests that PINN offers a promising path for machine learning-based failure prediction and, ultimately for improving our understanding of earthquake physics and prediction.

42 ENGINEERING↗

Fast and accurate machine learning prediction of phonon scattering rates and lattice thermal conductivity

Abstract Lattice thermal conductivity is important for many applications, but experimental measurements or first principles calculations including three-phonon and four-phonon scattering are expensive or even unaffordable. Machine learning approaches that can achieve similar accuracy have been a long-standing open question. Despite recent progress, machine learning models using structural information as descriptors fall short of experimental or first principles accuracy. This study presents a machine learning approach that predicts phonon scattering rates and thermal conductivity with experimental and first principles accuracy. The success of our approach is enabled by mitigating computational challenges associated with the high skewness of phonon scattering rates and their complex contributions to the total thermal resistance. Transfer learning between different orders of phonon scattering can further improve the model performance. Our surrogates offer up to two orders of magnitude acceleration compared to first principles calculations and would enable large-scale thermal transport informatics.

36 MATERIALS SCIENCE↗

An adaptive approach to machine learning for compact particle accelerators

Abstract Machine learning (ML) tools are able to learn relationships between the inputs and outputs of large complex systems directly from data. However, for time-varying systems, the predictive capabilities of ML tools degrade if the systems are no longer accurately represented by the data with which the ML models were trained. For complex systems, re-training is only possible if the changes are slow relative to the rate at which large numbers of new input-output training data can be non-invasively recorded. In this work, we present an approach to deep learning for time-varying systems that does not require re-training, but uses instead an adaptive feedback in the architecture of deep convolutional neural networks (CNN). The feedback is based only on available system output measurements and is applied in the encoded low-dimensional dense layers of the encoder-decoder CNNs. First, we develop an inverse model of a complex accelerator system to map output beam measurements to input beam distributions, while both the accelerator components and the unknown input beam distribution vary rapidly with time. We then demonstrate our method on experimental measurements of the input and output beam distributions of the HiRES ultra-fast electron diffraction (UED) beam line at Lawrence Berkeley National Laboratory, and showcase its ability for automatic tracking of the time varying photocathode quantum efficiency map. Our method can be successfully used to aid both physics and ML-based surrogate online models to provide non-invasive beam diagnostics.

97 MATHEMATICS AND COMPUTING↗

Cellular Decomposition Based Hybrid-Hierarchical Control Systems with Applications to Flight Management Systems

The work in this research project has been focused on the construction of a hierarchical hybrid control theory which is applicable to flight management systems. The motivation and underlying philosophical position for this work has been that the scale, inherent complexity and the large number of agents (aircraft) involved in an air traffic system imply that a hierarchical modelling and control methodology is required for its management and real time control. In the current work the complex discrete or continuous state space of a system with a small number of agents is aggregated in such a way that discrete (finite state machine or supervisory automaton) controlled dynamics are abstracted from the system's behaviour. High level control may then be either directly applied at this abstracted level, or, if this is in itself of significant complexity, further layers of abstractions may be created to produce a system with an acceptable degree of complexity at each level. By the nature of this construction, high level commands are necessarily realizable at lower levels in the system.

Caines, P. E.↗

Overcoming sparse datasets with multi-task learning as applied to high entropy alloys

Abstract The design of novel High Entropy Alloys for use in high-temperature applications is an area of active interest due to their potential to provide exceptional properties compared to conventional alloys. Since the increased popularity of machine learning, an important cog in the design process has been training surrogate models on alloy properties. However, these Single-Task models are trained on individual mechanical properties and do not take advantage of the relatedness between properties. Multi-Task models can capture the interdependencies between tasks, leading to potentially more accurate predictions for all tasks. In this paper, we investigate if Multi-Task models can show improvement over Single-Task models when used for predicting the mechanical properties of these alloys. To ensure fair evaluation between the models, we apply L 0 regularization and skip connections to the models, which allows them to adjust the number of model parameters and depth for optimal performance. We find that the Multi-Task models can leverage task relationships to perform better than Single-Task models, especially for high amounts of missing data in the tasks. Furthermore, adding simple auxiliary targets can boost Multi-Task performance even further despite not being effective as input descriptors to single-task models themselves. We anticipate that the proposed strategies can achieve more accurate predictions and consequently enable better design capabilities for such data-constrained domains without incurring much additional computational cost.

Debnath, Arindam (ORCID:0000000194274499)↗

Predictive models of the genetic bases underlying budding yeast fitness in multiple environments

Abstract The ability of organisms to adapt and survive depends on the effects of genes and the environment on fitness. However, the multigenic nature of fitness and genotype-by-environment interactions hinder our understanding of the genetic basis of fitness. Here, we established fitness prediction models for 35 environments using machine learning and existing fitness data and different genetic variant types for a Saccharomyces cerevisiae population. Models revealed that the predictive ability of genetic variants varied across environments, with copy number variants explaining the majority of fitness variation in most cases. Model interpretation showed that different variant types identified distinct gene sets associated with predictive variants. These gene sets were significantly enriched in experimentally validated genes affecting fitness in only a subset of environments, indicating that many genes influencing fitness remain unexplored. Notably, non-experimentally validated genes were more important than validated ones for fitness predictions. Gene contributions to predictions were both isolate- and environment-dependent, pointing to gene-by-gene and gene-by-environment interactions. Furthermore, models uncovered experimentally validated and novel candidate genetic interactions for a well-characterized stress, the fungicide benomyl. These findings highlight the feasibility of identifying the genetic basis of fitness by using different genetic variant types and offer novel targets for future functional analysis.

DNA copy number variations↗

Predicting the oxidation states of Mn ions in the oxygen-evolving complex of photosystem II using supervised and unsupervised machine learning

Abstract Serial Femtosecond Crystallography at the X-ray Free Electron Laser (XFEL) sources enabled the imaging of the catalytic intermediates of the oxygen evolution reaction of Photosystem II (PSII). However, due to the incoherent transition of the S-states, the resolved structures are a convolution from different catalytic states. Here, we train Decision Tree Classifier and K-means clustering models on Mn compounds obtained from the Cambridge Crystallographic Database to predict the S-state of the X-ray, XFEL, and CryoEM structures by predicting the Mn’s oxidation states in the oxygen-evolving complex. The model agrees mostly with the XFEL structures in the dark S 1 state. However, significant discrepancies are observed for the excited XFEL states (S 2 , S 3, and S 0 ) and the dark states of the X-ray and CryoEM structures. Furthermore, there is a mismatch between the predicted S-states within the two monomers of the same dimer, mainly in the excited states. We validated our model against other metalloenzymes, the valence bond model and the Mn spin densities calculated using density functional theory for two of the mismatched predictions of PSII. The model suggests designing a more optimized sample delivery and illumiation systems are crucial to precisely resolve the geometry of the advanced S-states to overcome the noncoherent S-state transition. In addition, significant radiation damage is observed in X-ray and CryoEM structures, particularly at the dangler Mn center (Mn4). Our model represents a valuable tool for investigating the electronic structure of the catalytic metal cluster of PSII to understand the water splitting mechanism.

Plant Sciences↗

A review of artificial intelligence applications in manufacturing operations

Abstract Artificial intelligence (AI) and machine learning (ML) can improve manufacturing efficiency, productivity, and sustainability. However, using AI in manufacturing also presents several challenges, including issues with data acquisition and management, human resources, infrastructure, as well as security risks, trust, and implementation challenges. For example, getting the data needed to train AI models can be difficult for rare events or costly for large datasets that need labeling. AI models can also pose security risks when integrated into industrial control systems. In addition, some industry players may be hesitant to use AI due to a lack of trust or understanding of how it works. Despite these challenges, AI has the potential to be extremely helpful in manufacturing, particularly in applications such as predictive maintenance, quality assurance, and process optimization. It is important to consider the specific needs and capabilities of each manufacturing scenario when deciding whether and how to use AI in manufacturing. This review identifies current developments, challenges, and future directions in AI/ML relevant to manufacturing, with the goal of improving understanding of AI/ML technologies available for solving manufacturing problems, providing decision‐support for prioritizing and selecting appropriate AI/ML technologies, and identifying areas where further research can yield transformational returns for the industry. Early experience suggests that AI/ML can have significant cost and efficiency benefits in manufacturing, especially when combined with the ability to capture enormous amounts of data from manufacturing systems.

Plathottam, Siby Jose↗

The Phenix‐AlphaFold webservice: Enabling AlphaFold predictions for use in Phenix

Abstract Advances in machine learning have enabled sufficiently accurate predictions of protein structure to be used in macromolecular structure determination with crystallography and cryo‐electron microscopy data. The Phenix software suite has AlphaFold predictions integrated into an automated pipeline that can start with an amino acid sequence and data, and automatically perform model‐building and refinement to return a protein model fitted into the data. Due to the steep technical requirements of running AlphaFold efficiently, we have implemented a Phenix‐AlphaFold webservice that enables all Phenix users to run AlphaFold predictions remotely from the Phenix GUI starting with the official 1.21 release. This webservice will be improved based on how it is used by the research community and the future research directions for Phenix.

Poon, Billy K.↗

Machine learning nonequilibrium electron forces for spin dynamics of itinerant magnets

Abstract We present a generalized potential theory for conservative as well as nonconservative forces for the Landau-Lifshitz magnetization dynamics. Importantly, this formulation makes possible an elegant generalization of the Behler-Parrinello machine learning (ML) approach, which is a cornerstone of ML-based quantum molecular dynamics methods, to the modeling of force fields in adiabatic spin dynamics of out-of-equilibrium itinerant magnetic systems. We demonstrate our approach by developing a deep-learning neural network that successfully learns the electron-mediated exchange fields in a driven s-d model computed from the nonequilibrium Green’s function method. We show that dynamical simulations with forces predicted from the neural network accurately reproduce the voltage-driven domain-wall propagation. Our work also lays the foundation for ML modeling of spin transfer torques and opens a avenue for ML-based multi-scale modeling of nonequilibrium dynamical phenomena in itinerant magnets and spintronics.

36 MATERIALS SCIENCE↗

Software for Checking Statecharts

HiVy is a software tool set that enables verification through model checking of designs represented as finite-state machines or statecharts. HiVy provides automated translation of (1) statecharts created by use of the MathWorks Stateflow program to (2) Promela, the input language of the Spin model checker, which can then be used to verify, or trace logical errors in, distributed software systems. HiVy can operate directly on Stateflow models, or its abstract syntax of hierarchical sequential automata (HSA) can be used independently as an intermediate format for translation to Promela. In a typical design application, HiVy parses and reformats Stateflow model file data using the programs SfParse and sf2hsa, respectively. If the parsing effort is successful, an abstract syntax tree is delivered into a file named with the extension .hsa. If the design comprises several model files, they may be merged into one .hsa file before translation into Promela. Stateflow scope is preserved, and name clashes are avoided in the merge process. The HiVy program hsa2pr translates the model from the intermediate HSA format into Promela. Additionally, HiVy provides through translation a list of all statechart model propositions that are the means for formalizing linear temporal logic (LTL) properties about the model for Spin verification.

Pingree, Paula↗

A machine learning Automated Recommendation Tool for synthetic biology

Abstract Synthetic biology allows us to bioengineer cells to synthesize novel valuable molecules such as renewable biofuels or anticancer drugs. However, traditional synthetic biology approaches involve ad-hoc engineering practices, which lead to long development times. Here, we present the Automated Recommendation Tool (ART), a tool that leverages machine learning and probabilistic modeling techniques to guide synthetic biology in a systematic fashion, without the need for a full mechanistic understanding of the biological system. Using sampling-based optimization, ART provides a set of recommended strains to be built in the next engineering cycle, alongside probabilistic predictions of their production levels. We demonstrate the capabilities of ART on simulated data sets, as well as experimental data from real metabolic engineering projects producing renewable biofuels, hoppy flavored beer without hops, fatty acids, and tryptophan. Finally, we discuss the limitations of this approach, and the practical consequences of the underlying assumptions failing.

59 BASIC BIOLOGICAL SCIENCES↗

A novel random forest approach to revealing interactions and controls on chlorophyll concentration and bacterial communities during coastal phytoplankton blooms

Abstract Increasing occurrence of harmful algal blooms across the land–water interface poses significant risks to coastal ecosystem structure and human health. Defining significant drivers and their interactive impacts on blooms allows for more effective analysis and identification of specific conditions supporting phytoplankton growth. A novel iterative Random Forests (iRF) machine-learning model was developed and applied to two example cases along the California coast to identify key stable interactions: (1) phytoplankton abundance in response to various drivers due to coastal conditions and land-sea nutrient fluxes, (2) microbial community structure during algal blooms. In Example 1, watershed derived nutrients were identified as the least significant interacting variable associated with Monterey Bay phytoplankton abundance. In Example 2, through iRF analysis of field-based 16S OTU bacterial community and algae datasets, we independently found stable interactions of prokaryote abundance patterns associated with phytoplankton abundance that have been previously identified in laboratory-based studies. Our study represents the first iRF application to marine algal blooms that helps to identify ocean, microbial, and terrestrial conditions that are considered dominant causal factors on bloom dynamics.

59 BASIC BIOLOGICAL SCIENCES↗

USSR Space Life Sciences Digest, issue 25

This is the twenty-fifth issue of NASA's Space Life Sciences Digest. It contains abstracts of 42 journal papers or book chapters published in Russian and of 3 Soviet monographs. Selected abstracts are illustrated with figures and tables from the original. The abstracts in this issue have been identified as relevant to 26 areas of space biology and medicine. These areas include: adaptation, body fluids, botany, cardiovascular and respiratory systems, developmental biology, endocrinology, enzymology, equipment and instrumentation, exobiology, gravitational biology, habitability and environmental effects, human performance, immunology, life support systems, man-machine systems, mathematical modeling, metabolism, microbiology, musculoskeletal system, neurophysiology, nutrition, operational medicine, psychology, radiobiology, reproductive system, and space biology and medicine.

Hooke, Lydia Razran↗

Band gap predictions of double perovskite oxides using machine learning

Abstract The compositional and structural variety inherent to oxide perovskites spawn wide-ranging applications. In perovskites, the band gap E g , a key material parameter for these applications, can be optimally controlled by varying the composition. Here, we implement a hierarchical screening process in which two cross-validated and predictive machine learning models for band gap classification and regression, trained using exhaustive datasets that span 68 elements of the periodic table, are applied sequentially. The classification model separates wide band gap materials, with E g ≥ 0.5 eV, from materials which have zero or relatively small band gaps, namely E g < 0.5 eV, and the second regression model quantitatively predicts the gap value of the wide band gap compounds. The study down-selects 13,589 cubic oxide perovskite compositions that are predicted to be experimentally formable, thermodynamically stable, and have a wide band gap. Of these, a subset of 310 compounds, which are predicted to be stable and formable with a confidence greater than 90%, are identified for further investigation. Our models are methodically analyzed via performance metrics and inter-dependence of model features to gain physical insight into the band gap prediction problem. Design maps to identify the variation of band gap with substitution of different elements are also presented.

36 MATERIALS SCIENCE↗