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At least 343 records · Page 19

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↗

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↗

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↗

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↗

Effects of isoalcohol blending with gasoline on autoignition behavior in a rapid compression machine: Isopropanol and isobutanol

Alcohols, and particularly isoalcohols, are potentially advantageous blendstocks towards achieving efficient, low-carbon intensity internal combustion engines. Their use in advanced configurations, such as boosted spark-ignition or spark-assisted compression ignition, requires a comprehensive understanding of their blending effects on the low- and intermediate-temperature autoignition behavior of petroleum-derived gasoline. This work reports an experimental and modeling study of such autoignition characteristics quantified in a twin-piston rapid compression machine. Isopropanol and isobutanol are blended into a research-grade gasoline (FACE-F) at oxygenate blend levels of 0 to 30% vol/vol, with tests conducted at pressures of 20 and 40 bar, temperatures from 700 to 1000 K, and dilute stoichiometric fuel loadings. Changes to overall reactivity, including first-stage and main ignition times, and preliminary exothermicity are established, with comparisons made to previous measurements with ethanol-blended FACE-F gasoline. Furthermore, it is found that at low-temperature/NTC conditions (700–860 K) the isoalcohols suppress first-stage reactivity and associated heat release while main ignition times are extended. At NTC/intermediate-temperature (860–1000 K) conditions changes to fuel reactivity are less significant with isopropanol slightly suppressing reactivity and isobutanol promoting ignition. Detailed chemical kinetic modeling is used to interpret the experimental measurements. Overall trends of suppression or promotion in the blending behavior are reasonably captured by the model. Sensitivity and rate of production analyses indicate that at lower temperatures H-atom abstraction reactions from the surrogate fuel molecules (e.g., cyclopentane, isooctane) and the isoalcohols via OH are important leading to TC 3 H 6 OH and IC 4 H 8 OH–C radicals, for isopropanol and isobutanol respectively, which act as scavengers in the system. At higher temperatures, similar chemistries are dominant, but there is an increasing importance of abstraction by HO 2 . The kinetic modeling also indicates that the promoting effect of isobutanol at higher temperatures is due to the increased abstractions at the γ-sites, while at lower temperatures abstraction at the α-site leads to greater reactivity suppression.

36 MATERIALS SCIENCE↗

An improved detailed chemical kinetic model for C3-C4 linear and iso-alcohols and their blends with gasoline at engine-relevant conditions

Propanol and butanol isomers have received significant research attention as promising fuel additives or neat biofuels. Robust chemical kinetic models are needed that can provide accurate and efficient predictions of combustion performance across a wide range of engine relevant conditions. Herein, this study seeks to improve the understanding of ignition and combustion behavior of pure C3-C4 linear and iso-alcohols, and their blends with gasoline at engine-relevant conditions. In this work, a kinetic model with improved thermochemistry and reaction kinetics was developed based on recent theoretical calculations of H-atom abstraction and peroxy radical reaction rates. Kinetic model validations are reported, and the current model reproduces the ignition delay times of the C3 and C4 alcohols well. Variations in reactivity over a wide range of temperatures and other operating conditions are also well predicted by the current model. Recent ignition delay time measurements from a rapid compression machine of neat iso-propanol and iso-butanol [Cheng et al., Proc. Combust Inst. (2020)] and blends with a research grade gasoline [Goldsborough et al., Proc. Combust Inst. (2020)] at elevated pressure (20–40 bar) and intermediate temperatures (780–950 K) were used to demonstrate the accuracy of the current kinetic model at conditions relevant to boosted spark-ignition engines. The effects of alcohol blending with gasoline on the autoignition behavior are discussed. The current model captures the suppression of reactivity in the low-temperature and negative-temperature-coefficient (NTC) region when either isopropanol and isobutanol are added to a research grade gasoline. Sensitivity and reaction flux analysis were performed to provide insights into the relevant fuel chemistry of the C3-C4 alcohols.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Simulated Evaluation of Powder Flowability Through a Partially Obstructed Consumable in Blown Powder Directed Energy Deposition Systems

Abstract In the interest of continued industrialization of metal additive manufacturing in modern production environments, cost is often referenced as a primary deterrent to new adopters. Conventional economic models for additive systems, processes, and supply chains often focus on specific process applications with little generalizability, or they neglect significant costs associated with production such as machine maintenance and consumable part replacement. Compounding the latter issue are substantial knowledge gaps in consumable part wear characterization for additive and other convergent manufacturing systems. In coaxial blown powder directed energy deposition systems, gas atomized metal powder is wasted during material deposition at a rate that is partly dependent on present wear phenomena in a consumable nozzle housed in the cladding head assembly. The price and lead time required to replace the nozzle incentivizes its reuse even when visibly worn. Often this initiates a process quality decline in the form of underbuilt geometry and internal defects due to losses in powder catchment efficiency. While depositing H13 steel using a hybrid manufacturing machine tool equipped with such a deposition system, a unique partial clog with a bridge-like structure formed at the consumable nozzle exit when supporting argon gas flows failed mid-process. To further understand coaxial multi-phase powder flow in the event of support gas failure, a computational fluid dynamics simulation is tailored to relevant process parameters, H13 powder material profile, and machine operator observations collected after the incident. The resulting differences in powder flow compared to control gas flow parameters is presented and discussed. The powder flowability and performance of the clogged nozzle is then assessed by using an optical profilometer to extract the profile of the clog and recreate the clog geometry within the simulation environment. In past work this simulation has been experimentally validated for a 316L steel powder material profile and used specifically for analyzing powder stream geometry and catchment efficiency. After the initial powder flow characterization, the clog is removed, and the nozzle is reprofiled. After removing the obstructing clog, the newly unobstructed nozzle geometry, the original off the shelf nozzle geometry, and additional nozzle profiles exploring different consumable refurbishment strategies are reevaluated in the simulation. Powder catchment efficiency for all variant nozzle geometries and relevant flow variables are compared and discussed, along with potential mitigation strategies for optimizing powder flowability with worn consumables. This work expands on the known morphology of blown powder obstructions and wear defects present in consumable coaxial nozzles while discussing pragmatic simulation driven responses to unanticipated subsystem failure in hybrid manufacturing machining platforms.

DeWitte, Lisa↗

Insights into coordination and ligand trends of lanthanide complexes from the Cambridge Structural Database

Abstract Understanding lanthanide coordination chemistry can help develop new ligands for more efficient separation of lanthanides for critical materials needs. The Cambridge Structural Database (CSD) contains tens of thousands of single crystal structures of lanthanide complexes that can serve as a training ground for both fundamental chemical insights and future machine learning and generative artificial intelligence models. This work aims to understand the currently available structures of lanthanide complexes in CSD by analyzing the coordination shell, donor types, and ligand types, from the perspective of rare-earth element (REE) separations. We obtain four sets of lanthanide complexes from CSD: Subset 1, all Ln-containing complexes (49472 structures); Subset 2, mononuclear Ln complexes (27858 structures); Subset 3, mononuclear Ln complexes without cyclopentadienyl ligands (Cp) (26156 structures); Subset 4, Ln complexes with at least one 1,10-phenanthroline (phen) or its derivative as a coordinating ligand (2226 structures). The subsequent analysis of lanthanide complexes in these subsets examines the trends in coordination numbers and first shell distances as well as identifies and characterizes the ligands and donor groups. In addition, examples of Ln-complexes with commercially available complexants and phen-based ligands are interrogated in detail. This systematic investigation lays the groundwork for future data-driven ligand designs for REE separations based on the structural insights into the lanthanide coordination chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Machine learned synthesizability predictions aided by density functional theory

Abstract A grand challenge of materials science is predicting synthesis pathways for novel compounds. Data-driven approaches have made significant progress in predicting a compound’s synthesizability; however, some recent attempts ignore phase stability information. Here, we combine thermodynamic stability calculated using density functional theory with composition-based features to train a machine learning model that predicts a material’s synthesizability. Our model predicts the synthesizability of ternary 1:1:1 compositions in the half-Heusler structure, achieving a cross-validated precision of 0.82 and recall of 0.82. Our model shows improvement in predicting non-half-Heuslers compared to a previous study’s model, and identifies 121 synthesizable candidates out of 4141 unreported ternary compositions. More notably, 39 stable compositions are predicted unsynthesizable while 62 unstable compositions are predicted synthesizable; these findings otherwise cannot be made using density functional theory stability alone. This study presents a new approach for accurately predicting synthesizability, and identifies new half-Heuslers for experimental synthesis.

Lee, Andrew (ORCID:0000000153014295)↗

All-purpose, all-sky photometric redshifts for the Legacy Imaging Surveys Data Release 8

ABSTRACT In this paper, we present photometric redshift (photo-z) estimates for the Dark Energy Spectroscopic Instrument (DESI) Legacy Imaging Surveys, currently the most sensitive optical survey covering the majority of the extragalactic sky. Our photo-z methodology is based on a machine-learning approach, using sparse Gaussian processes augmented with Gaussian mixture models (GMMs) that allow regions of parameter space to be identified and trained separately in a purely data-driven way. The same GMMs are also used to calculate cost-sensitive learning weights that mitigate biases in the spectroscopic training sample. By design, this approach aims to produce reliable and unbiased predictions for all parts of the parameter space present in wide area surveys. Compared to previous literature estimates using the same underlying photometry, our photo-zs are significantly less biased and more accurate at z > 1, with negligible loss in precision or reliability for resolved galaxies at z < 1. Our photo-z estimates offer accurate predictions for rare high-value populations within the parent sample, including optically selected quasars at the highest redshifts (z > 6), as well as X-ray or radio continuum selected populations across a broad range of flux (densities) and redshift. Deriving photo-z estimates for the full Legacy Imaging Surveys Data Release 8, the catalogues provided in this work offer photo-z estimates predicted to be of high quality for ≳9 × 108 galaxies over ${\sim}19\, 400\, \text{deg}^{2}$ and spanning 0 < z ≲ 7, offering one of the most extensive samples of redshift estimates ever produced.

79 ASTRONOMY AND ASTROPHYSICS↗

Applying Machine‐Learning Methods to Laser Acceleration of Protons: Lessons Learned From Synthetic Data

ABSTRACT In this study, we consider three different machine‐learning methods—a three‐hidden‐layer neural network, support vector regression, and Gaussian process regression—and compare how well they can learn from a synthetic data set for proton acceleration in the Target Normal Sheath Acceleration regime. The synthetic data set was generated from a previously published theoretical model by Fuchs et al. 2005 that we modified. Once trained, these machine‐learning methods can assist with efforts to maximize the peak proton energy, or with the more general problem of configuring the laser system to produce a proton energy spectrum with desired characteristics. In our study, we focus on both the accuracy of the machine‐learning methods and the performance on one GPU including memory consumption. Although it is arguably the least sophisticated machine‐learning model we considered, support vector regression performed very well in our tests.

Desai, Ronak↗

Amortized simulation-based frequentist inference for tractable and intractable likelihoods

Abstract High-fidelity simulators that connect theoretical models with observations are indispensable tools in many sciences. If the likelihood is known, inference can proceed using standard techniques. However, when the likelihood is intractable or unknown, a simulator makes it possible to infer the parameters of a theoretical model directly from real and simulated observations when coupled with machine learning. We introduce an extension of the recently proposed likelihood-free frequentist inference ( LF2I ) approach that makes it possible to construct confidence sets with the p -value function and to use the same function to check the coverage explicitly at any given parameter point. Like LF2I , this extension yields provably valid confidence sets in parameter inference problems for which a high-fidelity simulator is available. The utility of our algorithm is illustrated by applying it to three pedagogically interesting examples: the first is from cosmology, the second from high-energy physics and astronomy, both with tractable likelihoods, while the third, with an intractable likelihood, is from epidemiology 3 3 Code to reproduce all of our results is available on https://github.com/AliAlkadhim/ALFFI . .

Computer Science↗