Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Language”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,477 records · Page 82

Use of machine learning to analyze chemistry card sort tasks

Education researchers are deeply interested in understanding the way students organize their knowledge. Card sort tasks, which require students to group concepts, are one mechanism to infer a student’s organizational strategy. However, the limited resolution of card sort tasks means they necessarily miss some of the nuance in a student’s strategy. Here in this work, we propose new machine learning strategies that leverage a potentially richer source of student thinking: free-form written language justifications associated with student sorts. Using data from a university chemistry card sort task, we use vectorized representations of language and unsupervised learning techniques to generate qualitatively interpretable clusters, which can provide unique insight in how students organize their knowledge. We compared these to machine learning analysis of the students’ sorts themselves. Machine learning-generated clusters revealed different organizational strategies than those built into the task; for example, sorts by difficulty or even discipline. There were also many more categories generated by machine learning for what we would identify as more novice-like sorts and justifications than originally built into the task, suggesting students’ organizational strategies converge when they become more expert-like. Finally, we learned that categories generated by machine learning for students’ justifications did not always match the categories for their sorts, and these cases highlight the need for future research on students’ organizational strategies, both manually and aided by machine learning. In sum, the use of machine learning to analyze results from a card sort task has helped us gain a more nuanced understanding of students’ expertise, and demonstrates a promising tool to add to existing analytic methods for card sorts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

SNS Proton Beam Window Disposal

In order to support the disposal of the proton beam window assembly of the Spallation Neutron Source beamline to the target station, waste classification analyses are performed. The window has a limited life-time due to radiation-induced material damage. Here, analyses include calculation of the radionuclide inventory and shielding analyses for the transport package/container to ensure that the container is compliant with the transportation and waste management regulations. In order to automate this procedure and minimize manual work a script in Perl language was written.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Automatic log analysis with NLP for the CMS workflow handling

The central Monte-Carlo production of the CMS experiment utilizes the WLCG infrastructure and manages daily thousands of tasks, each up to thousands of jobs. The distributed computing system is bound to sustain a certain rate of failures of various types, which are currently handled by computing operators a posteriori. Within the context of computing operations, and operation intelligence, we propose a Machine Learning technique to learn from the operators with a view to reduce the operational workload and delays. This work is in continuation of CMS work on operation intelligence to try and reach accurate predictions with Machine Learning. We present an approach to consider the log files of the workflows as regular text to leverage modern techniques from Natural Language Processing (NLP). In general, log files contain a substantial amount of text that is not human language. Therefore, different log parsing approaches are studied in order to map the log files’ words to high dimensional vectors. These vectors are then exploited as feature space to train a model that predicts the action that the operator has to take. This approach has the advantage that the information of the log files is extracted automatically and the format of the logs can be arbitrary. In this work the performance of the log file analysis with NLP is presented and compared to previous approaches.

Layer, Lukas↗

Fractional charge and spin errors in self-consistent Green’s function theory

We examine fractional charge and spin errors in self-consistent Green’s function theory within a second-order approximation (GF2). For GF2, it is known that the summation of diagrams resulting from the self-consistent solution of the Dyson equation removes the divergences pathological to second-order Møller-Plesset (MP2) theory for strong correlations. In the language often used in density functional theory contexts, this means GF2 has a greatly reduced fractional spin error relative to MP2. The natural question then is what effect, if any, does the Dyson summation have on the fractional charge error in GF2? To this end, we generalize our previous implementation of GF2 to open-shell systems and analyze its fractional spin and charge errors. We find that like MP2, GF2 possesses only a very small fractional charge error, and consequently minimal many electron self-interaction error. This shows that GF2 improves on the critical failings of MP2, but without altering the positive features that make it desirable. Furthermore, we find that GF2 has both less fractional charge and fractional spin errors than typical hybrid density functionals as well as random phase approximation with exchange.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A practical field guide to thermoelectrics: Fundamentals, synthesis, and characterization

The study of thermoelectric materials spans condensed matter physics, materials science and engineering, and solid-state chemistry. The diversity of the participants and the inherent complexity of the topic mean that it is difficult, if not impossible, for a researcher to be fluent in all aspects of the field. This review, which grew out of a one-week summer school for graduate students, aims to provide an introduction and practical guidance for selected conceptual, synthetic, and characterization approaches and to craft a common umbrella of language, theory, and experimental practice for those engaged in the field of thermoelectric materials. This review does not attempt to cover all major aspects of thermoelectric materials research or review state-of-the-art thermoelectric materials. Rather, the topics discussed herein reflect the expertise and experience of the authors. We begin by discussing a universal approach to modeling electronic transport using Landauer theory. The core sections of the review are focused on bulk inorganic materials and include a discussion of effective strategies for powder and single crystal synthesis, the use of national synchrotron sources to characterize crystalline materials, error analysis, and modeling of transport data using an effective mass model, and characterization of phonon behavior using inelastic neutron scattering and ultrasonic speed of sound measurements. The final core section discusses the challenges faced when synthesizing carbon-based samples and the measuring or interpretation of their transport properties. We conclude this review with a brief discussion of some of the grand challenges and opportunities that remain to be addressed in the study of thermoelectrics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

PhysBERT: A text embedding model for physics scientific literature

The specialized language and complex concepts in physics pose significant challenges for information extraction through Natural Language Processing (NLP). Central to effective NLP applications is the text embedding model, which converts text into dense vector representations for efficient information retrieval and semantic analysis. In this work, we introduce PhysBERT, the first physics-specific text embedding model. Pre-trained on a curated corpus of 1.2 × 106 arXiv physics papers and fine-tuned with supervised data, PhysBERT outperforms leading general-purpose models on physics-specific tasks, including the effectiveness in fine-tuning for specific physics subdomains.

Hellert, Thorsten (ORCID:0000000227970926)↗

Dynamic in-context learning with conversational models for data extraction and materials property prediction

The advent of natural language processing and large language models (LLMs) has revolutionized the extraction of data from unstructured scholarly papers. However, ensuring data trustworthiness remains a significant challenge. In this paper, we introduce PropertyExtractor, an open-source tool that leverages advanced conversational LLMs such as Google gemini-pro and OpenAI gpt-4, blends zero-shot with few-shot in-context learning, and employs engineered prompts for the dynamic refinement of structured information hierarchies—enabling autonomous, efficient, scalable, and accurate identification, extraction, and verification of material property data. Our tests on material data demonstrate precision and recall that exceed 95% with an error rate of ∼9%, highlighting the effectiveness and versatility of the toolkit. Finally, databases for 2D material thicknesses, a critical parameter for device integration, and energy bandgap values are developed using PropertyExtractor. In particular, for the thickness database, the rapid evolution of the field has outpaced both experimental measurements and computational methods, creating a significant data gap. Our work addresses this gap and showcases the potential of PropertyExtractor as a reliable and efficient tool for the autonomous generation of various material property databases, advancing the field.

Ekuma, Chinedu E. (ORCID:0000000258527556)↗

Book Review: What Makes a Good Experiment? Reasons and Roles in Science

Classification is an arduous and sometimes controversial undertaking because of its inherent cultural particularity. One famous literary example is the fictitious nomenclature of animals found in Jorge Luis Borges’s ‘The Analytical Language of John Wilkins’. According to Borges, that taxonomy was discovered by a translator, F. Kuhn, in a Chinese source and divides all animals into fourteen categories, starting with ‘those that belong to the Emperor’ and ending with ‘those that from a long way off look like flies’. Physics of the twentieth century is a ramified full-fledged technical culture, and it should surprise no one that physics experiments can be classified in different ways, allowing certain experiments to belong to more than one category. Allan Franklin’s analysis of experiments is based on his classification, which substantially grasps the essence of the experimental enterprise. Although Franklin does not offer an explicit answer to the question posed in the title, he does include a detailed examination of several important physics and biology experiments in history

Pronskikh, Vitaly↗

GeoAI: spatially explicit artificial intelligence techniques for geographic knowledge discovery and beyond

Recent progress in Artificial Intelligence (AI) techniques, the large-scale availability of high-quality data, as well as advances in both hardware and software to efficiently process these data, are transforming a range of fields from computer vision and natural language processing to autonomous driving and healthcare. For example, the availability of high-resolution geographic data and high-performance computing techniques together with deep learning fuel progress in fast and accurate object detection. Recent examples of GeoAI work include the detections of terrain features and densely-distributed building footprints, information extraction from scanned historical maps, semantic classification (e.g. LiDAR point clouds), novel methods for spatial interpolation, and advances in traffic forecasting. Similarly, machine learning and natural language processing are facilitating the extraction of geographic information from unstructured (textual) data, such as news articles and Wikipedia as well as the matching of natural features in multiple gazetteers.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

ALGORITHMS AND PROGRAMS FOR STRONG GRAVITATIONAL LENSING IN KERR SPACE-TIME INCLUDING POLARIZATION

Active galactic nuclei (AGNs) and quasars are important astrophysical objects to understand. Recently, microlensing observations have constrained the size of the quasar X-ray emission region to be of the order of 10 gravitational radii of the central supermassive black hole. For distances within a few gravitational radii, light paths are strongly bent by the strong gravity field of the central black hole. If the central black hole has nonzero angular momentum (spin), then a photon’s polarization plane will be rotated by the gravitational Faraday effect. The observed X-ray flux and polarization will then be influenced significantly by the strong gravity field near the source. Consequently, linear gravitational lensing theory is inadequate for such extreme circumstances. We present simple algorithms computing the strong lensing effects of Kerr black holes, including the effects on polarization. Our algorithms are realized in a program “KERTAP” in two versions: MATLAB and Python. The key ingredients of KERTAP are a graphic user interface, a backward ray-tracing algorithm, a polarization propagator dealing with gravitational Faraday rotation, and algorithms computing observables such as flux magnification and polarization angles. Our algorithms can be easily realized in other programming languages such as FORTRAN, C, and C++. The MATLAB version of KERTAP is parallelized using the MATLAB Parallel Computing Toolbox and the Distributed Computing Server. The Python code was sped up using Cython and supports full implementation of MPI using the “mpi4py” package. As an example, we investigate the inclination angle dependence of the observed polarization and the strong lensing magnification of AGN X-ray emission. We conclude that it is possible to perform complex numerical-relativity related computations using interpreted languages such as MATLAB and Python.

79 ASTRONOMY AND ASTROPHYSICS↗

Mathematical solutions in internal dose assessment: A comparison of Python-based differential equation solvers in biokinetic modeling

Abstract In biokinetic modeling systems employed for radiation protection, biological retention and excretion have been modeled as a series of discretized compartments representing the organs and tissues of the human body. Fractional retention and excretion in these organ and tissue systems have been mathematically governed by a series of coupled first-order ordinary differential equations (ODEs). The coupled ODE systems comprising the biokinetic models are usually stiff due to the severe difference between rapid and slow transfers between compartments. In this study, the capabilities of solving a complex coupled system of ODEs for biokinetic modeling were evaluated by comparing different Python programming language solvers and solving methods with the motivation of establishing a framework that enables multi-level analysis. The stability of the solvers was analyzed to select the best performers for solving the biokinetic problems. A Python-based linear algebraic method was also explored to examine how the numerical methods deviated from an analytical or semi-analytical method. Results demonstrated that customized implicit methods resulted in an enhanced stable solution for the inhaled 60 Co (Type M) and 131 I (Type F) exposure scenarios for the inhalation pathway of the International Commission on Radiological Protection (ICRP) Publication 130 Human Respiratory Tract Model (HRTM). The customized implementation of the Python-based implicit solvers resulted in approximately consistent solutions with the Python-based matrix exponential method ( expm ). The differences generally observed between the implicit solvers and expm are attributable to numerical precision and the order of numerical approximation of the numerical solvers. This study provides the first analysis of a list of Python ODE solvers and methods by comparing their usage for solving biokinetic models using the ICRP Publication 130 HRTM and provides a framework for the selection of the most appropriate ODE solvers and methods in Python language to implement for modeling the distribution of internal radioactivity.

61 RADIATION PROTECTION AND DOSIMETRY↗

Late-time structure of the Bunch-Davies de Sitter wavefunction

We examine the late time behavior of the Bunch-Davies wavefunction for interacting light fields in a de Sitter background. We use perturbative techniques developed in the framework of AdS/CFT, and analytically continue to compute tree and loop level contributions to the Bunch-Davies wavefunction. We consider self-interacting scalars of general mass, but focus especially on the massless and conformally coupled cases. We show that certain contributions grow logarithmically in conformal time both at tree and loop level. We also consider gauge fields and gravitons. The four-dimensional Fefferman-Graham expansion of classical asymptotically de Sitter solutions is used to show that the wavefunction contains no logarithmic growth in the pure graviton sector at tree level. Finally, assuming a holographic relation between the wavefunction and the partition function of a conformal field theory, we interpret the logarithmic growths in the language of conformal field theory.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Energy and momentum conservation in the Euler–Poincaré formulation of local Vlasov–Maxwell-type systems

The action principle by Low for the classic Vlasov–Maxwell system contains a mix of Eulerian and Lagrangian variables. This renders the Noether analysis of reparametrization symmetries inconvenient, especially since the well-known energy- and momentum-conservation laws for the system are expressed in terms of Eulerian variables only. While an Euler–Poincaré formulation of Vlasov–Maxwell-type systems, effectively starting with Low's action and using constrained variations for the Eulerian description of particle motion, has been known for a while Cendra et al, it is hard to come by a documented derivation of the related energy- and momentum-conservation laws in the spirit of the Euler–Poincaré machinery. To our knowledge only one such derivation exists in the literature so far, dealing with the so-called guiding-center Vlasov–Darwin system Sugama et al. The present exposition discusses a generic class of local Vlasov–Maxwell-type systems, with a conscious choice of adopting the language of differential geometry to exploit the Euler–Poincaré framework to its full extent. After reviewing the transition from a Lagrangian picture to an Eulerian one, we demonstrate how symmetries generated by isometries in space lead to conservation laws for linear- and angular-momentum density and how symmetry by time translation produces a conservation law for energy density. Here, we also discuss what happens if no symmetries exist. Finally, two explicit examples will be given—the classic Vlasov–Maxwell and the drift-kinetic Vlasov–Maxwell—and the results expressed in the language of regular vector calculus for familiarity.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Attention-based quantum tomography

Abstract With rapid progress across platforms for quantum systems, the problem of many-body quantum state reconstruction for noisy quantum states becomes an important challenge. There has been a growing interest in approaching the problem of quantum state reconstruction using generative neural network models. Here we propose the ‘attention-based quantum tomography’ (AQT), a quantum state reconstruction using an attention mechanism-based generative network that learns the mixed state density matrix of a noisy quantum state. AQT is based on the model proposed in ‘Attention is all you need’ by Vaswani et al (2017 NIPS ) that is designed to learn long-range correlations in natural language sentences and thereby outperform previous natural language processing (NLP) models. We demonstrate not only that AQT outperforms earlier neural-network-based quantum state reconstruction on identical tasks but that AQT can accurately reconstruct the density matrix associated with a noisy quantum state experimentally realized in an IBMQ quantum computer. We speculate the success of the AQT stems from its ability to model quantum entanglement across the entire quantum system much as the attention model for NLP captures the correlations among words in a sentence.

97 MATHEMATICS AND COMPUTING↗

Plug & play directed evolution of proteins with gradient-based discrete MCMC

Abstract A long-standing goal of machine-learning-based protein engineering is to accelerate the discovery of novel mutations that improve the function of a known protein. We introduce a sampling framework for evolving proteins in silico that supports mixing and matching a variety of unsupervised models, such as protein language models, and supervised models that predict protein function from sequence. By composing these models, we aim to improve our ability to evaluate unseen mutations and constrain search to regions of sequence space likely to contain functional proteins. Our framework achieves this without any model fine-tuning or re-training by constructing a product of experts distribution directly in discrete protein space. Instead of resorting to brute force search or random sampling, which is typical of classic directed evolution, we introduce a fast Markov chain Monte Carlo sampler that uses gradients to propose promising mutations. We conduct in silico directed evolution experiments on wide fitness landscapes and across a range of different pre-trained unsupervised models, including a 650 M parameter protein language model. Our results demonstrate an ability to efficiently discover variants with high evolutionary likelihood as well as estimated activity multiple mutations away from a wild type protein, suggesting our sampler provides a practical and effective new paradigm for machine-learning-based protein engineering.

59 BASIC BIOLOGICAL SCIENCES↗

Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning

Abstract Motivation Creating knowledge bases and ontologies is a time consuming task that relies on manual curation. AI/NLP approaches can assist expert curators in populating these knowledge bases, but current approaches rely on extensive training data, and are not able to populate arbitrarily complex nested knowledge schemas. Results Here we present Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES), a Knowledge Extraction approach that relies on the ability of Large Language Models (LLMs) to perform zero-shot learning and general-purpose query answering from flexible prompts and return information conforming to a specified schema. Given a detailed, user-defined knowledge schema and an input text, SPIRES recursively performs prompt interrogation against an LLM to obtain a set of responses matching the provided schema. SPIRES uses existing ontologies and vocabularies to provide identifiers for matched elements. We present examples of applying SPIRES in different domains, including extraction of food recipes, multi-species cellular signaling pathways, disease treatments, multi-step drug mechanisms, and chemical to disease relationships. Current SPIRES accuracy is comparable to the mid-range of existing Relation Extraction methods, but greatly surpasses an LLM’s native capability of grounding entities with unique identifiers. SPIRES has the advantage of easy customization, flexibility, and, crucially, the ability to perform new tasks in the absence of any new training data. This method supports a general strategy of leveraging the language interpreting capabilities of LLMs to assemble knowledge bases, assisting manual knowledge curation and acquisition while supporting validation with publicly-available databases and ontologies external to the LLM. Availability and implementation SPIRES is available as part of the open source OntoGPT package: https://github.com/monarch-initiative/ontogpt.

59 BASIC BIOLOGICAL SCIENCES↗

Cropbox: a declarative crop modelling framework

Abstract We introduce Cropbox, a novel modelling framework that supports various aspects of crop modelling in a unique yet concise style. Building a crop model can be easily riddled with technical details looking trivial at first but later becoming major obstacles that hamper the whole development or application process. This is particularly the case when implementing models from scratch without relying on an established framework. Cropbox adopts a declarative approach providing a domain-specific language to reduce technical debt and assist modellers to focus on high-level abstraction formed by relations between variables and enclosing systems, rather than tinkering with low-level implementation details. The syntax of Cropbox framework is based on the Julia programming language and is deliberately constrained to avoid unintended side effects caused by common mistakes while its architecture remains open to extension. We highlight key capabilities of the framework through case studies featuring a leaf gas-exchange model and a whole-plant simulation model. We also illustrate potential extensions for supporting functional-structural plant modelling by demonstrating a 3D root architectural model as an example.

Yun, Kyungdahm (ORCID:0000000322894386)↗

The Human Phenotype Ontology in 2024: phenotypes around the world

The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs.

59 BASIC BIOLOGICAL SCIENCES↗