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At least 541 records · Page 30

Digital Analytics, Causal Knowledge Acquisition and Reasoning for Technical Language Processing

Complex engineering systems such as nuclear power plants (NPPs) generate and collect large amounts of equipment reliability (ER) data elements that contain information on the status of components, assets, and systems. Some of this information is textual in form and can be found in documents such as incident reports (IRs) and work orders (WOs). Analyses of textual data in current NPPs-using natural language processing (NLP) methods-have been expanded over the last decade, and it is only recently that the true potential of such analyses has emerged. So far, applications of NLP methods have mostly been limited to classification and prediction, the goal being to identify the nature of the textual element (e.g., safety or non-safety related). Here, we target a more complex problem: automatically extracting knowledge from a textual element in order to assist system engineers in conducting system health assessments. Knowledge extraction is a very broad concept, and its definition may vary depending on the application context. Our methods are a blend of both rule-based and machine learning (ML) algorithms. For our purposes, knowledge extraction means identifying the systems or assets mentioned in a given textual element, as well as the type of event described (e.g., component failure or maintenance activity). In addition, we want to capture details such as measured quantities and the temporal/cause-effect relations between events. In this tool, we also demonstrate how textual data elements are preprocessed in order to handle typos, acronyms, and abbreviations. One main feature of these methods is that they are not based solely on data, but are in fact model-based. In other words, they also rely on MBSE models that are designed to capture-from a functional point of view-the architecture of the systems/assets under consideration. The main purpose of such models is to digitally emulate system engineers' knowledge of system and asset architecture and to identify dependencies among systems, assets, and components. Provided these models, analyses of textual and numeric ER data can be performed by first identifying the OPM model elements to which the ER data elements are referring. The relationships between ER data elements are then identified by checking for any temporal or logical dependencies.

Mandelli, Diego [Idaho National Laboratory (INL), ↗

UWLi (Universal Workflow Language Interface) [SWR-24-12]

UWLi is a user interface for modifying Universal Workflow Language (UWL) files. UWL is a data format used to represent high fidelity scientific procedures in a generalized, field agnostic workflow format. See related publication: https://arxiv.org/pdf/2409.05899

Epps, Robert↗

SysCaps (Language Interfaces for Simulation Surrogates of Complex Systems) [SWR-24-97]

You've found the official code repository for the paper "SysCaps: Language Interfaces for Simulation Surrogates of Complex Systems," presented at the Foundation Models for Science: Progress, Opportunities, and Challenges workshop at NeurIPS 2024. Our paper conjectures that interfaces (both text templates as well as conversational) makes interacting with simulation surrogate models for complex systems more intuitive and accessible for both non-experts and experts. "System captions", or SysCaps, are text-based descriptions of systems based on information contained in simulation metadata. Our paper's goal is to train multimodal regression models that take text inputs (SysCaps) and timeseries inputs (exogenous system conditions such as hourly weather) and regress timeseries simulation outputs (e.g. hourly building energy consumption). The experiments in our paper with building and wind farm simulators, which can be reproduced using this codebase, aim to help us understand whether a) accurate regression in this setting is possible and b) if so, how well can we do it. Paper: https://arxiv.org/abs/2405.19653

Emami, Patrick↗

Mitigative Strategies for Recovering From Large Language Model Trust Violations

In this study, we investigated strategies to address trust issues arising from errors in large language models (LLMs). The study examined the impact of confidence scores, system capability explanations, and user feedback on trust restoration post-error. 68 participants viewed the responses of an LLM to 20 general trivia questions, with an error introduced on the third trial. Each participant was presented with one mitigation strategy. Participants rated their overall trust in the model and the reliability of the answer. Results showed an immediate drop in trust after the error; however, there were no differences across the three strategies in trust recovery. All conditions had a logarithmic trend in trust recovery following error. Differences in overall trust were predicted by perceived reliability of the answer, suggesting that participants were evaluating results critically and using that to inform their trust in the model. Qualitative data supported this finding; participants expressed lasting distrust despite the LLM’s later accuracy. Results showcase the need to prioritize accuracy in LLM deployment, because early errors may irrevocably damage user trust calibration and later adoption.

97 MATHEMATICS AND COMPUTING↗

SBOL Visual: A Graphical Language for Genetic Designs

Synthetic Biology Open Language (SBOL) Visual is a graphical standard for genetic engineering. We report that it consists of symbols representing DNA subsequences, including regulatory elements and DNA assembly features. These symbols can be used to draw illustrations for communication and instruction, and as image assets for computer-aided design. SBOL Visual is a community standard, freely available for personal, academic, and commercial use (Creative Commons CC0 license). We provide prototypical symbol images that have been used in scientific publications and software tools. We encourage users to use and modify them freely, and to join the SBOL Visual community: http://www.sbolstandard.org/visual.

59 BASIC BIOLOGICAL SCIENCES↗

Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2

Rule-based modeling is an approach that permits constructing reaction networks based on the specification of rules for molecular interactions and transformations. These rules can encompass details such as the interacting sub-molecular domains and the states and binding status of the involved components. Conceptually, fine-grained spatial information such as locations can also be provided. Through “wildcards” representing component states, entire families of molecule complexes sharing certain properties can be specified as patterns. This can significantly simplify the definition of models involving species with multiple components, multiple states, and multiple compartments. The systems biology markup language (SBML) Level 3 Multi Package Version 1 extends the SBML Level 3 Version 1 core with the “type” concept in the Species and Compartment classes. Therefore, reaction rules may contain species that can be patterns and exist in multiple locations. Multiple software tools such as Simmune and BioNetGen support this standard that thus also becomes a medium for exchanging rule-based models. This document provides the specification for Release 2 of Version 1 of the SBML Level 3 Multi package. No design changes have been made to the description of models between Release 1 and Release 2; changes are restricted to the correction of errata and the addition of clarifications.

59 BASIC BIOLOGICAL SCIENCES↗

Stan : A Probabilistic Programming Language

Stan is a probabilistic programming language for specifying statistical models. A Stan program imperatively defines a log probability function over parameters conditioned on specified data and constants. As of version 2.14.0, Stan provides full Bayesian inference for continuous-variable models through Markov chain Monte Carlo methods such as the No-U-Turn sampler, an adaptive form of Hamiltonian Monte Carlo sampling. Penalized maximum likelihood estimates are calculated using optimization methods such as the limited memory Broyden-Fletcher-Goldfarb-Shanno algorithm. Stan is also a platform for computing log densities and their gradients and Hessians, which can be used in alternative algorithms such as variational Bayes, expectation propagation, and marginal inference using approximate integration. To this end, Stan is set up so that the densities, gradients, and Hessians, along with intermediate quantities of the algorithm such as acceptance probabilities, are easily accessible. Stan can also be called from the command line using the cmdstan package, through R using the rstan package, and through Python using the pystan package. All three interfaces support sampling and optimization-based inference with diagnostics and posterior analysis. rstan and pystan also provide access to log probabilities, gradients, Hessians, parameter transforms, and specialized plotting.

97 MATHEMATICS AND COMPUTING↗

Understanding the Inner-Workings of Language Models Through Representation Dissimilarity

We use model stitching to understand the internal representations of language models. Similar to vision models, we find that "more is better," and representations learned with more data and larger width can improve the performance of weaker models via stitching. We likewise find that certain architecture choices, using GeLU vs SoLU activation functions, influence the quality of learned representations. Finally, model stitching (as opposed to other model diagnostic methods, like mode connectivity) can localize the different generalization strategies of text classifiers under domain shift to certain hidden layers.

Brown, Davis R.↗

Monte Carlo Thought Search: Large Language Model Querying for Complex Scientific Reasoning in Catalyst Design

Discovering novel catalysts requires complex reasoning involving multiple chemical properties and resultant trade-offs, leading to a combinatorial growth in the search space. While large language models (LLM) have demonstrated novel capabilities for chemistry through complex instruction following capabilities and high quality reasoning, a goal-driven combinatorial search using LLMs has not been explored in detail. In this work, we present a Monte Carlo Tree Search-based approach that improves beyond state-of-the-art chain-of-thought prompting variants to augment scientific reasoning. We introduce two new reasoning datasets: 1) a curation of computational chemistry simulations, and 2) diverse questions written by catalysis researchers for reasoning about novel chemical conversion processes. We improve over the best baseline by 25.8\% and find that our approach can augment scientist's reasoning and discovery process with novel insights.\footnote{All resources will be publicly available upon publication.

Sprueill, Henry W.↗

Domain Specific Language Support for Exascale

Domain-Specific Languages (DSLs) offer an attractive path to Exascale software since they provide expressive power through appropriate abstractions and enable domain-specific optimizations. But the advantages of a DSL compete with the difficulties of implementing a DSL, even for a narrowly defined domain. The DTEC project addresses how a variety of DSLs can be easily implemented to leverage existing compiler analysis and transformation capabilities within the ROSE open source compiler as part of a research program focusing on Exascale challenges. The OSU contributions to the DTEC project are in the area of code generation from high-level DSL descriptions, as well as verification of the automatically-generated code.

97 MATHEMATICS AND COMPUTING↗

Domain Specific Language for Exascale

The focus of this project was the development of the infrastructure supporting DSLs. The goal is that DSLs can be built easily and economically to address the requirements of future HPC software development on Exascale architectures. We proposed to use a novel integrated approach to support the lifecycle of DSL development and involve all major players including HPC programmers, domain algorithm experts, DSL designers, implementation experts. The resulting software artifacts and processes will include components supporting application migration, DSL specifications, DSL language parsing, compiler construction, refinement and transformation, performance analysis, runtime support, as well as parameterizing abstract extreme-scale machines.

97 MATHEMATICS AND COMPUTING↗

A Domain-Specific Language for High-Consequence Control Software

While most software development for control systems is directed at what the system is supposed to do (i.e., function), high-consequence controls must account for what the system is not supposed to do (i.e., safety, security and reliability requirements). A Domain Specific Language (DSL) for high-consequence digital controls is proposed. As with similar tools for the design of controls, the DSL will have plug-in modules for common controller functions. However, the DSL will also augment these modules with attendant "templates" that aid in the proof of safety, security and reliability requirements, not available in current tools. The object is to create a development methodology that makes construction of high-assurance control systems as easy as controls that are designed for function alone.

97 MATHEMATICS AND COMPUTING↗

Reference Interoperability Procurement Language

Achieving interoperability involves reaching agreement on common interfaces and promoting interoperability through performance specifications. Effective integration practices are a simple, effective, and direct way of addressing the challenge. By deciding on an integration approach with well-defined interfaces and selecting systems and devices that conform to that approach and choosing integrators that have experience implementing the chosen approach, many problems can be avoided. No integration effort is seamless but by specifying interoperability requirements during the procurement process typical problems from ad hoc approaches can be avoided or reduced. By continuing this approach to its conclusion at the end of the procurement process, these same interoperability requirements may lead themselves to specified performance criteria that can be used to measure interoperability during implementation. The contractual language may contain performance incentives and penalties tied to these requirements as appropriate.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Evaluation of Programming Language-Aware Diffs for Improving Developer Productivity

As the number of supported platforms for SNL software increases, so do the testing requirements. This increases the total time spent between when a developer submits code for testing, and when tests are completed. This in turn leads developers to hold off submitting code for testing, meaning that when code is ready for testing there's a lot more of it. This increases the likelihood of merge conflicts which the developer must resolve by hand -- because someone else touched the files near the lines the developer touched. Current text-based diff tools often have trouble resolving conflicts in these cases. Work in Europe and Japan has demonstrated that, using programming language aware diff tools (e.g., using the abstract syntax tree (AST) a compiler might generate) can reduce the manual labor necessary to resolve merge conflicts. These techniques can detect code blocks which have moved, as opposed than current text-based diff tools, which only detect insertions / deletions of text blocks. In this study, we evaluate one such tool, GumTree, and see how effective it is as a replacement for traditional text-based diff approaches.

97 MATHEMATICS AND COMPUTING↗

Active Learning for Language Modeling

Foreign disinformation campaigns undermine national security. Various supervised language modeling techniques in NLP can help to understand and dismantle these campaigns, but they rely heavily on large, labeled (often by humans) datasets. This work provides a solution to this problem in the form of an active learning (AL) framework, which is used to generate labeled datasets and leverage human input for detecting disinformation. The developed AL framework utilizes task adaptive pretraining to fully leverage the unlabeled data and boost the performance of the classifier used for labeling. A disinformation rhetoric metric was developed to measure the presence of common rhetorical techniques used in text that are meant to deceive, for both the classifier and human to use in the task of identifying disinformation. This metric was combined with an uncertainty criterion to create a hybrid acquisition method for AL, and this hybrid method was tested alongside other acquisition functions. A sophisticated and robust stopping strategy was developed to signal the AL process should terminate, saving human time from being wasted on iterations that would not significantly benefit classifier performance.

99 GENERAL AND MISCELLANEOUS↗

CALORIE: A Constraint Language and Optimizing Runtime for Exascale Power Management (Final Report)

This final technical report summarizes the key accomplishments on the CALORIE project, a DOE Early Career award received by PI Henry Hoffmann at the University of Chicago. CALORIE’s main goal was to create principled methodologies, tools, and practices to help scientists and high-performance computing (HPC) operators maximize the performance and insights obtained from scientific computing applications in the face of exascale power constraints. The project accomplished these goals by completing the following objectives: • Designing a language for describing application goals (including constraints and objectives) and system capabilities. The application goals will include things like which simulations or simulations plus in situ analysis will be run together, what the power constraints are, and what requirements there are for in situ analysis (for example, a desired frame rate for visualization). The system capabilities include all components that can be adjusted to tradeoff power and performance. • Designing a runtime system that takes specified goals and capabilities and dynamically determines what capabilities to use to meet the goals. This runtime adapts to changes in goals, application behavior, or available capabilities to automatically maintain the goals despite unexpected disturbances. • Developing a foundational understanding of how power constraints affect the problem of scheduling applications in large-scale systems. This report provides an overview of the accomplishments related to each of these key objectives.

97 MATHEMATICS AND COMPUTING↗