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At least 973 records · Page 54

Accelerating crystal structure determination with iterative AlphaFold prediction

Experimental structure determination can be accelerated with artificial intelligence (AI)-based structure-prediction methods such as AlphaFold . Here, an automatic procedure requiring only sequence information and crystallographic data is presented that uses AlphaFold predictions to produce an electron-density map and a structural model. Iterating through cycles of structure prediction is a key element of this procedure: a predicted model rebuilt in one cycle is used as a template for prediction in the next cycle. This procedure was applied to X-ray data for 215 structures released by the Protein Data Bank in a recent six-month period. In 87% of cases our procedure yielded a model with at least 50% of C α atoms matching those in the deposited models within 2 Å. Predictions from the iterative template-guided prediction procedure were more accurate than those obtained without templates. It is concluded that AlphaFold predictions obtained based on sequence information alone are usually accurate enough to solve the crystallographic phase problem with molecular replacement, and a general strategy for macromolecular structure determination that includes AI-based prediction both as a starting point and as a method of model optimization is suggested.

59 BASIC BIOLOGICAL SCIENCES↗

Are humans still necessary? Expanding the discussion

The rise of automation, artificial intelligence (AI), and autonomous systems raises important questions about the future role of humans and the field of human factors/ergonomics in workplaces. This paper builds on Dr. Peter Hancock’s 2023 ‘Are Humans Still Necessary?’ article published in the Ergonomics journal. Using a multi-method approach that included a debate, opinion polling, roundtable discussions, and AI queries, the current effort examined the necessity of human involvement in future work environments. Debate team members presented arguments for and against the need for human workers, considering human factors, technology, and socioeconomic factors. Observations indicate that while AI may handle routine tasks, humans will likely remain essential for complex decision making, creativity, and ethical considerations. The paper advocates for viewing workplace dynamics as collaborative human-AI partnerships rather than competition, highlighting the need for a transdisciplinary approach in which human factors/ergonomics professionals play a vital role in enhancing these relationships.

99 - GENERAL AND MISCELLANEOUS↗

ReVise: A Human-AI Interface for Incremental Algorithmic Recourse

The recent adoption of artificial intelligence in socio-technical systems raises concerns about the black-box nature of the resulting decisions in fields such as hiring, finance, admissions, etc. If data subjects—such as job applicants, loan applicants, and students—receive an unfavorable outcome, they may be interested in algorithmic recourse, which involves updating certain features to yield a more favorable result when re-evaluated by algorithmic decision-making. Unfortunately, when individuals do not fully understand the incremental steps needed to change their circumstances, they risk following misguided paths that can lead to significant, long-term adverse consequences. Existing recourse approaches focus exclusively on the final recourse goal but neglect the possible incremental steps to reach the goal with real-life constraints, user preferences, and model artifacts. To address this gap, we formulate a visual analytic workflow for incremental recourse planning in collaboration with AI/ML experts and contribute an interactive visualization interface that helps data subjects efficiently navigate the recourse alternatives and make an informed decision. We also present one of the many usage scenarios, developed during exploratory feedback sessions with twelve graduate students using a real-world dataset, which demonstrates that our approach can be instrumental for data subjects in choosing a suitable recourse path.

algorithmic recourse↗

Generative AI for design of nanoporous materials: review and future prospects

Generative artificial intelligence (AI) is emerging as a powerful tool for advancing the design of nanoporous materials such as metal–organic frameworks, covalent–organic frameworks, and zeolites. These materials have potential application in important areas such as carbon capture, catalysis, gas storage, chemical separation, and drug delivery due to their modular, tunable structures, and their performance in these areas depends on precise control over their structure, chemical functionalities, and properties. Herein, we provide a review of generative AI algorithms that are emerging as powerful tools for the design of nanoporous materials, namely generative adversarial networks, variational autoencoders, diffusion models, genetic algorithms, reinforcement learning, and large language models. Some models are particularly good at generating diverse and high-quality designs, while others excel at exploring large design spaces or optimizing materials with desired properties. Certain algorithms also allow for efficient transitions between different designs, and some offer versatility in generating materials based on textual input. We discuss the advantages, limitations, and applications of these algorithms in porous material design and emphasize the future potential of integrating AI with experimental workflows to accelerate the development and validation of AI-generated materials.

36 MATERIALS SCIENCE↗

Perspectives for self-driving labs in synthetic biology

Self-driving labs (SDLs) combine fully automated experiments and data collection with artificial intelligence (AI) and control algorithms that decide not only the set of parameters for the next experiment, but also potentially which scientific hypotheses to test. Taken to their ultimate expression, SDLs could usher a new paradigm of scientific research, where the world is probed, interpreted, and explained by machines for human benefit. Whereas there are functioning SDLs in the fields of chemistry and materials science, we contend that synthetic biology provides a unique opportunity since the genome provides a single, easily accessible, target for affecting the incredibly wide repertoire of biological cell behavior. Since they can provide large amounts of high-quality data, SDLs can be a platform for AI to develop approaches to systematically convert data into scientific knowledge systems. These knowledge systems can be used both to understand the biological world and to design bioengineered systems to fit a desired specification (inverse design). However, the level of investment required for the creation of biological SDLs is only warranted if directed towards solving difficult and enabling biological questions. Here, we discuss challenges and opportunities in creating SDLs for synthetic biology.

59 BASIC BIOLOGICAL SCIENCES↗

Generalist multimodal AI: A review of architectures, challenges and opportunities

Multimodal models are expected to be a critical component to future advances in artificial intelligence. Here, this field is starting to grow rapidly with a surge of new design elements motivated by the success of foundation models in natural language processing (NLP) and vision. It is widely hoped that further extending the foundation models to multiple modalities (e.g., text, image, video, sensor, time series, graph, etc.) will ultimately lead to generalist multimodal models, i.e. one model across different data modalities and tasks. However, there is little research that systematically analyzes recent multimodal models (particularly the ones that work beyond text and vision) with respect to the underling architecture proposed. Therefore, this work provides a fresh perspective on generalist multimodal models (GMMs) via a novel architecture and training configuration specific taxonomy. This includes factors such as Unifiability, Modularity, and Adaptability that are pertinent and essential to the wide adoption and application of GMMs. The review further highlights key challenges and prospects for the field and guide the researchers into the new advancements.

Artificial intelligence (AI)↗

Towards Next-Generation Urban Decision Support Systems through AI-Powered Construction of Scientific Ontology Using Large Language Models—A Case in Optimizing Intermodal Freight Transportation

The incorporation of Artificial Intelligence (AI) models into various optimization systems is on the rise. However, addressing complex urban and environmental management challenges often demands deep expertise in domain science and informatics. This expertise is essential for deriving data and simulation-driven insights that support informed decision-making. In this context, we investigate the potential of leveraging the pre-trained Large Language Models (LLMs) to create knowledge representations for supporting operations research. By adopting ChatGPT-4 API as the reasoning core, we outline an applied workflow that encompasses natural language processing, Methontology-based prompt tuning, and Generative Pre-trained Transformer (GPT), to automate the construction of scenario-based ontologies using existing research articles and technical manuals of urban datasets and simulations. From these ontologies, knowledge graphs can be derived using widely adopted formats and protocols, guiding various tasks towards data-informed decision support. The performance of our methodology is evaluated through a comparative analysis that contrasts our AI-generated ontology with the widely recognized pizza ontology, commonly used in tutorials for popular ontology software. We conclude with a real-world case study on optimizing the complex system of multi-modal freight transportation. Our approach advances urban decision support systems by enhancing data and metadata modeling, improving data integration and simulation coupling, and guiding the development of decision support strategies and essential software components.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

A framework to enhance disaster debris estimation with AI and aerial photogrammetry

This study addresses the critical need to enhance disaster preparedness and response, focusing on hurricane impact assessment and debris estimation. Accurate assessments in this context are critical for post-event search-and-rescue (SAR) operations and resource distribution. Recent computing advancements are revealing the potential of unmanned aerial vehicles (UAVs) and artificial intelligence (AI) technologies in collecting data and assisting with post-hurricane reconnaissance. However, the use of AI and UAV photogrammetry for accurate disaster impact analysis remains underexplored. To this end, this study proposes a damage and debris analysis framework harnessing reality capture through aerial imagery and photogrammetry. Within this framework, a region-based neural network is leveraged to detect debris locations in aerial imagery with favorable performance. In a testbed within the Beaumont-Port Arthur region, in Southeast Texas, this study performs 3D reality captures of the built environment. Since the accuracy of the 3D reality capture is of importance in research areas associated with time-sensitive disaster response, we further investigate the optimal 2D aerial imagery overlap ratio required to generate a sufficiently accurate 3D model for disaster impact analysis and debris volume estimation. Results indicate that, in the case of aerial imagery for infrastructure systems, a minimum of 60 % overlap is recommended for damage assessment and debris analysis. In contrast, for flat green areas, a minimum of 50 % overlap is adequate. Overall, for disaster response applications, our study reveals that an overlap ratio between 60 % and 70 % is optimal for achieving a balance between time efficiency and data quality in aerial data collection. Furthermore, these quantitative recommendations are crucial for enabling efficient disaster response efforts. Additionally, our study outcomes will improve disaster impact analysis and facilitating timely and effective response strategies.

Artificial intelligence↗

Hierarchical Conceptual Model Event and Activity Domains for Forecasting State-Sponsored Civil Nuclear Power Activities

In FY20, the Savannah River National Laboratory and the Sanghani Center for Artificial Intelligence and Data Analytics (Virginia Tech) entered a collaboration funded by the Department of Energy’s Office of Defense Nuclear Nonproliferation Research and Development to develop a machine learning based modeling pipeline to extract proliferation events of interest from open data sources. The prototype modeling pipeline that was developed relies on the use of time dependent word embedding models to identify contextual shifts in key words and phrases that act as indicators of events of interest. The FY20- 21 efforts were focused on a narrow topical domain of forecasting “fissile core fabrication” at the Savannah River Site prior to its official announcement in 2018. In FY22, the research team was funded to continue development of the modeling pipeline by applying it to the problem of forecasting new, and/or significant changes to existing, civil nuclear power reactors around the world. In this effort, the development will focus on proving applicability to a broader topical domain and in data environments that may contain more sparse information, relative to the United States. In this report, the worldwide landscape of civil nuclear reactors is outlined, the timeline of interest is defined, and a hierarchical conceptual model is established to identify the activity domains of interest and the event domains of interest. This preliminary effort will guide the curation of a glossary of key terms for data acquisition, as well as the downstream modeling efforts.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Optimal vocabulary selection approaches for privacy-preserving deep NLP model training for information extraction and cancer epidemiology

With the use of artificial intelligence and machine learning techniques for biomedical informatics, security and privacy concerns over the data and subject identities have also become an important issue and essential research topic. Without intentional safeguards, machine learning models may find patterns and features to improve task performance that are associated with private personal information. The privacy vulnerability of deep learning models for information extraction from medical textural contents needs to be quantified since the models are exposed to private health information and personally identifiable information. The objective of the study is to quantify the privacy vulnerability of the deep learning models for natural language processing and explore a proper way of securing patients’ information to mitigate confidentiality breaches. The target model is the multitask convolutional neural network for information extraction from cancer pathology reports, where the data for training the model are from multiple state population-based cancer registries. This study proposes the following schemes to collect vocabularies from the cancer pathology reports; (a) words appearing in multiple registries, and (b) words that have higher mutual information. We performed membership inference attacks on the models in high-performance computing environments. The comparison outcomes suggest that the proposed vocabulary selection methods resulted in lower privacy vulnerability while maintaining the same level of clinical task performance.

59 BASIC BIOLOGICAL SCIENCES↗

Extending High-Level Synthesis with AI/ML Methods

Artificial Intelligence (AI) and Machine Learning (ML) methods provide significant opportunities of improving quality of results when performing high-level synthesis (HLS). For example, they can be used to model and predict metrics of the final design (e.g., area, considering aspects such as interconnect overhead for different device technologies), facilitating exploration when searching for the best design trade-offs. They can also enable identifying hidden correlations across the various phases of the synthesis and the various optimizations performed, identifying the most effective pipelines. Finally, in more general terms, bio-inspired heuristic algorithms can improve the design space exploration for the synthesis process in terms of time and quality of the result. This paper discusses opportunities and challenges to augment HLS with AI/ML using as example flow the SODA Synthesizer, an open-source hardware generation toolchain which includes SODA-OPT, a hardware/software partitioning and pre-optimization tool developed with the MLIR framework, and PandA-Bambu, a state-of-the art HLS tool. SODA interfaces with OpenROAD to provide a complete end-to-end toolchain.

artificial intelligence↗

Increasing the Reproducibility and Replicability of Supervised AI/ML in the Earth Systems Science by Leveraging Social Science Methods

Artificial intelligence (AI) and machine learning (ML) pose a challenge for achieving science that is both reproducible and replicable. The challenge is compounded in supervised models that depend on manually labeled training data, as they introduce additional decision-making and processes that require thorough documentation and reporting. We address these limitations by providing an approach to hand labeling training data for supervised ML that integrates quantitative content analysis (QCA)—a method from social science research. The QCA approach provides a rigorous and well-documented hand labeling procedure to improve the replicability and reproducibility of supervised ML applications in Earth systems science (ESS), as well as the ability to evaluate them. Specifically, the approach requires (a) the articulation and documentation of the exact decision-making process used for assigning hand labels in a “codebook” and (b) an empirical evaluation of the reliability” of the hand labelers. In this paper, we outline the contributions of QCA to the field, along with an overview of the general approach. We then provide a case study to further demonstrate how this framework has and can be applied when developing supervised ML models for applications in ESS. With this approach, we provide an actionable path forward for addressing ethical considerations and goals outlined by recent AGU work on ML ethics in ESS.

58 GEOSCIENCES↗

AI Improves the Accuracy, Reliability, and Economic Value of Continental‐Scale Flood Predictions

Accurate flood early warnings are critical to minimize damage and loss of life. Current large‐scale operational forecasting systems, however, have limited accuracy, description of uncertainty, and computational efficiency. While Artificial intelligence (AI) can address these limitations in principle, the accuracy and reliability of AI forecasts have thus far proven insufficient. Here we present a novel hybrid framework that integrates AI‐based machinery termed Errorcastnet (ECN) with the National Water Model (NWM) to showcase the potential of ensemble AI flood forecasts over the contiguous U.S. ECN boosts prediction accuracy four‐ to six‐fold across lead times of 1–10 days, while providing uncertainty quantification. It also outperforms Google's state‐of‐the‐art global AI model. ECN‐based forecasts offer superior economic value (up to four‐fold) for decision‐making as compared to those from NWM alone. ECN performs well in varied ecoregions, physiography, and land management conditions. The framework is computationally efficient, enabling national‐scale ensemble forecasts in minutes.

artificial intelligence↗

ChemComp: A Compilation Framework for Computing with Chemical Reaction Networks

The acceleration of scientific computation, data analytics, and artificial intelligence is driving a surge in computational requirements. Yet, state-of-the-art high-performance computing systems are approaching physical limitations that impede further significant improvements in energy efficiency. As we move towards post-exascale computing systems, innovative approaches are necessary to overcome this barrier in power consumption. Novel analog and hybrid digital-analog architectures hold promise for enhancing energy efficiency by several orders of magnitude. Biochemical computation stands out among the various solutions being explored due to its potential to enable new classes of devices with immense computational capabilities. These devices can capitalize on the inherent efficacy of biological cells in solving optimization problems and are scalable through increasing reaction system size or vessel capacity, potentially satisfying scientific computing's high-performance requirements. Nonetheless, several theoretical and practical limitations persist, including problem formulation and mapping to chemical reaction networks (CRNs) and implementation of actual CRN devices. In this paper, we propose a framework for biochemical computation using systems chemistry. We present the initial components of our approach: an abstract chemical reaction dialect implemented as a multi-level intermediate representation (MLIR) compiler extension and a pathway to represent mathematical problems with CRNs. To showcase the potential of this approach, we emulate a simplified chemical reservoir device. This work lays the groundwork for leveraging chemistry's computing potential in creating energy-efficient, high-performance computing systems tailored to contemporary computational needs.

artificial intelligence↗

Scalable Technologies Achieving Risk-Informed Condition-Based Predictive Maintenance Enhancing the Economic Performance of Operating Nuclear Power Plants

The primary objective of the research presented in this report is to develop scalable technologies that are deployable across plant assets and across the nuclear fleet to achieve risk-informed predictive maintenance (PdM) strategies at commercial nuclear power plants (NPPs). Over the years, the nuclear fleet has relied on labor-intensive and time-consuming preventive maintenance (PM) programs, driving up operation and maintenance (O&M) costs to achieve high capacity factors. A well-constructed risk-informed PdM approach for an identified plant asset has been developed in this research, taking advantage of advancements in data analytics, machine learning (ML), artificial intelligence (AI), physics-informed modeling, and visualization. These technologies would allow commercial NPPs to reliably transition from current labor-intensive PM programs to a technology driven PdM program, eliminating unnecessary O&M costs. The work presented in the report is being developed as part of a collaborative research effort between Idaho National Laboratory and Public Service Enterprise Group Nuclear, LLC. This report (1) reflects the results of work by LWRS Program researchers with PSEG, Nuclear LLC-owned Salem and Hope Creek Nuclear Power Plants; (2) presents utilization of circulating water system (CWS) heterogeneous data and fault modes from both the Salem and Hope Creek nuclear power plant sites to develop salient fault signatures associated with each fault mode; (3) describes the integration of component-level predictive models into a robust system-level model enabled by the federated-transfer learning; (4) describes the development of physics-informed model of circulating water pump and motor; (5) develops a scalable risk and economic model; and (6) outlines the development of a user-centric visualization application. The outcomes presented in this report lays the foundation and provides a much-needed technical basis to focus on explainability and trustworthiness of ML and AI-based technologies, as part of future research.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Computational tools and data integration to accelerate vaccine development: challenges, opportunities, and future directions

The development of effective vaccines is crucial for combating current and emerging pathogens. Despite significant advances in the field of vaccine development there remain numerous challenges including the lack of standardized data reporting and curation practices, making it difficult to determine correlates of protection from experimental and clinical studies. Significant gaps in data and knowledge integration can hinder vaccine development which relies on a comprehensive understanding of the interplay between pathogens and the host immune system. In this review, we explore the current landscape of vaccine development, highlighting the computational challenges, limitations, and opportunities associated with integrating diverse data types for leveraging artificial intelligence (AI) and machine learning (ML) techniques in vaccine design. We discuss the role of natural language processing, semantic integration, and causal inference in extracting valuable insights from published literature and unstructured data sources, as well as the computational modeling of immune responses. Furthermore, we highlight specific challenges associated with uncertainty quantification in vaccine development and emphasize the importance of establishing standardized data formats and ontologies to facilitate the integration and analysis of heterogeneous data. Through data harmonization and integration, the development of safe and effective vaccines can be accelerated to improve public health outcomes. Looking to the future, we highlight the need for collaborative efforts among researchers, data scientists, and public health experts to realize the full potential of AI-assisted vaccine design and streamline the vaccine development process.

60 APPLIED LIFE SCIENCES↗

Beyond Optimization: Exploring Novelty Discovery in Autonomous Experiments

Autonomous experiments (AEs) are transforming how scientific research is conducted by integrating artificial intelligence with automated experimental platforms. Current AEs primarily focus on the optimization of a predefined target; while accelerating this goal, such an approach limits the discovery of unexpected or unknown physical phenomena. Here, we introduce a novel framework, INS 2 ANE (Integrated Novelty Score−Strategic Autonomous Non-Smooth Exploration), to enhance the discovery of novel phenomena in autonomous microscopy experimentation. Our method integrates two key components: (1) a novelty scoring system that evaluates the uniqueness of experimental results and (2) a strategic sampling mechanism that promotes exploration of under-sampled regions even if they appear less promising by conventional criteria. We validate this approach on a preacquired data set with a known ground truth comprising of image−spectral pairs. We further implement the process on autonomous scanning probe microscopy experiments. INS 2 ANE significantly increases the diversity of explored phenomena in comparison to conventional optimization routines, enhancing the likelihood of discovering previously unobserved phenomena. These results demonstrate the potential for autonomous microscopy experiments to enhance the scientific discovery by navigating complex experimental spaces to uncover novel phenomena.

Materials↗

A Hybrid AI/ML and Computational Mechanics Based Approach for Time-Series State and Fatigue Life Estimation of Nuclear Reactor Components

Environmental fatigue modeling is a complex problem due to multiple failure modes and their intermixing. The failure modes are function of various underlying causes in addition to the corrosive effect of reactor coolant environment. Some of the major causes are time-dependence of material associated with cyclic loading, load sequence effect associated with random/variable amplitude loading, effect of strain amplitude and rates, effect of varying temperature (along both temporal and spatial directions) and the effect of mean strain and stress. The nonlinear intermixing of failure modes associated with above mentioned causing parameters makes the environmental fatigue modeling is a challenging task. Because of this challenge, fatigue is traditionally being modeled based on experimental data. However, test based empirical approach often requires hundreds of fatigue tests to model the above-mentioned intermixing failure causes even for a single material system. The problem is further exaggerated for reactor component made from multi-material systems such as made from both carbon and stainless-steel base metals and their similar and dissimilar metal welds. With the difficulty of conducting hundreds of fatigue tests to capture the above-mentioned intermixing failure causes, fatigue modeling approaches often depends on empirical models based on limited available test data such as available through ASME code and NUREG 6909. However, these limited test-data-based models may not be enough to accurately predict the life of reactor components. Accurate prediction of life of reactor component would become a necessity, particularly when the license of the reactors to be extended for long-term-operation (LTO) that is for well beyond its original design life of 40 years. The requirement of extending the license of reactor under LTO requires hundreds of fatigue tests to be conducted to understand the mechanism associated with the above-mentioned interdependent failure causes. However, conducting large number of fatigue tests is not a feasibility due to the cost involved. To address this issues Argonne National Laboratory (ANL) with the sponsorship of DOE Light Water Reactor Sustainability (LWRS) program trying to develop a hybrid predictive modeling approach. This is based on limited experiment-data, Artificial-intelligence (AI) – Machine-Learning (ML) - Deep-Learning (DL) based techniques and Multiphysics-computational-mechanics based modeling tools. The hybrid approach not-only can improve the accuracy of the existing stress analysis and fatigue modeling approach but also can reduce the over-dependency on test-based approach. Towards this goal following are some of the major contributions based on ANL’s FY-20 environmental fatigue modeling activities: 1) A cyclic plasticity material model database for 82/182 dissimilar metal weld, which can be readily shared with US nuclear industry and regulatory agency on request. 2) A well validated analytical modeling methodology to perform cycle-by-cycle stress prediction under both constant amplitude fatigue loading and variable amplitude fatigue loading (with load-sequence effect). 3) An AI/ML/DL based methodology to predict unmeasurable cyclic strain based on other available sensor signals. This type of approach can be used for estimating strain in real reactor components from other sensor readings. 4) An AI/ML based approach to improve the US capability on environmental fatigue testing. This is by improving ANL’s existing environmental fatigue testing capacity to conduct ASME required strain-controlled tests (by controlling strain amplitudes and its rate), while not measuring the strain (due to the difficulty of placing an extensometer in a narrow autoclave in a PWR-water-test system). 5) A simulation and experiment based probabilistic modeling methodology for time-series fatigue state and life estimation of reactor metal such as dissimilar metal weld.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗