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Machine learning-led semi-automated medium optimization reveals salt as key for flaviolin production in Pseudomonas putida

Although synthetic biology can produce valuable chemicals in a renewable manner, its progress is still hindered by a lack of predictive capabilities. Media optimization is a critical, and often overlooked, process which is essential to obtain the titers, rates and yields needed for commercial viability. Here, we present a molecule- and host-agnostic active learning process for media optimization that is enabled by a fast and highly repeatable semi-automated pipeline. Its application yielded 60% and 70% increases in titer, and 350% increase in process yield in three different campaigns for flaviolin production in Pseudomonas putida KT2440. Explainable Artificial Intelligence techniques pinpointed that, surprisingly, common salt (NaCl) is the most important component influencing production. The optimal salt concentration is very high, comparable to seawater and close to the limits that P. putida can tolerate. The availability of fast Design-Build-Test-Learn (DBTL) cycles allowed us to show that performance improvements for active learning are rarely monotonous. This work illustrates how machine learning and automation can change the paradigm of current synthetic biology research to make it more effective and informative, and suggests a cost-effective and underexploited strategy to facilitate the high titers, rates and yields essential for commercial viability.

59 BASIC BIOLOGICAL SCIENCES

Postearthquake Damage Mapping via Remote Sensing: Lessons From the 2023 Türkiye Disaster

This review addresses the urgent need for scalable, accurate, and reproducible remote sensing solutions following the February 2023 Türkiye earthquakes. It synthesizes the contributions of five peer-reviewed studies published in the IEEE JSTARS Special Issue on postearthquake damage and risk assessment. These studies cover areas such as damage classification with deep learning, fusion of multisource remote sensing data, creation of benchmark datasets, detailed damage mapping, and analysis of geophysical signals using outgoing longwave radiation. The article summarizes the methodological approaches and the practical relevance of the reviewed studies for detecting, evaluating, and quantifying damage, and outlines key challenges, including model generalization, class ambiguity, and data integration. It also discusses emerging trends, including explainable artificial intelligence, multimodal data fusion, and open-data platforms. This synthesis provides a foundation for building robust, interpretable, and real-time disaster response systems and aims to guide future research in earthquake-related Earth observation and rapid damage assessment.

Taskin, Gulsen [Istanbul Technical University] (OR

Transcripts and genomic intervals associated with variation in metabolite abundance in maize leaves under field conditions

Abstract Plants exhibit extensive environment-dependent intraspecific metabolic variation, which likely plays a role in determining variation in whole plant phenotypes. However, much of the work seeking to use natural variation to link genes and transcript’s impacts on plant metabolism has employed data from controlled environments. Here, we generated and analyzed data on the variation in the abundance of 26 metabolites across 660 maize inbred lines under field conditions. We employ these data and previously published transcript and whole plant phenotype data reported for the same field experiment to identify both genomic intervals (through genome-wide association studies (GWAS)) and transcripts (using both transcriptome-wide association studies (TWAS) and an explainable artificial intelligence (AI) approach based on random forest (RF)) associated with variation in metabolite abundance. Both genome-wide association and random forest-based methods identified substantial numbers of significant associations including genes with plausible links to the metabolites they are associated with. In contrast, the transcriptome-wide association identified only six significant associations. In three cases, genetic markers associated with metabolic variation in our study colocalized with markers linked to variation in non-metabolic traits scored in the same experiment. We speculate that the poor performance of transcriptome-wide association studies in identifying transcript-metabolite associations may reflect a high prevalence of non-linear interactions between transcripts and metabolites and/or a bias towards rare transcripts playing a large role in determining intraspecific metabolic variation.

Mathivanan, Ramesh Kanna

ATTRACTOR: Autonomy Teaming and TRAjectories for Complex Trusted Operational Reliability

Autonomous systems (AS) are crucial to realizing the vision of new, complex transportation modes, such as advanced air mobility (AAM) and urban air mobility (UAM). A chief barrier to induction of AS into aviation is insufficient understanding of AS reliability in time-critical and safety-critical environments—an obstacle to certification. ATTRACTOR is aimed at building a basis for certification of classes of autonomous cyber-physical-human systems (CPHS) via establishing metrics and models of trustworthiness and trust in multi-agent team interactions, analyzable trajectories, explainability of computational algorithms (explainable artificial intelligence, or XAI), and persistent modeling and simulation, in the context of missions planning and operation. By “building a basis for certification,” we mean acquiring an understanding of when a system is trustworthy and developing computable means to estimate trustworthiness and trust in order to eventually inform functional requirements that contribute to certification. The outcomes are applicable not just to aviation but to all domains that rely on autonomous systems.

Autonomy

A Data-Driven Approach for High-Impedance Fault Localization in Distribution Systems

Accurate and quick identification of high-impedance faults (HIFs) is critical for the reliable operation of distribution systems. Unlike other faults in power grids, HIFs are very difficult to detect by conventional overcurrent relays due to the low fault current. Although HIFs can be affected by various factors, the voltage-current characteristics can substantially imply how the system responds to the disturbance and thus provides opportunities to effectively localize HIFs. In this work, we propose a data-driven approach for the identification of HIF events. To tackle the nonlinearity of the voltage-current trajectory, first, we formulate optimization problems to approximate the trajectory with piecewise functions. Then we collect the function features of all segments as inputs and use the support vector machine approach to efficiently identify HIFs at different locations. Numerical studies on the IEEE 123-node test feeder demonstrate the validity and accuracy of the proposed approach for real-time HIF identification.

explainable artificial intelligence

Chemical classification program synthesis using generative artificial intelligence

Accurately classifying chemical structures is essential for cheminformatics and bioinformatics, including tasks such as identifying bioactive compounds of interest, screening molecules for toxicity to humans, finding non-organic compounds with desirable material properties, or organizing large chemical libraries for drug discovery or environmental monitoring. However, manual classification is labor-intensive and difficult to scale to large chemical databases. Existing automated approaches either rely on manually constructed classification rules, or are deep learning methods that lack explainability. This work presents an approach that uses generative artificial intelligence to automatically write chemical classifier programs for classes in the Chemical Entities of Biological Interest (ChEBI) database. These programs can be used for efficient deterministic run-time classification of SMILES structures, with natural language explanations. The programs themselves constitute an explainable computable ontological model of chemical class nomenclature, which we call the ChEBI Chemical Class Program Ontology (C3PO). We validated our approach against the ChEBI database, and compared our results against deep learning models and a naive SMARTS pattern based classifier. C3PO outperforms the naive classifier, but does not reach the performance of state of the art deep learning methods. However, C3PO has a number of strengths that complement deep learning methods, including explainability and reduced data dependence. C3PO can be used alongside deep learning classifiers to provide an explanation of the classification, where both methods agree. The programs can be used as part of the ontology development process, and iteratively refined by expert human curators.

Artificial Intelligence

XSub: Explanation-Driven Adversarial Attack against Blackbox Classifiers via Feature Substitution

Despite its significant benefits in enhancing the transparency and trustworthiness of artificial intelligence (AI) systems, explainable AI (XAI) can unintentionally provide adversaries with insights into blackbox models, increasing their vulnerability to various attacks. In this paper, we develop a novel explanation-driven adversarial attack against blackbox classifiers based on feature substitution, called XSub. The key idea of XSub is to strategically replace important features (identified via XAI) in the original sample with corresponding important features of a different label, thereby increasing the likelihood of the model misclassifying the perturbed sample. XSub only requires a minimal number of queries and can be easily extended to launch backdoor attacks in case the attacker has access to the model's training data. Our evaluation shows that XSub is not only effective and stealthy but also low-cost, showcasing its feasibility across a wide range of AI applications.

adversarial attack

Serious Gaming for Building a Basis of Certification via Trust and Trustworthiness of Autonomous Systems

Autonomous systems governed by a variety of adaptive and nondeterministic algorithms are being planned for inclusion into safety-critical environments, such as unmanned aircraft and space systems in both civilian and military applications. However, until autonomous systems are proven and perceived to be capable and resilient in the face of unanticipated conditions, humans will be reluctant or unable to delegate authority, remaining in control aided by machine-based information and decision support. Proving capability, or trustworthiness, is a necessary component of certification. Perceived capability is a component of trust. Trustworthiness is an attribute of a cyber-physical system that requires context-driven metrics to prove and certify. Trust is an attribute of the agents participating in the system and is gained over time and multiple interactions through trustworthy behavior and transparency. Historically, artificial intelligence and machine learning systems provide answers without explanation - without a rationale or insight into the machine “thinking”. In order to function as trusted teammates, machines must be able to explain their decisions and actions. This transparency is a product of both content and communication. NASA’s Autonomy Teaming & TRAjectories for Complex Trusted Operational Reliability (ATTRACTOR) project seeks to build a basis for certification of autonomous systems via establishing metrics for trustworthiness and trust in multi-agent team interactions, using AI (Artificial Intelligence) explainability and persistent modeling and simulation, in the context of mission planning and execution, with analyzable trajectories. Inspired by Massively Multiplayer Online Role Playing Games (MMORPG) and Serious Gaming, the proposed ATTRACTOR modeling and simulation environment is similar to online gaming environments in which player (aka agent) participants interact with each other, affect their environment, and expect the simulation to persist and change regardless of any individual agent’s active participation. This persistent simulation environment will accommodate individual agents, groups of self-organizing agents, and large-scale infrastructure behavior. The effects of the emerging adaptation and coevolution can be observed and measured to building a basis of measurable trustworthiness and trust, toward certification of safety-critical autonomous systems.

Allen, B. Danette

Using a Large Language Model for Accurate Technical Language Generation in the Predictive Maintenance of Circulating Water Systems in Nuclear Power Plants

Machine learning (ML) methods for predictive maintenance (PdM) are emerging as effective proactive strategies for diagnosing equipment degradation and enabling effective decision-making. However, explainability and trustworthiness of artificial intelligence are two salient challenges that need to be addressed for wider deployment of these technologies in nuclear power plants (NPPs). Large language models (LLMs) offer a unique approach to tackle these challenges by explaining PdM, work orders, diagnosis results, and ML algorithms to users, who may not be familiar with ML and PdM in general. Moreover, by dynamically retrieving relevant information from technical documents and evaluating factuality of LLM generation, the accuracy and relevance of LLM generations can be improved. This work demonstrates using LLMs to explain the causes and consequences of circulating water system failures based on multiyear NPP work orders. This work tests the capability of multimodal LLM approaches in explaining the differences in the circulating water system from both the Salem and Hope Creek NPPs using both text and image resources. This work also demonstrates the use of multimodal LLMs in describing the diagnosis tab of a predictive maintenance software named VIsualization for PrEdictive maintenance Recommendation (VIPER) to users.

22 - GENERAL STUDIES OF NUCLEAR REACTORS

Plan-Property Dependencies are Useful: A User Study

The trade-offs between different desirable plan properties –e. g. PDDL temporal plan preferences – are often difficult to understand. Recent work proposes to address this by iterative planning with explanations elucidating the dependencies between such plan properties. Users can ask questions of the form “Why does the plan you suggest not satisfy property p?”, which are answered by “Because then we would have to forego q” where ¬q is entailed by p in plan space. It has been shown that such plan-property dependencies can be computed reasonably efficiently. But is this form of explanation actually useful for users? We contribute a user study evaluating that question. We design use cases from three domains and run a large user study (N= 40 for each domain, ca. 40 minutes work time per user and domain) on the internet platform Prolific. Comparing users with vs. without access to the explanations, we find that the explanations tend to enable users to identify better trade-offs between the plan properties, indicating an improved understanding of the task.

Explainable Planning

Demystifying Cyberattacks: Potential for Securing Energy Systems With Explainable AI : Preprint

Modernization of energy systems has led to in- creased interactions among multiple critical infrastructures and diverse stakeholders making the challenge of operational decision making more complex and at times beyond cognitive capabilities of human operators. The state-of-the-art machine learning and deep learning approaches show promise of supporting users with complex decision-making challenges, such as those occurring in our rapidly transforming cyber-physical energy systems. However, successful adoption of data-driven decision support technology for critical infrastructure will be dependent on the ability of these technologies to be trustworthy and contextually interpretable. In this paper, we investigate the feasibility of implementing XAI for interpretable detection of cyberattacks in the energy system. Leveraging a proof-of-concept simulation use case of detection of a data falsification attack on a photovoltaic system using XGBoost algorithm, we demonstrate how Local Interpretable Model-Agnostic Explanations (LIME), a flavor XAI approach, can help provide contextual and actionable interpretation of cyberattack detection.

artificial intelligence

Human Factors Considerations in Artificial Intelligence Applications for Nuclear Power Plants

In recent years, there has been a wave of artificial intelligence (AI) technologies that offer to solve problems from shopping habits to mortgage approvals to critical systems operations. The rapidity of the development of these systems has led to both excitement and apprehension about the roles these systems should play in our modern societies. Furthermore, this paper focuses on the critical infrastructure industry, in general, and nuclear power generation, in particular, and seeks to scrutinize how we can leverage these novel technologies in human-centered ways to maintain or enhance the established high levels of reliability and resilience in these industries. First, we discuss the broader aspects of cognitive systems and activities that are critical to understanding the human-AI space. Then we explore different approaches to explainability in AI and the notions of trust. We then move on to discuss several human factors concepts and methods and how they can support the design of human-AI teams. We then explore recent research related to nuclear power that has been undertaken and evaluate the current industry and regulatory landscapes. Finally, we discuss identified research gaps and recommendations for solving these for the critical infrastructure space.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS

NuGraph2 with explainability: post-hoc explanations for geometric neural network predictions

With the growing popularity of artificial intelligence (AI) used for scientific applications, the ability of attribute a result to a reasoning process from the network is in high demand for robust scientific generalizations to hold. In this work we aim to motivate the need for and demonstrate the use of post-hoc explainability methods when applied to AI methods used in scientific applications. To this end, we introduce explainability add-ons to the existing graph neural network (GNN) for neutrino tagging, NuGraph2. The explanations take the form of a suite of techniques examining the output of the network (node classifications) and the edge connections between them, and probing of the latent space using novel general-purpose tools applied to this network. We show how none of these methods are singularly sufficient to show network ‘understanding’, but together can give insights into the processes used in classification. While these methods are tested on the NuGraph2 application, they can be applied to a broad range of networks, not limited to GNNs. The code for this work is publicly available on GitHub at https://github.com/voetberg/XNuGraph.

Voetberg, Margaret [Fermilab] (ORCID:0009000527154

Role of Uncertainty Quantification in the Explainability of Large Language Models for the Nuclear Industry

The meteoric rise of generative artificial intelligence (AI) large language models (LLMs) has created an opportunity to utilize them to increase efficiencies in a multitude of industries. While LLMs carry great potential to revolutionize the manner in which work is performed, numerous known deficiencies limit their utility, including the black box nature of the models, the stochastic nature of the response (i.e., presenting the same prompt multiple times results in different responses), and the potential for hallucination. Widespread adoption of LLMs in safety-critical industries such as nuclear will require some form of explainability to assure end users that the LLM’s response to a given query is valid. Model uncertainty is inherently linked to the concepts of trust and explainability, and can be used to identify situations in which the model is insufficiently certain about its answer. Although uncertainty is not enough in and of itself to determine the suitability of an answer—a model can be very certain of an inaccurate answer—it still provides valuable supporting information. Practical methodologies for gauging or quantifying the uncertainty in LLM outputs are presented herein, along with examples based on nuclear-specific prompts.

22 - GENERAL STUDIES OF NUCLEAR REACTORS

TCR-H: explainable machine learning prediction of T-cell receptor epitope binding on unseen datasets

Artificial-intelligence and machine-learning (AI/ML) approaches to predicting T-cell receptor (TCR)-epitope specificity achieve high performance metrics on test datasets which include sequences that are also part of the training set but fail to generalize to test sets consisting of epitopes and TCRs that are absent from the training set, i.e., are ‘unseen’ during training of the ML model. We present TCR-H, a supervised classification Support Vector Machines model using physicochemical features trained on the largest dataset available to date using only experimentally validated non-binders as negative datapoints. TCR-H exhibits an area under the curve of the receiver-operator characteristic (AUC of ROC) of 0.87 for epitope ‘hard splitting’ (i.e., on test sets with all epitopes unseen during ML training), 0.92 for TCR hard splitting and 0.89 for ‘strict splitting’ in which neither the epitopes nor the TCRs in the test set are seen in the training data. Furthermore, we employ the SHAP (Shapley additive explanations) eXplainable AI (XAI) method for post hoc interrogation to interpret the models trained with different hard splits, shedding light on the key physiochemical features driving model predictions. TCR-H thus represents a significant step towards general applicability and explainability of epitope:TCR specificity prediction.

60 APPLIED LIFE SCIENCES

NASA Framework for the Ethical Use of Artificial Intelligence (AI)

The NASA Framework for the Ethical Use of Artificial Intelligence (AI) provides six key principles to guide NASA's use of AI. The principles are NASA's AI must be 1. Fair, 2., Explainable and transparent, 3. Accountable, 4. Secure and safe, 5. Human-centric and societally beneficial, and 6. Scientifically and technically robust. The framework describes each ethical AI principle, and then applies that principle to NASA work. The framework also includes a list of questions practitioners should use to guide their AI work. Finally, the framework focuses on concrete, practical considerations for the next five - ten years, while also beginning to lay the foundation for longer-term disruptive change as human-level (or beyond) AI is created.

Artificial Intelligence