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Enhanced accuracy through ensembling of randomly initialized auto-regressive models for dynamical systems

Computational mechanics simulations using traditional finite element methods (FEM) require prohibitively expensive computational resources for real-time engineering applications, design optimization, and digital twin implementations. While machine learning (ML) surrogate models offer significant computational speedups, autoregressive ML models for time-dependent mechanical systems suffer from error accumulation that compromises long-term prediction reliability - a critical concern for engineering applications where accuracy over extended time horizons is essential for safety and performance assessments. Here, we propose a deep ensemble framework specifically designed to address this challenge in computational mechanics applications, where multiple ML surrogate models with random weight initializations are trained in parallel and their predictions aggregated during inference. This approach leverages statistical diversity to maximize information gain from a fixed set of training data and to mitigate error propagation, while maintaining the computational efficiency that makes ML surrogates attractive for engineering practice. We validate the framework on three representative problems spanning critical areas of computational mechanics: stress field evolution in heterogeneous microstructures under complex loading (relevant to advanced materials design and composite analysis), planetary-scale shallow water dynamics (applicable to environmental and geotechnical engineering), and Gray-Scott reaction-diffusion systems (relevant to mass transport and chemical process engineering). Across all test cases, the ensemble approach demonstrates consistent error reduction of 15-33% compared to individual models. The codes for this work are available on GitHub (https://github.com/Graham-Brady-Research-Group/AutoregressiveEnsemble_SpatioTemporal_Evolution).

autoregressive prediction↗

AMIA KDDM Working Group Collaborative Workshop: Enriching Electronic Health Records with Social Determinants of Health to Improve Outcomes and Health Equity

Prior research has demonstrated that social determinants of health (SDoH) are major drivers of health outcomes and contributors to widespread health inequities. It was estimated that, in the United States, SDoH could be responsible for up to 40% of all preventable deaths, significantly higher than the 10-15% for which better medical care is responsible. Public health interventions that target SDoH are instrumental for improving health outcomes and reducing long-standing health inequities. Currently, most mainstream EHR vendors have implemented SDoH screeners in their EHR systems. However, the utility of the screeners is low, rendering patient-level SDoH still widely unavailable in the structured fields. SDoH are sometimes mentioned in free-text clinical notes (e.g., social context section) where natural language processing (NLP) can be applied to extract relevant information. Contextual-level SDoH can be identified from multiple data sources, many of which are publicly available and spatiotemporally linked to EHR data. As such, there is an opportunity for the KDDM research community to create innovative solutions to draw meaningful insights by creating and using rich data with SDoH to improve health outcomes while reducing disparities. In this workshop organized by AMIA Knowledge Discovery and Data Mining Working Group (AMIA KDDM WG), we will invite world-leading experts from academia, national laboratories, and life science industry with varied backgrounds in biomedical informatics, epidemiology, data science, machine learning, natural language processing, and pediatric cardiology to discuss the best practice of capturing, standardizing, and using SDoH information in various applications aiming at improving outcomes and health equity.

He, Zhe↗

Applications of fuzzy logic and best-worst method for tritium sensor selection

Accurate assessment of tritium as a fuel source is critical in fusion reactions, necessitating effective sensor evaluation methods. This study investigates a multi-criteria decision-making framework for selecting tritium sensors, integrating fuzzy logic to enhance decision quality. Initial attempts at applying fuzzy logic were found to be too elementary and failed to capture the complexity of multi-criteria selection; this prompted a refined approach that incorporated expert insights and advanced ranking techniques for sensor evaluation. The research used a two-stage methodology. In the first stage, important criteria and sub-criteria for sensor performance were identified and defined. These criteria were then weighted and scored using a fuzzy best-worst method, drawing upon expert opinions to ensure relevance and validity. The second stage involved interpreting information about varying sensors to rank them based on their overall criteria scores, encouraging the selection of the most suitable options. The result of the study is a proposed method for effective sensor selection in fusion reactors, which in turn will significantly improve the reliability of tritium monitoring in fusion applications.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

A Managed Tokens Service for Securely Keeping and Distributing Grid Tokens

Fermilab is transitioning authentication and authorization for grid operations to using bearer tokens based on the WLCG Common JWT (JSON Web Token) Profile. One of the functionalities that Fermilab experimenters rely on is the ability to automate batch job submission, which in turn depends on the ability to securely refresh and distribute the necessary credentials to experiment job submit points. Thus, with the transition to using tokens for grid operations, we needed to create a service that would obtain, refresh, and distribute tokens for experimenters' use. This service would avoid the need for experimenters to be experts in obtaining their own tokens and would better protect the most sensitive long-lived credentials. Further, the service needed to be widely scalable, as Fermilab hosts many experiments, each of which would need their own credentials. To address these issues, we created and deployed a Managed Tokens Service. The service is written in Go, taking advantage of that language's native concurrency primitives to easily be able to scale operations as we onboard experiments. The service uses as its first credentials a set of kerberos keytabs, stored on the same secure machine that the Managed Tokens service runs on. These kerberos credentials allow the service to use htgettoken via condor_vault_storer to store vault tokens in the HTCondor credential managers (credds) that run on the batch system scheduler machines (HTCondor schedds); as well as downloading a local, shorter-lived copy of the vault token. The kerberos credentials are then also used to distribute copies of the locally-stored vault tokens to experiment submit points.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

AutoLabs: cognitive multi-agent systems with self-correction for autonomous chemical experimentation

The automation of chemical research through self-driving laboratories (SDLs) promises to accelerate scientific discovery, yet the reliability and granular performance of the underlying AI agents remain critical, under-examined challenges. In this work, we introduce AutoLabs, a self-correcting, multi-agent architecture designed to autonomously translate natural-language instructions into executable protocols for a high-throughput liquid handler. The system engages users in dialogue, decomposes experimental goals into discrete tasks for specialized agents, performs tool-assisted stoichiometric calculations, and iteratively self-corrects its output before generating a hardware-ready file. We present a comprehensive evaluation framework featuring five benchmark experiments of increasing complexity, from simple sample preparation to multi-plate timed syntheses. Through a systematic ablation study of 20 agent configurations, we assess the impact of reasoning capacity, architectural design (single- vs. multi-agent), tool use, and self-correction mechanisms. Our results demonstrate that agent reasoning capacity is the most critical factor for success, reducing quantitative errors in chemical amounts (nRMSE) by over 85% in complex tasks. When combined with a multi-agent architecture and iterative self-correction, AutoLabs approaches expert-authored reference procedures on the benchmark (F1-score > 0.89) on challenging multi-plate syntheses. These findings establish a clear blueprint for developing robust and trustworthy AI partners for autonomous laboratories, highlighting the synergistic effects of modular design, advanced reasoning, and self-correction to ensure both performance and reliability in high-stakes scientific applications. Code: https://github.com/pnnl/autolabs

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A pre-training and self-training approach for biomedical named entity recognition

Named entity recognition (NER) is a key component of many scientific literature mining tasks, such as information retrieval, information extraction, and question answering; however, many modern approaches require large amounts of labeled training data in order to be effective. This severely limits the effectiveness of NER models in applications where expert annotations are difficult and expensive to obtain. In this work, we explore the effectiveness of transfer learning and semi-supervised self-training to improve the performance of NER models in biomedical settings with very limited labeled data (250-2000 labeled samples). We first pre-train a BiLSTM-CRF and a BERT model on a very large general biomedical NER corpus such as MedMentions or Semantic Medline, and then we fine-tune the model on a more specific target NER task that has very limited training data; finally, we apply semi-supervised self-training using unlabeled data to further boost model performance. We show that in NER tasks that focus on common biomedical entity types such as those in the Unified Medical Language System (UMLS), combining transfer learning with self-training enables a NER model such as a BiLSTM-CRF or BERT to obtain similar performance with the same model trained on 3x-8x the amount of labeled data. We further show that our approach can also boost performance in a low-resource application where entities types are more rare and not specifically covered in UMLS.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Microgrid Conceptual Design Guidebook | 2022

This guide is meant to assist communities – from residents to energy experts to decision makers – in developing a conceptual microgrid design that meets site-specific energy resilience goals. Using the framework described in this guidebook, stakeholders can come together and start to quantify site-specific vulnerabilities, identify the most significant risks to delivery of electricity, and establish electric outage tolerances across the community. In addition to establishing minimum service needs, this framework encourages communities to consider broader sustainability goals and policy constraints and begin to estimate up-front costs associated with the installation of alternative microgrid solutions. The framework guides a community through data collection and a high-level assessment of its needs, constraints, and priorities, prior to engaging engineers, vendors, and contractors. The first sections of this guidebook provide a high-level primer on electric systems. The latter sections include guidance for step-by-step data gathering and analysis of site conditions. The ultimate product resulting from the stepwise approach is a conceptual microgrid design. A conceptual design is defined as an initial design (10%-20% complete) that considers the specific threats, needs, limitations, and investment options for a given location. Going through this exercise and developing the conceptual microgrid design as a community ensures the same community members who will ultimately live with the solution are the developers of its foundational design. Often, these are also the very same people who understand system tolerances and needs the best and are therefore the ideal candidates for establishing these criteria. Especially when it comes to evaluating critical infrastructure, it is the community that best understands the most critical services. The framework is intended to facilitate a systematic approach to planning for resilience and provide a deeper understanding of how to use a framework to make decisions around microgrid solutions. Like many processes where tradeoffs need to be considered, this is often an iterative process. If this guide serves to help educate and empower communities who are beginning the process of deploying a microgrid, it has met the goal of its authors.

24 POWER TRANSMISSION AND DISTRIBUTION↗

A Multilevel Approach To Addressing Emerging Technologies In Nuclear Security

Emerging technologies present a unique set of challenges to operators and regulators. Although emerging technologies can be used to strengthen nuclear security systems, they also can increase risks to nuclear facilities. The disruptive nature of emerging technologies could also leave operators unprepared for threats to nuclear materials or facilities. To address the potentially dangerous consequences associated with these innovations, strong adaptive mechanisms and international cooperation on threat mitigation and technological integration are vital. This paper examines the nuclear security implications of emerging technologies from an institutional (as opposed to technology-specific) perspective. Drawing on insights from a recent workshop series hosted by the Stimson Center and the National Nuclear Security Administration’s Office of Global Material Security, as well as research funded by Global Material Security and separate research conducted by Stimson, the paper begins with a definition of emerging technology that bounds the scope of the problem while leaving some margin for expert interpretation. The subsequent sections highlight the challenges as well as potential benefits that these technologies pose at each level of the nuclear security establishment, from the operators of sites hosting radiological or nuclear material, to regulators and national policy makers, to international institutions. Each section also includes specific recommendations for incorporating emerging technologies into radiological and nuclear security planning.

Andrews, Ian↗

Active learning of a crystal plasticity flow rule from discrete dislocation dynamics simulations

Continuum-scale material deformation models, such as crystal plasticity (CP), can significantly enhance their predictive accuracy by incorporating input from lower-scale (i.e. mesoscale) models. The procedure to generate and extract the relevant information is however typically complex and ad hoc, involving decision and intervention by domain experts, leading to long development times. In this study, we develop a principled approach for calibration of continuum-scale models using lower scale information by representing a CP flow rule as a Gaussian process model. This representation allows for efficient parameter space exploration, guided by the uncertainty embedded in the model through a process known as Bayesian optimization (BO). We demonstrate a semi-autonomous BO loop which instantiates discrete dislocation dynamics simulations whose initial conditions are automatically chosen to optimize the uncertainty of a model CP flow rule. Our self-guided computational pipeline efficiently generated a dataset and corresponding model whose error, uncertainty, and physical feature sensitivities were validated with comparison to an independent dataset four times larger, demonstrating a valuable and efficient active learning implementation readily transferable to similar material systems.

36 MATERIALS SCIENCE↗

Energy Resilient Recovery in Puerto Rico: Hurricane Maria Recovery Support

This report covers microgrids as a special application of distributed energy resources (DERs) in Puerto Rico. This is one of a series of reports describing the U.S. Department of Energy (DOE) multi-laboratory efforts undertaken. To ensure the sustainable, long-term recovery of Puerto Rico's electric power grid from hurricanes Maria and Irma and to build capacity to manage future potential natural disasters in the most secure and resilient way, DOE convened experts from multiple national laboratories to develop a comprehensive set of data, models, analytic tools, and studies, considering inputs from a wide variety of stakeholder groups, to support technically sound recommendations for Puerto Rico's energy investment decisions. In Phase 1 of the multi-laboratory effort to support Puerto Rico's recovery, the National Renewable Energy Laboratory (NREL) provided the utility company Puerto Rico Electric Power Authority (PREPA) recommendations for a new framework of interconnection standards to accelerate the integration of utility-scale, transmission-connected, renewable electrical generation and energy storage that ensure cross-technology compatibility and enable high deployment levels without compromising grid reliability, safety, or security (https://www.nrel.gov/docs/fy19osti/73848.pdf). In Phase 2, NREL published a report focused on the interconnection of distributed energy resources (DERs) to the electric distribution system in Puerto Rico (https://www.nrel.gov/docs/fy21osti/77127.pdf). This report familiarized the reader with Puerto Rico's distribution infrastructure and operational practices and procedures that are relevant to DER interconnection. The report also provided considerations for streamlining the interconnection process given the expected increase in deployments resulting from Puerto Rico's renewable portfolio standard goal of 100% renewables by 2050. Accordingly, the report identifies considerations and concerns associated with the increase in intermittent generation, strategies for DER interconnection best practices, and the potential use of the latest technological solutions identified in the latest revision of the Institute of Electrical and Electronics Engineers 1547-2018 interconnection standard. Additionally, the report identified ways to improve the physical resiliency of installed DERs. This task describes how distributed energy systems may participate in and contribute to improving the resiliency of Puerto Rico's energy infrastructure in the future. This report presents an analysis of the Puerto Rico grid to illustrate the possible different microgrid and minigrid scenarios. The capability to form sustained microgrids and minigrids has the potential to provide a high level of resiliency during disturbances on the grid. DERs, on the other hand, have the capability to aid in the microgrid operation by providing grid support as well as grid-forming functionality. Other tasks in Phase 3 include voltage regulation in distribution networks using DERs and transmission-and-distribution co-simulation.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DEEPEN Global Standardized Categorical Exploration Datasets for Magmatic Plays

DEEPEN stands for DE-risking Exploration of geothermal Plays in magmatic ENvironments. As part of the development of the DEEPEN 3D play fairway analysis (PFA) methodology for magmatic plays (conventional hydrothermal, superhot EGS, and supercritical), weights needed to be developed for use in the weighted sum of the different favorability index models produced from geoscientific exploration datasets. This was done using two different approaches: one based on expert opinions, and one based on statistical learning. This GDR submission includes the datasets used to produce the statistical learning-based weights. While expert opinions allow us to include more nuanced information in the weights, expert opinions are subject to human bias. Data-centric or statistical approaches help to overcome these potential human biases by focusing on and drawing conclusions from the data alone. The drawback is that, to apply these types of approaches, a dataset is needed. Therefore, we attempted to build comprehensive standardized datasets mapping anomalies in each exploration dataset to each component of each play. This data was gathered through a literature review focused on magmatic hydrothermal plays along with well-characterized areas where superhot or supercritical conditions are thought to exist. Datasets were assembled for all three play types, but the hydrothermal dataset is the least complete due to its relatively low priority. For each known or assumed resource, the dataset states what anomaly in each exploration dataset is associated with each component of the system. The data is only a semi-quantitative, where values are either high, medium, or low, relative to background levels. In addition, the dataset has significant gaps, as not every possible exploration dataset has been collected and analyzed at every known or suspected geothermal resource area, in the context of all possible play types. The following training sites were used to assemble this dataset: - Conventional magmatic hydrothermal: Akutan (from AK PFA), Oregon Cascades PFA, Glass Buttes OR, Mauna Kea (from HI PFA), Lanai (from HI PFA), Mt St Helens Shear Zone (from WA PFA), Wind River Valley (From WA PFA), Mount Baker (from WA PFA). - Superhot EGS: Newberry (EGS demonstration project), Coso (EGS demonstration project), Geysers (EGS demonstration project), Eastern Snake River Plain (EGS demonstration project), Utah FORGE, Larderello, Kakkonda, Taupo Volcanic Zone, Acoculco, Krafla. - Supercritical: Coso, Geysers, Salton Sea, Larderello, Los Humeros, Taupo Volcanic Zone, Krafla, Reyjanes, Hengill. **Disclaimer: Treat the supercritical fluid anomalies with skepticism. They are based on assumptions due to the general lack of confirmed supercritical fluid encounters and samples at the sites included in this dataset, at the time of assembling the dataset. The main assumption was that the supercritical fluid in a given geothermal system has shared properties with the hydrothermal fluid, which may not be the case in reality. Once the datasets were assembled, principal component analysis (PCA) was applied to each. PCA is an unsupervised statistical learning technique, meaning that labels are not required on the data, that summarized the directions of variance in the data. This approach was chosen because our labels are not certain, i.e., we do not know with 100% confidence that superhot resources exist at all the assumed positive areas. We also do not have data for any known non-geothermal areas, meaning that it would be challenging to apply a supervised learning technique. In order to generate weights from the PCA, an analysis of the PCA loading values was conducted. PCA loading values represent how much a feature is contributing to each principal component, and therefore the overall variance in the data.

15 GEOTHERMAL ENERGY↗

Renewable energy and biological conservation in a changing world

Without a shift to renewable energy sources, climate change will have adverse effects on many terrestrial and aquatic species. On the other hand, replacing fossil fuels with renewable energy will have different effects on wildlife, some negative. To protect biota, while navigating the complexities surrounding the transition to renewable energy, will require sharing knowledge between energy experts and wildlife experts, as well as policy makers and resource managers. This special issue is intended to advance the conversation. Interactions between renewable energy facilities and fauna are complex. Each source of renewable energy has its own conservation concerns, and each presents its own set of opportunities for mitigation; Other concerns and mitigations are shared. In this overview, we review climate risks to biota, clarify the complementarities among renewables for the conservation community, and summarize research on energy effects on biota for the energy community. The papers invited for this special issue address fossil (coal, oil, natural gas) and renewable energy (terrestrial biomass energy, hydropower, marine-hydrokinetic energy, wind energy, solar energy) and affected fauna. Finally, we hope that the results of these studies, and others like them, set us on a path toward low-carbon energy systems that provide society with energy while protecting future biodiversity.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

A Guide to Conquer the Biological Network Era Using Graph Theory

Networks are one of the most common ways to represent biological systems as complex sets of binary interactions or relations between different bioentities. In this article, we discuss the basic graph theory concepts and the various graph types, as well as the available data structures for storing and reading graphs. In addition, we describe several network properties and we highlight some of the widely used network topological features. We briefly mention the network patterns, motifs and models, and we further comment on the types of biological and biomedical networks along with their corresponding computer- and human-readable file formats. Finally, we discuss a variety of algorithms and metrics for network analyses regarding graph drawing, clustering, visualization, link prediction, perturbation, and network alignment as well as the current state-of-the-art tools. We expect this review to reach a very broad spectrum of readers varying from experts to beginners while encouraging them to enhance the field further.

59 BASIC BIOLOGICAL SCIENCES↗

"Source Term Modeling for Advanced Gas Micro-Reactors"

Maintaining the safety of the public, environment, and operating personnel is the most important factor in designing, operating, maintaining, and decommissioning nuclear reactors. In recent years, there has been a growing interest in the development of micro-reactors employing TRi-structural ISOtropic (TRISO)-coated particle fuel. In gas reactors, TRISO fuel plays an important role in the safety case for high temperature reactors because of the fission product retention properties of the fuel. This ability enables the use of a functional containment strategy for the reactor where multiple barriers are used to prevent fission product release to the environment. Part of the safety analysis of these advanced reactors is the assessment of radionuclide releases under normal and accident conditions through the multiple credited safety barriers. Using conservative assumptions, a mechanistic analysis can be performed to quantify these releases that combines the probabilistic assessment of failure with analytic solutions to radionuclide transport equations. Source term modeling for TRISO fuel has been performed for previous reactor designs; however, these models are outdated, in many cases proprietary, and need updates to be applied to the current state of TRISO fuel technology and alternative gas reactor core configurations [1]. Currently, the only publicly available source term assessment for gas reactors is an expert-based Monte Carlo simulation based on the effectiveness of the fuel kernel, coating layers, and graphite block in a modular high temperature gas reactor [2]. Thus, there is a need to develop a simple, versatile, and mechanistic model of fission product release and transport in gas reactor cores that could be applied to a variety of reactors through user inputs and reactor-specific radionuclide inventories. The release is calculated by the diffusion of the key safety important fission products through the kernel, silicon carbide (SiC), graphite for both intact and defective TRISO particles based on fuel and graphite temperatures in the reactor under normal operation. These releases from the fuel enter the coolant where they can plate-out on cooler surfaces. A clean-up model is included for designs with a coolant purification system to remove fission gases. This initial distribution of fission products in the reactor serves as an initial condition for potential releases under postulated accident conditions. The model then can calculate the fission product release for any transient temperature profile and fission product releases can then be used to assess radiological dose to the workers and the public using conventional dose tools. Data on the diffusion of fission products is based on historic German TRISO experiments and the more current Department of Energy (DOE) Advanced Gas Reactor (AGR) TRISO fuel development program. The model is coded in python with inputs and outputs in excel spreadsheets, as well as python plotting utilities to aid in the interpretation of the results. References: [1] INL, NGNP Mechanistic Source Term White Paper, INL-10-17997, July 2010. [2] David A. Petti, Richard R. Hobbins, Peter Lowry, Hans Gougar, “Representative Source Terms and The Influence of Reactor Attributes on Functional Containment in Modular High Temperature Gas-cooled Reactors,” Nuclear Technology, Vol. 184, p. 181-197, Nov. 2013.

07 ISOTOPE AND RADIATION SOURCES↗

Dara: Automated Multiple-Hypothesis Phase Identification and Refinement from Powder X-ray Diffraction

Powder X-ray diffraction (XRD) is a foundational technique for characterizing crystalline materials. However, the reliable interpretation of XRD patterns, particularly in multiphase systems, remains a manual and expertise-demanding task. As a characterization method that only provides structural information, multiple reference phases can often be fit to a single pattern, leading to potential misinterpretation when alternative solutions are overlooked. To ease humans’ efforts and address the challenge, we introduce Dara (data-driven automated Rietveld analysis), a framework designed to automate the robust identification and refinement of multiple phases from powder XRD data. Dara performs an exhaustive tree search over all plausible phase combinations within a given chemical space and validates each hypothesis using the BGMN Rietveld refinement routine. Key features include structural database filtering, automatic clustering of isostructural phases during tree expansion, and peak-matching-based scoring to identify promising phases for refinement. When ambiguity exists, Dara generates multiple hypothesis which can then be decided between by human experts or with further characterization tools. By enhancing the reliability and accuracy of phase identification, Dara enables scalable analysis of realistic complex XRD patterns and provides a foundation for integration into multimodal characterization workflows, moving toward fully self-driving materials discovery.

Biological databases↗

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↗

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↗

The Human Phenotype Ontology in 2021

The Human Phenotype Ontology (HPO, https://hpo.jax.org) was launched in 2008 to provide a comprehensive logical standard to describe and computationally analyze phenotypic abnormalities found in human disease. The HPO is now a worldwide standard for phenotype exchange. The HPO has grown steadily since its inception due to considerable contributions from clinical experts and researchers from a diverse range of disciplines. Here, we present recent major extensions of the HPO for neurology, nephrology, immunology, pulmonology, newborn screening, and other areas. For example, the seizure subontology now reflects the International League Against Epilepsy (ILAE) guidelines and these enhancements have already shown clinical validity. We present new efforts to harmonize computational definitions of phenotypic abnormalities across the HPO and multiple phenotype ontologies used for animal models of disease. These efforts will benefit software such as Exomiser by improving the accuracy and scope of cross-species phenotype matching. The computational modeling strategy used by the HPO to define disease entities and phenotypic features and distinguish between them is explained in detail. We also report on recent efforts to translate the HPO into indigenous languages. Finally, we summarize recent advances in the use of HPO in electronic health record systems.

59 BASIC BIOLOGICAL SCIENCES↗