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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Mondo: integrating disease terminology across communities

Precision medicine aims to enhance diagnosis, treatment, and prognosis by integrating multimodal data at the point of care. However, challenges arise due to the vast number of diseases, differing methods of classification, and conflicting terminological coding systems and practices used to represent molecular definitions of disease. This lack of interoperability artificially constrains the potential for diagnosis, clinical decision support, care outcome analysis, as well as data linkage across research domains to support the development or repurposing of therapeutics. There is a clear and pressing need for a unified system for managing disease entities⁠—including identifiers, synonyms, and definitions. To address these issues, we created the Mondo disease ontology—a community-driven, open-source, unified disease classification system that harmonizes diverse terminologies into a consistent, computable framework. Mondo integrates key medical and biomedical terminologies, including Online Mendelian Inheritance in Man (OMIM), Orphanet, Medical Subject Headings (MeSH), National Cancer Institute Thesaurus (NCIt), and more, to provide a comprehensive and accurate representation of disease concepts with fully provenanced and attributed links back to the sources. Mondo can be used as the handle for curation of gene–disease associations utilized in diagnostic applications, research applications such as computational phenotyping, and in clinical coding systems in clinical decision support by pointing the clinician to the numerous knowledge resources linked to the Mondo identifier. Mondo's community-centric approach, stewarded by the Monarch Initiative's expertise in ontologies, ensures that the ontology remains adaptable to the evolving needs of biomedical research and clinical communities, as well as the knowledge providers.

biomedical informatics↗
DOE OSTI2025

Supporting Information for manuscript: “A latitudinal gradient in S/G lignin monomer ratio driven by laccase in natural poplar variants”

Lignin composition plays a crucial role in plant structural integrity and environmental adaptation. However, the genetic and molecular mechanisms underlying natural variation in lignin composition remain poorly understood. This study investigates the syringyl-to-guaiacyl (S/G) lignin monomer ratio across a natural population of Populus trichocarpa spanning a latitudinal gradient along the Northwest coast of North America. By integrating biochemical, genomic, and geographic analysis, we identify key gene variants associated with S/G ratio differences. These datasets provide valuable insights into the evolutionary and functional genomics of lignin composition and serve as a resource for developing poplar variants optimized for forestry and bioenergy applications.

Poplar, lignin composition, laccases, latitude, ad↗
DOE OSTI2022

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↗
DOE OSTI2025

Modeling inter‐reader variability in clinical target volume delineation for soft tissue sarcomas using diffusion model

Abstract Background Accurate delineation of the clinical target volume (CTV) is essential in the radiotherapy treatment of soft tissue sarcomas. However, this process is subject to inter‐reader variability due to the need for clinical assessment of risk and extent of potential microscopic spread. This can lead to inconsistencies in treatment planning, potentially impacting treatment outcomes. Most existing automatic CTV delineation methods do not account for this variability and can only generate a single CTV for each case. Purpose This study aims to develop a deep learning‐based technique to generate multiple CTV contours for each case, simulating the inter‐reader variability in the clinical practice. Methods We employed a publicly available dataset consisting of fluorodeoxyglucose positron emission tomography (FDG‐PET), x‐ray computed tomography (CT), and pre‐contrast T1‐weighted magnetic resonance imaging (MRI) scans from 51 patients with soft tissue sarcoma, along with an independent validation set containing five additional patients. An experienced reader drew a contour of the gross tumor volume (GTV) for each patient based on multi‐modality images. Subsequently, two additional readers, together with the first one, were responsible for contouring three CTVs in total based on the GTV. We developed a diffusion model‐based deep learning method that is capable of generating arbitrary number of different and plausible CTVs to mimic the inter‐reader variability in CTV delineation. The proposed model incorporates a separate encoder to extract features from the GTV masks, leveraging the critical role of GTV information in accurate CTV delineation. Results The proposed diffusion model demonstrated superior performance with the highest Dice Index (0.902 compared to values below 0.881 for state‐of‐the‐art models) and the best generalized energy distance (GED) (0.209 compared to values exceeding 0.221 for state‐of‐the‐art models). It also achieved the second‐highest recall and precision metrics among the compared ambiguous image segmentation models. Results from both datasets exhibited consistent trends, reinforcing the reliability of our findings. Additionally, ablation studies exploring different model structures and input configurations highlighted the significance of incorporating prior GTV information for accurate CTV delineation. Conclusions The proposed diffusion model successfully generates multiple plausible CTV contours for soft tissue sarcomas, effectively capturing inter‐reader variability in CTV delineation.

Dong, Yafei [Yale Biomedical Imaging Institute Yal↗
DOE OSTI2024

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↗
DOE OSTI2025

Cross‐Cultural Validation of the Binge Eating Disorder Screener‐7 ( BEDS ‐7) Across 42 Countries

ABSTRACT Objective This study aimed to evaluate the reliability and validity of the Binge Eating Disorder Screener‐7 (BEDS‐7) across 42 countries and 26 languages, assessing its reliability and validity as a screening tool for binge‐eating disorder (BED) in diverse cultural contexts. Specifically, it sought to enhance early recognition of BED symptoms in primary care settings globally, contributing to a standardized framework for assessing BED. Method The International Sex Survey, a cross‐sectional online study, was conducted in 42 countries and 26 languages. A diverse community sample of 82,243 participants, aged 18 years or older, completed the BEDS‐7 and measures of sexuality, mental health, substance use, and sociodemographic characteristics. Confirmatory factor analyses and tests of measurement invariance were employed to evaluate the reliability and validity of the BEDS‐7 across languages, countries, genders, and sexual orientations. Results The BEDS‐7 demonstrated scalar factorial invariance across languages and countries, indicating consistent factor loadings and item intercepts. In contrast, the screener showed residual invariance across gender and sexual orientation groups, supporting its robustness across these demographics. Kruskal–Wallis tests revealed significant differences in BED symptoms across languages, countries, genders, and sexual orientations, with the highest BED scores observed among queer, pansexual, and gender‐diverse individuals. The BEDS‐7 also demonstrated adequate reliability (Cronbach's alpha > 0.80) and moderate criterion validity. Discussion The findings provide further evidence of the reliability and validity of the BEDS‐7 as a potential screening tool for identifying probable cases of BED globally, facilitating early intervention in primary care settings.

Gewirtz‐Meydan, Ateret [School of Social Work, Fac↗
DOE OSTI2025

Leveraging Large Language Models for Real-World Data Evidence: A Framework for Automated Treatment Extraction and Data Harmonization

Background: The ability to comprehensively collect treatment information from cancer patient medical records would enable studies to evaluate real-world benefits and risks tied to specific treatments. Currently, it is difficult to system- atically collect high-quality treatment information because it is often stored in unstructured text. Manually extracting and standardizing drug and regimen data is time-intensive. Recent advances in large language models (LLMs) offer a potential solution for automated extraction of structured treatment information from clinical text. Objective: This study systematically evaluates the utility of four LLMs from the Llama family for automated extraction of oncology treatment information from clinical text. This information can guide researchers using cancer registry data to provide insights into cancer care and outcomes beyond clinical trials. Methods: Four instruction-tuned Llama models with varying parameter counts (1B, 3B, 8B, and 70B) were evaluated for their ability to extract treatment information from clinical documents. A unified oncology knowledge base integrating seven major public data sources was developed to standardize and normalize extracted entities—a critical step for harmonizing data from diverse sources. Extracted treatment data were compared against expert-annotated ground truth. Model performance was assessed using accuracy metrics (Precision, Recall, F1-Score) and opera- tional feasibility metrics, including processing speed and structural compliance of the output. Results: A strong positive correlation was observed between model size and extraction accuracy. F1-score improved from 0.609 for the 1B model to 0.710 (3B), 0.807 (8B), and 0.828 (70B). While larger models demonstrated superior accuracy and compliance, they incurred higher computational costs. The modest performance difference between 8B and 70B suggests diminishing returns with increasing model size. Conclusions: LLMs represent a viable technology for automating oncology treatment extraction. The 8B-parameter model emerged as a highly effective option, balancing high accuracy and computational efficiency. Selecting an appropriate LLM for deployment in cancer registries involves a trade-off between desired accuracy and available operational resources. Harmonizing extracted entities with the oncology knowledge base facilitates standardized integration into common data models, enhancing data quality for real-world evidence analyses.

artificial intelligence↗