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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

CAHS: Context-Aware Homology Search

Protein homology search is foundational to bioinformatics: it supports annotation transfer, structure/function inference, and evolutionary analysis over rapidly expanding sequence repositories (e.g., UniProtKB). Profile hidden Markov models (pHMMs), as implemented in HMMER, remain the most widely trusted approach because they provide statistically calibrated E-values; however, their gap behavior is fixed once a profile is trained, despite biological evidence that insertion/deletion tolerance varies across flexible loops and intrinsically disordered regions. We present CAHS (Context-Aware Homology Search), a lightweight query-time adapter for pHMM search that incorporates learned and biologically motivated signals without changing HMMER's downstream search pipeline or its calibrated E-value reporting. Given a query sequence, CAHS computes per-residue representations from a protein language model and a disorder predictor, maps these to profile coordinates, and modulates only match-state transition rows (gap-open and gap-extension probabilities) while preserving Plan7 constraints. We comprehensively evaluate CAHS across six structurally diverse protein families and multi-domain architectures against a 570k-sequence target corpus. CAHS expands detection capability, retrieving thousands of additional remote homologs at relaxed thresholds by maintaining alignment quality through flexible regions. For multi-domain proteins, context-aware modulation resolves 94% of fragmented alignments. Crucially, CAHS preserves hit-set invariance at stringent operating points (E<10-10), demonstrating increased statistical confidence without inflating false positives. Furthermore, sharper statistical distinction between homologs and background noise during early filter stages yields up to a 3.87× acceleration in end-to-end wall-clock time on high-performance computing clusters. Overall, CAHS illustrates a practical AI-for-science design pattern: augmenting a trusted probabilistic model with query-specific learned signals to improve interpretable, reproducible inference in data-rich biology.

Bhattaram, Swethasree [Georgia Institute of Techno↗
DOE OSTI2026

NuGraph2 with context-aware inputs: physics-inspired improvements in semantic segmentation

Graph neural networks have recently shown strong promise for event reconstruction tasks in Liquid Argon Time Projection Chambers, yet their performance remains limited for underrepresented classes of particles, such as Michel electrons. In this work, we investigate physics-informed strategies to improve semantic segmentation within the NuGraph2 architecture. We explore three complementary approaches: (i) enriching the input representation with context-aware features derived from detector geometry and track continuity, (ii) introducing auxiliary decoders to capture class-level correlations, and (iii) incorporating energy-based regularization terms motivated by Michel electron energy distributions. Experiments on MicroBooNE public datasets show that physics-inspired feature augmentation yields the largest gains, particularly boosting Michel electron precision and recall by disentangling overlapping latent space regions. In contrast, auxiliary decoders and energy-regularization terms provided limited improvements, partly due to the hit-level nature of NuGraph2, which lacks explicit particle- or event-level representations. Our findings highlight that embedding physics context directly into node-level inputs is more effective than imposing task-specific auxiliary losses, and suggest that future hierarchical architectures such as NuGraph3, with explicit particle- and event-level reasoning, will provide a more natural setting for advanced decoders and physics-based regularization. The code for this work is publicly available on Github at https://github.com/vitorgrizzi/nugraph_phys/tree/main_phys.

Other Experiments↗
DOE OSTI2015

Online updating of context-aware landmark detectors for prostate localization in daily treatment CT images

Purpose: In image guided radiation therapy, it is crucial to fast and accurately localize the prostate in the daily treatment images. To this end, the authors propose an online update scheme for landmark-guided prostate segmentation, which can fully exploit valuable patient-specific information contained in the previous treatment images and can achieve improved performance in landmark detection and prostate segmentation. Methods: To localize the prostate in the daily treatment images, the authors first automatically detect six anatomical landmarks on the prostate boundary by adopting a context-aware landmark detection method. Specifically, in this method, a two-layer regression forest is trained as a detector for each target landmark. Once all the newly detected landmarks from new treatment images are reviewed or adjusted (if necessary) by clinicians, they are further included into the training pool as new patient-specific information to update all the two-layer regression forests for the next treatment day. As more and more treatment images of the current patient are acquired, the two-layer regression forests can be continually updated by incorporating the patient-specific information into the training procedure. After all target landmarks are detected, a multiatlas random sample consensus (multiatlas RANSAC) method is used to segment the entire prostate by fusing multiple previously segmented prostates of the current patient after they are aligned to the current treatment image. Subsequently, the segmented prostate of the current treatment image is again reviewed (or even adjusted if needed) by clinicians before including it as a new shape example into the prostate shape dataset for helping localize the entire prostate in the next treatment image. Results: The experimental results on 330 images of 24 patients show the effectiveness of the authors’ proposed online update scheme in improving the accuracies of both landmark detection and prostate segmentation. Besides, compared to the other state-of-the-art prostate segmentation methods, the authors’ method achieves the best performance. Conclusions: By appropriate use of valuable patient-specific information contained in the previous treatment images, the authors’ proposed online update scheme can obtain satisfactory results for both landmark detection and prostate segmentation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

CALMS: CONTEXT-AWARE LANGUAGE MODEL FOR SCIENCE

Context-Aware Language Model for Science (CALMS) is designed to assist scientists with instrument operations and complex experimentation. CALMS consists of a large-language model (LLM) augmented with context and tool use abilities. With the ability to retrieve relevant information from facility documentation, CALMS can answer simple questions on scientific capabilities and other operational procedures. With the ability to interface with software tools and experimental hardware, CALMS can operate scientific instruments in a conversational manner.

CHERUKARA, MATTHEW↗
DOE OSTI2025

CareWELL: Multimodal Region Representation Learning with Spatial Contexts for Urban Health

Rapid urbanization affects living environments by intensifying exposure to air pollution, heat, noise, and urban dynamics, which together contribute to uneven health outcomes across neighborhoods. For instance, cardiovascular, respiratory, and mental health conditions are each influenced by distinct exposures such as air pollution, extreme temperatures, or limited access to green space. These heterogeneous patterns require understanding the characteristics of geographic regions in order to explain why urban health risks vary across urban areas. Recent work in self-supervised region representation learning provides a promising way to model such characteristics from multimodal geospatial data. However, existing methods face two major limitations: (i) they often depend on non-public datasets, limiting reproducibility and applicability, and (ii) their generic pretraining objectives overlook health-relevant determinants, including temporal variability in environmental exposures and inequalities in social conditions. To address these gaps, we propose Context-Aware Region rEpresentation with Weather, Environment, and Location Learning (CareWELL). CareWELL leverages large language models to encode seasonal variability in weather, employs contrastive learning to align geo-coordinate and weather representations, and introduces a context-aware objective that integrates socio-demographic factors while preserving spatial correlations. We evaluate CareWELL by predicting six urban health outcomes in Manhattan, New York City, and demonstrate that CareWELL consistently outperforms state-of-the-art baselines as well as a traditional spatial computing method. These results suggest the importance of context-aware pretraining objectives for learning health-relevant region representations.

Namgung, Min [ORNL]↗
DOE OSTI2024

Review of Technical Photovoltaic Key Performance Indicators and the Importance of Data Quality Routines

Technical key performance indicators (KPIs) are important metrics used to assess and quantitatively summarize various aspects of photovoltaic (PV) systems, including long-term performance, economic viability, and carbon footprint. Herein, a group of experts of the International Energy Agency's Photovoltaic Power Systems Programme Task 13 collect and describ the most important technical KPIs used in the industry. Thereby, a set of best practices for reliably handling PV system data is presented and the impact of data quality and climatic variability on KPI calculation is investigated. Further, the effective use of technical KPIs allows triggering data-driven and informed decisions to optimize PV systems and providing a comprehensive overview of how PV systems operate across different conditions and climates. With the worldwide growth of the PV industry, more companies operate/own PV systems in different regions, where the climatic and seasonal profiles differ. This requires context-aware evaluation of KPIs, or the judicious application of multiple KPIs, to ensure that each asset is evaluated correctly. Beyond that, there is untapped potential in the utilization of KPIs through geospatial mapping and extrapolation of fleet KPIs. This study demonstrates that the uncertainty in KPI estimation is not well understood and depends on data quality, climatic variability, and system configuration.

14 SOLAR ENERGY↗
DOE OSTI2023

CholecTriplet2021: A benchmark challenge for surgical action triplet recognition

Context-aware decision support in the operating room can foster surgical safety and efficiency by leveraging real-time feedback from surgical workflow analysis. Most existing works recognize surgical activities at a coarse-grained level, such as phases, steps or events, leaving out fine-grained interaction details about the surgical activity; yet those are needed for more helpful AI assistance in the operating room. Recognizing surgical actions as triplets of ‹ instrument, verb, target › combination delivers more comprehensive details about the activities taking place in surgical videos. This paper presents CholecTriplet2021: an endoscopic vision challenge organized at MICCAI 2021 for the recognition of surgical action triplets in laparoscopic videos. Here, the challenge granted private access to the large-scale CholecT50 dataset, which is annotated with action triplet information. In this paper, we present the challenge setup and the assessment of the state-of-the-art deep learning methods proposed by the participants during the challenge. Here, a total of 4 baseline methods from the challenge organizers and 19 new deep learning algorithms from the competing teams are presented to recognize surgical action triplets directly from surgical videos, achieving mean average precision (mAP) ranging from 4.2% to 38.1%. This study also analyzes the significance of the results obtained by the presented approaches, performs a thorough methodological comparison between them, in-depth result analysis, and proposes a novel ensemble method for enhanced recognition. Our analysis shows that surgical workflow analysis is not yet solved, and also highlights interesting directions for future research on fine-grained surgical activity recognition which is of utmost importance for the development of AI in surgery.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Developing Scenario‐Based Strategies for Health, Climate, and Environmental Preparedness: The One Health, One Earth Approach

Climate change amplifies many threats to human health. Despite advances in understanding climate change dynamics and impacts, there remains a critical gap in translating scientific knowledge into equitable, and community-driven health interventions. The inaugural One Earth, One Health workshop sought to explore this gap through human-centered design exercises involving interdisciplinary researchers from climate and Earth sciences, engineering, epidemiology, microbiology, and environmental health. Although participants did not co-develop solutions with affected communities, they used stakeholder role-playing to guide ideation and lay groundwork for actionable plans. Through these methods, participants identified community needs and proposed prototype solutions to alleviate health threats exacerbated by global environmental change. Prototypes were organized around infectious diseases, extreme weather, and air quality, as illustrative themes rather than an exhaustive set of risks. Key solutions included strategies for anticipatory systems and early warning (e.g., integrating environmental signals with health data), inclusive communication and infrastructure needs for responding to extreme weather events, and integrated platforms visualizing air quality trends to support tailored, context-aware guidance beyond one-size-fits-all alerts. The workshop highlighted opportunities such as leveraging machine learning, Earth observation, and real-time surveillance to protect communities, but also noted barriers including data quality, technological redundancy, privacy, and governance challenges. Additionally, participants emphasized the need for interdisciplinary teams capable of collaborating across sectors, breaking down silos and addressing gaps in training and education. Overall, the workshop illustrates how process-driven, human-centered approaches can help surface user needs and generate testable prototype concepts, while underscoring the importance of direct community partnership for implementation.

Abadi, Azar M. [University of Alabama, Birmingham,↗
DOE OSTI2024

Opportunities for retrieval and tool augmented large language models in scientific facilities

Upgrades to advanced scientific user facilities such as next-generation x-ray light sources, nanoscience centers, and neutron facilities are revolutionizing our understanding of materials across the spectrum of the physical sciences, from life sciences to microelectronics. However, these facility and instrument upgrades come with a significant increase in complexity. Driven by more exacting scientific needs, instruments and experiments become more intricate each year. This increased operational complexity makes it ever more challenging for domain scientists to design experiments that effectively leverage the capabilities of and operate on these advanced instruments. Large language models (LLMs) can perform complex information retrieval, assist in knowledge-intensive tasks across applications, and provide guidance on tool usage. Using x-ray light sources, leadership computing, and nanoscience centers as representative examples, we describe preliminary experiments with a Context-Aware Language Model for Science (CALMS) to assist scientists with instrument operations and complex experimentation. With the ability to retrieve relevant information from facility documentation, CALMS can answer simple questions on scientific capabilities and other operational procedures. With the ability to interface with software tools and experimental hardware, CALMS can conversationally operate scientific instruments. By making information more accessible and acting on user needs, LLMs could expand and diversify scientific facilities’ users and accelerate scientific output.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

GALIC: hybrid multi-qubitwise pauli grouping for quantum computing measurement

Abstract Observable estimation is a core primitive in NISQ-era algorithms targeting quantum chemistry applications. To reduce the state preparation overhead required for accurate estimation, recent works have proposed various simultaneous measurement schemes to lower estimator variance. Two primary grouping schemes have been proposed: full commutativity (FC) and qubit-wise commutativity (QWC), with no compelling means of interpolation. In this work we propose a generalized framework for designing and analyzing context-aware hybrid FC/QWC commutativity relations. We use our framework to propose a noise-and-connectivity aware grouping strategy: Generalized backend-Aware pauLI Commutation (GALIC). We demonstrate how GALIC interpolates between FC and QWC, maintaining estimator accuracy in Hamiltonian estimation while lowering variance by an average of 20% compared to QWC. We also explore the design space of near-term quantum devices using the GALIC framework, specifically comparing device noise levels and connectivity. We find that error suppression has a more than 10 × larger impact on device-aware estimator variance than qubit connectivity with even larger correlation differences in estimator biases.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Gaia: An AI-enabled genomic context–aware platform for protein sequence annotation

Protein sequence similarity search is fundamental to biology research, but current methods are typically not able to consider crucial genomic context information indicative of protein function, especially in microbial systems. Here, we present Gaia (Genomic AI Annotator), a sequence annotation platform that enables rapid, context-aware protein sequence search across genomic datasets. Gaia leverages gLM2, a mixed-modality genomic language model trained on both amino acid sequences and their genomic neighborhoods to generate embeddings that integrate sequence-structure-context information. This approach allows for the identification of functionally and/or evolutionarily related genes that are found in conserved genomic contexts, which may be missed by traditional sequence- or structure-based search alone. Gaia enables real-time search of a curated database comprising more than 85 million protein clusters from 131,744 microbial genomes. We compare the homolog retrieval performance of Gaia search against other embedding and alignment-based approaches. We provide Gaia as a web-based, freely available tool.

Jha, Nishant↗
DOE OSTI2024

Live cell imaging of cellular dynamics in poplar wood using computational cannula microscopy

This study presents significant advancements in computational cannula microscopy for live imaging of cellular dynamics in poplar wood tissues. Leveraging machine-learning models such as pix2pix for image reconstruction, we achieved high-resolution imaging with a field of view of 55µm using a 50µm-core diameter probe. Our method allows for real-time image reconstruction at 0.29 s per frame with a mean absolute error of 0.07. We successfully captured cellular-level dynamics in vivo , demonstrating morphological changes at resolutions as small as 3µm. We implemented two types of probabilistic neural network models to quantify confidence levels in the reconstructed images. This approach facilitates context-aware, human-in-the-loop analysis, which is crucial for in vivo imaging where ground-truth data is unavailable. Using this approach we demonstrated deep in vivo computational imaging of living plant tissue with high confidence (disagreement score ⪅0.2). This work addresses the challenges of imaging live plant tissues, offering a practical and minimally invasive tool for plant biologists.

Ingold, Alexander (ORCID:0009000752380016)↗
DOE OSTI2024

National Security Programs - Cyber: MMAREJBLIGE – Modular Multi Agent Grid Emulation for Joined Breakdowns in Linked Generative Emulations - 23-0644

Modular Multi Agent Grid Emulations for Joined Breakdowns in Linked Generative Emulations (MMAREJBLIGE) introduces an agent-based modeling framework into real-time cyber-physical emulation to achieve a context-aware environment that introduces operator/attacker/external-condition variability to improve emulation fidelity and testing rigor. We detail our agent framework design, internal communication via message passing, and time synchronization, as well as the individual components of the system. We include a brief analysis of several scenarios run on a real-time, hardware-in-the-loop, Industrial Control Systems (ICS) test-bed which include normal operation, physical disruption, disruption with mitigation, and disruption with mitigation during a cyber denial-of-service (DOS) attack.

42 ENGINEERING↗
DOE OSTI2025

Masked Symbol Modeling for Demodulation of Oversampled Baseband Communication Signals in Impulsive Noise-Dominated Channels

Recent breakthroughs in natural language processing show that attention mech- anism in Transformer networks, trained via masked-token prediction, enables models to capture the semantic context of the tokens and internalize the grammar of language. While the application of Transformers to communication systems is a burgeoning field, the notion of context within physical waveforms remains under-explored. This paper addresses that gap by re-examining inter-symbol con- tribution (ISC) caused by pulse-shaping overlap. Rather than treating ISC as a nuisance, we view it as a deterministic source of contextual information embedded in oversampled complex baseband signals. We propose Masked Symbol Model- ing (MSM), a framework for the physical (PHY) layer inspired by Bidirectional Encoder Representations from Transformers methodology. In MSM, a subset of symbol-aligned samples is randomly masked, and a Transformer predicts the missing symbol identifiers using the surrounding “in-between” samples. Through this objective, the model learns the latent syntax of complex baseband waveforms. We illustrate MSM’s potential by applying it to the task of demodulating sig- nals corrupted by impulsive noise, where the model infers corrupted segments by leveraging the learned context. Our results suggest a path toward receivers that interpret, rather than merely detect communication signals, opening new avenues for context-aware PHY layer design.

Bedir, Oguz↗
DOE OSTI2026

Knowledge Graph of RB-Tnseq Data from Fitness Browser (KP-DP1)

Motivation: Predicting microbial gene fitness across environmental conditions remains a central challenge for predictive phenomics and autonomous experimentation. Fitness assays generate large volumes of genotype–phenotype measurements difficult to integrate with experimental metadata and biological function in a form that supports mechanistic reasoning. Knowledge graphs offer a semantic framework for unifying modalities and enabling context-aware inference. Results: We build GIMME (Graph Inference for Microbial Metabolism Exploration), a semantically grounded knowledge graph that unifies gene fitness measurements spanning 10 Pseudomonas species with experimental metadata and biological context. Media are decomposed into chemical components and experiments carry structured links to natural-language descriptions. The resulting graph supports two inference modes: (1) symbolic graph traversal to surface candidate gene–environment and gene–chemical associations, and (2) learned inference using heterogeneous graph neural networks that propagate information across neighborhoods. We formulate link regression over (gene, media, experiment) triplets, combining learned gene embeddings with pretrained LLM sourced text embeddings of node descriptions to predict gene fitness. We then augment a baseline MLP with an auxiliary message-passing encoder (GraphSAGE/GAT) that propagates information over gene–protein–function and media–chemical subgraphs, and fuse the two pathways with a gated residual connection. This approach produces strong agreement with held-out fitness measurements (GraphSAGE Pearson r 0.74) while also highlighting inference challenges in extreme-fitness regimes. We aggregate GAT edge-attention weights by relation type and layer to estimate which biological and environmental relations most influence fitness predictions. Conclusion: This work explores using knowledge graphs as “context graphs” for microbial phenotype prediction. They provide a rich substrate which enables explainable retrieval of supporting evidence, and provides a natural bridge to autonomous workflows that prioritize the next experiment.

59 BASIC BIOLOGICAL SCIENCES↗