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DOE OSTI2025

Replacing non-biomedical concepts improves embedding of biomedical concepts

Embeddings are semantically meaningful representations of words in a vector space, commonly used to enhance downstream machine learning applications. Traditional biomedical embedding techniques often replace all synonymous words representing biological or medical concepts with a unique token, ensuring consistent representation and improving embedding quality. However, the potential impact of replacing non-biomedical concept synonyms has received less attention. Embedding approaches often employ concept replacement to replace concepts that span multiple words, such as non-small-cell lung carcinoma, with a single concept identifier (e.g., D002289). Also, all synonyms of each concept are merged into the same identifier. Here, we additionally leveraged WordNet to identify and replace sets of non-biomedical synonyms with their most common representatives. This combined approach aimed to reduce embedding noise from non-biomedical terms while preserving the integrity of biomedical concept representations. We applied this method to 1,055 biomedical concept sets representing molecular signatures or medical categories and assessed the mean pairwise distance of embeddings with and without non-biomedical synonym replacement. A smaller mean pairwise distance was interpreted as greater intra-cluster coherence and higher embedding quality. Embeddings were generated using the Word2Vec algorithm applied to a corpus of 10 million PubMed abstracts. Our results demonstrate that the addition of non-biomedical synonym replacement reduced the mean intra-cluster distance by an average of 8%, suggesting that this complementary approach enhances embedding quality. Future work will assess its applicability to other embedding techniques and downstream tasks. Python code implementing this method is provided under an open-source license.

algorithms↗

NASA NTRSDate not supplied

Fast Aircraft Separation Calculations for Gradient Based Optimization of Airspace Simulations

Simulations of airspace operational concepts can play a significant role in determining future paradigms that would allow for a safe increase in airspace density. In particular, airspace simulations which are capable of handling large numbers of aircraft act as an enabling capability for the testing of proposed airspace operational concepts. Simulations allowing for gradient based optimization methods are particularly attractive, since they would potentially allow for an efficient and empirical means to derive best operational practices. These could also allow for vehicle multidisciplinary design and optimization studies to include air traffic management considerations as a discipline. But any large scale simulation of airspace operations must include some methodology for addressing airspace separation requirements, which in the most direct sense would be tracked in a manner that computationally grows as a quadratic function of the number of simulated aircraft. Efficient indirect methods have been developed in certain contexts to address this limitation. However, any means of addressing separation requirements in a gradient based optimization context should be implemented by functions which provide analytic derivative information to maximize numerical precision and computational efficiency. In this paper, a fast and differentiable separation metric is described in application to gradient based optimization of airspace operations. Rather than computing the separation distance between every pair of aircraft in a simulation, this method effectively reduces the problem to a smaller relevant set using a geometric decomposition. This method guarantees that the smallest distance at all points in simulated time is determined exactly. When used in an optimization constraint context, this guarantees that a minimum separation is maintained between all pairs of aircraft. The presented metric has logarithmic computational growth with respect to the number of simulated aircraft, and is shown to perform well in a series of notional 2D airspace optimization problems when used to enforce specified airborne separation constraints. Results show that this is notably faster than a direct pairwise distance computing metric for optimizations involving both small and large numbers of aircraft, yet enforce separation requirements to the same tolerance. It is shown that this favorable scalability is an enabling capability for more sophisticated air traffic management conceptual studies.

Optimization↗

DOE OSTI2026

Multidimensional scaling informed by F -statistic: Visualizing grouped microbiome data with inference

Multidimensional scaling (MDS) is a widely used dimensionality reduction technique in microbial ecology data analysis that captures the multivariate structure of the data while preserving pairwise distances between samples. While improvements in MDS have enhanced the ability to reveal group-specific data patterns, these MDS-based methods require prior assumptions for inference, limiting their application in general microbiome analysis. Here, in this study, we introduce a new MDS-based ordination method, “F-informed MDS,” which configures the data distribution based on the F-statistic, the ratio of dispersion between groups sharing common and different characteristics. Using semisynthetic datasets, we demonstrate that the proposed method is robust to hyperparameter selection while maintaining statistical significance throughout the ordination process. Various quality metrics for evaluating dimensionality reduction confirm that F-informed MDS is comparable to state-of-the-art methods in preserving both local and global data structures. Its application to a diatom-associated bacterial community suggests the role of this new method in interpreting the community’s response to the host. Our approach offers a well-founded refinement of MDS that aligns with statistical test results, which can be beneficial for broader multidimensional data analyses in microbiology and ecology. This new visualization tool can be incorporated into standard microbiome data analyses.

Biological and medical sciences↗

NASA NTRS1994

Efficient massively parallel simulation of dynamic channel assignment schemes for wireless cellular communications

Fast, efficient parallel algorithms are presented for discrete event simulations of dynamic channel assignment schemes for wireless cellular communication networks. The driving events are call arrivals and departures, in continuous time, to cells geographically distributed across the service area. A dynamic channel assignment scheme decides which call arrivals to accept, and which channels to allocate to the accepted calls, attempting to minimize call blocking while ensuring co-channel interference is tolerably low. Specifically, the scheme ensures that the same channel is used concurrently at different cells only if the pairwise distances between those cells are sufficiently large. Much of the complexity of the system comes from ensuring this separation. The network is modeled as a system of interacting continuous time automata, each corresponding to a cell. To simulate the model, conservative methods are used; i.e., methods in which no errors occur in the course of the simulation and so no rollback or relaxation is needed. Implemented on a 16K processor MasPar MP-1, an elegant and simple technique provides speedups of about 15 times over an optimized serial simulation running on a high speed workstation. A drawback of this technique, typical of conservative methods, is that processor utilization is rather low. To overcome this, new methods were developed that exploit slackness in event dependencies over short intervals of time, thereby raising the utilization to above 50 percent and the speedup over the optimized serial code to about 120 times.

Greenberg, Albert G.↗

DOE OSTI2024

Intra- and inter-subtype HIV diversity between 1994 and 2018 in southern Uganda: a longitudinal population-based study

There is limited data on human immunodeficiency virus (HIV) evolutionary trends in African populations. We evaluated changes in HIV viral diversity and genetic divergence in southern Uganda over a 24-year period spanning the introduction and scale-up of HIV prevention and treatment programs using HIV sequence and survey data from the Rakai Community Cohort Study, an open longitudinal population-based HIV surveillance cohort. Gag (p24) and env (gp41) HIV data were generated from people living with HIV (PLHIV) in 31 inland semi-urban trading and agrarian communities (1994–2018) and four hyperendemic Lake Victoria fishing communities (2011–2018) under continuous surveillance. HIV subtype was assigned using the Recombination Identification Program with phylogenetic confirmation. Inter-subtype diversity was evaluated using the Shannon diversity index, and intra-subtype diversity with the nucleotide diversity and pairwise TN93 genetic distance. Genetic divergence was measured using root-to-tip distance and pairwise TN93 genetic distance analyses. Demographic history of HIV was inferred using a coalescent-based Bayesian Skygrid model. Evolutionary dynamics were assessed among demographic and behavioral population subgroups, including by migration status. 9931 HIV sequences were available from 4999 PLHIV, including 3060 and 1939 persons residing in inland and fishing communities, respectively. In inland communities, subtype A1 viruses proportionately increased from 14.3% in 1995 to 25.9% in 2017 (P < .001), while those of subtype D declined from 73.2% in 1995 to 28.2% in 2017 (P < .001). The proportion of viruses classified as recombinants significantly increased by nearly four-fold from 12.2% in 1995 to 44.8% in 2017. Inter-subtype HIV diversity has generally increased. While intra-subtype p24 genetic diversity and divergence leveled off after 2014, intra-subtype gp41 diversity, effective population size, and divergence increased through 2017. Intra- and inter-subtype viral diversity increased across all demographic and behavioral population subgroups, including among individuals with no recent migration history or extra-community sexual partners. This study provides insights into population-level HIV evolutionary dynamics following the scale-up of HIV prevention and treatment programs. Continued molecular surveillance may provide a better understanding of the dynamics driving population HIV evolution and yield important insights for epidemic control and vaccine development.

60 APPLIED LIFE SCIENCES↗

NASA NTRS1990

Performance comparison of combined ECC/RLL codes

In this paper, we present a performance comparison of several combined error correcting/run-lenth limited (ECC/RLL) codes created by concatenating a convolutional code with a run-length limited code. In each case, encoding and decoding are accomplished using a single trellis based on the combined code. Half of the codes under investigation use conventionally (d,k) run-length limited codes, where d is the minimum and k is the maximum allowable run of 0's between 1's. The other half of the combined codes use a special class of (d,k) codes known as distance preserving codes. These codes have the property that pairwise Hamming distances out of the (d,k) encoder are at least as large as the corresponding distances into the encoder (i.e., the codes preserve distance). Thus a combined code, created using a convolutional code concatenated with a distance preserving (d,k) code, will have a free distance (dfree) no smaller than the free distance of the original convolutional code. It should be noted that this does not hold if the (d,k) code was not distance preserving. A computer simulation is used to compare the performance of these two types of codes over the binary symmetric channel for various (d,k) constraints, rates, free distances, and numbers of states. Of particular interest for magnetic recording applications are codes with run-length constraints (1,3), (1,7), and (2,7).

French, C.↗

DOE OSTI2025

Timing based clustering of childhood BMI trajectories reveals differential maturational patterns; Study in the Northern Finland Birth Cohorts 1966 and 1986

Children’s biological age does not always correspond to their chronological age. In the case of BMI trajectories, this can appear as phase variation, which can be seen as shift, stretch, or shrinking between trajectories. With maturation thought of as a process moving towards the final state - adult BMI, we assessed whether children can be divided into latent groups reflecting similar maturational age of BMI. The groups were characterised by early factors and time-related features of the trajectories. We used data from two general population birth cohort studies, Northern Finland Birth Cohorts 1966 and 1986 (NFBC1966 and NFBC1986). Height (n = 6329) and weight (n = 6568) measurements were interpolated in 34 shared time points using B-splines, and BMI values were calculated between 3 months to 16 years. Pairwise phase distances of 2999 females and 3163 males were used as a similarity measure in k-medoids clustering. We identified three clusters of trajectories in females and males (Type 1: females, n = 1566, males, n = 1669; Type 2: females, n = 1028, males, n = 973; Type 3: females, n = 405, males, n = 521). Similar distinct timing patterns were identified in males and females. The clusters did not differ by sex, or early growth determinants studied. Trajectory cluster Type 1 reflected to the shape of what is typically illustrated as the childhood BMI trajectory in literature. However, the other two have not been identified previously. Type 2 pattern was more common in the NFBC1966 suggesting a generational shift in BMI maturational patterns.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Exabiome: Advancing Microbial Science through Exascale Computing

The Exabiome project seeks to improve the understanding of microbiomes through the development of methods for accelerating metagenomic science using exascale computing. This article gives an overview of scientific impact of the three components of the project: metagenome assembly, protein family detection, and comparative analysis of metagenomes. Exabiome developed MetaHipMer, the only metagenome assembler capable of scaling to full exascale systems. MetaHipMer has enabled ground-breaking assemblies on the Frontier supercomputer, with many scientific benefits, such as the discovery of rare species and viral genomes. To investigate protein families, Exabiome developed two exascale tools, PASTIS and HipMCL. Together, these can utilize exascale resources to understand the functional diversity of billions of dark matter proteins and novel protein families. For comparative analysis, Exabiome developed kmerprof, a tool that can be used to compare huge metagenomes for many different scientific purposes, for example, grouping human microbiomes according to body location.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

A Class of Sparse Johnson–Lindenstrauss Transforms and Analysis of their Extreme Singular Values

The Johnson–Lindenstrauss (JL) lemma is a powerful tool for dimensionality reduction in modern algorithm design. The lemma states that any set of high-dimensional points in a Euclidean space can be projected into lower dimensions while approximately preserving pairwise Euclidean distances. Random matrices satisfying this lemma are called JL transforms (JLTs). Inspired by existing $s$-hashing JLTs with exactly $s$ nonzero elements on each column, the present work introduces an ensemble of sparse matrices encompassing so-called $s$-hashing-like matrices whose expected number of nonzero elements on each column is $s$. The independence of the sub-Gaussian entries of these matrices and the knowledge of their exact distribution play an important role in their analyses. Using properties of independent sub-Gaussian random variables, these matrices are demonstrated to be JLTs, and their smallest nontrivial singular values and largest singular values are estimated nonasymptotically using a technique from geometric functional analysis. As the dimensions of the matrix grow to infinity, these singular values are proved to converge almost surely to fixed quantities (by using the universal Bai–Yin law) and in distribution to the Gaussian orthogonal ensemble Tracy–Widom law after proper rescalings. Understanding the behaviors of extreme singular values is important in general because they are often used to define a measure of stability of matrix algorithms. For example, JLTs were recently used in derivative-free optimization algorithmic frameworks to select random subspaces in which are constructed random models or poll directions to achieve scalability, and hence estimating their smallest singular value in particular helps determine the dimension of these subspaces.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Torque Teno Sus Virus 1: A Potential Surrogate Pathogen to Study Pig-Transmitted Transboundary Animal Diseases

Understanding the epidemiology and transmission dynamics of transboundary animal diseases (TADs) among wild pigs (Sus scrofa) will aid in preventing the introduction or containment of TADs among wild populations. Given the challenges associated with studying TADs in free-ranging populations, a surrogate pathogen system may predict how pathogens may circulate and be maintained within wild free-ranging swine populations, how they may spill over into domestic populations, and how management actions may impact transmission. We assessed the suitability of Torque teno sus virus 1 (TTSuV1) to serve as a surrogate pathogen for molecular epidemiological studies in wild pigs by investigating the prevalence, persistence, correlation with host health status and genetic variability at two study areas: Archbold’s Buck Island Ranch in Florida and Savannah River Site in South Carolina. We then conducted a molecular epidemiological case study within Archbold’s Buck Island Ranch site to determine how analysis of this pathogen could inform transmission dynamics of a directly transmitted virus. Prevalence was high in both study areas (40%, n = 190), and phylogenetic analyses revealed high levels of genetic variability within and between study areas. Our case study showed that pairwise host relatedness and geographic distance were highly correlated to pairwise viral genetic similarity. Molecular epidemiological analyses revealed a distinct pattern of direct transmission from pig to pig occurring within and between family groups. Our results suggest that TTSuV1 is highly suitable for molecular epidemiological analyses and will be useful for future studies of transmission dynamics in wild free-ranging pigs.

60 APPLIED LIFE SCIENCES↗

NASA NTRS1980

Inventory estimation on the massively parallel processor

This paper describes algorithms for efficiently computing inventory estimates from satellite based images. The algorithms incorporate a one dimensional feature extraction which optimizes the pairwise sum of Fisher distances. Biases are eliminated with a premultiplication by the inverse of the analytically derived error matrix. The technique is demonstrated with a numerical example using statistics obtained from an actual Landsat scene. Attention was given to implementation of the Massively Parallel processor (MPP). A timing analysis demonstrates that the inventory estimation can be performed an order of magnitude faster on the MPP than on a conventional serial machine.

Argentiero, P. D.↗

NASA NTRSDate not supplied

Wake Disturbance-Based Separation Evaluation for Urban Air Mobility Aircraft

This paper builds upon previous research to evaluate Urban Air Mobility (UAM) flight dynamics in the presence of wake disturbances. A model for fixed-wing-generated wake effects is applied to a Revolutionary Vertical Lift Technology (RVLT) Lift+Cruise UAM trail aircraft operating in the fixed-wing Cruise configuration. The wake effects are evaluated at various longitudinal and latitudinal separation configurations to determine the most hazardous wake encounter situation. Trim calculations and closed-loop simulations show a trailing aircraft flying directly into a wake vortex as the most hazardous scenario. Furthermore, trailing behind a larger aircraft at similar speeds greatly increases the safe separation distance. These considerations indicate a need for dynamic pairwise separation criteria to enable dense Advanced Air Mobility (AAM) operations while maintaining safety.

Urban Air Mobility↗

NASA NTRS2006

Value, Cost, and Sharing: Open Issues in Constrained Clustering

Clustering is an important tool for data mining, since it can identify major patterns or trends without any supervision (labeled data). Over the past five years, semi-supervised (constrained) clustering methods have become very popular. These methods began with incorporating pairwise constraints and have developed into more general methods that can learn appropriate distance metrics. However, several important open questions have arisen about which constraints are most useful, how they can be actively acquired, and when and how they should be propagated to neighboring points. This position paper describes these open questions and suggests future directions for constrained clustering research.

constraints↗

NASA NTRS2017

Ensuring Interoperability between UAS Detect-and-Avoid and Manned Aircraft Collision Avoidance

The UAS community in the United States has identified the need for a collision avoidance region in which UAS Detect-and-Avoid (DAA) vertical guidance is restricted to preclude interoperability issues with manned aircraft collision avoidance system vertical resolution advisories (RAs). This paper documents the process by which the collision avoidance region was defined. Three candidate definitions were evaluated on 1.3 million simulated pairwise encounters between UAS and manned aircraft covering a wide range of horizontal and vertical closure rates, angles, and miss distances. They were evaluated with regard to UAS DAA interoperability with manned aircraft collision avoidance systems in terms of: 1) the primary objective of restricting DAA vertical guidance before RAs when the aircraft are close, and 2) the secondary objective of avoiding unnecessary restrictions of DAA vertical guidance at a DAA alert when the aircraft are further apart. The collision avoidance region definition that fully achieves the primary objective and best achieves the secondary objective was recommended to and accepted by the UAS community in the United States. By this definition, UAS and manned aircraft are in the collision avoidance region--during which DAA vertical guidance is restricted--when the time to closest point of approach is less than 50 seconds and either the time to co-altitude is less than 50 seconds or the current vertical separation is less than 800 feet.

collision avoidance↗

NASA NTRS2017

Ensuring Interoperability Between Unmanned Aircraft Detect-and-Avoid and Manned Aircraft Collision Avoidance

The Unmanned Aircraft Systems (UAS) community in the United States has identified the need for a collision avoidance region in which UAS Detect-and-Avoid (DAA) vertical guidance is restricted to preclude interoperability issues with manned aircraft collision avoidance system vertical resolution advisories (RAs). This paper documents the process by which the collision avoidance region was defined. Three candidate definitions were evaluated on 1.3 million simulated pairwise encounters between UAS and manned aircraft covering a wide range of horizontal and vertical closure rates, angles, and miss distances. Each definition was evaluated with regard to UAS DAA interoperability with manned aircraft collision avoidance in terms of how well it achieved: 1) the primary objective of restricting DAA vertical guidance prior to RAs when the aircraft are close, and 2) the secondary objective of avoiding unnecessary restrictions of DAA vertical guidance at DAA alerts when the aircraft are further apart. The collision avoidance region definition that fully achieves the primary objective and best achieves the secondary objective was recommended to and accepted by the UAS community in the United States. By this definition, UAS and manned aircraft are in the collision avoidance region where DAA vertical guidance is restricted when the time to closest point of approach (CPA) is less than 50 seconds and either the time to co-altitude is less than 50 seconds or the current vertical separation is less than 800 feet.

unmanned aircraft systems; collision avoidance; in↗

NASA NTRS1991

Archaebacterial rhodopsin sequences: Implications for evolution

It was proposed over 10 years ago that the archaebacteria represent a separate kingdom which diverged very early from the eubacteria and eukaryotes. It follows that investigations of archaebacterial characteristics might reveal features of early evolution. So far, two genes, one for bacteriorhodopsin and another for halorhodopsin, both from Halobacterium halobium, have been sequenced. We cloned and sequenced the gene coding for the polypeptide of another one of these rhodopsins, a halorhodopsin in Natronobacterium pharaonis. Peptide sequencing of cyanogen bromide fragments, and immuno-reactions of the protein and synthetic peptides derived from the C-terminal gene sequence, confirmed that the open reading frame was the structural gene for the pharaonis halorhodopsin polypeptide. The flanking DNA sequences of this gene, as well as those of other bacterial rhodopsins, were compared to previously proposed archaebacterial consensus sequences. In pairwise comparisons of the open reading frame with DNA sequences for bacterio-opsin and halo-opsin from Halobacterium halobium, silent divergences were calculated. These indicate very considerable evolutionary distance between each pair of genes, even in the dame organism. In spite of this, three protein sequences show extensive similarities, indicating strong selective pressures.

Lanyi, J. K.↗

NASA NTRS2018

Pairwise Trajectory Management (PTM): Concept Description and Documentation

Pairwise Trajectory Management (PTM) is an Interval Management (IM) concept that utilizes airborne and ground-based capabilities to enable the implementation of airborne pairwise spacing capabilities in oceanic regions. The goal of PTM is to use airborne surveillance and tools to manage an "at or greater than" inter-aircraft spacing. Due to the accuracy of Automatic Dependent Surveillance-Broadcast (ADS-B) information and the use of airborne spacing guidance, the minimum PTM spacing distance will be less than distances a controller can support with current automation systems that support oceanic operations. Ground tools assist the controller in evaluating the traffic picture and determining appropriate PTM clearances to be issued. Avionics systems provide guidance information that allows the flight crew to conform to the PTM clearance issued by the controller. The combination of a reduced minimum distance and airborne spacing management will increase the capacity and efficiency of aircraft operations at a given altitude or volume of airspace. This document provides an overview of the proposed application, a description of several key scenarios, a high level discussion of expected air and ground equipment and procedure changes, a description of a NASA human-machine interface (HMI) prototype for the flight crew that would support PTM operations, and initial benefits analysis results. Additionally, included as appendices, are the following documents: the PTM Operational Services and Environment Definition (OSED) document and a companion "Future Considerations for the Pairwise Trajectory Management (PTM) Concept: Potential Future Updates for the PTM OSED" paper, a detailed description of the PTM algorithm and PTM Limit Mach rules, initial PTM safety requirements and safety assessment documents, a detailed description of the design, development, and initial evaluations of the proposed flight crew HMI, an overview of the methodology and results of PTM pilot training requirements focus group and human-in-the-loop testing activities, and the PTM Pilot Guide.

Jones, Kenneth M.↗

NASA NTRS2017

Pairwise Trajectory Management (PTM): Concept Overview

Jones, Kenneth M.↗