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DOE OSTI2026

Chemical Recommender System: Replacement Suggestions for Small Molecules

The Chemical Recommender System (CRS) is an open-source, high-performance toolkit that enables real-time similarity searches across the complete PubChem database (over 50 million molecules) using commodity hardware. The CRS addresses critical limitations in existing chemical informatics platforms through a novel vector database infrastructure, extensible model integration capabilities, and complete algorithmic transparency. The system implements a vector database deployment with partitioned indexing that achieves a ~60x speedup over traditional approaches. A containerized model integration framework allows researchers to seamlessly incorporate custom predictive models into the full-scale search and scoring pipeline, while complete configurability of search parameters, filtering logic, and scoring functions provides capabilities not available in existing black-box solutions. Beyond structural similarity, the CRS integrates OPERA QSAR models for thermophysical and toxicity predictions, RDKit synthetic accessibility scoring, and user-defined models to compute weighted final replacement scores. The complete system is accessible through an interactive web application supporting real-time progress monitoring, post-processing score re-weighting, automated PDF reporting, and batch processing capabilities.

Nair, Parthiv Anand [Sandia National Laboratories ↗

NASA NTRS1992

Numerical classification of coding sequences

DNA sequences coding for protein may be represented by counts of nucleotides or codons. A complete reading frame may be abbreviated by its base count, e.g. A76C158G121T74, or with the corresponding codon table, e.g. (AAA)0(AAC)1(AAG)9 ... (TTT)0. We propose that these numerical designations be used to augment current methods of sequence annotation. Because base counts and codon tables do not require revision as knowledge of function evolves, they are well-suited to act as cross-references, for example to identify redundant GenBank entries. These descriptors may be compared, in place of DNA sequences, to extract homologous genes from large databases. This approach permits rapid searching with good selectivity.

Non-NASA Center↗

NASA NTRS1994

Supersonic and hypersonic shock/boundary-layer interaction database

An assessment is given of existing shock wave/tubulent boundary-layer interaction experiments having sufficient quality to guide turbulence modeling and code validation efforts. Although the focus of this work is hypersonic, experiments at Mach numbers as low as 3 were considered. The principal means of identifying candidate studies was a computerized search of the AIAA Aerospace Database. Several hundred candidate studies were examined and over 100 of these were subjected to a rigorous set of acceptance criteria for inclusion in the data-base. Nineteen experiments were found to meet these criteria, of which only seven were in the hypersonic regime (M is greater than 5).

Settles, Gary S.↗

NASA NTRS2003

Quantum Search in Hilbert Space

A proposed quantum-computing algorithm would perform a search for an item of information in a database stored in a Hilbert-space memory structure. The algorithm is intended to make it possible to search relatively quickly through a large database under conditions in which available computing resources would otherwise be considered inadequate to perform such a task. The algorithm would apply, more specifically, to a relational database in which information would be stored in a set of N complex orthonormal vectors, each of N dimensions (where N can be exponentially large). Each vector would constitute one row of a unitary matrix, from which one would derive the Hamiltonian operator (and hence the evolutionary operator) of a quantum system. In other words, all the stored information would be mapped onto a unitary operator acting on a quantum state that would represent the item of information to be retrieved. Then one could exploit quantum parallelism: one could pose all search queries simultaneously by performing a quantum measurement on the system. In so doing, one would effectively solve the search problem in one computational step. One could exploit the direct- and inner-product decomposability of the unitary matrix to make the dimensionality of the memory space exponentially large by use of only linear resources. However, inasmuch as the necessary preprocessing (the mapping of the stored information into a Hilbert space) could be exponentially expensive, the proposed algorithm would likely be most beneficial in applications in which the resources available for preprocessing were much greater than those available for searching.

Zak, Michail↗

NASA NTRSDate not supplied

New Ways of Facilitating Improved Data Discovery and Access for NASA's Suborbital Earth Science Observations

NASA conducts field research in various Earth Science disciplines utilizing airborne and other non-satellite platforms to acquire in situ and remotely sensed observations indicative of physical processes across a range of scales. Field efforts are key in the development and validation of instruments and satellite algorithm refinements. The heterogeneous data, with a range of file formats, scales, and acquisition methods, support research in several science areas. NASA’s archive process assigns data products to discipline-oriented Distributed Active Archive Centers (DAACs) for stewardship. Over time, individual DAACs have developed tools for data browsing and serving disparate user bases. As science becomes more interdisciplinary, researchers need to incorporate observations from multiple campaigns, and multiple DAACs, into their work. Motivated in part by this shifting paradigm of needs, the Catalog of Archived Suborbital Earth Science Investigations (CASEI) was created. CASEI provides a single starting point to browse, search, and discover airborne and field data. Contextual metadata are organized and inter-linked allowing intuitive, integrated exploration across all NASA DAACs. Campaign science objectives, platform and instrument configurations, geographical details, geophysical concepts, and more are tracked in CASEI’s database, facilitating multi-parameter search, browse, and discovery of relevant data products. Researchers are able to directly access associated data products, via DOI links, regardless of the DAAC where they reside. Significant events, key time periods of high science interest within the longer-duration campaign effort, are also indicated and allow for a more efficient identification of critical data subsets. This presentation describes CASEI’s development, intensive metadata curation process, and demonstrates the web interface experience. Initial content metrics and plans for continued maintenance will also be discussed.

metadata↗

NASA NTRSDate not supplied

Assessing the Use of UAS-Related Terms in ASRS Using Seed Topic Modeling

Context: The NASA Aviation Safety Reporting System (ASRS) is a voluntary confidential system that disseminates reports received from personnel involved in aviation operations after de-identifying them. These reports are used by the community to improve overall aviation system safety. Aim: We propose and execute an experiment to assess the use of seed term topic modeling over the database narratives to identify Unmanned Aircraft System (UAS) reports. The use of seed term topic modeling enables users to identify groups of conceptually similar narratives associated to a topic of their interest. Method: We use a collection of narratives, expert-selected words, and report metadata that separates UAS from non-UAS reports to assess if seed topic modeling can be used to improve ASRS searches. Results: For simpler queries, seed topic search observes a higher recall and lower precision than the existing DBOL (DataBase OnLine) search in operation. However, the best results are obtained when seed topic search is used as a search suggestion system to be executed on the DBOL. Conclusion: Utilizing a combination of both the existing method and the proposed method, users can expand their search vocabulary about subjects of interest while improving the quality of results.

Text Mining↗

NASA NTRSDate not supplied

Assessing the Use of UAS-Related Terms in ASRS using Seeds for Topic Modeling

LDA↗

NASA NTRS1994

Investigations into mirror fabrication metrology analysis

This final report describes the work performed under this delivery order from June 1993 through August 1994. The scope of work included three distinct tasks in support of the AXAF-I program. The objective of the first task was to perform investigations of the grinding and polishing characteristics of the zerodur material by fabricating several samples. The second task was to continue the development of the integrated optical performance modeling software for AXAF-I. The purpose of third and final task was to develop and update the database of AXAF technical documents for an easy and rapid access. The MSFC optical and metrology shops were relocated from the B-wing of Building 4487 to Room BC 144 of Building 4466 in the beginning of this contract. This included dismantling, packing, and moving the equipment from its old location, and then reassembling it at the new location. A total of 65 zerodur samples, measuring 1 inch x 2 inches x 6 inches were ground and polished to a surface figure of lambda/10 p-v, and a surface finish of 5A rms were fabricated for coating tests. A number of special purpose tools and metal mirrors were also fabricated to support various AXAF-I development activities. In the metrology area, the ZYGO Mark 4 interferometer was relocated and also upgraded with a faster and more powerful processor. Surface metrology work was also performed on the coating samples and other optics using ZYGO interferometer and WYKO profilometer. A number of new features have been added to the GRAZTRACE program to enhance its analysis and modeling capabilities. A number of new commands have been added to the command mode GRAZTRACE program to provide a better control to the user on the program execution and data manipulation. Some commands and parameter entries have been reorganized for a uniform format. The command mode version of the convolution program CONVOLVE has been developed. An on-line help system and a user's manual have also been developed for the benefit of the users. The database of AXAF technical documents continues to progress. The titles, company name, date, and location of over 390 documents have been entered in this database. This database provides both a data search and retrieval function, and a data adding function. These functions allow a user to quickly search the data files for documents or add new information. A detailed user's guide has also been prepared. This user guide includes a document classification guide, a list of abbreviations, and a list of acronyms, which have been used in compiling this database of AXAF-I technical documents.

Dimmock, John O.↗

NASA NTRS2011

From Science to e-Science to Semantic e-Science: A Heliosphysics Case Study

The past few years have witnessed unparalleled efforts to make scientific data web accessible. The Semantic Web has proven invaluable in this effort; however, much of the literature is devoted to system design, ontology creation, and trials and tribulations of current technologies. In order to fully develop the nascent field of Semantic e-Science we must also evaluate systems in real-world settings. We describe a case study within the field of Heliophysics and provide a comparison of the evolutionary stages of data discovery, from manual to semantically enable. We describe the socio-technical implications of moving toward automated and intelligent data discovery. In doing so, we highlight how this process enhances what is currently being done manually in various scientific disciplines. Our case study illustrates that Semantic e-Science is more than just semantic search. The integration of search with web services, relational databases, and other cyberinfrastructure is a central tenet of our case study and one that we believe has applicability as a generalized research area within Semantic e-Science. This case study illustrates a specific example of the benefits, and limitations, of semantically replicating data discovery. We show examples of significant reductions in time and effort enable by Semantic e-Science; yet, we argue that a "complete" solution requires integrating semantic search with other research areas such as data provenance and web services.

Narock, Thomas↗

NASA NTRS2000

A Systematic Search for Short-term Variability of EGRET Sources

The 3rd EGRET Catalog of High-energy Gamma-ray Sources contains 170 unidentified sources, and there is great interest in the nature of these sources. One means of determining source class is the study of flux variability on time scales of days; pulsars are believed to be stable on these time scales while blazers are known to be highly variable. In addition, previous work has demonstrated that 3EG J0241-6103 and 3EG J1837-0606 are candidates for a new gamma-ray source class. These sources near the Galactic plane display transient behavior but cannot be associated with any known blazers. Although, many instances of flaring AGN have been reported, the EGRET database has not been systematically searched for occurrences of short-timescale (approximately 1 day) variability. These considerations have led us to conduct a systematic search for short-term variability in EGRET data, covering all viewing periods through proposal cycle 4. Six 3EG catalog sources are reported here to display variability on short time scales; four of them are unidentified. In addition, three non-catalog variable sources are discussed.

Wallace, P. M.↗

NASA NTRS2018

Small Spacecraft Systems Virtual Institute's Federated Databases and State of the Art of Small Spacecraft Technology Report

NASA's Small Spacecraft Systems Virtual Institute (S3VI) is collaborating with the Air Force Research Laboratory and Space Dynamics Laboratory on the development of a small spacecraft parts database called SmallSat Parts On Orbit Now (SPOON). The SPOON database contains small spacecraft parts and technologies categorized by major satellite subsystems developed by industry, academia and government. The State of the Art of Small Spacecraft Technology report reflects small spacecraft parts submitted to the SPOON database and technologies compiled from other sources that were assessed as the current state of the art in each of the major subsystems. The report, first commissioned by NASA's Small Spacecraft Technology Program in mid-2013, is developed in response to the continuing growth in interest in using small spacecraft for many types of missions in Earth orbit and beyond. Due to the high market penetration of CubeSats, particular emphasis is placed on the state of the art of CubeSat-related technology. The 2018 report is planned for release in late summer. A review of SPOON database functionality, federation of additional NASA-internal and external databases along with a common search capability, as well as an overview of the State of the Art of Small Spacecraft Technology report will be presented. The S3VI is jointly sponsored by NASA's Space Technology Mission Directorate and Science Mission Directorate.

Small spacecraft↗

NASA NTRS2004

Aerodynamic Optimization of Rocket Control Surface Geometry Using Cartesian Methods and CAD Geometry

Aerodynamic design is an iterative process involving geometry manipulation and complex computational analysis subject to physical constraints and aerodynamic objectives. A design cycle consists of first establishing the performance of a baseline design, which is usually created with low-fidelity engineering tools, and then progressively optimizing the design to maximize its performance. Optimization techniques have evolved from relying exclusively on designer intuition and insight in traditional trial and error methods, to sophisticated local and global search methods. Recent attempts at automating the search through a large design space with formal optimization methods include both database driven and direct evaluation schemes. Databases are being used in conjunction with surrogate and neural network models as a basis on which to run optimization algorithms. Optimization algorithms are also being driven by the direct evaluation of objectives and constraints using high-fidelity simulations. Surrogate methods use data points obtained from simulations, and possibly gradients evaluated at the data points, to create mathematical approximations of a database. Neural network models work in a similar fashion, using a number of high-fidelity database calculations as training iterations to create a database model. Optimal designs are obtained by coupling an optimization algorithm to the database model. Evaluation of the current best design then gives either a new local optima and/or increases the fidelity of the approximation model for the next iteration. Surrogate methods have also been developed that iterate on the selection of data points to decrease the uncertainty of the approximation model prior to searching for an optimal design. The database approximation models for each of these cases, however, become computationally expensive with increase in dimensionality. Thus the method of using optimization algorithms to search a database model becomes problematic as the number of design variables is increased.

Nelson, Andrea↗

DOE OSTI2021

Prediction of DIII-D Pedestal Structure From Externally Controllable Parameters

The sharp increase of pressure at the edge of a high confinement mode (H-mode) plasma, the pedestal, strongly impacts overall plasma performance. Predicting the pedestal is a necessity to control and optimize tokamak operations. Here, an experimental data-driven machine learning (ML) approach is presented that predicts the pedestal heights and widths of electron density (n e ) and electron temperature (T e ) profiles as well as the separatrix ne from externally controllable parameters such as the plasma shape, heating method and power, and gas puff rate and integrated gas puff. The OMFIT framework was used with DIII-D data to efficiently, robustly, and automatically build a database of pedestal parameters to train machine learning models. Database creation was enabled by the search engine tool for DIII-D data, TokSearch, which parallelizes data fetching, enabling fast searches through basic signals of thousands of DIII-D shots and selection of relevant time intervals. Principal Component Analysis (PCA) separated the database into three clusters that represent classes of plasma shapes that are regularly used in DIII-D. The most important parameters for setting the pedestal structure were plasma current (I p ), toroidal magnetic field (B Φ ), neutral beam heating power (P NBI ) and shaping quantities. The Deep Jointly Informed Neural Networks (DJINN) algorithm was applied to identify suitable neural network (NN) architectures that appropriately capture the features of the pedestal database. Separate NNs were implemented for each pedestal parameter, and ensembling methods were used to improve the prediction accuracy and allowed estimation of the prediction uncertainty. The pedestal predictions of the test dataset lie within the measurement uncertainties of the pedestal parameters. The NN outperformed simple Linear Regression (LR) analysis, indicating non-linear dependencies in the pedestal structure. The presented achievements illustrate a promising path for future research, using feature extraction to infer experimental trends and thereby improve pedestal models as well as deploying NN for a fast pedestal prediction in DIII-D scenario development.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

Prediction of DIII-D Pedestal Structure from Externally Controllable Parameters

The sharp increase of pressure at the edge of a high confinement mode (H-mode) plasma, the pedestal, strongly impacts overall plasma performance. Predicting the pedestal is a necessity to control and optimize tokamak operations. An experimental data-driven machine learning (ML) approach is presented that predicts the pedestal heights and widths of electron density (ne) and electron temperature (Te) profiles as well as the separatrix ne from externally controllable parameters such as the plasma shape, heating method and power, and gas puff rate and integrated gas puff. The OMFIT framework was used with DIII-D data to efficiently, robustly, and automatically build a database of pedestal parameters to train machine learning models. Database creation was enabled by the search engine tool for DIII-D data, TokSearch, which parallelizes data fetching, enabling fast searches through basic signals of thousands of DIII-D shots and selection of relevant time intervals. Principal Component Analysis (PCA) separated the database into three clusters that represent classes of plasma shapes that are regularly used in DIII-D. The most important parameters for setting the pedestal structure were plasma current (Ip), toroidal magnetic field (Bφ), neutral beam heating power (PNBI) and shaping quantities. The Deep Jointly Informed Neural Networks (DJINN) algorithm was applied to identify suitable neural network (NN) architectures that appropriately capture the features of the pedestal database. Separate NNs were implemented for each pedestal parameter, and ensembling methods were used to improve the prediction accuracy and allowed estimation of the prediction uncertainty. The pedestal predictions of the test dataset lie within the measurement uncertainties of the pedestal parameters. The NN outperformed simple Linear Regression (LR) analysis, indicating non-linear dependencies in the pedestal structure. The presented achievements illustrate a promising path for future research, using feature extraction to infer experimental trends and thereby improve pedestal models as well as deploying NN for a fast pedestal prediction in DIII-D scenario development.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

NASA NTRS1993

Bibliography on propulsion airframe integration technologies for high-speed civil transport applications, 1980-1991

NASA has initiated the High Speed Research (HSR) program with the goal to develop technologies for a new generation, economically viable, environmentally acceptable, supersonic transport (SST) called the High Speed Civil Transport (HSCT). A significant part of this effort is expected to be in multidisciplinary systems integration, such as in propulsion airframe integration (PAI). In order to assimilate the knowledge database on PAI for SST type aircraft, a bibliography on this subject was compiled. The bibliography with over 1200 entries, full abstracts, and indexes. Related topics are also covered, such as the following: engine inlets, engine cycles, nozzles, existing supersonic cruise aircraft, noise issues, computational fluid dynamics, aerodynamics, and external interference. All identified documents from 1980 through early 1991 are included; this covers the latter part of the NASA Supersonic Cruise Research (SCR) program and the beginnings of the HSR program. In addition, some pre-1980 documents of significant merit or reference value are also included. The references were retrieved via a computerized literature search using the NASA RECON database system.

Anderson, David J.↗

NASA NTRS2010

Integrating Variances into an Analytical Database

For this project, I enrolled in numerous SATERN courses that taught the basics of database programming. These include: Basic Access 2007 Forms, Introduction to Database Systems, Overview of Database Design, and others. My main job was to create an analytical database that can handle many stored forms and make it easy to interpret and organize. Additionally, I helped improve an existing database and populate it with information. These databases were designed to be used with data from Safety Variances and DCR forms. The research consisted of analyzing the database and comparing the data to find out which entries were repeated the most. If an entry happened to be repeated several times in the database, that would mean that the rule or requirement targeted by that variance has been bypassed many times already and so the requirement may not really be needed, but rather should be changed to allow the variance's conditions permanently. This project did not only restrict itself to the design and development of the database system, but also worked on exporting the data from the database to a different format (e.g. Excel or Word) so it could be analyzed in a simpler fashion. Thanks to the change in format, the data was organized in a spreadsheet that made it possible to sort the data by categories or types and helped speed up searches. Once my work with the database was done, the records of variances could be arranged so that they were displayed in numerical order, or one could search for a specific document targeted by the variances and restrict the search to only include variances that modified a specific requirement. A great part that contributed to my learning was SATERN, NASA's resource for education. Thanks to the SATERN online courses I took over the summer, I was able to learn many new things about computers and databases and also go more in depth into topics I already knew about.

Sanchez, Carlos↗

NASA NTRSDate not supplied

Implementation of A New Microwave Scattering Database and A Forward Model for Active Microwave Sensors in CRTM

Radiative transfer models are extensively used for the assimilation of satellite observations into NWP models as well as retrieving geophysical products from satellite measurements. CRTM is a community model developed by NOAA JCSDA and widely used for different purposes requiring RT calculations. CRTM requires bulk scattering lookup tables in order to perform all-sky RT calculations. However, the current CRTM lookup tables for microwave frequencies were generated based on the Mie theory by assuming spherical frozen particles. The scattering lookup tables generated using the DDA technique has shown to largely improve the RT scattering calculations in the MW region. This presentation targets (i) the implementation and validation of a DDA database that was originally developed for the ARTS RT model into CRTM, and (ii) developing the CRTM active sensor module that takes advantage of the backscattering coefficients computed using the DDA method. The DDA database only provides single scattering properties of different habits, while CRTM requires bulk scattering properties. The CRTM cloud coefficients were previously generated based on the effective radius for representing the size of the particles. However, effective radius is neither measurable nor provided by the NWP models, thus need to be estimated from other geophysical variables such as water content. Therefore, in addition to calculating the CRTM bulk scattering properties from the DDA single scattering database, the CRTM was also largely modified to use cloud water content (kg.m-3), instead of effective radius, for performing the interpolation over size/mass of the particles. CRTM already requires water content as input, thus no extra variables are required for performing scattering calculations using the new ARTS DDA database. The CRTM scattering modules search for effective radius in cloud coefficient files and will use the cloud water content if the effective radius dimension is not found in the cloud coefficient files. Figure 1 shows the CRTM simulated brightness temperatures computed using different cloud coefficients versus ATMS observed values over Hurricane Irma on September 7, 2017 at 18:00 UTC. We used all the cloud water content values included in ERA5 with default CRTM/DDA habits for water, rain, snow, ice, hail, and graupel. ERA5 does not provide separate water content values for ice, hail, and graupel, thus the ice water content values were divided between ice, hail, and graupel clouds similar to what was explained in the previous section. In channels with a frequency lower than 90 GHz, emission from water and rain clouds can compensate for cloud scattering so that cloud contaminated Tbs are larger than corresponding clear sky Tbs. The DDA simulations for channels 1-7 largely perform better than the Mie simulations. The DDA simulations show a mix of small negative and positive simulated minus observed values, while the Mie results show large negative biases. The weighting functions for some of the ATMS temperature sounding channels (channels 9-15) peak mostly above the clouds, therefore the measured Tbs become less sensitive to clouds so that the results of both Mie and DDA become very similar. The Mie lookup tables generate excessive scattering for channel 16, but not enough scattering for the water vapor channels. In the specific case of Hurricane Maria, the DDA lookup tables do not generate enough scattering for channel 16, but the DDA results are much more consistent with observations for water vapor channels than for channel 16. It should be noted that the results may vary if we use other habits to represent snow, hail, and graupel in the DDA simulations. Although these results clearly show the advantage of the DDA database over the Mie dataset, different error sources such as error in the observations, displacement of clouds in the ERA5 reanalysis, and also lack of convective clouds or in general errors in the input atmospheric and cloud profiles contribute to the differences between the simulated and observed values. Aside from the improvements in the simulations, a major advantage of the new dataset is a large number of habits that can be used to tune the data assimilation systems to perform well in different weather conditions.

Isaac Moradi↗

DOE OSTI2021

iBLAST: Incremental BLAST of new sequences via automated e-value correction

Search results from local alignment search tools use statistical scores that are sensitive to the size of the database to report the quality of the result. For example, NCBI BLAST reports the best matches using similarity scores and expect values (i.e., e-values) calculated against the database size. Given the astronomical growth in genomics data throughout a genomic research investigation, sequence databases grow as new sequences are continuously being added to these databases. As a consequence, the results (e.g., best hits) and associated statistics (e.g., e-values) for a specific set of queries may change over the course of a genomic investigation. Thus, to update the results of a previously conducted BLAST search to find the best matches on an updated database, scientists must currently rerun the BLAST search against the entire updated database, which translates into irrecoverable and, in turn, wasted execution time, money, and computational resources. To address this issue, we devise a novel and efficient method to redeem past BLAST searches by introducing iBLAST. iBLAST leverages previous BLAST search results to conduct the same query search but only on the incremental (i.e., newly added) part of the database, recomputes the associated critical statistics such as e-values, and combines these results to produce updated search results. Our experimental results and fidelity analyses show that iBLAST delivers search results that are identical to NCBI BLAST at a substantially reduced computational cost, i.e., iBLAST performs (1 + δ )/ δ times faster than NCBI BLAST, where δ represents the fraction of database growth. We then present three different use cases to demonstrate that iBLAST can enable efficient biological discovery at a much faster speed with a substantially reduced computational cost.

59 BASIC BIOLOGICAL SCIENCES↗