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At least 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Knowledge Oriented Graph Unified Transformer (KOGUT) v0.1

KOGUT — Knowledge Oriented Graph Unified Transformer KOGUT implements the Relational Graph Transformer (RelGT) architecture for knowledge graph link prediction in biological domains, with a primary focus on microbial growth media prediction. While the original RelGT (arXiv:2505.10960) targets relational tables, time series, and multi-table databases, KOGUT adapts this architecture for heterogeneous biological knowledge graphs, providing first-in-class AI predictive models for microbial cultivation. Key Adaptations Beyond Original RelGT: - Knowledge Graph Focus: Applied to biological KGs with semantic node types (taxa, chemicals, media, phenotypes, environments) versus generic relational database tables, trained on the KG-Microbe knowledge graph (1.3M entities, 2.9M edges, 24 relation types). - Multimodal Node Encoding: Integrates node labels, categories, descriptions, and synonyms from KG metadata through learned embedding layers—adapting relational column features to graph node attributes with textual semantics. - Extended K-Hop Subgraph Strategy: Optimized neighborhood sampling (3-hop default, configurable up to 200 nodes) tuned for sparse biological networks, building on the original local-global attention framework with biological relation preservation. - Biolink Predicate Preservation: Type-specific transformations for 24 biological edge semantics (occurs_in, consumes, produces, has_phenotype, subclass_of) beyond standard relational foreign keys, enabling multi-relation link prediction. - Inductive Learning Support: Enables zero-shot predictions for novel taxa through feature-based embeddings (temperature, oxygen requirements, gram stain, cell shape), extending the original transductive relational benchmark scope to uncultured microorganisms. CheapSOTA Performance Optimizations (This Distribution): - VQ-EMA Centroid Attention: Vector quantization with exponential moving average for improved global context modeling (+5-10% MRR improvement). - HDF5 Precomputed Data Loading: One-time preprocessing of k-hop subgraphs to eliminate redundant graph traversals (2-5× training speedup). - Distributed Data Parallel Training: Multi-GPU support for scaling to larger knowledge graphs (tested on 4× NVIDIA A100 GPUs at NERSC Perlmutter). - Mixed Precision Training: Automatic mixed precision (AMP) for memory efficiency and faster training. Advantages Over Standard Knowledge Graph Embedding Models: Combines RelGT's proven multi-element tokenization (features, type, hop, structure) with graph-native biological representations, enabling interpretable link prediction across heterogeneous entities that standard embedding models (TransE, RotatE, ComplEx) and table-based transformers cannot directly model. Achieves near-perfect performance on microbial growth media prediction (MRR: 0.9966, Precision@1: 0.9932, Hit@10: 1.0000) while maintaining explainability through attention-based reasoning over biological pathways. Training Data: - KG-Microbe merged knowledge graph: 1,379,337 nodes, 2,960,472 edges - 24 biological relation types including taxonomic hierarchies, metabolic interactions, phenotype associations, and environmental relationships - Primary prediction task: Growth media suitability for microbial taxa (biolink:occurs_in, 50K edges) - Multi-relation capability: Predicts links for any of the 24 relation types, including chemical consumption/production, phenotype associations, and taxonomic classification Citation: Original RelGT Architecture: Dwivedi et al., "Relational Graph Transformer", arXiv:2505.10960, 2025 KOGUT Implementation: Knowledge Oriented Graph Unified Transformer for Microbial Growth Media Prediction Developed at Lawrence Berkeley National Laboratory (LBNL) Trained on NERSC Perlmutter supercomputer

Joachimiak, Marcin [Lawrence Berkeley National Lab↗
DOE OSTI2021

Biogeography of microbial bile acid transformations along the murine gut

Bile acids, which are synthesized from cholesterol by the liver, are chemically transformed along the intestinal tract by the gut microbiota, and the products of these transformations signal through host receptors, affecting overall host health. These transformations include bile acid deconjugation, oxidation, and 7α-dehydroxylation. An understanding of the biogeography of bile acid transformations in the gut is critical because deconjugation is a prerequisite for 7α-dehydroxylation and because most gut microorganisms harbor bile acid transformation capacity. Here, we used a coupled metabolomic and metaproteomic approach to probe in vivo activity of the gut microbial community in a gnotobiotic mouse model. Results revealed the involvement of Clostridium scindens in 7α-dehydroxylation, of the genera Muribaculum and Bacteroides in deconjugation, and of six additional organisms in oxidation (the genera Clostridium, Muribaculum, Bacteroides, Bifidobacterium, Acutalibacter, and Akkermansia). Furthermore, the bile acid profile in mice with a more complex microbiota, a dysbiosed microbiota, or no microbiota was considered. For instance, conventional mice harbor a large diversity of bile acids, but treatment with an antibiotic such as clindamycin results in the complete inhibition of 7α-dehydroxylation, underscoring the strong inhibition of organisms that are capable of carrying out this process by this compound. Finally, a comparison of the hepatic bile acid pool size as a function of microbiota revealed that a reduced microbiota affects host signaling but not necessarily bile acid synthesis. In this study, bile acid transformations were mapped to the associated active microorganisms, offering a systematic characterization of the relationship between microbiota and bile acid composition.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Dose-Rate Effects of Protons and Light Ions for DNA Damage Induction, Survival and Transformation in Apparently Normal Primary Human Fibroblasts

In this work, we report on effects of low-dose exposures of accelerated protons delivered at high-dose rate (HDR) or a simulated solar-particle event (SPE) like low-dose rate (LDR) on immediate DNA damage induction and processing, survival and in vitro transformation of low passage NFF28 apparently normal primary human fibroblasts. Cultures were exposed to 50, 100 and 1,000 MeV monoenergetic protons in the Bragg entrance/plateau region and cesium-137 γ rays at 20 Gy/h (HDR) or 1 Gy/h (LDR). DNA double-strand breaks (DSB) and clustered DNA damages (containing oxypurines and abasic sites) were measured using transverse alternating gel electrophoresis (TAFE) and immunocytochemical detection/scoring of colocalized γ-H2AX pS139/53BP1 foci, with their induction being linear energy transfer (LET) dependent and dose-rate sparing observed for the different damage classes. Relative biological effectiveness (RBE) values for cell survival after proton irradiation at both dose-rates ranged from 0.61–0.73. Transformation RBE values were dose-rate dependent, ranging from ~1.8–3.1 and ~0.6–1.0 at low doses (≤30 cGy) for HDR and LDR irradiations, respectively. However peak transformation frequencies were significantly higher (1.3–7.3-fold) for higher doses of 0.5–1 Gy delivered at SPE-like LDR. Cell survival and transformation frequencies measured after low-dose 500 MeV/n He-4, 290 MeV/n C-12 and 600 MeV/n Si-28 ion irradiations also showed an inverse dose-rate effect for transformation at SPE-like LDR. This work demonstrates the existence of inverse dose-rate effects for proton and light-ion-induced postirradiation cell survival and in vitro transformation for space mission-relevant doses and dose rates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Solid State Transformer Architecture and Control Compensation for Common Mode Currents

A high-altitude electromagnetic pulse (HEMP) or similar geomagnetic disturbance (GMD) has the potential to impact the operation of large-scale electric power grids. By introducing low-frequency common-mode (CM) currents, these events can degrade the performance of critical system components, such as large power transformers by introducing CM currents which can lead to magnetic saturation of the transformer core. In this work, a solid-state transformer (SST) is developed to replace susceptible equipment and improve grid resiliency by safely absorbing these CM disturbances. This device will be referred to as a common-mode solid-state transformer (CM-SST). An SST architecture based on a four-legged AC/DC converter is developed. This architecture enables active control of CM signals without disturbing the AC voltages or the real and reactive power delivery capabilities. A system-level model of this architecture is created, and time-domain simulations are performed to evaluate the SST’s performance in response to simulated CM disturbances. A control strategy for mitigating CM current is also investigated. Hamiltonian surface shaping and power flow control (HSSPFC) is used to design a nonlinear controller for the SST’s output inverter. The objectives of the controller are to suppress CM-induced AC current offsets and regulate AC currents to desired setpoints. Nonlinear system analysis is applied to design and validate the controller. Two cases are tested: (a) the proposed four-leg inverter and (b) a standard three-leg inverter. The results show that the proposed controller rapidly mitigates CM disturbances while maintaining high-quality AC current waveforms in the four-leg configuration. Finally, the hardware performance of an SST prototype is evaluated. In particular, the ability of the SST to safely redirect and absorb CM currents is demonstrated, showing how it can protect neighboring conventional transformers in the system. The study confirms that appropriate control laws allow the SST to protect both itself and adjacent transformers during a HEMP or GMD event.

24 POWER TRANSMISSION AND DISTRIBUTION↗
NASA NTRS1972

Low-temperature solid-state phase transformations in 2H silicon carbide

Single crystals of 2H SiC were observed to undergo phase transformations at temperatures as low as 400 C. Some 2H crystals transformed to a structure with one-dimensional disorder along the crystal c axis. Others transformed to a faulted cubic/6H structure. The transformation is time and temperature dependent and is greatly enhanced by dislocations. Observations indicate that the transformation takes place by means of a slip process perpendicular to the c axis. Cubic SiC crystals were observed to undergo a solid state transformation above 1400 C.

Will, H. A.↗
NASA NTRS1972

Low-temperature solid-state phase transformations in 2H silicon carbide.

Study of the phase transformations taking place in 2H SiC single crystals at temperatures as low as 400 C. Some crystals transformed to a structure with one-dimensional disorder along the crystal c axis. Others transformed to a faulted cubic/6H structure. The transformation is time and temperature dependent, and is greatly enhanced by dislocations. The transformation takes place by means of a slip process perpendicular to the c axis. Cubic SiC crystals were observed to undergo a solid-state transformation above 1400 C.

Powell, J. A.↗
NASA NTRS1975

On the Laplace transform for distributions

A new characterization of the Laplace transform for Schwartz distributions is developed, using sequences of linear transformations on the space of distributions. The standard theorems on analyticity, uniqueness and invertibility of the transform are proved, using the new characterization as the definition of the Laplace transform. It is shown that this sequential definition is equivalent to Schwartz's extension of the ordinary Laplace transform to distributions which he obtained from the Fourier transform.

Price, D. B.↗
NASA NTRS1975

The transformation of aerodynamic stability derivatives by symbolic mathematical computation

The formulation of mathematical models of aeronautical systems for simulation or other purposes, involves the transformation of aerodynamic stability derivatives. It is shown that these derivatives transform like the components of a second order tensor having one index of covariance and one index of contravariance. Moreover, due to the equivalence of covariant and contravariant transformations in orthogonal Cartesian systems of coordinates, the transformations can be treated as doubly covariant or doubly contravariant, if this simplifies the formulation. It is shown that the tensor properties of these derivatives can be used to facilitate their transformation by symbolic mathematical computation, and the use of digital computers equipped with formula manipulation compilers. When the tensor transformations are mechanised in the manner described, man-hours are saved and the errors to which human operators are prone can be avoided.

Howard, J. C.↗
NASA NTRS1982

Discrete Fourier transforms of nonuniformly spaced data

Time series or spatial series of measurements taken with nonuniform spacings have failed to yield fully to analysis using the Discrete Fourier Transform (DFT). This is due to the fact that the formal DFT is the convolution of the transform of the signal with the transform of the nonuniform spacings. Two original methods are presented for deconvolving such transforms for signals containing significant noise. The first method solves a set of linear equations relating the observed data to values defined at uniform grid points, and then obtains the desired transform as the DFT of the uniform interpolates. The second method solves a set of linear equations relating the real and imaginary components of the formal DFT directly to those of the desired transform. The results of numerical experiments with noisy data are presented in order to demonstrate the capabilities and limitations of the methods.

Swan, P. R.↗
NASA NTRS1983

Development of a rotary power transformer and inverter drive for spacecraft

Many future satellites and spacecraft with spun and despun configurations will require the transfer of power across rotating interfaces in lieu of slip-rings and/or flexures. This is particularly true of spacecraft that have to demonstrate a long life expectancy. The rotary transformer has the desirable characteristics of high reliability and low noise, which qualify it as a potential replacement for slip rings. Development of a rotary power transformer follows the successful completion of a task to develop rotary signal-level transformers for the Galileo Spacecraft Project. The physical configuration of a rotary power transformer has a significant effect on its magnetic and electrical characteristics and therefore impacts the design of the dc/ac inverter driver. Important characteristics addressed during this development effort include: operating frequency, efficiency, transformer gap size, leakage inductance, and leakage flux. A breadboard inverter and rotary transformer were designed, fabricated and tested.

Mclyman, W. T.↗
NASA NTRS1984

Use of the TM tasseled cap transform for interpretation of spectral contrasts in an urban scene

Investigations are being conducted with the objective to develop automated numerical image analysis procedures. In this context, an examination is performed of physically-based multispectral data transforms as a means to incorporate a priori knowledge of land radiance properties in the analysis process. A physically-based transform of TM observations was developed. This transform extends the Landsat MSS Tasseled Cap transform reported by Kauth and Thomas (1976) to TM data observations. The present study has the aim to examine the utility of the TM Tasseled Cap transform as applied to TM data from an urban landscape. The analysis conducted is based on 512 x 512 subset of the Washington, DC November 2, 1982 TM scene, centered on Springfield, VA. It appears that the TM tasseled cap transformation provides a good means to explain land physical attributes of the Washington scene. This result provides a suggestion regarding a direction by which a priori knowledge of landscape spectral patterns may be incorporated into numerical image analysis.

Goward, S. N.↗
NASA NTRS1986

Mechanisms and depths of atlantic transform earthquakes

Mechanisms and depths of 40 earthquakes on major transforms along the Mid-Atlantic Ridge are studied in order to identify events that deviate from the transform-parallel strike-slip motion. Long and short period waves and Rayleigh wave spectral amplitudes are used to analyze focal mechanisms, depths, source time functions, and seismic moments of earthquakes. The relationship between centroid depths and transform thermal structures is examined. The data reveal that transform earthquake centroid depths occur above the predicted 400 C isotherms and the oceanic intraplate depths extend to the 750 C isotherm. Slip rates inferred from seismic moment releases are compared to those predicted by plate motions and good correlation is detected. The difference in the centroid depths of transform and interplate seismicity indicates transforms are either weaker or higher temperatures than expected.

Engeln, J. F.↗
NASA NTRS1986

Optimal block cosine transform image coding for noisy channels

The two dimensional block transform coding scheme based on the discrete cosine transform was studied extensively for image coding applications. While this scheme has proven to be efficient in the absence of channel errors, its performance degrades rapidly over noisy channels. A method is presented for the joint source channel coding optimization of a scheme based on the 2-D block cosine transform when the output of the encoder is to be transmitted via a memoryless design of the quantizers used for encoding the transform coefficients. This algorithm produces a set of locally optimum quantizers and the corresponding binary code assignment for the assumed transform coefficient statistics. To determine the optimum bit assignment among the transform coefficients, an algorithm was used based on the steepest descent method, which under certain convexity conditions on the performance of the channel optimized quantizers, yields the optimal bit allocation. Comprehensive simulation results for the performance of this locally optimum system over noisy channels were obtained and appropriate comparisons against a reference system designed for no channel error were rendered.

Vaishampayan, V.↗
NASA NTRS1989

Data compression properties of the Hartley transform

The data compression performance of the Hartley transform on a Markov-1 signal is theoretically compared to that of the Fourier transform. Covariance distribution and residue correlation measurements have been computed for the Hartley, Fourier, and cosine transforms. The Hartley transform achieves better coding performance than the Fourier transform, but is inferior to the cosine transform.

Yeh, Pen-Shu↗
NASA NTRS1988

A kinematic model of ridge-transform geometry evolution

A simple kinematic model is used to study the effects of various parameters on the evolution of zero-offset transforms and very-long-offset transforms. Consideration is given to the effects of initial configuration, degree of asymmetry, and degree of bias in asymmetry on the generation of these ridge transform geometries and on the possible steady-state nature of the transform length spectra. Of the parameters tests, only lack of 'memory' of zero-offset transforms affects transform length distribution.

Stoddard, Paul R.↗
NASA NTRS1991

A two-dimensional time domain near zone to far zone transformation

In a previous paper, a time domain transformation useful for extrapolating 3-D near zone finite difference time domain (FDTD) results to the far zone was presented. In this paper, the corresponding 2-D transform is outlined. While the 3-D transformation produced a physically observable far zone time domain field, this is not convenient to do directly in 2-D, since a convolution would be required. However, a representative 2-D far zone time domain result can be obtained directly. This result can then be transformed to the frequency domain using a Fast Fourier Transform, corrected with a simple multiplicative factor, and used, for example, to calculate the complex wideband scattering width of a target. If an actual time domain far zone result is required it can be obtained by inverse Fourier transform of the final frequency domain result.

Luebbers, Raymond J.↗
NASA NTRS1991

A two-dimensional time domain near zone to far zone transformation

A time domain transformation useful for extrapolating three dimensional near zone finite difference time domain (FDTD) results to the far zone was presented. Here, the corresponding two dimensional transform is outlined. While the three dimensional transformation produced a physically observable far zone time domain field, this is not convenient to do directly in two dimensions, since a convolution would be required. However, a representative two dimensional far zone time domain result can be obtained directly. This result can then be transformed to the frequency domain using a Fast Fourier Transform, corrected with a simple multiplicative factor, and used, for example, to calculate the complex wideband scattering width of a target. If an actual time domain far zone result is required, it can be obtained by inverse Fourier transform of the final frequency domain result.

Luebbers, Raymond J.↗
NASA NTRS1995

Neoplastic transformation of human cells

The goal of this project was to gain a better understanding of the cellular mechanisms of cancer induction by ionizing radiation as a risk assessment for workers subjected to high LET irradiation such as that found in space. The following ions were used for irradiation: Iron, Argon, Neon, and Lanthanum. Two tests were performed: growth in low serum and growth in agar were used as indicators of cell transformation. The specific aims of this project were to: (1) compare the effectiveness of various ions on degree of transformation of a single dose of the same RBE; (2) determine if successive irradiations with the same ion (Ge 600 MeV/u) increases the degree of transformation; (3) test if clones with the greatest degree of transformation produce tumors in nude mice; and (4) construct a cell hybrid of a transformed and control (non-transformed) clone. The cells used for this work are human mammary epithelial cells with an extended lifespan and selected for growth in MEM + 10% serum.

Goth-Goldstein, Regine↗