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Results for “network alignment”

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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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

Dynamic Provisioning for Terascale Science Applications Using Hybrid Circuit/Packet Technologies and 100G Transmission Systems (Final Report)

This project investigated dynamic hybrid circuit/packet network architectures and examined technologies that are beneficial to enhance the performance of Future Internet architectures with a specific emphasis on their potential deployment in the Department of Energy (DOE) Energy Sciences Network (ESnet). Our research was very much aligned with the new “OpenFlow Network Architecture” which has caught the attention of the telecom networking industry.

Mukherjee, Biswanath↗
DOE OSTI2025

ecospec v0.1.0

Bespoke software for segmenting plants in ecoFABs to monitor growth and health. Contains python libraries for image alignment, training neural networks and running inference.

Zwart, PetrusH [Lawrence Berkeley National Laborat↗
DOE OSTI2023

Compositions having reduced thermal conductivities and methods of making the same

The present disclosure relates to a composition that includes a film having a network of randomly aligned carbon nanotubes, where the carbon nanotubes have an average diameter between about 0.6 nm and about 2.0 nm and the carbon nanotubes form bundles having an average diameter between about 3 nm and about 50 nm. In addition, the composition is characterized by a power factor α 2 σ between 1 μW/mK 2 and about 3500 μW/mK 2 and by ZT=α 2 σT/k between about 0.02 and about 2.0 over a temperature range between about 100 K and about 500 K.

Blackburn, Jeffrey Lee↗
DOE OSTI2019

ManiNetCluster: a novel manifold learning approach to reveal the functional links between gene networks

BACKGROUND:The coordination of genomic functions is a critical and complex process across biological systems such as phenotypes or states (e.g., time, disease, organism, environmental perturbation). Understanding how the complexity of genomic function relates to these states remains a challenge. To address this, we have developed a novel computational method, ManiNetCluster, which simultaneously aligns and clusters gene networks (e.g., co-expression) to systematically reveal the links of genomic function between different conditions. Specifically, ManiNetCluster employs manifold learning to uncover and match local and non-linear structures among networks, and identifies cross-network functional links. RESULTS:We demonstrated that ManiNetCluster better aligns the orthologous genes from their developmental expression profiles across model organisms than state-of-the-art methods (p-value <2.2×10-16). This indicates the potential non-linear interactions of evolutionarily conserved genes across species in development. Furthermore, we applied ManiNetCluster to time series transcriptome data measured in the green alga Chlamydomonas reinhardtii to discover the genomic functions linking various metabolic processes between the light and dark periods of a diurnally cycling culture. We identified a number of genes putatively regulating processes across each lighting regime. CONCLUSIONS:ManiNetCluster provides a novel computational tool to uncover the genes linking various functions from different networks, providing new insight on how gene functions coordinate across different conditions. ManiNetCluster is publicly available as an R package at https://github.com/daifengwanglab/ManiNetCluster.

Comparative network analysis↗
DOE OSTI2022

Artificial intelligence inferred microstructural properties from voltage–capacity curves

Abstract The quantification of microstructural properties to optimize battery design and performance, to maintain product quality, or to track the degradation of LIBs remains expensive and slow when performed through currently used characterization approaches. In this paper, a convolution neural network-based deep learning approach (CNN) is reported to infer electrode microstructural properties from the inexpensive, easy to measure cell voltage versus capacity data. The developed framework combines two CNN models to balance the bias and variance of the overall predictions. As an example application, the method was demonstrated against porous electrode theory-generated voltage versus capacity plots. For the graphite|LiMn $$_2$$ 2 O $$_4$$ 4 chemistry, each voltage curve was parameterized as a function of the cathode microstructure tortuosity and area density, delivering CNN predictions of Bruggeman’s exponent and shape factor with 0.97 $$R^2$$ R 2 score within 2 s each, enabling to distinguish between different types of particle morphologies, anisotropies, and particle alignments. The developed neural network model can readily accelerate the processing-properties-performance and degradation characteristics of the existing and emerging LIB chemistries.

25 ENERGY STORAGE↗
DOE OSTI2014

Core and filament formation in magnetized, self-gravitating isothermal layers

We examine the role of the gravitational instability in an isothermal, self-gravitating layer threaded by magnetic fields on the formation of filaments and dense cores. Using a numerical simulation, we follow the non-linear evolution of a perturbed equilibrium layer. The linear evolution of such a layer is described in the analytic work of Nagai et al. We find that filaments and dense cores form simultaneously. Depending on the initial magnetic field, the resulting filaments form either a spiderweb-like network (for weak magnetic fields) or a network of parallel filaments aligned perpendicular to the magnetic field lines (for strong magnetic fields). Although the filaments are radially collapsing, the density profile of their central region (up to the thermal scale height) can be approximated by a hydrodynamical equilibrium density structure. Thus, the magnetic field does not play a significant role in setting the density distribution of the filaments. The density distribution outside of the central region deviates from the equilibrium. The radial column density distribution is then flatter than the expected power law of r {sup –4} and similar to filament profiles observed with Herschel. Our results do not explain the near constant filament width of ∼0.1pc. However, our model does not include turbulent motions. It is expected that the accretion-driven amplification of these turbulent motions provides additional support within the filaments against gravitational collapse. Finally, we interpret the filamentary network of the massive star forming complex G14.225-0.506 in terms of the gravitational instability model and find that the properties of the complex are consistent with being formed out of an unstable layer threaded by a strong, parallel magnetic field.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Sn-InAs Nanowire Shadow-Defined Josephson Junctions

Hybrid superconductor–semiconductor platforms are foundational to advancing quantum information technologies, motivating the integration of materials with clean interfaces, robust superconductivity, and scalable architectures. Here, in this work, we report the synthesis and analysis of inclined InAs nanowires, conformally coated with β-Sn shells. These nanowires extend in opposite in-plane directions, forming a self-aligned, criss-cross network. This enables the deterministic formation of nanowire-shadow Josephson junctions through angle-controlled, low-temperature Sn deposition. Structural characterization shows uniform polycrystalline β-Sn shells forming a sharp, diffusion-free interface with InAs. Low-temperature transport measurements reveal a hard induced superconducting gap ≈ 600 μeV, switching currents up to ≈ 500 nA, and parallel magnetic field resilience beyond 1T. These results establish β-Sn/InAs nanowire networks as a promising platform for superconducting qubits, low-noise microwave devices, and the exploration of exotic superconducting phases including triplet pairing and topological superconductivity.

B-Sn↗
DOE OSTI2024

Gene-Metabolite Association Prediction with Interactive Knowledge Transfer Enhanced Graph for Metabolite Production

Identifying gene targets for enhancing metabolite production in metabolic engineering is challenging due to the vast research literature and the approximation in genome-scale metabolic model (GEM) simulations. Here, to address this, we propose the Gene-Metabolite Association Prediction task, which automates gene discovery for given metabolite-gene pairs, accompanied by a benchmark dataset of 2474 metabolites and 1947 genes for Saccharomyces cerevisiae (SC) and Issatchenkia orientalis (IO). This task is complicated by incomplete metabolic graphs and metabolic heterogeneity. We introduce an Interactive Knowledge Transfer mechanism based on Metabolism Graphs (IKT4Meta) to enhance prediction accuracy by integrating cross-metabolism knowledge. Using Pretrained Language Models (PLMs) to generate inter-graph links mitigates heterogeneity issues, while intra-graph links are propagated via these anchors. Gene-metabolite predictions are then performed on the enriched graphs integrating multiple microorganisms’ knowledge. Experiments show that IKT4Meta outperforms baselines by up to 12.3% in link prediction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Machine Learning Approaches for Nuclear Material Accounting Data from Irradiation and Reprocessing

We are currently exploring data analysis methods for their ability to strengthen the synthesis and evaluation of information generated within domestic and international safeguard regimes. Safeguard data typically includes rich heterogenous datasets amenable to advanced data analytics methods, such as machine learning. We have converted transactional data containing both numerical and categorical attributes from a domestic nuclear material control and accountability (NMC&A) system into a low-dimensional numerical structure via linear principal component analysis. This data representation allows for global structure discovery via cluster analysis, which can characterize the typical behavior of each of the primary types of transaction events. Furthermore, the structure of the top principal components captures the “typical behavior” of the data and is thus amenable to anomaly detection through statistical hypothesis testing. We explored this capability by generating erroneous permutations of the data and computing the Q-residual quantity increase associated with the information loss when these data are projected into the low-dimensional principal component analysis space representative of typical transactions.Future work will focus on identifying data transformations (e.g., graph networks) that more closely align with the inherent structure of these transactions to explain more salient information and disambiguate the underlying nuclear process—in this case, irradiation and reprocessing—from artifacts of NMC&A system transactional record keeping data.

Drescher, Adam↗
DOE OSTI2012

Permeability Calculation in a Fracture Network - 12197

Laminar flow of a viscous fluid in the pore space of a saturated fractured rock medium is considered to calculate the effective permeability of the medium. The effective permeability is determined from the flow field which is calculated numerically by using the finite element method. The computation of permeability components is carried out with a few different discretizations for a number of fracture arrangements. Various features such as flow field in the fracture channels, the convergence of permeability, and the variation of permeability among different fracture networks are discussed. The longitudinal permeability in general appears greater than the transverse ones. The former shows minor variations with fracture arrangement whereas the latter appears to be more sensitive to the arrangement. From the calculations of the permeability in a rock medium with a fracture network (two parallel fractures aligned in the direction of 45-deg counterclockwise from the horizontal and two connecting fractures(narrowing, parallel and widening) the following conclusions are drawn. 1. The permeability of fractured medium not only depends on the primary orientation of the main fractures but also is noticeably influenced by the connecting fractures in the medium. 2. The transverse permeability (the permeability in the direction normal to the direction of the externally imposed macro-scale pressure gradient) is only a fraction of the longitudinal one, but is sensitive to the arrangement of the connecting fractures. 3. It is important to figure out the pattern of the fractures that connect (or cross) the main fractures for reliable calculation of the transverse permeability. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2023

Smart Data Mapping for Connecting Power System Model and Geospatial Data

Knowing the geospatial locations of power system model elements is the foundation for analyzing system vulnerability to natural hazards and connecting loads with end users and their communities. However, power system models and geospatial data for power grid assets may have been developed asynchronously without close coordination. Creating a direct mapping between the two may be a challenging task, considering heterogeneous data structures, target uses, historical legacies, and human errors. This work aims to build an automatic data mapping workflow to connect power system model elements and geospatial data for transmission network, and to support energy grid resilience studies for Puerto Rico. The primary steps in this workflow include constructing graphs using geospatial data, and aligning them to the transmission networks defined in the power system data. The results have been evaluated against existing manual mapping practices for part of the Puerto Rico Power Grid model to illustrate the performance of such auto-mapping solutions.

Resilience, geospatial data, grid transmission net↗
DOE OSTI2020

Multi-Channel Entity Alignment via Name Uniqueness Estimation

When searching for adversarial activity within multiple networks, one of the greatest challenges is how to accurately align entities across different channels of information. This task becomes increasingly difficult when minimal additional information is known about each individual besides a name. Within this study, we analyze name rarity and how it can be used to align people on three distinct data channels: Venmo financial transactions, Reddit online discussions, and a bibliographic data source of academic writings. We explore how the uniqueness of a name can be used to decide if a person is likely the same as another across networks, in the absence of any additional ground truth. While 100 percent confidence cannot be gained, we can use this information to clarify when a possible alignment is more or less likely to be the same individual, increasing our confidence of accurately detecting adversarial behavioral patterns. From the data collected, we found that 0.1% of people had the same name across data sets, and 22.5% of those names are considered rare by our threshold. In our study, we also examine the accuracy of our method and show how real names can be extracted from account usernames, and compared in a similar manner.

Orren, Miquette J.↗
DOE OSTI2019

Data-driven efficient network and surveillance-based immunization

Given a contact network and coarse-grained diagnostic information such as electronic Healthcare Reimbursement Claims (eHRC) data, can we develop efficient intervention policies from data to control an epidemic? Immunization is an important problem in multiple areas, especially epidemiology and public health. However, most existing studies rely on assuming prior epidemiological models to develop pre-emptive strategies, which may fail to adapt to the change in new epidemiological patterns and the availability of rich data such as eHRC. In practice, disease spread is usually complicated, hence assuming an underlying model may deviate from true spreading patterns, leading to possibly inaccurate interventions. Additionally, the abundance of health care surveillance data (such as eHRC) makes it possible to study data-driven strategies without too many restrictive assumptions. Therefore, such a data-driven intervention approach can help public-health experts take more practical decisions. In this work, we take into account propagation log and contact networks for controlling propagation. Furthermore, different from previous model-based approaches, our solutions are solely data driven in a sense that we develop immunization strategies directly from the network and eHRC without assuming classical epidemiological models. In particular, we formulate the novel and challenging data-driven immunization problem. To solve it, we first propose an efficient sampling approach to align surveillance data with contact networks, then develop an efficient algorithm with the provably approximate guarantee for immunization. Finally, we show the effectiveness and scalability of our methods via extensive experiments on multiple datasets, and conduct case studies on nation-wide real medical surveillance data.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

SIMILE enables alignment of tandem mass spectra with statistical significance

Abstract Interrelating small molecules according to their aligned fragmentation spectra is central to tandem mass spectrometry-based untargeted metabolomics. Current alignment algorithms do not provide statistical significance and compounds that have multiple delocalized structural differences and therefore often fail to have their fragment ions aligned. Here we align fragmentation spectra with both statistical significance and allowance for multiple chemical differences using Significant Interrelation of MS/MS Ions via Laplacian Embedding (SIMILE). SIMILE yields spectral alignment inferred structural connections in molecular networks that are not found with cosine-based scoring algorithms. In addition, it is now possible to rank spectral alignments based on p-values in the exploration of structural relationships between compounds and enhance the chemical connectivity that can be obtained with molecular networking.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

The NSLS-II Control Network Design

The required positioning tolerances are an essential part of the survey and alignment design. The following tables show the requirement of storage ring. Table 1 provides the required global tolerances, while Table 2 outlines the relative tolerances for the NSLS-II girder-to-girder positioning. These tolerances dictate the instruments and methods necessary to obtain the positioning goals. The global tolerance is a little bit relaxed, but the ± 0.10 mm positioning requirement of adjacent girders is rather strict if the larger dimension and probable foundation settlement is considered. control network. Therefore, whether the goals can be obtained is mainly dependent on the performance of control network. The shape of control network defines the global alignment accuracy, while the relative position relationships of monuments determine the relative positioning accuracy between girders. When deciding the strategy of survey and alignment techniques, the instrumentation and approach of light sources have been built and are still in construction are investigated. State-of-the art equipment and methods will be employed. NSLS-II covers an area of about one-eighth of a square kilometer with a radius of ~126 m and a circumference of ~792 m. Depending on the size of the system to be constructed, primary and secondary control networks are required to achieve these tolerances. Primary control network will provide global control for different tunnels, and it should possess a relative point accuracy of better than ± 3 mm for all the storage ring monuments. Secondary control network will direct the alignment of girders in tunnel with the ability to ensure the final ± 0.10 mm positioning accuracy. The experiences from accomplished light source indicate that: for a dimension like NSLS2, primary control network can obtain a point accuracy of better than ± 1 mm easily, while secondary control network can obtain a relative point accuracy of ± 0.08 mm. With this expectation, the tolerance can be achieved for both the global and relative situation. Take the relative positioning requirement as an example, with 2 control network error of ± 0.08 mm, instrument tie-in error of ± 0.04 mm, and residual error of ± 0.04 mm, according to error propagation formula, the final alignment error should be better than ± 0.1 mm. Correspondingly, if a better control network accuracy can be achieved, the requirement for the residuals can be looser. The further alignment accuracy improvement will be realized by a smoothing process to assure the better position relationship between adjacent girders. The following simulation will perform error analysis to evaluate the estimated accuracy of NSLS II control network.

36 MATERIALS SCIENCE↗
DOE OSTI2022

End-to-end learning of multiple sequence alignments with differentiable Smith–Waterman

Abstract Motivation Multiple sequence alignments (MSAs) of homologous sequences contain information on structural and functional constraints and their evolutionary histories. Despite their importance for many downstream tasks, such as structure prediction, MSA generation is often treated as a separate pre-processing step, without any guidance from the application it will be used for. Results Here, we implement a smooth and differentiable version of the Smith–Waterman pairwise alignment algorithm that enables jointly learning an MSA and a downstream machine learning system in an end-to-end fashion. To demonstrate its utility, we introduce SMURF (Smooth Markov Unaligned Random Field), a new method that jointly learns an alignment and the parameters of a Markov Random Field for unsupervised contact prediction. We find that SMURF learns MSAs that mildly improve contact prediction on a diverse set of protein and RNA families. As a proof of concept, we demonstrate that by connecting our differentiable alignment module to AlphaFold2 and maximizing predicted confidence, we can learn MSAs that improve structure predictions over the initial MSAs. Interestingly, the alignments that improve AlphaFold predictions are self-inconsistent and can be viewed as adversarial. This work highlights the potential of differentiable dynamic programming to improve neural network pipelines that rely on an alignment and the potential dangers of optimizing predictions of protein sequences with methods that are not fully understood. Availability and implementation Our code and examples are available at: https://github.com/spetti/SMURF. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗