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At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Using Machine Learning for Quantum Annealing Accuracy Prediction

Quantum annealers, such as the device built by D-Wave Systems, Inc., offer a way to compute solutions of NP-hard problems that can be expressed in Ising or quadratic unconstrained binary optimization (QUBO) form. Although such solutions are typically of very high quality, problem instances are usually not solved to optimality due to imperfections of the current generations quantum annealers. In this contribution, we aim to understand some of the factors contributing to the hardness of a problem instance, and to use machine learning models to predict the accuracy of the D-Wave 2000Q annealer for solving specific problems. We focus on the maximum clique problem, a classic NP-hard problem with important applications in network analysis, bioinformatics, and computational chemistry. By training a machine learning classification model on basic problem characteristics such as the number of edges in the graph, or annealing parameters, such as the D-Wave’s chain strength, we are able to rank certain features in the order of their contribution to the solution hardness, and present a simple decision tree which allows to predict whether a problem will be solvable to optimality with the D-Wave 2000Q. We extend these results by training a machine learning regression model that predicts the clique size found by D-Wave.

97 MATHEMATICS AND COMPUTING↗
NASA NTRSDate not supplied

Quantum Distributed Algorithms for Approximate Steiner Trees and Directed Minimum Spanning Trees

We present two algorithms in the Quantum CONGEST- CLIQUE model of distributed computation that succeed with high probability; one for producing an approximately optimal Steiner Tree, and one for producing an exact directed minimum spanning tree, each of which uses O ̃(n1/4) rounds of communication and O ̃(n9/4) messages, achieving a lower asymptotic round and message complexity than any known algorithms in the classical CONGEST-CLIQUE model. At a high level, we achieve these results by combining classical algorithms with fast quantum subroutines. Additionally, we characterize the constants and logarithmic factors involved in our algorithms, as well as related classical algorithms, revealing that advances are needed to render both practical.

quantum computing↗
NASA NTRSDate not supplied

Quantum Distributed Algorithms for Approximate Steiner Trees and Directed Minimum Spanning Trees​

We present two algorithms in the Quantum CONGEST- CLIQUE model of distributed computation that succeed with high probability; one for producing an approximately optimal Steiner Tree, and one for producing an exact directed minimum spanning tree, each of which uses O ̃(n 1/4 ) rounds of communication and O ̃(n 9/4 ) messages, achieving a lower asymptotic round and message complexity than any known algorithms in the classical CONGEST-CLIQUE model. At a high level, we achieve these results by combining classical algorithms with fast quantum subroutines. Additionally, we characterize the constants and logarithmic factors involved in our algorithms, as well as related classical algorithms, revealing that advances are needed to render both practical.

quantum computing↗
DOE OSTI2023

Better Than Worst-Case Decoding for Quantum Error Correction

The overheads of classical decoding for quantum error correction in cryogenic quantum systems grow rapidly with the number of logical qubits and their correction code distance. Decoding at room temperature is bottlenecked by refrigerator I/O bandwidth while cryogenic on-chip decoding is limited by area/power/thermal budget. To overcome these overheads, we are motivated by the observation that in the common case (over 90% of the time), error correction 'syndromes' are fairly trivial with high redundancy / sparsity, since the error correction codes are over-provisioned to be able to correct for uncommon worst-case complex scenarios (to ensure substantially low logical error rates). If suitably exploited, these trivial scenarios can be handled with insignificant overhead, thereby alleviating any bottlenecks towards handling the worst-case scenarios by state-of-the-art means. Here, we propose Better Than Worst-Case Decoding for Quantum Error Correction, targeting cryogenic quantum systems and Surface Code, consisting of: On-chip Clique Decoder: An extremely lightweight decoder for correcting trivial common-case errors, designed for the cryogenic domain. The decoder is implemented and evaluated for SFQ logic. Statistical Off-chip Bandwidth Allocation: A statistical confidence-based technique for allocation of off-chip decoding bandwidth, to efficiently handle the rare complex decodes that are not covered by the Clique Decoder. Decode-Overflow Execution Stalling: A method to stall circuit execution, for the worst-case scenarios in which the provisioned off-chip bandwidth is insufficient to complete all requested off-chip decodes. In all, BTWC decoding achieves 70-99+% off-chip bandwidth elimination across a range of logical and physical error rates, without significantly sacrificing the accuracy of a state-of-the-art off-chip decoder. Further, it achieves 10-1000x bandwidth reduction over prior bandwidth reduction techniques, as well as 15-37x resource overhead reduction compared to prior on-chip decoding.

cryogenic optimization↗
DOE OSTI2021

Orbital Conflict: Cutting Planes for Symmetric Integer Programs

Cutting planes have been an important factor in the impressive progress made by integer programming (IP) solvers in the past two decades. However, cutting planes have had little impact on improving performance for symmetric IPs. Rather, the main breakthroughs for solving symmetric IPs have been achieved by cleverly exploiting symmetry in the enumeration phase of branch and bound. In this work, we introduce a hierarchy of cutting planes that arise from a reinterpretation of symmetry-exploiting branching methods. There are too many inequalities in the hierarchy to be used efficiently in a direct manner. However, the lowest levels of this cutting-plane hierarchy can be implicitly exploited by enhancing the conflict graph of the integer programming instance and by generating inequalities such as clique cuts valid for the stable set relaxation of the instance. We provide computational evidence that the resulting symmetry-powered clique cuts can improve state-of-the-art symmetry-exploiting methods. Furthermore, the inequalities are then employed in a two-phase approach with high-throughput computations to solve heretofore unsolved symmetric integer programs arising from covering designs, establishing for the first time the covering radii of two binary-ternary codes.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS2003

cWINNOWER Algorithm for Finding Fuzzy DNA Motifs

The cWINNOWER algorithm detects fuzzy motifs in DNA sequences rich in protein-binding signals. A signal is defined as any short nucleotide pattern having up to d mutations differing from a motif of length l. The algorithm finds such motifs if multiple mutated copies of the motif (i.e., the signals) are present in the DNA sequence in sufficient abundance. The cWINNOWER algorithm substantially improves the sensitivity of the winnower method of Pevzner and Sze by imposing a consensus constraint, enabling it to detect much weaker signals. We studied the minimum number of detectable motifs qc as a function of sequence length N for random sequences. We found that qc increases linearly with N for a fast version of the algorithm based on counting three-member sub-cliques. Imposing consensus constraints reduces qc, by a factor of three in this case, which makes the algorithm dramatically more sensitive. Our most sensitive algorithm, which counts four-member sub-cliques, needs a minimum of only 13 signals to detect motifs in a sequence of length N = 12000 for (l,d) = (15,4).

Liang, Shoudan↗
DOE OSTI2024

Introducing Molecular Hypernetworks for Discovery in Multidimensional Metabolomics Data

Orthogonal separations of data from high-resolution mass spectrometry can provide insight into sample composition and address challenges of complete annotation of molecules in untargeted metabolomics. “Molecular networks” (MNs), as used in the Global Natural Products Social Molecular Networking platform, are a prominent strategy for exploring and visualizing molecular relationships and improving annotation. MNs are mathematical graphs showing the relationships between measured multidimensional data features. MNs also show promise for using network science algorithms to automatically identify targets for annotation candidates and to dereplicate features associated with a single molecular identity. Here, this paper introduces “molecular hypernetworks” (MHNs) as more complex MN models able to natively represent multiway relationships among observations. Compared to MNs, MHNs can more parsimoniously represent the inherent complexity present among groups of observations, initially supporting improved exploratory data analysis and visualization. MHNs also promise to increase confidence in annotation propagation, for both human and analytical processing. We first illustrate MHNs with simple examples, and build them from liquid chromatography- and ion mobility spectrometry-separated MS data. We then describe a method to construct MHNs directly from existing MNs as their “clique reconstructions”, demonstrating their utility by comparing examples of previously published graph-based MNs to their respective MHNs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Effect of tectonic processes on biosphere–geosphere feedbacks across a convergent margin

The subsurface is among Earth’s largest biomes, but the extent to which microbial communities vary across tectonic plate boundaries or interact with subduction-scale geological processes remains unknown. Here we compare bacterial community composition with deep-subsurface geochemistry from 21 hot springs across the Costa Rican convergent margin. We find that cation and anion compositions of the springs reflect the dip angle and position of the underlying tectonic structure and also correlate with the bacterial community. Co-occurring microbial cliques related to cultured chemolithoautotrophs that use the reverse tricarboxylic acid cycle (rTCA) as well as abundances of metagenomic rTCA genes correlate with concentrations of slab-volatilized carbon. This, combined with carbon isotope evidence, suggests that fixation of slab-derived CO2 into biomass may support a chemolithoautotrophy-based subsurface ecosystem. We calculate that this forearc subsurface biosphere could sequester 1.4 × 10 9 to 1.4 × 10 10 mol of carbon per year, which would decrease estimates of the total carbon delivered to the mantle by 2 to 22%. Furthermore, based on the observed correlations, we suggest that distribution and composition of the subsurface bacterial community are probably affected by deep tectonic processes across the Costa Rican convergent margin and that, by sequestering carbon volatilized during subduction, these chemolithoautotrophic communities could in turn impact the geosphere.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Scalable edge clustering of dynamic graphs via weighted line graphs

Timestamped relational datasets consisting of records (or connections) between pairs of entities are ubiquitous in network science. For applications like peer-to-peer communication, email, various social network interactions, and computer network security, it is useful to organize these records into groups based on how and when they are occurring. Weighted line graphs offer a natural way to model how records are related in such datasets but for large real-world graph topologies, building and utilizing the line graph is prohibitively expensive. Here, we present the framework to cluster the edges of a dynamic graph via the associated line graph that contains two major contributions. The first is a method to work with the line graph implicitly and the second is a distributed scale implementation of an agglomerative hierarchical graph clustering algorithm. We outline a novel hierarchical dynamic graph edge clustering approach that efficiently breaks massive relational datasets into small sets of edges containing events at various timescales. This is in stark contrast to traditional graph clustering algorithms that prioritize highly connected (clique-like) community structures. Our approach relies on constructing a sufficient subgraph of a weighted line graph and applying a hierarchical agglomerative clustering. This approach is related to scalable techniques from spatial clustering, nonlinear-dimension reduction, topological data analysis, and draws particular inspiration from HDBSCAN. As an edge clustering, this method yields an overlapping node clustering. Our algorithm is parallelizable and we demonstrate efficient clustering of a billion-scale, real-world dynamic graph into small edge sets that correlate in topology and time. The entire clustering process for a graph with tens of billions of edges takes just a few minutes of run time on 256 nodes of a distributed compute environment. We argue how the output of the edge clustering is useful for a multitude of data visualization and powerful machine learning tasks, both involving the original massive dynamic graph data and metadata associated with the nodes and edges. Finally, we describe how this approach can be extended to dynamic hypergraphs and dynamic graphs/hypergraphs with unstructured data living on vertices and edges.

Data Analysis↗
DOE OSTI2024

Picasso: Memory-Efficient Graph Coloring Using Palettes With Applications in Quantum Computing

A coloring of a graph is an assignment of colors to vertices such that no two neighboring vertices have the same color. The need for memory-efficient coloring algorithms is motivated by their application in computing clique partitions of graphs arising in quantum computations where the objective is to map a large set of Pauli strings into a compact set of unitaries. We present Picasso, a randomized memory-efficient iterative parallel graph coloring algorithm with theoretical sublinear space guarantees under practical assumptions. The parameters of our algorithm provide a trade-off between coloring quality and resource consumption. To assist the user, we also propose a machine learning model to predict the coloring algorithm’s parameters considering these trade-offs. We provide a sequential and a parallel implementation of the proposed algorithm. We perform an experimental evaluation on a 64-core AMD CPU equipped with 512 GB of memory and an Nvidia A100 GPU with 40GB of memory. For a small dataset where existing coloring algorithms can be executed within the 512 GB memory budget, we show up to 68× memory savings. On massive datasets we demonstrate that GPU-accelerated Picasso can process inputs with 49.5× more Pauli strings (vertex set in our graph) and 2,478× more edges than state-of-the-art parallel approaches.

artificial intelligence, quantum computing↗
DOE OSTI2022

Topological Simplifications of Hypergraphs

Here we study hypergraph visualization via its topological simplification. We explore both vertex simplification and hyperedge simplification of hypergraphs using tools from topological data analysis. In particular, we transform a hypergraph into its graph representations, known as the line graph and clique expansion. A topological simplification of such a graph representation induces a simplification of the hypergraph. In simplifying a hypergraph, we allow vertices to be combined if they belong to almost the same set of hyperedges, and hyperedges to be merged if they share almost the same set of vertices. Our proposed approaches are general and mathematically justifiable, and put vertex simplification and hyperedge simplification in a unifying framework.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Molecular Hypernetworks for Exploration of Multi-Dimensional Metabolomics Data (Chyper)

Orthogonal separations of data from high-resolution mass spectrometry can provide insight into sample composition and help address the challenge of complete annotation of molecules in untargeted metabolomics. “Molecular networks” (MNs), as used, for example, in the Global Natural Products Social Molecular Networking platform, are an increasingly popular computational strategy for exploring and visualizing molecular relationships and improving annotation. MNs use graph representations to show the relationships between measured multidimensional data features. MNs also show promise for using network science algorithms to automatically identify targets for annotation candidates and to dereplicate features associated to a single molecular identity. However, more advanced methods may better represent the complexity present in samples. Our work aims to increase confidence in annotation propagation by extending molecular network methods to include “molecular hypernetworks” (MHNs), able to natively represent multiway relationships among observations supporting both human and analytical processing. In this paper we first introduce MHNs illustrated with simple examples, and demonstrate how to build them from liquid chromatography- and ion mobility spectrometry- separated MS data. We then describe a method to construct MHNs directly from existing MNs as their “clique reconstructions”, demonstrating their utility by comparing examples of previously published graph-based MNs to their respective MHNs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Templates for Risk Informed Assurance with Curvature Embeddings (TRACE)

We investigate recovery of geometric structure from networks embedded in manifolds with spatially varying curvature, extending the constant-curvature framework of Lubold et al. (2023). Our work supports cascade risk assessment in critical infrastructure through the Templates for Risk-informed Assurance with Curvature Embeddings (TRACE) framework. Simulations on a bi-modal Gaussian surface show that constant-curvature methods yield weighted averages shaped by clique patterns, while hierarchical clustering identifies distinct regimes. Localized estimation, however, reveals boundary contamination in transitional regions. To address heterogeneity, we develop distance metrics for graphs with edge and node features, proving their metric validity, and validate them via deterministic graph generation from canonical tilings. We further propose a diffusion-based anomaly detection approach that treats networks as glued manifolds, using curvature discontinuities to detect structural anomalies. Employing the carré-du-champ operator and scalar curvature, we achieve robust anomaly discrimination, demonstrated on the Singapore Water Treatment (SWaT) dataset with joint network-traffic and sensor features. Integration with TRACE reveals how curvature shapes cascade dynamics: positive curvature impedes, while negative curvature accelerates propagation. This geometric perspective provides interpretable risk metrics and visualization tools for critical infrastructure managers. While full validation remains ongoing, our contributions establish a rigorous foundation for geometric analysis of network resilience and cascade vulnerability.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Genomic Metrics Applied to Rhizobiales ( Hyphomicrobiales ): Species Reclassification, Identification of Unauthentic Genomes and False Type Strains

Taxonomic decisions within the order Rhizobiales have relied heavily on the interpretations of highly conserved 16S rRNA sequences and DNA–DNA hybridizations (DDH). Currently, bacterial species are defined as including strains that present 95–96% of average nucleotide identity (ANI) and 70% of digital DDH (dDDH). Thus, ANI values from 520 genome sequences of type strains from species of Rhizobiales order were computed. From the resulting 270,400 comparisons, a ≥95% cut-off was used to extract high identity genome clusters through enumerating maximal cliques. Coupling this graph-based approach with dDDH from clusters of interest, it was found that: (i) there are synonymy between Aminobacter lissarensis and Aminobacter carboxidus, Aurantimonas manganoxydans and Aurantimonas coralicida, “Bartonella mastomydis,” and Bartonella elizabethae, Chelativorans oligotrophicus, and Chelativorans multitrophicus, Rhizobium azibense, and Rhizobium gallicum, Rhizobium fabae, and Rhizobium pisi, and Rhodoplanes piscinae and Rhodoplanes serenus; (ii) Chelatobacter heintzii is not a synonym of Aminobacter aminovorans; (iii) “Bartonella vinsonii” subsp. arupensis and “B. vinsonii” subsp. berkhoffii represent members of different species; (iv) the genome accessions GCF_003024615.1 (“Mesorhizobium loti LMG 6125T”), GCF_003024595.1 (“Mesorhizobium plurifarium LMG 11892T”), GCF_003096615.1 (“Methylobacterium organophilum DSM 760T”), and GCF_000373025.1 (“R. gallicum R-602 spT”) are not from the genuine type strains used for the respective species descriptions; and v) “Xanthobacter autotrophicus” Py2 and “Aminobacter aminovorans” KCTC 2477T represent cases of misuse of the term “type strain”. Aminobacter heintzii comb. nov. and the reclassification of Aminobacter ciceronei as A. heintzii is also proposed. To facilitate the downstream analysis of large ANI matrices, we introduce here ProKlust (“Prokaryotic Clusters”), an R package that uses a graph-based approach to obtain, filter, and visualize clusters on identity/similarity matrices, with settable cut-off points and the possibility of multiple matrices entries.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1978

The Lovasz bound and some generalizations

The zero error capacity of a discrete memoryless channel is defined as the largest rate at which information can be transmitted over the channel with zero error probability. One channel with five inputs and outputs whose zero capacity remained unsolved until very recently is considered. An extremely powerful and general technique phased in terms of graph theory, for studying combinatorial packing problems is presented. In particular, Delsarte's linear programming bound for cliques in association schemes appears as a special case of the Lovasz bound.

Mceliece, R. J.↗
NASA NTRS1990

Optimal parallel solution of sparse triangular systems

A method for the parallel solution of triangular sets of equations is described that is appropriate when there are many right-handed sides. By preprocessing, the method can reduce the number of parallel steps required to solve Lx = b compared to parallel forward or backsolve. Applications are to iterative solvers with triangular preconditioners, to structural analysis, or to power systems applications, where there may be many right-handed sides (not all available a priori). The inverse of L is represented as a product of sparse triangular factors. The problem is to find a factored representation of this inverse of L with the smallest number of factors (or partitions), subject to the requirement that no new nonzero elements be created in the formation of these inverse factors. A method from an earlier reference is shown to solve this problem. This method is improved upon by constructing a permutation of the rows and columns of L that preserves triangularity and allow for the best possible such partition. A number of practical examples and algorithmic details are presented. The parallelism attainable is illustrated by means of elimination trees and clique trees.

Alvarado, Fernando L.↗
NASA NTRS1990

Summary of presentation for research on social structure, agreement, and conflict in groups in extreme and isolated environments

Despite a vast amount of research, little is known concerning the effect of group structure, and individuals' understanding of that structure, on conflict in Antarctic groups. The overall objective of the research discussed is to determine the interrelationships of group structure, social cognition, and group function and conflict in isolated and extreme environments. In the two decades following WWII, a large body of research focused on the physiological, psychological, and social psychological factors affecting the functioning of individuals and groups in a variety of extreme and isolated environments in both the Arctic and Antarctic. There are two primary reasons for further research of this type. First, Antarctic polar stations are considered to be natural laboratories for the social and behavioral sciences and provide an opportunity to address certain theoretical and empirical questions concerned with agreement and conflict in social groups in general and group behavior in extreme, isolated environments in particular. Recent advances in the analysis of social networks and intracultural variation have improved the methods and have shifted the theoretical questions. The research is motivated by three classes of questions: (1) What are the characteristics of the social relations among individuals working and living together in extreme and isolated environments?; (2) What do individuals understand about their group, how does that understanding develop, and how is it socially distributed?; and (3) What is the relationship between that understanding and the functioning of the social group? Answers to these questions are important if we are to advance our knowledge of how individuals and groups adapt to extreme environments. Second, although Antarctic winter-over candidates may be evaluated as qualified on the basis of individual characteristics, they may fail to adapt because of certain characteristics of the social group. Consequently, the ability of winter-over-groups to adapt to these extreme conditions has varied dramatically from year to year. In the past, differences in personality, background, and social status have led to conflicts between individuals or cliques precipitating, in turn, an overall decline in morale, failure to accomplish work tasks, and increases in insomnia, depression, anxiety, and alcohol abuse. A better understanding of the role of group structure and social cognition in processes of group adaptation and conflict in Antarctica would contribute towards the revision of existing screening methods, potentially leading to a reduction of group conflict and improved performance of scientific research and support activities. An improved screening protocol for the Antarctic would also have applications for other isolated environments such as scientific outposts and the proposed NASA space station. In sum, this research will (1) contribute significantly to our theoretical understanding of the role of social structure and cognition in the functioning of groups in isolation; (2) complement current work on health and adaptation in polar environments; and (3) provide for models of the formation of group structure that will aid in the development of improved procedures for assembling groups for the Antarctic and other isolated environments (e.g., space stations).

Source record↗
NASA NTRS1992

Towards a fast implementation of spectral nested dissection

We describe the spectral nested dissection (SND) algorithm, a new algorithm for computing orderings appropriate for parallel factorization of sparse, symmetric matrices. The algorithm makes use of spectral properties of the Laplacian matrix associated with the given matrix to compute separators. We evaluate the quality of the spectral orderings with respect to several measures: fill, elimination tree height, height and weight balances of elimination trees, and clique tree heights. We use some very large structural analysis problems as test cases and demonstrate on these real applications (such as the Space Shuttle Solid Rocket Booster) that spectral orderings compare quite favorably with commonly used orderings, outperforming them by a wide margin for some of these measures. The only disadvantage of SND is its relatively long execution time. We will present some recent efforts to improve the execution time using both a multilevel and a hybrid approach. We use SND in computing a multifrontal numerical factorization with the different orderings on an eight processor Cray Y-MP and show its effectiveness. We believe that spectral nested dissection is a major breakthrough in terms of generating efficient sparse orderings for parallel machines.

Pothen, Alex↗