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At least 199 records · Page 11

Low-rank factorization of electron integral tensors and its application in electronic structure theory

In this letter, we introduce the reverse Cuthill-McKee (RCM) algorithm, which is often used for the bandwidth reduction of sparse tensors, to transform the two-electron integral tensors to their block diagonal forms. By further applying the pivoted Cholesky decomposition (CD) on each of the diagonal blocks, we are able to represent the high-dimensional two-electron integral tensors in terms of permutation matrices and low-rank Cholesky vectors. This representation facilitates the low-rank factorization of the high-dimensional tensor contractions that are usually encountered in post-Hartree-Fock calculations. In this letter, we discuss the second-order Møller-Plesset (MP2) method and linear coupled- cluster model with doubles (L-CCD) as two simple examples to demonstrate the efficiency of the RCM-CD technique in representing two-electron integrals in a compact form.

electronic structure theory↗

Nucleon axial-vector form factor and radius from radiatively corrected antineutrino scattering data

The nucleon axial-vector form factor, 𝐺 𝐴 , is critical to determine the electroweak interactions of leptons with nucleons. Important examples of processes influenced by 𝐺 𝐴 are elastic (anti)neutrino-nucleon scattering and muon capture by the proton. Sparse experimental data results in a large uncertainty on the momentum dependence of 𝐺 𝐴 and has motivated the consideration of new experimental probes and first-principles lattice quantum chromodynamics (QCD) evaluations. The comparison of new and precise theoretical predictions for 𝐺 𝐴 with future experimental data necessitates the application of radiative corrections to experimentally observable processes. We apply these corrections in the extraction of 𝐺 𝐴 and the associated axial-vector radius from the recent MINERvA antineutrino-hydrogen data, compare the effects from radiative corrections to other uncertainties in neutrino scattering experiments, and discuss the comparison of lattice QCD evaluations to experimental measurements.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Quantum block encoding for one-pair semiseparable matrices

Quantum block encoding (QBE) is a crucial step in the development of most quantum algorithms, as it provides an embedding of a given matrix into a suitable larger unitary matrix. Historically, the development of efficient techniques for QBE has mostly focused on sparse matrices; less effort has been devoted to data-sparse (e.g., rank-structured) matrices. In this work we examine a particular case of rank structure, namely, one-pair semiseparable matrices. We present a new block encoding approach that relies on a suitable factorization of the given matrix as the product of triangular and diagonal factors. To encode the matrix, the algorithm needs $2\log(N)+7$ ancillary qubits. Assuming that the data input oracles can be implemented with polylogarithmic depth, or that a QRAM input model is available, our proposed method requires $\mathcal{O}({\rm polylog} (N))$ time and has an error of $\mathcal{O}(N^2)$, where $N$ is the matrix size.

Antonioli, Giacomo [Pisa U.; CERN] (ORCID:00090000↗

Sparse Control Synthesis for Uncertain Responsive Loads With Stochastic Stability Guarantees

In this report, recent studies have demonstrated the potential of flexible loads in providing frequency response services, predominantly due to their availability and cost-effectiveness. However, uncertainty and variability in various weather-related and end-use behavioral factors often impact the reliability of demand-side control performance. This work addresses this problem with the design of a demand-side control to achieve frequency response under load uncertainties. Our approach involves modeling the load uncertainties via stochastic processes that appear as both multiplicative and additive in the power system dynamics. Recently developed mean square exponential stability (MSES) results for continuous-time linear stochastic systems are applied to pose the control synthesis problem which results in an LMI-based optimization problem. Additional costs and constraints are added to the LMI-based controller synthesis to ensure MSES, improve closed-loop transient performance, maximize tolerable uncertainties, and promote sparsity in the controller. Additionally, the fundamental limitations between the tolerable uncertainties and control efforts while ensuring MSES are discussed. Further, the control synthesis problem for the case of the full-state measurement is generalized to the case of partial-state measurements. The proposed control synthesis is illustrated on an IEEE 39 bus system with rigorous studies to demonstrate the role of sparsity, closed-loop transient performance, tolerable uncertainties, and control efforts while ensuring MSES and achieving frequency response.

42 ENGINEERING↗

An Algebraic Sparsified Nested Dissection Algorithm Using Low-Rank Approximations

Here, we propose a new algorithm for the fast solution of large, sparse, symmetric positive-definite linear systems, spaND (sparsified Nested Dissection). It is based on nested dissection, sparsification, and low-rank compression. After eliminating all interiors at a given level of the elimination tree, the algorithm sparsifies all separators corresponding to the interiors. This operation reduces the size of the separators by eliminating some degrees of freedom but without introducing any fill-in. This is done at the expense of a small and controllable approximation error. The result is an approximate factorization that can be used as an efficient preconditioner. We then perform several numerical experiments to evaluate this algorithm. We demonstrate that a version using orthogonal factorization and block-diagonal scaling takes fewer CG iterations to converge than previous similar algorithms on various kinds of problems. Furthermore, this algorithm is provably guaranteed to never break down and the matrix stays symmetric positive-definite throughout the process. We evaluate the algorithm on some large problems show it exhibits near-linear scaling. The factorization time is roughly $\mathcal{O}$(N), and the number of iterations grows slowly with N.

97 MATHEMATICS AND COMPUTING↗

Algorithms for solving large sparse systems of simultaneous linear equations on vector processors

Very efficient algorithms for solving large sparse systems of simultaneous linear equations have been developed for serial processing computers. These involve a reordering of matrix rows and columns in order to obtain a near triangular pattern of nonzero elements. Then an LU factorization is developed to represent the matrix inverse in terms of a sequence of elementary Gaussian eliminations, or pivots. In this paper it is shown how these algorithms are adapted for efficient implementation on vector processors. Results obtained on the CYBER 200 Model 205 are presented for a series of large test problems which show the comparative advantages of the triangularization and vector processing algorithms.

David, R. E.↗

The fractional Fourier transform and applications

This paper describes the 'fractional Fourier transform', which admits computation by an algorithm that has complexity proportional to the fast Fourier transform algorithm. Whereas the discrete Fourier transform (DFT) is based on integral roots of unity e exp -2(pi)i/n, the fractional Fourier transform is based on fractional roots of unity e exp -2(pi)i(alpha), where alpha is arbitrary. The fractional Fourier transform and the corresponding fast algorithm are useful for such applications as computing DFTs of sequences with prime lengths, computing DFTs of sparse sequences, analyzing sequences with noninteger periodicities, performing high-resolution trigonometric interpolation, detecting lines in noisy images, and detecting signals with linearly drifting frequencies. In many cases, the resulting algorithms are faster by arbitrarily large factors than conventional techniques.

Bailey, David H.↗

Asymmetry parameters of the phase function for densely packed scattering grains

Spatial correlation among densely packed particles can substantially change their single-scattering properties, thus making questionable the applicability of the independent scattering approximation in calculations of light scattering by planetary regoliths. The same problem arises in geophysics in light scattering computations for snow, frosts, and bare soil. In this paper, we use a dense-medium light-scattering theory based on the introduction of the static structure factor to calculate asymmetry parameters of the phase function for densely packed particles with real refractive indices 1.31 and 1.66, approximating water ice and soil particles, respectively, and imaginary refractive indices 0, 0.01, and 0.3. For sparsely distributed, independently scattering grains, the calculated asymmetry parameters are always positive and always larger than those for densely packed particles. For densely packed grains, the asymmetry parameters may be negative but only for radius-to-wavelength ratios from about 0.1 to about 0.4. With decreasing particle size, the calculated asymmetry parameters tend to zero independently of the compaction state. In the geometrical optics regime, the asymmetry parameters for densely packed scatterers are positive and very close to those for independently scattering grains. These results may have important implications for remote sensing of the Earth and solid planetary surfaces. In particular, it is demonstrated that negative asymmetry parameters derived with some approximate multiple-scattering theories may be physically irrelevant and can be the result of using an inaccurate bidirectional reflection function combined with the ill-conditionally of the inverse scattering problem.

Mishchenko, Michael I.↗

Integration and validation of some modules for modelling of high-speed chemically reactive flows in two-phase gas-droplet mixtures

Three modules are integrated into the built-in OpenFOAM rhoCentralFoam solver towards accurate and efficient modelling of high-speed chemically reactive flows in two-phase gas-droplet mixtures within the OpenFOAM 10.0 framework. The first module is the mixture-averaged diffusion model. The second module is the built-in OpenFOAM Lagrangian solver coupled with optimised droplet drag coefficient and convective heat transfer coefficient sub-models. The last module is a sparse stiff chemistry solver based on dynamic adaptive hybrid integration (AHI-S). The optimised droplet sub-models are first verified in correct implementation for subsequent simulations in this work. Further, they show good accuracy against experimental and analytical data in the modelling of ammonia droplet acceleration and cooling in the flowing and/or low-temperature air. The accuracy and efficiency gains related to the mixture-averaged diffusion model and the AHI-S chemistry solver are examined by simulating 1-D detonation propagation in ammonia droplet-free/laden ammoniaoxygen mixtures. Numerical results of detonation propagation speed, gaseous temperature, density, and species distributions around the induction zone show good agreement with experimental data and analytical solutions. Compared to the built-in OpenFOAM diffusion model, the mixture-averaged diffusion model provides different numerical predictions of pulsating instabilities in detonation propagation. It shows better accuracy in depicting the detonation structure within the droplet-free section attributed to improved multi-component diffusion modelling. Compared to the built-in OpenFOAM solver EulerImplicit (backward Euler), the AHI-S chemistry solver reduces the computational cost by around 50%. It achieves satisfactory accuracy in calculating detonation propagation speed within the droplet-free section with the optimal efficiency when the safety factor, β, equals 0.5.

42 ENGINEERING↗

Analytical gradients for tensor hyper-contracted MP2 and SOS-MP2 on graphical processing units

Analytic energy gradients for tensor hyper-contraction (THC) are derived and implemented for second-order Møller-Plesset perturbation theory (MP2), with and without the scaled-opposite-spin (SOS)-MP2 approximation. By exploiting the THC factorization, the formal scaling of MP2 and SOS-MP2 gradient calculations with respect to system size is reduced to quartic and cubic, respectively. An efficient implementation has been developed that utilizes both graphics processing units and sparse tensor techniques exploiting spatial sparsity of the atomic orbitals. THC-MP2 has been applied to both geometry optimization and ab initio molecular dynamics (AIMD) simulations. Furthermore, the resulting energy conservation in micro-canonical AIMD demonstrates that the implementation provides accurate nuclear gradients with respect to the THC-MP2 potential energy surfaces.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Nucleon-Pion Spectroscopy from Sparsened Correlators

Neutrino oscillation experiments require accurate reconstructions of neutrino energies, which depend in part on a theoretical understanding of the axial $N\rightarrow\Delta$ transition form factors. A lattice QCD study of this transition will require construction of all hadronic states with energies up to $m_\Delta$, which at the physical point includes $N\pi$ and $N\pi\pi$. Building interpolating operators from sparse grids at the source and sink is a versatile method that allows construction of a wide range of diagram topologies and has successfully been used in other multi-hadron calculations. We will discuss application of this method to nucleon-pion systems and present preliminary results.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Incorporating Social Vulnerability Variables in Measures to Quantify Access to Opportunities

Herein this study quantifies access to travel opportunities to understand what societal factors are linked with local access and to identify communities with reduced access. We introduce a method to compare accessibility across all census tracts in the United States that can be used across geographically diverse communities ranging from sparsely to densely populated areas. This study considers six key opportunities which we consider essential for all communities (grocery stores, public schools, daycares, primary care doctors, pharmacies, and parks), and six additional destinations which can be viewed as a social safety net (homeless shelters, women’s shelters, food pantries, libraries, vocational schools, and banks). We quantify accessibility to these opportunities within a 15 min walk, transit trip, bicycle ride, and automobile drive for every census tract in the United States, and observe a decrease in vehicle miles traveled and vehicle ownership in tracts with increased walkability. Through analysis at the census tract level, this study incorporates variables of social vulnerability with these cumulative opportunity metrics to better understand diminished accessibility as attributed to social and racial inequities. As example findings, we find decreased access to financial services in communities with high minority and limited English speaking populations, no apparent change in access for childcare in communities with high percentages of single-parent families, and potentially increased or decreased access to women’s healthcare resources for Black women depending on the travel mode.

99 GENERAL AND MISCELLANEOUS↗

A spectral algorithm for envelope reduction of sparse matrices

A new algorithm for reducing the envelope of a sparse matrix is presented. This algorithm is based on the computation of eigenvectors of the Laplacian matrix associated with the graph of the sparse matrix. A reordering of the sparse matrix is determined based on the numerical values of the entries of an eigenvector of the Laplacian matrix. Numerical results show that the new reordering algorithm can in some cases reduce the envelope by more than a factor of two over the current standard algorithms such as Gibbs-Poole-Stockmeyer (GPS) or SPARSPAK's reverse Cuthill-McKee (RCM).

Barnard, Stephen T.↗

Predictive Modeling for Differential Diagnosis and Mortality Risk Assessment

The prevalence of electronic health record (EHR) systems has brought prodigious biomedical informatics opportunity. Automated machine learning methods can effectively utilize such data and have become common tools for healthcare predictive modeling. Researches in medical informatics have explored the potential of deep learning and classical models in emergent care scenarios. In particular, predicting differential diagnoses for admissions have proven useful in decreasing unnecessary lab tests and improving inpatient triage decision-making. Moreover, identification of high-risk patients for in-hospital mortality is vitally important to maximize allocation of medical resources.The Medical Information Mart for Intensive Care (MIMIC-III) database, containing de-identified critical care inpatient was used in our study. This data set captures hospital patient laboratory measurements, pharmacologic prescriptions, diagnostic data and procedure event recordings. When considering adult patients and discounting admissions with ICU length of stay less than 24 hours, there were 37,787 unique admissions and 30,414 total patients. We examined the top 25 most prevalent ICD-9 group-level disease specificities in MIMIC-III using a multi-label classification model. In-hospital mortality was modeled as binary classification with 4,155 (13%) adult patients that expired, of which 3,138 (75.5%) were in the ICU setting. The metrics AUC, F1 score, sensitivity and specificity values calculated for each disease label measured prediction performance.The usage of ICD-9 group codes reduced feature dimension from 14,567 to 942 and greatly improved distribution of patient diagnostic categories. Disease temporal patterns were captured by considering the most frequently sampled 6 vital signs and 13 laboratory values. Missing data were imputed at each time-stamp. Time-series raw hourly average values were converted into 5 summary features (mean, standard deviation, number of observations, min & max values). Patient demographic variables such as age, gender, marital status and ethnicity were also factored into the modeling. Choi et al showed that contextual embedding of medical data, diagnostic and procedural codes alone can predict future diagnoses with sensitivity as high as 0.79. We utilized an embedding technique called word2vec which allowed sparse representations of medical history to be transformed into dense word vectors. The mappings captured contextual information by treating each admission as a sentence and learning the most likely neighboring words in a sliding window fashion. Binary and multi-label classification was achieved via collapse models, which do not consider temporal information, as well as recurrent neural networks with regularization, Softmax output layer activation together with categorical cross-entropy as the loss function.

US Army collaboration↗

Discrete anisotropic radiative transfer modelling of solar-induced chlorophyll fluorescence: Structural impacts in geometrically explicit vegetation canopies

Solar-induced fluorescence (SIF) is a subtle but informative optical signal of vegetation photosynthesis. Remotely sensed SIF integrates environmental, physiological and structural changes that alter photosynthesis at leaf, plant and canopy scales. Radiative transfer models are ideally suited to investigate the complex sources of variability in the SIF signal to guide the interpretation of SIF retrievals from airborne and space-borne platforms. Here, we coupled the Fluspect-Cx model of leaf optical properties and chlorophyll-a fluorescence with the Discrete Anisotropic Radiative Transfer (DART) model to upscale SIF from individual leaves to three-dimensional (3D) structurally explicit canopies. For one-dimensional homogeneous (turbid-like) canopies, DART-SIF was nearly identical to SIF simulated in two existing models, SCOPE and mSCOPE (RMSE <0.221 W./sq.m.μm.sr). DART simulations in geometrically explicit 3D canopies offered four important insights regarding the influence of vegetation structure on the multi-angular top-of-canopy SIF signal. First, changes in the 3D canopy architecture of maize crops, represented by leaf density (leaf area index), and plant clumping (canopy closure) had a larger impact on SIF than the modelled photosynthetic efficiency distinction between sun-adapted and shade-adapted foliage. Second, clumping of leaves at the crop and stand levels was identified as one of the key driving factors of multi-angular anisotropy of red and far-red SIF (686 and 740 nm) for both maize and eucalyptus canopies. Third, non-photosynthetic woody material had a significant impact on top-of-canopy SIF in modelled 3D forest stands. Wood shadowing decreased the photosynthetically active radiation absorbed by green leaves, and consequently the SIF emissions, by 10% in sparse and 17% in dense eucalyptus stands. The wood obstruction (blocking) effect, quantified as a relative difference of SIF escape probabilities from canopies with and without wood in the nadir viewing direction, decreased far-red SIF by 4–6% but it had a smaller and sometimes positive influence (by less than 2%) on red SIF. Fourth, DART 3D radiative budget profiles revealed that the majority of the SIF signal from a dense eucalyptus stand originated from the top 25% of the simulated canopy. Interestingly, the introduction of bark-covered woody elements did not alter the simulated balance and omnidirectional escape factor of red SIF in this upper canopy part but did raise significantly both of them in case of far-red SIF. These results demonstrate the importance of 3D radiative transfer and radiative budget simulations for investigating SIF interactions in structurally complex plant canopies and for a better understanding of spatiotemporal and multi-angular remote sensing SIF observations.

Zbyněk Malenovský↗

Compact video content representation for video coding using low multi-linear tensor rank approximation with dynamic core tensor order

Tensor is a multi-way representation of an entity that is widely used in many applications of mathematics and physics. The wide range of tensor algebra operations attract the researchers of graphical and vision field to identify unique methods for various applications such as segmentation, compression, indexing and so on. In this paper, low multi-linear rank approximation of a tensor is used for decomposition so as to perform compression on a video that is represented as a 4D tensor. Thus, the encoder has blocks for (1) multilinear rank approximation method so as to aid decomposition, (2) sparsity removal of residual data to reduce the required memory storage to a small level, (3) quantization on the sparse less residual data and (4) LZ77 dictionary coding for the video. The decoder uses a tensor reconstruction block along with residual error correction block that reduces loss/error in the reconstructed video. The size of core tensor is an important factor in rank approximation. It is identified at run time depending on the video contents. This size is determined adaptively using Tikhonov’s regularization method. The best value of core tensor size is identified with the corner of L-curve which preserves the video contents from heavy loss/error. Experimental results of the proposed work on comparison with H.264/AVC compression method indicate that the proposed method achieves up to 10% improvement in compression ratio with the least amount of loss and a maximum signal to noise ratio of 0.14. The proposed system gives better compression ratio than H.265 for videos with more number of frames without compromising quality.

97 MATHEMATICS AND COMPUTING↗

An Algorithm for the Extraction of Tafel Slopes

Though bacteriophages (phages) are known to play a crucial role in bacterial fitness and virulence, our knowledge about the genetic basis of their interaction, cross-resistance and host-range is sparse. Here, we employed genome-wide screens in Salmonella enterica serovar Typhimurium to discover host determinants involved in resistance to eleven diverse lytic phages including 4 new phages isolated from a therapeutic phage cocktail. We uncovered 301 diverse host factors essential in phage infection, many of which are shared between multiple phages demonstrating potential cross-resistance mechanisms. We validate many of these novel findings and uncover the intricate interplay between RpoS, the virulence-associated general stress response sigma factor and RpoN, the nitrogen starvation sigma factor in phage cross-resistance. Finally, the infectivity pattern of eleven phages across a panel of 23 genome sequenced Salmonella strains indicates that additional constraints and interactions beyond the host factors uncovered here define the phage host range.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Novel Application of Machine Learning Techniques for Rapid Source Apportionment of Aerosol Mass Spectrometer Datasets

In this work, we apply machine learning approaches sparse multinomial logistic regression to classify aerosol mass spectrometer (AMS) unit mass resolution (UMR) data followed by an ensemble regression technique for source apportionment of organic aerosols (OA). The classifier was trained on 60 well characterized laboratory and positive matrix factorization (PMF) deconvolved reference spectra to identify eight OA types. These include four laboratory-derived secondary organic aerosol (SOA) spectra, which include isoprene photooxidation SOA, isoprene epoxydiols (IEPOX) SOA, a monoterpene SOA type that includes a-pinene and ß-pinene SOA, and aromatic SOA from oxidation of naphthalene and m-xylene precursors, as well as PMF deconvolved spectra for three primary organic aerosol (POA) types, namely, hydrocarbon-like organic aerosol (HOA), biomass burning organic aerosol (BBOA), and cooking OA (COA), and a more oxidized oxygenated OA type (MO-OOA). A 5-fold cross-validation strategy, repeated 10 times, was used to assess the classifier’s performance. The classifier had high classification accuracy for COA, aromatic SOA, and isoprene SOA spectra but incorrectly classified ~9% by number of MO-OOA spectra as BBOA, 12% of BBOA spectra as HOA (and vice versa), and 18% of IEPOX-SOA spectra as aromatic SOA. Next, an ensemble regression model was trained on an artificially generated dataset consisting of mixtures of different OA types to assess its ability to predict fractional mass abundances from classification probabilities of various OA species obtained from the multinomial logistic regression classifier trained on the reference spectra. Ultimately, the proposed approach was applied for source apportionment of aircraft-based AMS measurements of OA UMR spectra during the HI-SCALE field campaign. On two representative days (May 6th and 18th, 2016), the algorithm determined that ~50-60% of OA by mass was MO-OOA, which represented a highly aged organic aerosol mixture from different sources. On both days, BBOA was determined to contribute less than 10% to OA by mass. However, on May 18th, the aromatic SOA fraction was higher compared to that on May 6th. The proposed approach is capable of rapidly analyzing AMS data in real time, making it suitable for applications where rapid source apportionment of AMS OA spectra is desirable.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗