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At least 73 records · Page 4

ADEPT: a domain independent sequence alignment strategy for gpu architectures

Bioinformatic workflows frequently make use of automated genome assembly and protein clustering tools. At the core of most of these tools, a significant portion of execution time is spent in determining optimal local alignment between two sequences. This task is performed with the Smith-Waterman algorithm, which is a dynamic programming based method. With the advent of modern sequencing technologies and increasing size of both genome and protein databases, a need for faster Smith-Waterman implementations has emerged. Multiple SIMD strategies for the Smith-Waterman algorithm are available for CPUs. However, with the move of HPC facilities towards accelerator based architectures, a need for an efficient GPU accelerated strategy has emerged. Existing GPU based strategies have either been optimized for a specific type of characters (Nucleotides or Amino Acids) or for only a handful of application use-cases. In this paper, we present ADEPT, a new sequence alignment strategy for GPU architectures that is domain independent, supporting alignment of sequences from both genomes and proteins. Our proposed strategy uses GPU specific optimizations that do not rely on the nature of sequence. We demonstrate the feasibility of this strategy by implementing the Smith-Waterman algorithm and comparing it to similar CPU strategies as well as the fastest known GPU methods for each domain. ADEPT’s driver enables it to scale across multiple GPUs and allows easy integration into software pipelines which utilize large scale computational systems. We have shown that the ADEPT based Smith-Waterman algorithm demonstrates a peak performance of 360 GCUPS and 497 GCUPs for protein based and DNA based datasets respectively on a single GPU node (8 GPUs) of the Cori Supercomputer. Overall ADEPT shows 10x faster performance in a node-to-node comparison against a corresponding SIMD CPU implementation. ADEPT demonstrates a performance that is either comparable or better than existing GPU strategies. We demonstrated the efficacy of ADEPT in supporting existing bionformatics software pipelines by integrating ADEPT in MetaHipMer a high-performance denovo metagenome assembler and PASTIS a high-performance protein similarity graph construction pipeline. Our results show 10% and 30% boost of performance in MetaHipMer and PASTIS respectively.

59 BASIC BIOLOGICAL SCIENCES↗

Cluster compression algorithm: A joint clustering/data compression concept

The Cluster Compression Algorithm (CCA), which was developed to reduce costs associated with transmitting, storing, distributing, and interpreting LANDSAT multispectral image data is described. The CCA is a preprocessing algorithm that uses feature extraction and data compression to more efficiently represent the information in the image data. The format of the preprocessed data enables simply a look-up table decoding and direct use of the extracted features to reduce user computation for either image reconstruction, or computer interpretation of the image data. Basically, the CCA uses spatially local clustering to extract features from the image data to describe spectral characteristics of the data set. In addition, the features may be used to form a sequence of scalar numbers that define each picture element in terms of the cluster features. This sequence, called the feature map, is then efficiently represented by using source encoding concepts. Various forms of the CCA are defined and experimental results are presented to show trade-offs and characteristics of the various implementations. Examples are provided that demonstrate the application of the cluster compression concept to multi-spectral images from LANDSAT and other sources.

Hilbert, E. E.↗

Accurate and efficient open-source implementation of domain-based local pair natural orbital (DLPNO) coupled-cluster theory using a t1-transformed Hamiltonian

We present an efficient, open-source formulation for coupled-cluster theory through perturbative triples with domain-based local pair natural orbitals [DLPNO-CCSD(T)]. Similar to the implementation of the DLPNO-CCSD(T) method found in the ORCA package, the most expensive integral generation and contraction steps associated with the CCSD(T) method are linear-scaling. In this work, we show that the t1-transformed Hamiltonian allows for a less complex algorithm when evaluating the local CCSD(T) energy without compromising efficiency or accuracy. Our algorithm yields sub-kJ mol−1 deviations for relative energies when compared with canonical CCSD(T), with typical errors being on the order of 0.1 kcal mol−1, using our TightPNO parameters. We extensively tested and optimized our algorithm and parameters for non-covalent interactions, which have been the most difficult interaction to model for orbital (PNO)-based methods historically. To highlight the capabilities of our code, we tested it on large water clusters, as well as insulin (787 atoms).

Chemistry↗

Hidden orders and phase transitions for the fully packed quantum loop model on the triangular lattice

Abstract Quantum loop and dimer models are prototypical correlated systems with local constraints, which are not only intimately connected to lattice gauge theories and topological orders but are also widely applicable to the broad research areas of quantum materials and quantum simulation. Employing our sweeping cluster quantum Monte Carlo algorithm, we reveal the complete phase diagram of the triangular-lattice fully packed quantum loop model. Apart from the known lattice nematic (LN) solid and the even$${{\mathbb{Z}}}_{2}$$ Z 2 quantum spin liquid (QSL) phases, we discover a hidden vison plaquette (VP) phase, which had been overlooked and misinterpreted as a QSL for more than a decade. Moreover, the VP-to-QSL continuous transition belongs to the (2 + 1)D cubic * universality class, which offers a lattice realization of the (fractionalized) cubic fixed point that had long been considered as irrelevant towards the O(3) symmetry until corrected recently by conformal bootstrap calculations. Our results are therefore of relevance to recent developments in both experiments and theory, and facilitate further investigations of hidden phases and transitions.

Physics↗

Archetypal TRMM Radar Profiles Identified Through Cluster Analysis

It is widely held that identifiable 'convective regimes' exist in nature, although precise definitions of these are elusive. Examples include land / Ocean distinctions, break / monsoon beahvior, seasonal differences in the Amazon (SON vs DJF), etc. These regimes are often described by differences in the realized local convective spectra, and measured by various metrics of convective intensity, depth, areal coverage and rainfall amount. Objective regime identification may be valuable in several ways: regimes may serve as natural 'branch points' in satellite retrieval algorithms or data assimilation efforts; one example might be objective identification of regions that 'should' share a similar 2-R relationship. Similarly, objectively defined regimes may provide guidance on optimal siting of ground validation efforts. Objectively defined regimes could also serve as natural (rather than arbitrary geographic) domain 'controls' in studies of convective response to environmental forcing. Quantification of convective vertical structure has traditionally involved parametric study of prescribed quantities thought to be important to convective dynamics: maximum radar reflectivity, cloud top height, 30-35 dBZ echo top height, rain rate, etc. Individually, these parameters are somewhat deficient as their interpretation is often nonunique (the same metric value may signify different physics in different storm realizations). Individual metrics also fail to capture the coherence and interrelationships between vertical levels available in full 3-D radar datasets. An alternative approach is discovery of natural partitions of vertical structure in a globally representative dataset, or 'archetypal' reflectivity profiles. In this study, this is accomplished through cluster analysis of a very large sample (0[107) of TRMM-PR reflectivity columns. Once achieved, the rainconditional and unconditional 'mix' of archetypal profile types in a given location and/or season provides a description of the local convective spectrum which retains vertical structure information. A further cluster analysis of these 'mixes' can identify recurrent convective spectra. These are a first step towards objective identification of convective regimes, and towards answering the question: 'What are the most convectively similar locations in the world?'

Boccippio, Dennis J.↗

Parallel processing for scientific computations

The scope of this project dealt with the investigation of the requirements to support distributed computing of scientific computations over a cluster of cooperative workstations. Various experiments on computations for the solution of simultaneous linear equations were performed in the early phase of the project to gain experience in the general nature and requirements of scientific applications. A specification of a distributed integrated computing environment, DICE, based on a distributed shared memory communication paradigm has been developed and evaluated. The distributed shared memory model facilitates porting existing parallel algorithms that have been designed for shared memory multiprocessor systems to the new environment. The potential of this new environment is to provide supercomputing capability through the utilization of the aggregate power of workstations cooperating in a cluster interconnected via a local area network. Workstations, generally, do not have the computing power to tackle complex scientific applications, making them primarily useful for visualization, data reduction, and filtering as far as complex scientific applications are concerned. There is a tremendous amount of computing power that is left unused in a network of workstations. Very often a workstation is simply sitting idle on a desk. A set of tools can be developed to take advantage of this potential computing power to create a platform suitable for large scientific computations. The integration of several workstations into a logical cluster of distributed, cooperative, computing stations presents an alternative to shared memory multiprocessor systems. In this project we designed and evaluated such a system.

Alkhatib, Hasan S.↗

Entropy-Assisted Quality Pattern Identification in Finance

Short-term patterns in financial time series form the cornerstone of many algorithmic trading strategies, yet extracting these patterns reliably from noisy market data remains a formidable challenge. In this paper, we propose an entropy-assisted framework for identifying high-quality, non-overlapping patterns that exhibit consistent behavior over time. We ground our approach in the premise that historical patterns, when accurately clustered and pruned, can yield substantial predictive power for short-term price movements. To achieve this, we incorporate an entropy-based measure as a proxy for information gain: patterns that lead to high one-sided movements in historical data yet retain low local entropy are more “informative” in signaling future market direction. Compared to conventional clustering techniques such as K-means and Gaussian Mixture Models (GMMs), which often yield biased or unbalanced groupings, our approach emphasizes balance over a forced visual boundary, ensuring that quality patterns are not lost due to over-segmentation. By emphasizing both predictive purity (low local entropy) and historical profitability, our method achieves a balanced representation of Buy and Sell patterns, making it better suited for short-term algorithmic trading strategies. This paper offers an in-depth illustration of our entropy-assisted framework through two case studies on Gold vs. USD and GBPUSD. While these examples demonstrate the method’s potential for extracting high-quality patterns, they do not constitute an exhaustive survey of all possible asset classes.

Physics↗

A circuit-generated quantum subspace algorithm for the variational quantum eigensolver

Recent research has shown that wavefunction evolution in real and imaginary time can generate quantum subspaces with significant utility for obtaining accurate ground state energies. Inspired by these methods, we propose combining quantum subspace techniques with the variational quantum eigensolver (VQE). In our approach, the parameterized quantum circuit is divided into a series of smaller subcircuits. The sequential application of these subcircuits to an initial state generates a set of wavefunctions that we use as a quantum subspace to obtain high-accuracy groundstate energies. We call this technique the circuit subspace variational quantum eigensolver (CSVQE) algorithm. By benchmarking CSVQE on a range of quantum chemistry problems, we show that it can achieve significant error reduction in the best case compared to conventional VQE, particularly for poorly optimized circuits, greatly improving convergence rates. Furthermore, we demonstrate that when applied to circuits trapped at local minima, CSVQE can produce energies close to the global minimum of the energy landscape, making it a potentially powerful tool for diagnosing local minima.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Implementation and Testing of the First Prompt Search for Electromagnetic Counterparts to Gravitational Wave Transients

A transient astrophysical event observed in both gravitational wave (OW) and electromagnetic (EM) channels would yield rich scientific rewards. A first program initiating EM follow-ups to possible transient OW events has been developed and exercised by the LIGO and Virgo community in association with several partners. In this paper, we describe and evaluate the methods used to promptly identify and localize OW event candidates and to request images of targeted sky locations. Methods. During two observing periods (Dec 172009 to Jan 8 2010 and Sep 2 to Oct 20 2010), a low-latency analysis pipeline was used to identify OW event candidates and to reconstruct maps of possible sky locations. A catalog of nearby galaxies and Milky Way globular clusters was used to select the most promising sky positions to be imaged, and this directional information was delivered to EM observatories with time lags of about thirty minutes. A Monte Carlo simulation has been used to evaluate the low-latency OW pipeline's ability to reconstruct source positions correctly. Results. For signals near the detection threshold, our low-latency algorithms often localized simulated GW burst signals to tens of square degrees, while neutron star/neutron star inspirals and neutron star/black hole inspirals were localized to a few hundred square degrees. Localization precision improves for moderately stronger signals. The correct sky location of signals well above threshold and originating from nearby galaxies may be observed with approx.50% or better probability with a few pointings of wide-field telescopes. Key words. gravitational waves - methods: observational

Camp, Jordan↗

Implementation and Testing of the First Prompt Search for Gravitational Wave Transients with Electromagnetic Counterparts

Aims. A transient astrophysical event observed in both gravitational wave (GW) and electromagnetic (EM) channels would yield rich scientific rewards. A first program initiating EM follow-ups to possible transient GW events has been developed and exercised by the LIGO and Virgo community in association with several partners. In this paper, we describe and evaluate the methods used to promptly identify and localize GW event candidates and to request images of targeted sky locations. Methods. During two observing periods (Dec. 17, 2009 to Jan. 8, 2010 and Sep. 2 to Oct. 20, 2010), a low-latency analysis pipeline was used to identify GW event candidates and to reconstruct maps of possible sky locations. A catalog of nearby galaxies and MilkyWay globular clusters was used to select the most promising sky positions to be imaged, and this directional information was delivered to EM observatories with time lags of about thirty minutes. A Monte Carlo simulation has been used to evaluate the low-latency GW pipeline's ability to reconstruct source positions correctly. Results. For signals near the detection threshold, our low-latency algorithms often localized simulated GW burst signals to tens of square degrees, while neutron star/neutron star inspirals and neutron star/black hole inspirals were localized to a few hundred square degrees. Localization precision improves for moderately stronger signals. The correct sky location of signals well above threshold and originating from nearby galaxies may be observed with ∼50% or better probability with a few pointings of wide-field telescopes.

testing↗

The Future Electron-Ion Collider

Generalized Parton Distributions include rich information and became a powerful tool for studying hadron structure. Deeply Virtual Compton Scattering is the golden channel to access GPDs. The development of high luminosity and high-acceptance detectors (Electron-Ion Collider) allows physicists to overcome the difficulty of DVCS measurements. The outstanding performance of the accelerator performs the eA collisions at the center of mass energy from 20 to 140 GeV, while the luminosity at the scale of 1034 cm?2s?1. The new type of high-density crystal, PWO-II, produced by CRYTUR in 2×2×20 cm3 will be utilized in the calorimeter. The transparency of PWO-II crystals is > 70% at 620 nm, > 60% at 420 nm, and >35% at 360 nm. The crystals also show good radiation hardness under 30 Gy radiation exposure. Ten PWO-II crystals have a uniform light yield at 30 p.e./MeV, providing sufficient light yield to reduce the fluctuation of the energy measurements. Near 3000 crystals were constructed inside the 12-sided polygon supporting structure in the simulation. The island clustering algorithm was used for reconstructed the energy. The energy resolution study by the particle gun shows the stochastic term and constant term are 1.8% and 1.2%, respectively. The spatial resolution of NEEMC varies from 5% to 15% of the crystal?s width depending on the particle?s incident angle. The pion rejection of NEEMC can reach 103 with electron efficiency > 85% when the particle?s energy is larger than 1GeV. The Pi0- identified efficiency study can be interpreted as finding the local maxima in the single cluster caused by two high energy close photons. The study results show that efficiency is nearly 100% for pi0 energy is smaller than 10 GeV, and efficiency drops to 30% with 20 GeV pi0. The new type of 3x3 pixelated AC-LGAD were wire bonded to ALTIROC for performance test. The cross-talk between the adjacent channels is about 20% for VPA and 10% for TZ. A series of the TDC characteristic measurements show that the jitter for both preamplifiers is about 20 ps, and the time-walk effect is mild for inject charge > 12 pF. Furthermore, the beta source radiation results quantify the sharing scale of the 3x3 pixels AC-LGAD (? 20%). The electronics simulation study results show no significant changes in the spatial resolution, whether ADC resolution is 8, 10, or 12 bits. The 8-bit ADC is decided to use in the EICROC as it has a smaller size and power consumption than the 10-bit and 12-bit ADC. The ECCE is one of the full detector proposals for EIC. The new type of DVCS generator, called TOPEG, is used to generate the high acceptance beam configurations of 18×110 GeV2 electron and 4He. The acceptance study shows a -1.8 < ? < -1.4 gap between the BEMC and EEMC. The 10?x,y geometry cut is applied on the Roman Pots, so the acceptance of Roman Pots quickly drops to 0% when the polar angle of the recoiled 4He < 2 mrad. This primary ECCE simulation study suggests extending the acceptance of BEMC longitudinally as the structure limits the radial size of EEMC. The acceptance of the Roman Pots is still challenging. In 2023, The overall design of ePIC was finalized by merging two full detector proposals (ECCE and ATHENA) after a series of intensive simulation studies.

Wang, Pu-Kai↗

Implementation and Testing of the First Prompt for Electromagnetic Counterparts to Gravitational Wave Transients

A transient astrophysical event observed in both gravitational wave (GW) and electromagnetic (EM) channels would yield rich scientific rewards. A first program initiating EM follow-ups to possible transient GW events has been developed and exercised by the LIGO and Virgo community in association with several partners. In this paper, we describe and evaluate the methods used to promptly identify and localize GW event candidates and to request images of targeted sky locations. Methods. During two observing periods (Dec 17 2009 to Jan 8 2010 and Sep 2 to Oct 20 2010), a low-latency analysis pipeline was used to identify GW-event candidates and to reconstruct-maps of possible sky locations. A catalog of nearby galaxies and Milky Way globular clusters was used to select the most promising sky positions to be imaged, and this directional information was delivered to EM observatories with time lags of about thirty minutes. A Monte Carlo simulation has been used to evaluate the low-latency GW pipeline s ability to reconstruct source positions correctly. Results. For signals near the detection threshold, our low-latency algorithms often localized simulated GW burst signals to tens of square degrees, while neutron star/neutron star inspirals and neutron star/black hole inspirals were localized to a few hundred square degrees. Localization precision improves for moderately stronger signals. The correct sky location of signals well above threshold and originating from nearby galaxies may be observed with 50% or better probability with a few pointings of wide-field telescopes.

Abadie, J.↗

Distributed Hierarchical Contour Trees

Contour trees are a significant tool for data analysis as they capture both local and global variation. However, their utility has been limited by scalability, in particular for distributed computation and storage. We report a distributed data structure for storing the contour tree of a data set distributed on a cluster, based on a fan-in hierarchy, and an algorithm for computing it based on the boundary tree that represents only the superarcs of a contour tree that involve contours that cross boundaries between blocks. This allows us to limit the communication cost for contour tree computation to the complexity of the block boundaries rather than of the entire data set.

Carr, Hamish A↗

Explicit structure-preserving geometric particle-in-cell algorithm in curvilinear orthogonal coordinate systems and its applications to whole-device 6D kinetic simulations of tokamak physics

Explicit structure-preserving geometric particle-in-cell (PIC) algorithm in curvilinear orthogonal coordinate systems is developed. The work reported represents a further development of the structure-preserving geometric PIC algorithm achieving the goal of practical applications in magnetic fusion research. The algorithm is constructed by discretizing the field theory for the system of charged particles and electromagnetic field using Whitney forms, discrete exterior calculus, and explicit non-canonical symplectic integration. In addition to the truncated infinitely dimensional symplectic structure, the algorithm preserves exactly many important physical symmetries and conservation laws, such as local energy conservation, gauge symmetry and the corresponding local charge conservation. As a result, the algorithm possesses the long-term accuracy and fidelity required for first-principles-based simulations of the multiscale tokamak physics. The algorithm has been implemented in the SymPIC code, which is designed for high-efficiency massively-parallel PIC simulations in modern clusters. The code has been applied to carry out whole-device 6D kinetic simulation studies of tokamak physics. A self-consistent kinetic steady state for fusion plasma in the tokamak geometry is numerically found with a predominately diagonal and anisotropic pressure tensor. The state also admits a steady-state sub-sonic ion flow in the range of 10 km s -1 , agreeing with experimental observations and analytical calculations Kinetic ballooning instability in the self-consistent kinetic steady state is simulated. It is shown that high-n ballooning modes have larger growth rates than low-n global modes, and in the nonlinear phase the modes saturate approximately in 5 ion transit times at the 2% level by the E × B flow generated by the instability. These results are consistent with early and recent electromagnetic gyrokinetic simulations.

43 PARTICLE ACCELERATORS↗

MatLab Package for Whispering Gallery Mode Data

Dye-doped whispering gallery mode resonator (WGMR) microspheres yield highly structured emission spectra that are extremely sensitive to their environment and are of intense interest for use in a variety of sensing applications. Efforts to leverage the unique sensitivities of WGMRs have relied on stringent experimental requirements to correlate specific spectral shifts/changes to an analyte/stimulus such as 1) precise positional knowledge, 2) reference spectra for each microsphere, and 3) high mechanical stability. Consequently, these can hinder adequate mixing or incorporation of analytes and creates challenges for remote sensing. The MATLAB codes provided here are to be used in conjunction with a continuous flow technique for measuring WGM spectra of dye-doped microspheres suspended in solution. One MATLAB script, smooths the data, automatically baseline corrects it to isolate the whispering gallery modes (WGM) from the unwanted bulk emission, and assesses the similarity of each spectrum to aid in selecting a set of unique WGM spectra for further analysis. The next script is designed to analyze WGM spectra to determine the size of the resonator and the refractive index (RI) of its local environment without a priori knowledge of the individual microsphere. The final script allows the user to cluster spheres based on the product of their RI and radius and the contrast ratio of the RI of the sphere material and that of its environment by using a shared nearest neighbor spectral clustering algorithm.

Lilley, Laura↗

Unsupervised learning of representative local atomic arrangements in molecular dynamics data

Molecular dynamics (MD) simulations present a data-mining challenge, given that they can generate a considerable amount of data but often rely on limited or biased human interpretation to examine their information content. By not asking the right questions of MD data we may miss critical information hidden within it. Here we combine dimensionality reduction (UMAP) and unsupervised hierarchical clustering (HDBSCAN) to quantitatively characterize prevalent coordination environments of chemical species within MD data. By focusing on local coordination, we significantly reduce the amount of data to be analyzed by extracting all distinct molecular formulas within a given coordination sphere. We then efficiently combine UMAP and HDBSCAN with alignment or shape-matching algorithms to partition these formulas into structural isomer families indicating their relative populations. The method was employed to reveal details of cation coordination in electrolytes based on molecular liquids.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Metals and Quantum Materials with Spin-orbit Interactions by Quantum Monte Carlo methods

The key goals of this project were as follows: 1) Analysis and benchmarks of electron correlation effects recovered in the fixed-node approximation that is inherent to quantum Monte Carlo (QMC) method as applied to metallic states; 2) development of new algorithms for electron spin-degrees of freedom to be treated as explicit quantum variables; 3) designing electronic structure QMC algorithm for efficient evaluation of spin-orbit effects in systems with heavy atoms; 4) adapting the algorithm to complex wave functions and developing corresponding fixed-phase approximation; 5) design and testing of algorithm for valence-only non-local spin-orbit operators; 6) analysis of fixed-node vs fixed-phase errors and their comparisons. The key accomplishments: i) We carried out a systematic study of Li systems by the fixed-node diffusion Monte Carlo method. This involved Li atom, molecule, cluster and solid calculated by the full range of QMC methods including fixed-node QMC.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Data Analysis of the 2020 Central Idaho Mainshock-Aftershock Sequence

In an effort to inform the Senior Seismic Hazard Analysis Committee for the Idaho National Laboratory, we provide an improved aftershock catalog related to the March 31, 2020, Mw6.5 Stanley, Idaho earthquake from picks related to a temporary network of two real-time and 15 non-telemetered seismometers within the epicentral area. From the permanent and temporary (XP) real-time network, the USGS cataloged 1,946 aftershocks between April 1, 2020 and October 31, 2020. To improve aftershock location and magnitudes, we manually picked arrival times of P and S waves from off-line stations in the XP temporary network, generated a new crustal velocity model, and independently relocated each event using the HypoDD double-difference earthquake algorithm. We created our new velocity model from existing broadband and active source seismic campaign data that were acquired near the epicentral region prior to the 2020 earthquake. We compare arrival time differences, epicentral locations and depths between aftershocks recorded with the two catalogs. We find the addition of local stations provides tighter aftershock clustering that suggests an improved aftershock locations. To detect lower magnitude events, we employed deep learning. Our method solves common problems associated with detecting many events that have a low signal-to-noise ratio. From the machine learning database, we detected more than 74,000 aftershocks. Based on the number of identified earthquakes and Gutenberg-Richter relationships derived from the USGS catalog, we estimate that we have reduced the completion magnitude for the Stanley earthquake sequence to below M1 using this machine learning approach. We located each aftershock with our new velocity model. Our new velocity model and picks suggests aftershocks occurred mostly at shallower depths than assessed in the USGS catalog. These aftershocks align along two linear trends that suggest the activation of two unnamed primary faults.

58 GEOSCIENCES↗