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At least 847 records · Page 47
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

ppdx : Automated modeling of protein–protein interaction descriptors for use with machine learning

This paper describes ppdx, a python workflow tool that combines protein sequence alignment, homology modeling, and structural refinement, to compute a broad array of descriptors for characterizing protein–protein interactions. The descriptors can be used to predict various properties of interest, such as protein–protein binding affinities, or inhibitory concentrations (IC 50 ), using approaches that range from simple regression to more complex machine learning models. The software is highly modular. It supports different protocols for generating structures, and 95 descriptors can be currently computed. More protocols and descriptors can be easily added. The implementation is highly parallel and can fully exploit the available cores in a single workstation, or multiple nodes on a supercomputer, allowing many systems to be analyzed simultaneously. As an illustrative application, ppdx is used to parametrize a model that predicts the IC 50 of a set of antigens and a class of antibodies directed to the influenza hemagglutinin stalk.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Target–decoy false discovery rate estimation using Crema

Assigning statistical confidence estimates to discoveries produced by a tandem mass spectrometry proteomics experiment is critical to enabling principled interpretation of the results and assessing the cost/benefit ratio of experimental follow-up. The most common technique for computing such estimates is to use target-decoy competition (TDC), in which observed spectra are searched against a database of real (target) peptides and a database of shuffled or reversed (decoy) peptides. TDC procedures for estimating the false discovery rate (FDR) at a given score threshold have been developed for application at the level of spectra, peptides, or proteins. Although these techniques are relatively straightforward to implement, it is common in the literature to skip over the implementation details or even to make mistakes in how the TDC procedures are applied in practice. Here we present Crema, an open-source Python tool that implements several TDC methods of spectrum-, peptide- and protein-level FDR estimation. Crema is compatible with a variety of existing database search tools and provides a straightforward way to obtain robust FDR estimates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

PlantCV v4: Image analysis software for high‐throughput plant phenotyping

PlantCV is an open-source Python project aimed at developing tools to address a range of image-based, plant phenotyping questions. PlantCV has been used for more than 10 years to automate trait collection from image data, and the newest release, PlantCV version 4, continues to lower the barrier to entry for users without substantial coding experience through extensive example use-case tutorials and simplified installation. In addition to usability, we document added functionality since the release of PlantCV v2, including support for more image types such as fluorescence, thermal, and hyperspectral data. Finally, we describe the development of a new subpackage focused on morphological trait measurements like leaf angle, and demonstrate its utility as compared to more manual methods of data collection.

Schuhl, Haley [Donald Danforth Plant Science Cente↗
DOE OSTI2024

AEcroscopy: A Software–Hardware Framework Empowering Microscopy Toward Automated and Autonomous Experimentation

Microscopy has been pivotal in improving the understanding of structure-function relationships at the nanoscale and is by now ubiquitous in most characterization labs. However, traditional microscopy operations are still limited largely by a human-centric click-and-go paradigm utilizing vendor-provided software, which limits the scope, utility, efficiency, effectiveness, and at times reproducibility of microscopy experiments. Here, in this work, a coupled software–hardware platform is developed that consists of a software package termed AEcroscopy (short for Automated Experiments in Microscopy), along with a field-programmable-gate-array device with LabView-built customized acquisition scripts, which overcome these limitations and provide the necessary abstractions toward full automation of microscopy platforms. The platform works across multiple vendor devices on scanning probe microscopes and electron microscopes. It enables customized scan trajectories, processing functions that can be triggered locally or remotely on processing servers, user-defined excitation waveforms, standardization of data models, and completely seamless operation through simple Python commands to enable a plethora of microscopy experiments to be performed in a reproducible, automated manner. This platform can be readily coupled with existing machine-learning libraries and simulations, to provide automated decision-making and active theory-experiment optimization to turn microscopes from characterization tools to instruments capable of autonomous model refinement and physics discovery.

47 OTHER INSTRUMENTATION↗
DOE OSTI2025

Fragme∩t: An Open‐Source Framework for Multiscale Quantum Chemistry Based on Fragmentation

Fragment-based quantum chemistry offers a means to circumvent the nonlinear computational scaling of conventional electronic structure calculations, by partitioning a large calculation into smaller subsystems then considering the many-body interactions between them. Variants of this approach have been used to parameterize classical force fields and machine learning potentials, applications that benefit from interoperability between quantum chemistry codes. However, there is a dearth of software that provides interoperability yet is purpose-built to handle the combinatorial complexity of fragment-based calculations. To fill this void we introduce “Fragme∩t”, an open-source software application that provides a tool for community validation of fragment-based methods, a platform for developing new approximations, and a framework for analyzing many-body interactions. Fragme∩t includes algorithms for automatic fragment generation and structure modification, and for distance- and energy-based screening of the requisite subsystems. Checkpointing, database management, and parallelization are handled internally and results are archived in a portable database. Interfaces to various quantum chemistry engines are easy to write and exist already for Q-Chem, PySCF, xTB, Orca, CP2K, MRCC, Psi4, NWChem, GAMESS, and MOPAC. Applications reported here demonstrate parallel efficiencies around 96% on more than 1000 processors but also showcase that the code can handle large-scale protein fragmentation using only workstation hardware, all with a codebase that is designed to be usable by non-experts. Fragme∩t conforms to modern software engineering best practices and is built upon well established technologies including Python, SQLite, and Ray. The source code is available under the Apache 2.0 license.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Investigation of Main Bearing Fatigue Estimate Sensitivity to Synthetic Turbulence Models Using a Novel Drivetrain Model Implemented in OpenFAST

ABSTRACT A coupled medium‐fidelity drivetrain model is developed and implemented in OpenFAST for a 10‐MW land‐based reference turbine. The implementation is verified against a fully coupled multibody wind turbine model, including a detailed drivetrain. The new model can simultaneously and accurately estimate main bearing loads and represent elastic bending of the drivetrain. It has low computational cost and is useful for early design phases, sensitivity analyses and complex systems like wind farms (where computational expense must be expended elsewhere). Here, the model is implemented for a monopile offshore wind turbine and used to investigate the sensitivity of main bearing basic rating life to different synthetic turbulence models. Large‐eddy simulations (LES) targeting stable, neutral, and unstable atmospheric conditions at below‐, near‐ and above‐rated wind speeds are used as a reference. The turbulence models recommended by the International Electrotechnical Commission, the Mann spectral tensor model, and the Kaimal spectral model with exponential coherence are fitted to the LES data. Additionally, a constrained turbulence generator, PyConTurb (short for Python Constrained Turbulence ), based on LES data, is applied in the aero‐hydro‐servo‐elastic simulations. Taking PyConTurb as the baseline, the Kaimal model significantly underestimates fatigue of the downwind main bearing, with between 10% and 40% less damage. The Mann model also underestimates the downwind main bearing fatigue by up to 30%. The upwind main bearing damage is driven by mean loads, and differences between models are less significant, although the trends are similar. Reasons for these discrepancies are investigated and attributed to differences in spatial and temporal variations among the turbulence models.

17 WIND ENERGY↗
DOE OSTI2024

The Data Mine model for accessible partnerships in data science

Abstract The Data Mine at Purdue University is a pioneering experiential learning community for undergraduate and graduate students of any background to learn data science. The first data‐intensive experience embedded in a large learning community, The Data Mine had nearly 1300 students in academic year (AY) 2022–2023 and nearly 1700 students for AY 2023–2024. The Data Mine embodies data‐infused education, research, and collaboration. Students learn Python, R, SQL, and shell‐scripting, while working on weekly projects within a high‐performance computing (HPC) cluster. In the Corporate Partners cohort, students work on teams of 5–15 students, led by a paid student team leader. Each cohort follows an Agile approach, working on data‐intensive projects provided by industry partners and mentored by company employees. Students develop professional and data skills throughout the academic year, from August through April. Many students return in subsequent years to the program, increasing their tenure with a Corporate Partner. Student teams are inherently interdisciplinary; students from 133 different majors are involved in the program, ranging from new incoming students through PhD level students. These interdisciplinary teams of students bring new perspectives to challenging problems in which data science is a key part of the solution. The interdisciplinary teams foster an environment of synthesis with ideas and solutions. Students come together with different life experiences, different levels of technical skill, but also varying ways they navigate paths to solutions because of the variety of majors represented, resulting in a more creative and robust solution than a traditional data science program. This article is categorized under: Applications of Computational Statistics > Education in Computational Statistics

Betz, Margaret A.↗
DOE OSTI2020

Hypergraph Analytics of Domain Name System Relationships

We report on the use of novel mathematical methods in hypergraph analytice over a large quantity of DNS data. Hypergraphs generalize graphs, as used in network science, to better model complex multiway relations in cyber data. Specifically, casting DNS data from Georgia Tech's ActiveDNS repository as hypergraphs allows us to fully represent the interactions between {\em collections} of domains and IP addresses. To facilitate large-scale analytics, we fielded an analytical pipeline of two capabilities. HyperNetX (HNX) is a Python package for the exploration and visualization of hypergraphs, acting as a frontend. For the backend, the Chapel HyperGraph Library (CHGL) is a library for high performance hypergraph analytics written in the exascale programming language Chapel. CHGL was used to process gigascale DNS data, performing compute-intensive calculations for data reduction and segmentation. Identified portions are then sent to HNX for both exploratory analysis and knowledge discovery targeting known tactics, techniques, and procedures.

Joslyn, Cliff A.↗
DOE OSTI2020

Sparse Matrix-Based HPC Tomography

Tomographic imaging has benefited from advances in X-ray sources, detectors and optics to enable novel observations in science, engineering and medicine. These advances have come with a dramatic increase of input data in the form of faster frame rates, larger fields of view or higher resolution, so high performance solutions are currently widely used for analysis. Tomographic instruments can vary significantly from one to another, including the hardware employed for reconstruction: from single CPU workstations to large scale hybrid CPU/GPU supercomputers. Furthermore, flexibility on the software interfaces and reconstruction engines are also highly valued to allow for easy development and prototyping. This paper presents a novel software framework for tomographic analysis that tackles all aforementioned requirements. The proposed solution capitalizes on the increased performance of sparse matrix-vector multiplication and exploits multi-CPU and GPU reconstruction over MPI. Furthermore, the solution is implemented in Python and relies on CuPy for fast GPU operators and CUDA kernel integration, and on SciPy for CPU sparse matrix computation. As opposed to previous tomography solutions that are tailor-made for specific use cases or hardware, the proposed software is designed to provide flexible, portable and high-performance operators that can be used for continuous integration at different production environments, but also for prototyping new experimental settings or for algorithmic development. The experimental results demonstrate how our implementation can even outperform state-of-the-art software packages used at advanced X-ray sources worldwide.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

The SENSEI Generic In Situ Interface: Tool and Processing Portability at Scale [Book Chapter]

One key challenge when doing in situ processing is the investment required to add code to numerical simulations needed to take advantage of in situ processing. Such instrumentation code is often specialized, and tailored to a specific in situ method or infrastructure. Then, if a simulation wants to use other in situ tools, each of which has its own bespoke API [4], then the simulation code team will quickly become overwhelmed with having a different set of instrumentation APIs, one per in situ tool or method. In an ideal situation, such instrumentation need happen only once, and then the instrumentation API provides access to a large diversity of tools. In this way, a data producer’s instrumentation need not be modified if the user desires to take advantage of a different set of in situ tools. The SENSEI generic in situ interface addresses this challenge, which means that SENSEI-instrumented codes enjoy the benefit of being able to use a diversity of tools at scale, tools that include Libsim, Catalyst, Ascent, as well as user-defined methods written in C++ or Python. SENSEI has been shown to scale to greater than 1M-way concurrency on HPC platforms, and provides support for a rich and diverse collection of common scientific data models. Furthermore, this chapter presents the key design challenges that enable tool and processing portability at scale, some performance analysis, and example science applications of the methods.

Bethel, E. Wes↗
DOE OSTI2021

ThickBrick: optimal event selection and categorization in high energy physics. Part I. Signal discovery

We provide a prescription called ThickBrick to train optimal machine-learning-based event selectors and categorizers that maximize the statistical significance of a potential signal excess in high energy physics (HEP) experiments, as quantified by any of six different performance measures. For analyses where the signal search is performed in the distribution of some event variables, our prescription ensures that only the information complementary to those event variables is used in event selection and categorization. This eliminates a major misalignment with the physics goals of the analysis (maximizing the significance of an excess) that exists in the training of typical ML-based event selectors and categorizers. In addition, this decorrelation of event selectors from the relevant event variables prevents the background distribution from becoming peaked in the signal region as a result of event selection, thereby ameliorating the challenges imposed on signal searches by systematic uncertainties. Our event selectors (categorizers) use the output of machine-learning-based classifiers as input and apply optimal selection cutoffs (categorization thresholds) that are functions of the event variables being analyzed, as opposed to flat cutoffs (thresholds). These optimal cutoffs and thresholds are learned iteratively, using a novel approach with connections to Lloyd’s k-means clustering algorithm. We provide a public, Python implementation of our prescription, also called ThickBrick, along with usage examples.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

cymyc: $\underline{C}$alabi-$\underline{Y}$au $\underline{M}$etrics, $\underline{Y}$ukawas, and $\underline{C}$urvature

We introduce cymyc, a high-performance Python library for numerical investigation of the geometry of a large class of string compactification manifolds and their associated moduli spaces. We develop a well-defined geometric ansatz to numerically model tensor fields of arbitrary degree on a large class of Calabi-Yau manifolds. cymyc includes a machine learning component which incorporates this ansatz to model tensor fields of interest on these spaces by finding an approximate solution to the system of partial differential equations they should satisfy.

differential and algebraic geometry↗
DOE OSTI2021

Probing small-scale power spectra with pulsar timing arrays

Models of Dark Matter (DM) can leave unique imprints on the Universe’s small scale structure by boosting density perturbations on small scales. We study the capability of Pulsar Timing Arrays to search for, and constrain, subhalos from such models. The models of DM we consider are ordinary adiabatic perturbations in ΛCDM, QCD axion miniclusters, models with early matter domination, and vector DM produced during inflation. We show that ΛCDM, largely due to tidal stripping effects in the Milky Way, is out of reach for PTAs. Axion miniclusters may be within reach, although this depends crucially on whether the axion relic density is dominated by the misalignment or string contribution. Models where there is matter domination with a reheat temperature below 1 GeV may be observed with future PTAs. Lastly, vector DM produced during inflation can be detected if it is lighter than 10 16 GeV. We also make publicly available a Python Monte Carlo tool for generating the PTA time delay signal from any model of DM substructure.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2026

Implementing the finite-volume three-pion scattering formalism across all non-maximal isospins

We present a numerical exploration of the relativistic-field-theory (RFT) formalism for three pions with all possible values of non-maximal isospin, I πππ = 2, 1 and 0. Using the generic-isospin extension of the RFT formalism [1] and applying our open-source Python library to implement the framework, we predict a range of three-pion energies for illustrative values of the two-to-two scattering amplitudes for various finite-volume irreps also with non-zero total momentum P in the finite-volume frame. The results restrict attention to the case of a vanishing intrinsic three-body interaction so that the spectra can be understood as a baseline. In future lattice QCD calculations, deviations from these values will be translated into evidence for intrinsic three-body effects in the various scattering channels.

hadronic spectroscopy↗
DOE OSTI2024

Effective theory tower for μ → e conversion

We present theoretical predictions for μ → e conversion rates using a tower of effective field theories connecting the UV to nuclear physics scales. The interactions in nuclei are described using a recently developed nonrelativistic effective theory (NRET) that organizes contributions according to bound nucleon and muon velocities, ${\overrightarrow{v}}_N$ and ${\overrightarrow{v}}_μ$, with |${\overrightarrow{v}}_N$| > |${\overrightarrow{v}}_μ$|. To facilitate the top-down matching, we enlarge the set of Lorentz covariant nucleon-level interactions mapped onto the NRET operators to include those mediated by tensor interactions, in addition to the scalar and vector interactions already considered previously, and then match NRET nonperturbatively onto the Weak Effective Theory (WET). At the scale μ ≈ 2 GeV WET is formulated in terms of u, d, s quarks, gluons and photons as the light degrees of freedom, along with the flavor-violating leptonic current. We retain contributions from WET operators up to dimension 7, which requires the full set of 26 NRET operators. The results are encoded in the open-source Python- and Mathematica-based software suite MuonBridge, which we make available to the theoretical and experimental communities interested in μ → e conversion.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Island for gravitationally prepared state and pseudo entanglement wedge

We consider spacetime initiated by a finite-sized initial boundary as a generalization of the Hartle-Hawking no-boundary state. We study entanglement entropy of matter state prepared by such spacetime. We find that the entanglement entropy for large subregion is given either by the initial state entanglement or the entanglement island, preventing the entropy to grow arbitrarily large. Consequently, the entanglement entropy is always bounded from above by the boundary area of the island, leading to an entropy bound in terms of the island. The island I is located in the analytically continued spacetime, either at the bra or the ket part of the spacetime in Schwinger-Keldysh formalism. The entanglement entropy is given by an average of complex pseudo generalized entropy for each entanglement island. We find a necessary condition of the initial state to be consistent with the strong sub-additivity, which requires that any probe degrees of freedom are thermally entangled with the rest of the system. We then find a large parameter region where the spacetime with finite-sized initial boundary, which does not have the factorization puzzle at leading order, dominates over the Hartle-Hawking no-boundary state or the bra ket wormhole. Due to the absence of a moment of time reflection symmetry, the island in our setup is a generalization of the entanglement wedge, called pseudo entanglement wedge. In pseudo entanglement wedge reconstruction, we consider reconstructing the bulk matter transition matrix on A ∪ I, from a fine-grained state on A. The bulk transition matrix is given by a thermofield double state with a projection by the initial state. We also provide an AdS/BCFT model by considering EOW branes with corners. We also find the exponential hardness of such reconstruction task using a generalization of Python’s lunch conjecture to pseudo generalized entropy.

2D gravity↗
DOE OSTI2023

Identifying crack tip position and stress intensity factors from displacement data

Fracture prognosis and characterization efforts require knowledge of crack tip position and the Stress Intensity Factors (SIFs) acting in the vicinity of the crack. Here, in this work, we present an efficient numerical approach to infer both of these characteristics under a consistent theoretical framework from noisy, unstructured displacement data. The novel approach utilizes the separability of the asymptotic linear elastic fracture mechanics fields to expedite the search for crack tip position and is particularly useful for noisy displacement data. The manuscript begins with an assessment of the importance of accurately locating crack tip position when quantifying the SIFs from displacement data. Next, the proposed separability approach for quickly inferring crack tip position is introduced. Comparing to the widely used displacement correlation approach, the performance of the separability approach is assessed. Cases involving both noisy data and systematic deviation from the asymptotic linear elastic fracture mechanics model are considered, e.g. inelastic material behavior and finite geometries. An open source python implementation of the proposed approach is available for use by those doing field and laboratory work involving digital image correlation and simulations, e.g. finite element, discrete element, molecular dynamics and peridynamics, where the crack tip position is not explicitly defined.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Efficient estimation of the modified Gromov–Hausdorff distance between unweighted graphs

Abstract Gromov–Hausdorff distances measure shape difference between the objects representable as compact metric spaces, e.g. point clouds, manifolds, or graphs. Computing any Gromov–Hausdorff distance is equivalent to solving an NP-hard optimization problem, deeming the notion impractical for applications. In this paper we propose a polynomial algorithm for estimating the so-called modified Gromov–Hausdorff (mGH) distance, a relaxation of the standard Gromov–Hausdorff (GH) distance with similar topological properties. We implement the algorithm for the case of compact metric spaces induced by unweighted graphs as part of Python library , and demonstrate its performance on real-world and synthetic networks. The algorithm finds the mGH distances exactly on most graphs with the scale-free property. We use the computed mGH distances to successfully detect outliers in real-world social and computer networks.

Oles, Vladyslav (ORCID:0000000188727463)↗