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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

A scalable stochastic programming approach for the design of flexible systems

We study the problem of designing systems in order to minimize cost while meeting a given flexibility target. Flexibility is attained by enforcing a joint chance constraint, which ensures that the system will exhibit feasible operation with a given target probability level. Unfortunately, joint chance constraints are complicated mathematical objects that often need to be reformulated using mixed-integer programming (MIP) techniques. In this work, we cast the design problem as a conflict resolution problem that seeks to minimize cost while maximizing flexibility. We propose a purely continuous relaxation of this problem that provides a significantly more scalable approach relative to MIP methods and show that the formulation delivers solutions that closely approximate the Pareto set of the original joint chance-constrained problem.

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

Similarity Metric for Data Optimization and Efficient Training of Reactive Machine Learning Force Fields for Hydrocarbon Radiolysis

Radiolysis is a common approach to sterilize polymers, chemically modify them for upcycling, and accelerate their decomposition for recycling purposes. Reactive molecular dynamics (MD) simulations provide a powerful tool to generate atomic-level trajectories of the reactive processes and quantify radiolytic chemical degradation pathways. For this, machine learning (ML) surrogate models for reactive force fields with quantum mechanical accuracy are now widely used, which require ML training data sets that can provide information on atomic environments for target chemical systems. However, radiolysis chemistry can be highly complex and diverse, which poses significant challenges for generating training data to parametrize ML models. In this regard, we developed a method for optimizing the training data set using a cosine similarity metric to help guide training set selection for radiolysis of polyethylene, a model hydrocarbon polymer, as well as to enhance the transferability of our reactive ML force field (MLFF) to a variety of molecular and polymeric systems. Our approach performs atom-by-atom comparisons between local atomic environments to pinpoint important data points associated with rare and localized events, such as radiolysis damage within structures. We apply this approach to train the Chebyshev Interaction Model for Efficient Simulation (ChIMES) MLFF model, which expresses the atomic interaction potentials in terms of linear combinations of many-body Chebyshev polynomials. We first show that our method can reduce our training set size by ∼70% while improving overall accuracy compared to more standard MD model fitting approaches. We then validate our optimum model against diverse hydrocarbon simulation data, including simple alkanes and systems with unsaturated carbon bonds, over a wide range of thermodynamic conditions. Finally, we use our ChIMES model to perform MD simulations of radiolytic damage with large-scale systems that help avoid system size effects. Overall, our approach yields an MD force field that retains most of the accuracy of the underlying quantum method while yielding many orders of improvement in computational efficiency. In conclusion, our efforts will have impact on future hydrocarbon polymer radiolysis studies, where the chemical details of the polymer–radiation interactions can have a strong effect on the resulting products observed in experiments.

Hydrocarbons↗
DOE OSTI2019

Assessing Electronic Structure Methods for Long-Range Three-Body Dispersion Interactions: Analysis and Calculations on Well-Separated Metal Atom Trimers

Three-body dispersion interactions are much weaker than their two-body counterpart. However, their importance grows quickly as the number of interacting monomers rises. To explore the numerical performance of correlation methods for long-range three-body dispersion, we performed calculations on eight very simple dispersion-dominated model metal trimers: Na 3 , Mg 3 , Zn 3 , Cd 3 , Hg 3 , Cu 3 , Ag 3 , and Au 3 . One encouraging aspect is that relatively small basis sets of augmented triple-ζ size appear to be adequate for three-body dispersion in the long-range. Coupled cluster calculations were performed at high levels to assess MP3, CCSD, CCSD(T), empirical density functional theory dispersion (D3), and the many-body dispersion (MBD) approach. We found that the accuracy of CCSD(T) was generally significantly lower than for two-body interactions, with errors sometimes reaching 20% in the investigated systems, while CCSD and particularly MP3 were generally more erratic. MBD is found to perform better than D3 at large distances, whereas the opposite is true at shorter distances. When computing reference numbers for three-body dispersion, care should be taken to appropriately represent the effect of the connected triple excitations, which are significant in most cases and incompletely approximated by CCSD(T).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Curated Collection of More than 20,000 Experimentally Reported One-Dimensional Metal–Organic Frameworks

Herein, a collection of more than 20,000 experimentally derived crystal structures for metal–organic frameworks (MOFs) that do not have two- or three-dimensional covalently bonded networks has been developed from the materials available at the Cambridge Crystallographic Data Centre. Of these 20,000 1D MOFs, more than 12,000 structures have been verified to be solvent-free and in exact agreement with the stoichiometry of the synthesized materials. More than 10% of the complete data set comprise materials including two or more distinct metals. The band gaps of more than 12,000 1D MOFs have been computed at the density functional theory-generalized gradient approximation level, finding more than 2000 materials that have a zero band gap. Molecular simulations of CH4 adsorption in a small number of 1D MOFs indicated that adsorbate-induced deformation plays a significant role in determining adsorption isotherms in these materials. As a result, methods that have been used previously for high-throughput predictions of molecular adsorption in 3D MOFs are not suitable for 1D MOFs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

REVISITING SPITZER TRANSIT OBSERVATIONS WITH INDEPENDENT COMPONENT ANALYSIS: NEW RESULTS FOR THE GJ 436 SYSTEM

We analyzed four Spitzer/IRAC observations at 3.6 and 4.5 μm of the primary transit of the exoplanet GJ 436b, by using blind source separation techniques. These observations are important for investigating the atmospheric composition of the planet GJ 436b. Previous analyses claimed strong inter-epoch variations of the transit parameters due to stellar variability, casting doubts on the possibility of conclusively extracting an atmospheric signal. Those analyses also reported discrepant results, hence the necessity of this reanalysis. The method we used has been proposed in Morello et al. to analyze 3.6 μm transit light curves of the hot Jupiter HD 189733b. It performes an Independent Component Analysis on a set of pixel light curves, i.e., time series read by individual pixels, from the same photometric observation. Our method only assumes the independence of instrumental and astrophysical signals, and therefore guarantees a higher degree of objectivity compared to parametric detrending techniques published in the literature. The data sets we analyzed in this paper represent a more challenging test than the previous ones. Contrary to previous results reported in the literature, our results (1) do not support any detectable inter-epoch variations of orbital and stellar parameters, (2) are photometrically stable at the level ∼10{sup −4} in the IR, and (3) the transit depth measurements at the two wavelengths are consistent within 1σ. We also (4) detect a possible transit duration variation of ∼80 s (2σ significance level) that has not been pointed out in the literature, and (5) confirm no transit timing variations ≳30 s.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

Probing cosmological isotropy with type Ia supernovae

We investigate the validity of the cosmological principle by mapping the cosmological parameters H{sub 0} and q{sub 0} through the celestial sphere. In our analysis, which is performed in a low-redshift regime to follow a model-independent approach, we use two compilations of type Ia Supernovae (SNe Ia), namely the Union2.1 and the JLA data sets. First, we show that the angular distributions for both SNe Ia data sets are statistically anisotropic at a high confidence level (p-value < 0.0001), particularly the JLA sample. Then we find that the cosmic expansion and acceleration are mainly of dipolar type, with maximal anisotropic expansion [acceleration] pointing toward (l,b)≃(326{sup ∘},12{sup ∘}) [(l,b)≃(174{sup ∘},27{sup ∘})], and (l,b)≃(58{sup ∘},−60{sup ∘}) [(l,b)≃(225{sup ∘},51{sup ∘})] for the Union2.1 and JLA data, respectively. Second, we use a geometrical method to test the hypothesis that the non-uniformly distributed SNe Ia events could introduce anisotropic imprints on the cosmological expansion and acceleration. For the JLA compilation, we found significant correlations between the celestial distribution of data points and the directional studies of H{sub 0} and q{sub 0}, suggesting that these results can be attributed to the intrinsic anisotropy of the sample. In the case of the Union2.1 data, nonetheless, these correlations are less pronounced, and we verify that the dipole asymmetry found in the H{sub 0} analyses coincides with the well-known bulk-flow motion of our local group. From these analyses, we conclude that the directional asymmetry on the cosmological parameter maps are mainly either of local origin or due to celestial incompleteness of current SNe Ia samples.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Quantitative comparison of opacities calculated using the R -matrix and distorted-wave methods: Fe xvii

ABSTRACT We present here a detailed calculation of opacities for Fe xvii at the physical conditions corresponding to the base of the Solar convection zone. Many ingredients are involved in the calculation of opacities. We review the impact of each ingredient on the final monochromatic and mean opacities (Rosseland and Planck). The necessary atomic data were calculated with the R-matrix and the distorted-wave (DW) methods. We study the effect of broadening, of resolution, of the extent of configuration sets and of configuration interaction to understand the differences between several theoretical predictions as well as the existing large disagreement with measurements. New Dirac R-matrix calculations including all configurations up to the n = 4, 5, and 6 complexes have been performed as well as corresponding Breit–Pauli DW calculations. The DW calculations have been extended to include autoionizing initial levels. A quantitative contrast is made between comparable DW and R-matrix models. We have reached self-convergence with n = 6 R-matrix and DW calculations. Populations in autoionizing initial levels contribute significantly to the opacities and should not be neglected. The R-matrix and DW results are consistent under the similar treatment of resonance broadening. The comparison with the experiment shows a persistent difference in the continuum while the filling of the windows shows some improvement. This study defines our path to the next generation of opacities and opacity tables for stellar modelling.

Delahaye, F.↗
DOE OSTI2022

Application of the ASME Boiler and Pressure Vessel Code in the Design of SRF Cavities at Fermilab

Jacketed Superconducting Radio Frequency (SRF) cavities structurally comprise of an inner niobium vessel surrounded by a liquid helium containment vessels. The pressure of the helium bath and/or its volume might be such that a jacketed SRF cavity shall be considered a system of pressure vessels. Thus, methods described in the American Society of Mechanical Engineers (ASME) Boiler and Pressure Vessel Code (BPVC) should be used to analyze the structural soundness of jacketed SRF cavities. This paper will report the use of the set of rules developed at Fermilab for the design of SRF cavities, such as jacketed 1.3 GHz cavities for LCLS-II HE and jacketed Single Spoke Resonator type~2 (SSR2) for PIP-II, to ensure a similar level of safety as prescribed by the ASME BPVC.

43 PARTICLE ACCELERATORS↗
DOE OSTI2018

Evaluating Equivalent Monte Carlo Calculations

We address several basic issues, primarily whether two sets of MCNP tallies are stochastically equivalent (i.e., that the sets of particle history scores follow the same statistical distribution) and, if di erent, quantify the signi cance level of the di erence. The underlying topics here are of longstanding interest to the statistical community, and no \new" theoretical work needs to be carried out to address them. Related comparisons are useful to code developers in assessing code modi cations and to code users in assessing other simulations and related physical measurements. However, these statistical methods must be applied with care to avoid obtaining misleading results, as we show in several examples. The text is written for MCNP practitioners.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

The Effect of the Flux Separability Approximation on Multigroup Neutron Transport

The angular dependence of flux-weighted multigroup cross sections is commonly neglected when generating multigroup libraries. The error of this flux separability approximation is typically not isolated from other error sources due to a lack of availability of library generation and corresponding solvers that cannot relax this approximation. These errors can now be isolated and quantified with the availability of a multigroup Monte Carlo transport and multigroup library-generation capability in the OpenMC Monte Carlo transport code. This work will discuss relevant details of the OpenMC implementation, provide an example case useful for detailing the type of errors one can expect from making the flux separability approximation, and end with more realistic problems which show the impact of the approximation and highlight how it can strongly arise from an energy-dependent resonance absorption effect. Since the angle-dependence is intrinsically linked to the energy group structure, these examples also show that relaxing the flux separability approximation with angle-dependent cross sections could be used to reduce either the fine-tuning required to set a multigroup energy structure for a specific reactor type or the number of energy groups required to obtain a desired level of accuracy for a given problem. This trade-off could increase the costs of generating multigroup cross sections, and has the potential to require more memory for storing the multigroup library during the transport calculations, but it can significantly reduce the computational time required since the runtime of a discrete ordinates or method of characteristics neutron transport solver scales roughly linearly with the number of groups.

42 ENGINEERING↗
DOE OSTI2015

JHR Project: a future Material Testing Reactor working as an International user Facility: The key-role of instrumentation in support to the development of modern experimental capacity

Research and development on fuel and material behaviour under irradiation is a key issue for sustainable nuclear energy in order to meet specific needs by keeping the best level of safety. These needs mainly deal with a constant improvement of performances and safety in order to optimize the fuel cycle and hence to reach nuclear energy sustainable objectives. A sustainable nuclear energy requires a high level of performances in order to meet specific needs such as: - Pursuing improvement of the performances and safety of present and coming water cooled reactor technologies. This will require a continuous R and D support following a long-term trend driven by the plant life management, safety demonstration, flexibility and economics improvement. Experimental irradiations of structure materials are necessary to anticipate these material behaviours and will contribute to their optimisation. - Upgrading continuously nuclear fuel technology in present and future nuclear power plants to achieve better performances and to optimise the fuel cycle keeping the best level of safety. Fuel evolution for generation II, III and III+ is a key stake requiring developments, qualification tests and safety experiments to ensure the competitiveness and safety: experimental tests exploring the full range of fuel behaviour determine fuel stability limits and safety margins, as a major input for the fuel reliability analysis. To perform such accurate and innovative progress and developments, specific and ad hoc instrumentation, irradiation devices, measurement methods are necessary to be set up inside or beside the material testing reactor (MTR) core. These experiments require beforehand in situ and on line sophisticated measurements to accurately determine different key parameters such as thermal and fast neutron fluxes and nuclear heating in order to precisely monitor and control the conducted assays. The new Material Testing Reactor JHR (Jules Horowitz Reactor) currently under construction at CEA Cadarache research centre in the south of France will represent a major Research Infrastructure for scientific studies regarding material and fuel behavior under irradiation. It will also be devoted to medical isotopes production. Hence JHR will offer a real opportunity to perform R and D programs regarding needs above and hence will crucially contribute to the selection, optimization and qualification of these innovative materials and fuels. The JHR reactor objectives, principles and main characteristics associated to specific experimental devices associated to measurement techniques and methodology, their performances, their limitations and field of applications will be presented and discussed. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2025

An MLCommons Scientific Benchmarks Ontology

Scientific machine learning research spans diverse domains and data modalities, yet existing benchmark efforts remain siloed and lack standardization. This makes novel and transformative applications of machine learning to critical scientific use-cases more fragmented and less clear in pathways to impact. This paper introduces an ontology for scientific benchmarking developed through a unified, community-driven effort that extends the MLCommons ecosystem to cover physics, chemistry, materials science, biology, climate science, and more. Building on prior initiatives such as XAI-BENCH, FastML Science Benchmarks, PDEBench, and the SciMLBench framework, our effort consolidates a large set of disparate benchmarks and frameworks into a single taxonomy of scientific, application, and system-level benchmarks. New benchmarks can be added through an open submission workflow coordinated by the MLCommons Science Working Group and evaluated against a six-category rating rubric that promotes and identifies high-quality benchmarks, enabling stakeholders to select benchmarks that meet their specific needs. The architecture is extensible, supporting future scientific and AI/ML motifs, and we discuss methods for identifying emerging computing patterns for unique scientific workloads. The MLCommons Science Benchmarks Ontology provides a standardized, scalable foundation for reproducible, cross-domain benchmarking in scientific machine learning. A companion webpage for this work has also been developed as the effort evolves: https://mlcommons-science.github.io/benchmark/

Hawks, Ben [Fermilab] (ORCID:0000000157000288)↗
DOE OSTI2023

Spatiotemporal Super-Resolution with Generative Machine Learning for Creating Renewable Energy Resource Data Under Climate Change Scenarios

As we plan for a future with higher penetrations of renewables and increasing electrification, it becomes more important to understand how the electricity grid will operate under a variety of weather events. We must also consider that the weather our future grid will experience will be different and possibly more extreme than the historical weather that we have extensive data for. We can use data from global climate models (GCMs) to help understand how our climate may change over the next several decades, but there is often a significant gap between the low-resolution GCM data and the high-resolution weather data required to study power systems under specific weather events. Therefore, our objective in this work is to develop tools that can bridge this gap by using low-resolution GCM data to create realistic high-resolution weather datasets that can be used to study renewable energy generation and electricity demand. To accomplish this objective, we have developed a set of generative machine learning models that can rapidly downscale GCM daily average output data at an approximate grid resolution of 100km to hourly data at an approximate 4 km grid resolution. The models can be used to create high resolution data from nearly any GCM included in the Coupled Model Intercomparison Project (CMIP) Phase 5 or 6. Our methods include all datasets regularly used to study the integration of wind and solar power plants as well as changes in electricity demand due to heating and cooling loads. These models and datasets enable power systems modelers to study climate change-influenced weather events and their impact on the grid. We have downscaled and validated wind, solar, temperature, and humidity data with very promising results. The generative machine learning methods are computationally efficient and produce data that has similar statistical characteristics to current state-of-the-art historical datasets. We have trained initial generative models and produced an initial dataset collectively referred to as Sup3rCC: Super-Resolved Renewable Energy Resource Data with Climate Change Impacts. The data covers a (mostly) historical period from 2015-2025 and a future period from 2050-2059. We have also taken hypothetical high-electrification load data and scaled the heating and cooling loads with respect to the 2050-2059 high-resolution Sup3rCC meteorology. The results show how future levels of renewable energy generation and electrified load may be impacted by climate change, setting the stage for capacity expansion models to consider a dynamic climate through model years.

climate change↗
DOE OSTI2015

DGDFT: A massively parallel method for large scale density functional theory calculations

We describe a massively parallel implementation of the recently developed discontinuous Galerkin density functional theory (DGDFT) method, for efficient large-scale Kohn-Sham DFT based electronic structure calculations. The DGDFT method uses adaptive local basis (ALB) functions generated on-the-fly during the self-consistent field iteration to represent the solution to the Kohn-Sham equations. The use of the ALB set provides a systematic way to improve the accuracy of the approximation. By using the pole expansion and selected inversion technique to compute electron density, energy, and atomic forces, we can make the computational complexity of DGDFT scale at most quadratically with respect to the number of electrons for both insulating and metallic systems. We show that for the two-dimensional (2D) phosphorene systems studied here, using 37 basis functions per atom allows us to reach an accuracy level of 1.3 × 10{sup −4} Hartree/atom in terms of the error of energy and 6.2 × 10{sup −4} Hartree/bohr in terms of the error of atomic force, respectively. DGDFT can achieve 80% parallel efficiency on 128,000 high performance computing cores when it is used to study the electronic structure of 2D phosphorene systems with 3500-14 000 atoms. This high parallel efficiency results from a two-level parallelization scheme that we will describe in detail.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Advanced instrumentation and analysis methods for in-pile thermal and nuclear measurements: from out-of-pile studies to irradiation campaigns

Research and development on nuclear fuel behavior under irradiations and accelerated ageing of structure materials is a key issue for sustainable nuclear energy in order to meet specific needs by keeping the best level of safety. A new Material Testing Reactor (MTR), the Jules Horowitz Reactor (JHR) currently under construction in the South of France in the CEA Cadarache research centre will offer a real opportunity to perform R and D programs and hence will crucially contribute to the selection, optimization and qualification of innovative materials and fuels. To perform such programs advanced accurate and innovative experiments, irradiation devices that contain material and fuel samples are required to be set up inside or beside the reactor core. These experiments needs beforehand in situ and on line sophisticated measurements to accurately reach specific and determining parameters such as thermal and fast neutron fluxes, nuclear heating and temperature conditions to precisely monitor and control the conducted assays. Consequently, since 2009 CEA and Aix-Marseille University collaborate in order to design and develop a new multi-sensor device which will be dedicated to measuring profiles of such conditions inside the experimental channels of the JHR. These works are performed in the framework of two complementary joint research programs called MAHRI-BETHY and INCORE. These programs couple experimental studies carried out both out-of nuclear fluxes (in laboratory) and under irradiation conditions (in OSIRIS MTR reactor in France and MARIA MTR reactor in Poland) with numerical works realized by thermal simulations (CAST3M code) and Monte Carlo simulations (MCNP code). These programs deal with three main aims. The first one corresponds to the design and/or the test of new in-pile instrumentation. The second one concerns the development of advanced calibration procedures in particular in the case of one specific sensor: a differential calorimeter used to quantify nuclear heating. The last one consists in the development of accurate measurement and analysis methods. The paper will be dedicated to a complete review of the experimental and numerical works performed since 2009 thanks to two parts. The first part will detail a new thermal approach implemented to improve nuclear heating measurements by radiometric calorimeters. New experimental tools (calorimeter prototypes and set-ups such BETHY Bench) developed to perform preliminary out-of-pile studies under suitable conditions will be presented (temperature and velocity of the external cooling fluid, heat source localization and intensity inside the calorimetric cells). Then the response of two kinds of sensors, their calibrations curves and their thermal behaviors will be compared for various parameters. Finally validated numerical thermal and Monte Carlo works will be discussed to propose new improvements. The second parts of the paper will focus on works realized in order to design, develop and test the first prototype of the multi-sensor device called CARMEN [7-9]. The two mock-ups dedicated respectively to neutron measurements and photon measurements will be detailed. The results obtained during two irradiation campaigns inside the periphery of OSIRIS reactor will be shown. The new analysis method will be discussed. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2016

SU-F-T-493: An Investigation Into the Feasibility of Using PipsPro Software with Film for Linac QA

Purpose: To determine the feasibility of using radiochromic and radiographic film with Pipspro software for quality assurance of linear accelerators with no on-board imaging. Methods: The linear accelerator being used is a Varian Clinac 21EX. All IGRT is performed using the BrainLab ExacTrac system. Because of the lack of on board imaging, certain monthly and annual TG-142 quality assurance tests are more difficult to perform and analyze to a high degree of accuracy. Pipspro was not designed to be used with hard film, and to our knowledge its use with film had not been investigated. The film used will be GafChromic EBT3 film and Kodak EDR2 film, scanned with an Epson V700 scanner. The following routine tests will be attempted: MLC picket fence, light vs. radiation field coincidence, starshots, and MLC transmission. Results: The only tests that gave accurate and reliable results were the couch, gantry, and collimator starshots. Typical MV and kV images are acquired with a much higher level of contrast between the irradiated and non-irradiated areas when compared to film. Pipspro relies on this level of contrast to be able to automatically detect the fiducial points from its phantom devices, leaf edges for picket fence and transmission tests, and jaw edges for light vs. radiation field tests. Because of this, certain tests gave erroneous results and others were not able to be performed in the software at all, with either type of film. The number of monitor units delivered to the film, the experimental setup, and the scan settings was not able to rectify the problem. Conclusion: For linear accelerators with no on-board imaging, it is not recommended to use hard film with PipsPro to perform TG-142 quality assurance tests. Other software or methods should instead be investigated.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

On the Sampling-Based Computation of Nash Equilibria Under Uncertainty via the Nikaido–Isoda Function

We consider the computation of an equilibrium of a stochastic Nash equilibrium problem, where the player objectives are assumed to be L 0 -Lipschitz continuous and convex, given rival decisions with convex and closed player-specific feasibility sets. To address this problem, we consider minimizing a suitably defined value function defined using the Nikaido–Isoda function. Such an avenue does not necessitate either monotonicity properties of the concatenated gradient map or potentiality requirements on the game but does require a suitable regularity requirement under which a stationary point is a Nash equilibrium. We design and analyze a sampling-enabled projected-gradient-response method, reliant on inexact resolution of a player-level best-response subproblem. Here, by deriving suitable Lipschitzian guarantees on the value function, we derive both asymptotic guarantees for the sequence of generated iterates as well as rate and complexity guarantees for computing a stationary point by appropriate choices of the sampling rate and inexactness sequence.

Nikaido-Isoda function↗
DOE OSTI2017

Automating cell detection and classification in human brain fluorescent microscopy images using dictionary learning and sparse coding

Background Immunofluorescence (IF) plays a major role in quantifying protein expression in situ and understanding cell function. It is widely applied in assessing disease mechanisms and in drug discovery research. Automation of IF analysis can transform studies using experimental cell models. However, IF analysis of postmortem human tissue relies mostly on manual interaction, often subjected to low-throughput and prone to error, leading to low inter and intra-observer reproducibility. Human postmortem brain samples challenges neuroscientists because of the high level of autofluorescence caused by accumulation of lipofuscin pigment during aging, hindering systematic analyses. We propose a method for automating cell counting and classification in IF microscopy of human postmortem brains. Our algorithm speeds up the quantification task while improving reproducibility. New method Dictionary learning and sparse coding allow for constructing improved cell representations using IF images. These models are input for detection and segmentation methods. Classification occurs by means of color distances between cells and a learned set. Results Our method successfully detected and classified cells in 49 human brain images. We evaluated our results regarding true positive, false positive, false negative, precision, recall, false positive rate and F1 score metrics. We also measured user-experience and time saved compared to manual countings. Comparison with existing methods We compared our results to four open-access IF-based cell-counting tools available in the literature. Lastly, our method showed improved accuracy for all data samples. Conclusion The proposed method satisfactorily detects and classifies cells from human postmortem brain IF images, with potential to be generalized for applications in other counting tasks.

59 BASIC BIOLOGICAL SCIENCES↗