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At least 55 records · Page 3

From Reproducible Edge–Cloud Experimentation to Real-World Practice: The E2Clab Experience

Reproducibility is already difficult in distributed systems; on the computing continuum, it becomes substantially harder. Applications that span sensing devices, edge and fog resources, and cloud platforms must be evaluated across heterogeneous hardware, variable network conditions, cross-layer orchestration decisions, and long-running workflow lifecycles. We use E2Clab as a case study to examine these challenges and their implications for experimental methodology. We explain why reproducible experimentation is harder on the continuum, then revisit E2Clab as an initial response based on explicit modeling of infrastructure, workflow lifecycle, and artifacts. Lastly, we discuss how its evolution toward more realistic application settings can be understood through the lens of Translational Computer Science. We argue that reproducible continuum experimentation requires methods that are rigorous enough for research while remaining adaptable to real-world practice.

42 ENGINEERING↗

Towards Redefining the Reproducibility in Quantum Computing: A Data Analysis Approach on NISQ Devices

Although the building of quantum computers has kept making rapid progress in recent years, noise is still the main challenge for any application to leverage the power of quantum computing. Existing works addressing noise in quantum devices proposed noise reduction when deploying a quantum algorithm to a specified quantum computer. The reproducibility issue of quantum algorithms has been raised since the noise levels vary on different quantum computers. Importantly, existing works largely ignore the fact that the noise of quantum devices varies as time goes by. Therefore, reproducing the results on the same hardware will even become a problem. We analyze the reproducibility of quantum machine learning (QML) algorithms based on daily model training and execution data collection. Our analysis shows a correlation between our QML models’ test accuracy and quantum computer hardware’s calibration features. We also demonstrate that noisy simulators for quantum computers are not a reliable tool for quantum machine learning applications.

Senapati, Priyabrata↗

Impacts of floating-point non-associativity on reproducibility for HPC and deep learning applications

Run to run variability in parallel programs caused by floating-point non-associativity has been known to significantly affect reproducibility in iterative algorithms, due to accumulating errors. Non-reproducibility can critically affect the efficiency and effectiveness of correctness testing for stochastic programs. Recently, the sensitivity of deep learning training and inference pipelines to floating-point non-associativity has been found to sometimes be extreme. It can prevent certification for commercial applications, accurate assessment of robustness and sensitivity, and bug detection. New approaches in scientific computing applications have coupled deep learning models with high-performance computing, leading to an aggravation of debugging and testing challenges. Here we perform an investigation of the statistical properties of floating-point non-associativity within modern parallel programming models, and analyze performance and productivity impacts of replacing atomic operations with deterministic alternatives on GPUs. We examine the recently-added deterministic options in PyTorch within the context of GPU deployment for deep learning, uncovering and quantifying the impacts of input parameters triggering run to run variability and reporting on the reliability and completeness of the documentation. Finally, we evaluate the strategy of exploiting automatic determinism that could be provided by deterministic hardware, using the Groq LPUTM accelerator for inference portions of the deep learning pipeline. We demonstrate the benefits that a hardware-based strategy can provide within reproducibility and correctness efforts.

Shanmugavelu, Sanjif↗

Consistency and reproducibility in atomic layer deposition

Atomic layer deposition (ALD) is a thin film synthesis technique that can provide exquisite accuracy and precision in film thickness and composition even on complex, large area substrates. Based on self-limiting surface chemistry, ALD can be insensitive to process conditions and reactor designs, allowing an ALD process developed in one lab to be easily reproduced in other labs. In practice, however, ALD is sometimes difficult to reproduce or replicate, and the results can vary substantially between ALD reactors and between labs. This is exemplified by large deviations in reports on the growth of, e.g., Al2O3, FeOx, and TiO2 given the same precursors under similar conditions. Furthermore, the problem of irreproducibility seems to be growing as ALD is adopted by more researchers and integrated into new applications. In this article, the authors highlight some of the major sources of variations and errors and common misconceptions related to ALD. In particular, the authors focus on issues related to precursors, substrates, and deposition tools. The authors illustrate these problems through examples from the literature, and they present results from numerical simulations that describe how nonidealities would manifest in thickness profiles in a typical cross-flow reactor. They also describe how reproducibility in ALD is linked to consistent experimental practice and reporting between labs. The authors’ hope is that by educating newcomers to ALD and advocating for consistent reporting of deposition conditions, they can minimize irreproducibility and enable ALD practitioners to realize the full potential afforded by self-limiting surface chemistry.

36 MATERIALS SCIENCE↗

Breaking the reproducibility barrier with standardized protocols for plant–microbiome research

Inter-laboratory replicability is crucial yet challenging in microbiome research. Leveraging microbiomes to promote soil health and plant growth requires understanding underlying molecular mechanisms using reproducible experimental systems. In a global collaborative effort involving five laboratories, we aimed to help advance reproducibility in microbiome studies by testing our ability to replicate synthetic community assembly experiments. Our study compared fabricated ecosystems constructed using two different synthetic bacterial communities, the model grass Brachypodium distachyon, and sterile EcoFAB 2.0 devices. All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure, where Paraburkholderia sp. OAS925 could dramatically shift microbiome composition. Comparative genomics and exudate utilization linked the pH-dependent colonization ability of Paraburkholderia, which was further confirmed with motility assays. The study provides detailed protocols, benchmarking datasets, and best practices to help advance replicable science and inform future multi-laboratory reproducibility studies.

Novak, Vlastimil↗

Reproducibility and Optimization Techniques for Evaluated Data in the Resolved Resonance Region [Slides]

This presentation discusses the experimental setup input parameters that are basic quantities for reproducibility. The goal is to increase quality of the evaluated data and decrease time needed for an evaluation. Full reproducibility should be achieved efficiently by including any type of constraints in the optimization procedure and to improve computational time to reach convergence. The goal of an automated reproducibility aligns to the goal of “certified” evaluated data, i.e., defined by a well-defined metric.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

A reproducibility study of "Augmenting Genetic Algorithms with Deep Neural Networks for Exploring the Chemical Space"

Nigam et al. reported a genetic algorithm (GA) utilizing the SELFIES representation and also propose an adaptive, neural network-based penalty that is supposed to improve the diversity of the generated molecules. The main claims of the paper are that this GA outperforms other generative techniques (as measured by the penalized logP) and that a neural network-based adaptive penalty increases the diversity of the generated molecules. In this work, we investigated the reproducibility of their claims. Overall, we were able to reproduce comparable results using the SELFIES-based GA, but mostly by exploiting deficiencies of the (easily optimizable) fitness function (i.e., generating long, sulfur containing chains). In addition, we reproduce results showing that the discriminator can be used to bias the generation of molecules to ones that are similar to the reference set. Lastly, we attempted to quantify the evolution of the diversity, understand the influence of some hyperparameters, and propose improvements to the adaptive penalty.

Jablonka, Kevin Maik↗

Image-based modeling of coupled electro-chemo-mechanical behavior of Li-ion battery cathode using an interface-modified reproducing kernel particle method

Abstract An interface-modified reproducing kernel particle method (IM-RKPM) is introduced in this work to allow for a direct model construction from image pixels of heterogeneous polycrystalline Li-ion battery microstructures. The interface-modified reproducing kernel (IM-RK) approximation is constructed through scaling of a kernel function by a regularized distance function in conjunction with strategic placement of interface node locations. This leads to RK shape functions with either weak or strong discontinuities across material interfaces, suitable for modeling various interface mechanics. With the placement of a triple junction node and distance-based scaling of kernel functions, the resulting IM-RK shape function also possesses proper discontinuities at the triple junctions. This IM-RK approximation effectively remedies the well-known Gibb’s oscillation in the smooth approximation of discontinuities. Different from the conventional meshfree approaches for interface discontinuities, this IM-RK approach is done without additional degrees of freedom associated with the enrichment functions, and it is formulated with the standard procedures in the RK shape function construction. This work focuses on identifying the accuracy and convergence properties of IM-RKPM for modeling the coupled electro-chemo-mechanical system. A linear patch test is formulated and numerically tested for the electro-chemo-mechanical coupled problem with a Butler–Volmer boundary condition representing the physical conditions in Li-ion battery microstructures. This is followed by verification of the optimal rates of convergence of IM-RKPM for solving the coupled problem with higher order solutions. The image-based modeling of Li-ion battery microstructures in the numerical examples demonstrates the applicability of the proposed method to realistic Li-ion battery materials modeling.

25 ENERGY STORAGE↗

A quasi-meshfree method for constructing boundary-aware reproducing bases on geometrically complex domains using manifold geodesics

In many applications, physical domains are geometrically complex making it challenging to perform coarse-scale approximation. A defeaturing process is often used to simplify the domain in preparation for approximation and analysis at the coarse scale. In this paper, a methodology is presented for constructing a coarse-scale reproducing basis on geometrically complex domains given an initial fine-scale mesh of the fully featured domain. The initial fine-scale mesh can be of poor quality and extremely refined. The construction of the basis functions begins with a coarse-scale covering of the domain and generation of weighting functions with local support. Manifold geodesics are used to define distances within the local support for general applicability to non-convex domains. Conventional moving least squares is used to construct the coarse-scale reproducing basis. Applications in quasi-interpolation and linear elasticity are presented.

97 MATHEMATICS AND COMPUTING↗

CUF-Links: Continuous and Ubiquitous FAIRness Linkages for Reproducible Research

Despite much creative work on methods and tools, reproducibility— the ability to repeat the computational steps used to obtain a research result—remains elusive. One reason for these difficulties is that extant tools for capturing research processes, while powerful, often fail to capture vital connections as research projects grow in extent and complexity. We explain here how these interstitial connections can be preserved via simple methods that integrate easily with current work practices to capture basic information about every data product consumed or produced in a project. By thus extending the scope of findable, accessible, interoperable, and reusable (FAIR) data in both time and space to enable the creation of a continuous chain of Continuous and Ubiquitous FAIRness linkages (CUFlinks) from inputs to outputs, such mechanisms can facilitate capture of the provenance linkages that are essential to reproducible research. Herein we give examples of mechanisms that can facilitate the use of these methods, and review how they have been applied in practice.

97 MATHEMATICS AND COMPUTING↗

Planetary normal mode computation: Parallel algorithms, performance and reproducibility

This report is an extension of work entitled “Computing planetary interior normal modes with a highly parallel polynomial filtering eigensolver.” by Shi et al., [1] originally presented at the SC18 conference. A highly parallel polynomial filtered eigensolver was developed and exploited to calculate the planetary normal modes. The proposed method is ideally suited for computing interior eigenpairs for large-scale eigenvalue problems as it greatly enhances memory and computational efficiency. In this article, the second-order finite element method is used to further improve the accuracy as only the first-order finite element method was deployed in the previous work. The parallel algorithm, its parallel performance up to 20k processors, and the great computational accuracy are illustrated. The reproducibility of the previous work was successfully performed on the Student Cluster Competition at the SC19 conference by several participant teams using a completely different Mars-model dataset on different clusters. Both weak and strong scaling performances of the reproducibility by the participant teams were impressive and encouraging. The analysis and reflection of their results are demonstrated and future direction is discussed.

97 MATHEMATICS AND COMPUTING↗

Efforts to enhance reproducibility in a human performance research project

Background: Ensuring the validity of results from funded programs is a critical concern for agencies that sponsor biological research. In recent years, the open science movement has sought to promote reproducibility by encouraging sharing not only of finished manuscripts but also of data and code supporting their findings. While these innovations have lent support to third-party efforts to replicate calculations underlying key results in the scientific literature, fields of inquiry where privacy considerations or other sensitivities preclude the broad distribution of raw data or analysis may require a more targeted approach to promote the quality of research output. Methods: We describe efforts oriented toward this goal that were implemented in one human performance research program, Measuring Biological Aptitude, organized by the Defense Advanced Research Project Agency's Biological Technologies Office. Our team implemented a four-pronged independent verification and validation (IV&V) strategy including 1) a centralized data storage and exchange platform, 2) quality assurance and quality control (QA/QC) of data collection, 3) test and evaluation of performer models, and 4) an archival software and data repository. Results: Our IV&V plan was carried out with assistance from both the funding agency and participating teams of researchers. QA/QC of data acquisition aided in process improvement and the flagging of experimental errors. Holdout validation set tests provided an independent gauge of model performance. Conclusions: In circumstances that do not support a fully open approach to scientific criticism, standing up independent teams to cross-check and validate the results generated by primary investigators can be an important tool to promote reproducibility of results.

59 BASIC BIOLOGICAL SCIENCES↗

A standards perspective on genomic data reusability and reproducibility

Genomic and metagenomic sequence data provides an unprecedented ability to re-examine findings, offering a transformative potential for advancing research, developing computational tools, enhancing clinical applications, and fostering scientific collaboration. However, effective and ethical reuse of genomics data is hampered by numerous technical and social challenges. The International Microbiome and Multi’Omics Standards Alliance (IMMSA, https://www.microbialstandards.org/) and the Genomic Standards Consortium (GSC, https://gensc.org) hosted a 5-part seminar series “A Year of Data Reuse” in 2024 to explore challenges and opportunities of data reuse and reproducibility across disparate domains of the genomic sciences. Addressing these challenges will require a multifaceted approach, including common metadata reporting, clear communication, standardized protocols, improved data management infrastructure, ethical guidelines, and collaborative policies that prioritize transparency and accessibility. We offer strategies to enable responsible and technically feasible data reuse, recognition of data reproducibility challenges, and emphasizing the importance of cross-disciplinary efforts in the pursuit of open science and data-driven innovation.

59 BASIC BIOLOGICAL SCIENCES↗

Neural Network-Enhanced Reproducing Kernel Particle Method for Image-Based Multiphysics Damage Modeling of Energy Storage Materials

Energy storage materials undergo significant stresses during charge/discharge cycling, which makes understanding their reliability and durability fundamental in predicting performance and service life. Strong electrochemical-mechanical coupling and highly anisotropic material properties contribute to the formation and propagation of micro-cracking, largely along material interfaces and grain boundaries. With microstructural images supplied by the National Renewable Energy Laboratory (NREL), image-based modeling techniques are used to represent the complex material microstructures that dictate the coupled physics of these systems. Traditional electrochemical-mechanical models rely on mesh-based finite element methods, which can lead to difficulties in capturing crack propagation due to mesh dependency. Additionally, commonly used damage models, such as the continuous damage model and the cohesive zone model, often have steep tradeoffs between discontinuous field accuracy and computational expense. In this work, a neural network-enhanced reproducing kernel particle method (NN-RKPM) [1] is leveraged to accurately capture damage and crack propagation throughout the material by learning the location, orientation, and sharpness of discontinuity while allowing for a coarser nodal distribution than that necessary for capturing sharp solution transitions using traditional mesh-based methods. NN-RKPM is used to inform how crack opening and closure in turn affect the coupled chemical equations and material microstructure. Reference: [1] Baek, J., Chen, J. S., Susuki, K., "Neural Network enhanced Reproducing Kernel Particle Method for Modeling Localizations," International Journal for Numerical Methods in Engineering, Vol. 123, pp 4422-4454, https://doi.org/10.1002/nme.7040, 2022.

damage modeling↗

How Reproducible are Surface Areas Calculated from the BET Equation?

Abstract Porosity and surface area analysis play a prominent role in modern materials science. At the heart of this sits the Brunauer–Emmett–Teller (BET) theory, which has been a remarkably successful contribution to the field of materials science. The BET method was developed in the 1930s for open surfaces but is now the most widely used metric for the estimation of surface areas of micro‐ and mesoporous materials. Despite its widespread use, the calculation of BET surface areas causes a spread in reported areas, resulting in reproducibility problems in both academia and industry. To prove this, for this analysis, 18 already‐measured raw adsorption isotherms were provided to sixty‐one labs, who were asked to calculate the corresponding BET areas. This round‐robin exercise resulted in a wide range of values. Here, the reproducibility of BET area determination from identical isotherms is demonstrated to be a largely ignored issue, raising critical concerns over the reliability of reported BET areas. To solve this major issue, a new computational approach to accurately and systematically determine the BET area of nanoporous materials is developed. The software, called “BET surface identification” (BETSI), expands on the well‐known Rouquerol criteria and makes an unambiguous BET area assignment possible.

36 MATERIALS SCIENCE↗

Demonstration of the Reproducibility Challenges in the Sintering Behavior of Lithium‐Stuffed Garnets in Scaling up Synthesis

Lithium-stuffed garnets, such as Li 7 La 3 Zr 2 O 12 (LLZO), are promising candidates for next-generation solid-state batteries because of their high room-temperature ionic conductivity and chemical stability against lithium metal anodes, which are crucial for achieving higher energy density. However, realizing LLZO's potential in practical devices requires synthesis methods that can be scaled reliably to large batch sizes for manufacturing. Herein, we investigate the sintering reproducibility of LLZO synthesized at larger scales using ultrasonic spray pyrolysis, a cost-effective and scalable synthesis route. Two 100 g batches of Al-doped LLZO are prepared and their sintering behavior is examined in detail. Both Al-LLZO batches contain over 90 wt.% cubic-phase LLZO, and both batches exhibit room temperature conductivities greater than 1 × 10 −4 S cm −1 at a relative density above 0.8. However, variations in secondary phases and subtle differences in Al content lead to significant differences in densification and microstructure. These results demonstrate that LLZO's sintering behavior is highly sensitive to small changes in secondary phases and Al content, creating reproducibility challenges when moving from laboratory- to manufacturing-scale synthesis.

36 MATERIALS SCIENCE↗

Sensitivity Analysis of Material Model Parameters to Reproduce Crushing of Composite Tubes

The ability to predict the behavior of composite structures under impact conditions is an important challenge for engineering analysis since it requires modeling beyond the elasticity and into failure initiation and propagation. Crushing of laminate composites is the result of a combination of several and complex failure mechanisms, which are not always possible to reproduce together in a single finite element analysis (FEA). In this paper, models based on lamina-level failure criteria have been used to predict the onset of damage; once failure initiates, the mechanisms of failure propagation require reducing the material properties using several degradation schemes. Among the composite material models available in LS-DYNA, MAT-ENHANCED-COMPOSITE-DAMAGE (MAT-54) has been chosen for modeling the axial crushing of composite tubes with various resistant sections and wall slope, given the reduced experimental input parameters to insert into the card definition. Comparison with experimental data shows that such material model is able to successfully reproduce the crushing behavior, even if the numerical results are strictly correlated with some model parameters which cannot be measured experimentally or are purely mathematical expedients. Therefore, extensive calibration of these parameters by trial-and-error is necessary to achieve successful simulation results. Once done it for a structure made of the same composite material, it is possible to adopt the same card configuration for all the other cases, obtaining good agreement between numerical and experimental results. After, the attempt to model the same geometries using the MAT-LAMINATED-COMPOSITE-FABRIC (MAT-58) card with the same parameter values previously calibrated has been done obtaining results comparable with the experimental data.

36 MATERIALS SCIENCE↗

Reproducible benchmark for the SNAP 8 experimental reactor at dry conditions

Here, this work provides fully reproducible benchmark models of the Systems for Nuclear Auxiliary Power (SNAP) 8 Experimental Reactor. Validation benchmarks of the criticality configuration experiments under dry conditions with no coolant are presented. In addition, relevant reactivity worth experiments, and measurement of power distributions are validated and presented here. Discrepancies between modeled and experimental results are at most 110 pcm for fuel and poison worths, and critical configurations that do not manipulate control elements are within 50 pcm. Larger discrepancies found in reflector element worth experiments are due to experimental methodology which was noted as being simplified due to limited calculational capabilities at the time, while discrepancy in the control element manipulated critical configuration is due the absence of structural components for modeling simplification. Power distributions closely follow what was observed in experiment with expected peaking in reflecting elements. All models are well documented with cited references describing and justifying assumptions, simplifications, and adjustments to reproduce the models with any nuclear safety codes; model inputs and outputs are stored in the snapReactors GitHub repository.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗