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1,284 results on '"A Pebay"'

1. A Communication- and Memory-Aware Model for Load Balancing Tasks

Author

Lifflander, Jonathan, Pebay, Philippe P., Slattengren, Nicole L., Pebay, Pierre L., Pfeiffer, Robert A., Kotulski, Joseph D., and McGovern, Sean T.

Subjects
Computer Science - Distributed, Parallel, and Cluster Computing
Abstract

While load balancing in distributed-memory computing has been well-studied, we present an innovative approach to this problem: a unified, reduced-order model that combines three key components to describe "work" in a distributed system: computation, communication, and memory. Our model enables an optimizer to explore complex tradeoffs in task placement, such as increased parallelism at the expense of data replication, which increases memory usage. We propose a fully distributed, heuristic-based load balancing optimization algorithm, and demonstrate that it quickly finds close-to-optimal solutions. We formalize the complex optimization problem as a mixed-integer linear program, and compare it to our strategy. Finally, we show that when applied to an electromagnetics code, our approach obtains up to 2.3x speedups for the imbalanced execution.

Published
2024

4. Distributed Asynchronous Contact Mechanics with DARMA/vt

Author

Morales, Nicolas, Jones, Reese, Lifflander, Jonathan, Pébaÿ, Philippe P., McGovern, Sean, Skrzyński, Cezary, Schilly, Caleb, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Diehl, Patrick, editor, Schuchart, Joseph, editor, Valero-Lara, Pedro, editor, and Bosilca, George, editor

Published
2024
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5. Sturm's Theorem with Endpoints

Author

Pébay, Philippe, Rojas, J. Maurice, and Thompson, David C.

Subjects
Computer Science - Symbolic Computation, Mathematics - Commutative Algebra
Abstract

Sturm's Theorem is a fundamental 19th century result relating the number of real roots of a polynomial $f$ in an interval to the number of sign alternations in a sequence of polynomial division-like calculations. We provide a short direct proof of Sturm's Theorem, including the numerically vexing case (ignored in many published accounts) where an interval endpoint is a root of $f$., Comment: 4 pages. A software implementation can be found in algorithm vtkPolynomialSolversUnivariate , within the VTK (Visualization Toolkit) software package

Published
2022

8. Wnt dose escalation during the exit from pluripotency identifies tranilast as a regulator of cardiac mesoderm

Author

Wu, Zhixuan, Shen, Sophie, Mizikovsky, Dalia, Cao, Yuanzhao, Naval-Sanchez, Marina, Tan, Siew Zhuan, Alvarez, Yanina D., Sun, Yuliangzi, Chen, Xiaoli, Zhao, Qiongyi, Kim, Daniel, Yang, Pengyi, Hill, Timothy A., Jones, Alun, Fairlie, David P., Pébay, Alice, Hewitt, Alex W., Tam, Patrick P.L., White, Melanie D., Nefzger, Christian M., and Palpant, Nathan J.

Published
2024
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14. Retinal ganglion cell-specific genetic regulation in primary open-angle glaucoma

Author

Daniszewski, Maciej, Senabouth, Anne, Liang, Helena H., Han, Xikun, Lidgerwood, Grace E., Hernández, Damián, Sivakumaran, Priyadharshini, Clarke, Jordan E., Lim, Shiang Y., Lees, Jarmon G., Rooney, Louise, Gulluyan, Lerna, Souzeau, Emmanuelle, Graham, Stuart L., Chan, Chia-Ling, Nguyen, Uyen, Farbehi, Nona, Gnanasambandapillai, Vikkitharan, McCloy, Rachael A., Clarke, Linda, Kearns, Lisa S., Mackey, David A., Craig, Jamie E., MacGregor, Stuart, Powell, Joseph E., Pébay, Alice, and Hewitt, Alex W.

Published
2022
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18. Two New Contributions to the Visualization of AMR Grids: I. Interactive Rendering of Extreme-Scale 2-Dimensional Grids II. Novel Selection Filters in Arbitrary Dimension

Author

Harel, Guénolé, Lekien, Jacques-Bernard, and Pébaÿ, Philippe P.

Subjects
Computer Science - Graphics
Abstract

We present here the result of continuation work, performed to further fulfill the vision we outlined in [Harel,Lekien,P\'eba\"y-2017] for the visualization and analysis of tree-based adaptive mesh refinement (AMR) simulations, using the hypertree grid paradigm which we proposed. The first filter presented hereafter implements an adaptive approach in order to accelerate the rendering of 2-dimensional AMR grids, hereby solving the problem posed by the loss of interactivity that occurs when dealing with large and/or deeply refined meshes. Specifically, view parameters are taken into account, in order to: on one hand, avoid creating surface elements that are outside of the view area; on the other hand, utilize level-of-detail properties to cull those cells that are deemed too small to be visible with respect to the given view parameters. This adaptive approach often results in a massive increase in rendering performance. In addition, two new selection filters provide data analysis capabilities, by means of allowing for the extraction of those cells within a hypertree grid that are deemed relevant in some sense, either geometrically or topologically. After a description of these new algorithms, we illustrate their use within the Visualization Toolkit (VTK) in which we implemented them. This note ends with some suggestions for subsequent work., Comment: Keywords: scientific visualization, interactive visualization, meshing, AMR, mesh refinement, tree-based, octree, VTK, parallel visualization, large scale visualization, HPC, data analysis

Published
2017

19. Visualization and Analysis of Large-Scale, Tree-Based, Adaptive Mesh Refinement Simulations with Arbitrary Rectilinear Geometry

Author

Harel, Guénolé, Lekien, Jacques-Bernard, and Pébaÿ, Philippe P.

Subjects
Computer Science - Graphics
Abstract

We present here the first systematic treatment of the problems posed by the visualization and analysis of large-scale, parallel adaptive mesh refinement (AMR) simulations on an Eulerian grid. When compared to those obtained by constructing an intermediate unstructured mesh with fully described connectivity, our primary results indicate a gain of at least 80\% in terms of memory footprint, with a better rendering while retaining similar execution speed. In this article, we describe the key concepts that allow us to obtain these results, together with the methodology that facilitates the design, implementation, and optimization of algorithms operating directly on such refined meshes. This native support for AMR meshes has been contributed to the open source Visualization Toolkit (VTK). This work pertains to a broader long-term vision, with the dual goal to both improve interactivity when exploring such data sets in 2 and 3 dimensions, and optimize resource utilization.

Published
2017

29. Quantification of Detergents Complexed with Membrane Proteins.

Author

Chaptal, Vincent, Delolme, Frédéric, Kilburg, Arnaud, Magnard, Sandrine, Montigny, Cédric, Picard, Martin, Prier, Charlène, Monticelli, Luca, Bornert, Olivier, Agez, Morgane, Ravaud, Stéphanie, Orelle, Cédric, Wagner, Renaud, Jawhari, Anass, Broutin, Isabelle, Pebay-Peyroula, Eva, Jault, Jean-Michel, Kaback, H Ronald, le Maire, Marc, and Falson, Pierre

Subjects
Membrane Proteins, Liposomes, Detergents, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Sensitivity and Specificity, Reproducibility of Results, Micelles, Models, Molecular, Models, Molecular, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
Abstract

Most membrane proteins studies require the use of detergents, but because of the lack of a general, accurate and rapid method to quantify them, many uncertainties remain that hamper proper functional and structural data analyses. To solve this problem, we propose a method based on matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS) that allows quantification of pure or mixed detergents in complex with membrane proteins. We validated the method with a wide variety of detergents and membrane proteins. We automated the process, thereby allowing routine quantification for a broad spectrum of usage. As a first illustration, we show how to obtain information of the amount of detergent in complex with a membrane protein, essential for liposome or nanodiscs reconstitutions. Thanks to the method, we also show how to reliably and easily estimate the detergent corona diameter and select the smallest size, critical for favoring protein-protein contacts and triggering/promoting membrane protein crystallization, and to visualize the detergent belt for Cryo-EM studies.

Published
2017

30. A semi-automated pipeline for quantifying drusen-like deposits in human induced pluripotent stem cell-derived retinal pigment epithelium cells

Author

Hall, J, Daniszewski, M, Cheung, S, Shobhana, K, Kumar, H, Liang, HH, Beetham, H, Cho, E, Abbott, C, Hewitt, AW, Simpson, KJ, Guymer, RH, Paull, D, Pebay, A, Lidgerwood, GE, Hall, J, Daniszewski, M, Cheung, S, Shobhana, K, Kumar, H, Liang, HH, Beetham, H, Cho, E, Abbott, C, Hewitt, AW, Simpson, KJ, Guymer, RH, Paull, D, Pebay, A, and Lidgerwood, GE

Abstract

Age-Related Macular Degeneration (AMD) is a highly prevalent form of retinal disease amongst Western communities over 50 years of age. A hallmark of AMD pathogenesis is the accumulation of drusen underneath the retinal pigment epithelium (RPE), a biological process also observable in vitro. The accumulation of drusen has been shown to predict the progression to advanced AMD, making accurate characterisation of drusen in vitro models valuable in disease modelling and drug development. More recently, deposits above the RPE in the subretinal space, called reticular pseudodrusen (RPD) have been recognized as a sub-phenotype of AMD. While in vitro imaging techniques allow for the immunostaining of drusen-like deposits, quantification of these deposits often requires slow, low throughput manual counting of images. This further lends itself to issues including sampling biases, while ignoring critical data parameters including volume and precise localization. To overcome these issues, we developed a semi-automated pipeline for quantifying the presence of drusen-like deposits in vitro, using RPE cultures derived from patient-specific induced pluripotent stem cells (iPSCs). Using high-throughput confocal microscopy, together with three-dimensional reconstruction, we developed an imaging and analysis pipeline that quantifies the number of drusen-like deposits, and accurately and reproducibly provides the location and composition of these deposits. Extending its utility, this pipeline can determine whether the drusen-like deposits locate to the apical or basal surface of RPE cells. Here, we validate the utility of this pipeline in the quantification of drusen-like deposits in six iPSCs lines derived from patients with AMD, following their differentiation into RPE cells. This pipeline provides a valuable tool for the in vitro modelling of AMD and other retinal disease, and is amenable to mid and high throughput screenings.

Published
2024

36. PSEN1ΔE9, APPswe, and APOE4 Confer Disparate Phenotypes in Human iPSC-Derived Microglia

Author

Konttinen, Henna, Cabral-da-Silva, Mauricio e Castro, Ohtonen, Sohvi, Wojciechowski, Sara, Shakirzyanova, Anastasia, Caligola, Simone, Giugno, Rosalba, Ishchenko, Yevheniia, Hernández, Damián, Fazaludeen, Mohammad Feroze, Eamen, Shaila, Budia, Mireia Gómez, Fagerlund, Ilkka, Scoyni, Flavia, Korhonen, Paula, Huber, Nadine, Haapasalo, Annakaisa, Hewitt, Alex W., Vickers, James, Smith, Grady C., Oksanen, Minna, Graff, Caroline, Kanninen, Katja M., Lehtonen, Sarka, Propson, Nicholas, Schwartz, Michael P., Pébay, Alice, Koistinaho, Jari, Ooi, Lezanne, and Malm, Tarja

Published
2019
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40. Optimization and NP_R-Completeness of Certain Fewnomials

Author

Pebay, Philippe, Rojas, J. Maurice, and Thompson, David C.

Subjects
Mathematics - Algebraic Geometry, Mathematics - Optimization and Control
Abstract

We give a high precision polynomial-time approximation scheme for the supremum of any honest n-variate (n+2)-nomial with a constant term, allowing real exponents as well as real coefficients. Our complexity bounds count field operations and inequality checks, and are polynomial in n and the logarithm of a certain condition number. For the special case of polynomials (i.e., integer exponents), the log of our condition number is quadratic in the sparse encoding. The best previous complexity bounds were exponential in the sparse encoding, even for n fixed. Along the way, we extend the theory of A-discriminants to real exponents and certain exponential sums, and find new and natural NP_R-complete problems., Comment: 9 pages, 7 figures (3 of them tiny). This is close to the final conference proceedings version

Published
2009

46. Single-Cell Profiling Identifies Key Pathways Expressed by iPSCs Cultured in Different Commercial Media

Author

Daniszewski, Maciej, Nguyen, Quan, Chy, Hun S., Singh, Vikrant, Crombie, Duncan E., Kulkarni, Tejal, Liang, Helena H., Sivakumaran, Priyadharshini, Lidgerwood, Grace E., Hernández, Damián, Conquest, Alison, Rooney, Louise A., Chevalier, Sophie, Andersen, Stacey B., Senabouth, Anne, Vickers, James C., Mackey, David A., Craig, Jamie E., Laslett, Andrew L., Hewitt, Alex W., Powell, Joseph E., and Pébay, Alice

Published
2018
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