16 papers · ranked by Valyu relevance
Minyu Cui, Νικέλα Παπαδοπούλου, Miquel Pericàs
In the high performance computing (HPC) domain, performance variability is a major scalability issue for parallel computing applications with heavy synchronization and communication. In this paper, we present an experimental performance analysis of OpenMP benchmarks regarding the variation of execution time, and…
Sören Henning, Adriano Vogel, Esteban Pérez-Wohlfeil, Otmar Ertl + 1 more
Benchmarks and performance experiments are frequently conducted in cloud environments. However, their results are often treated with caution, as the presumed high variability of performance in the cloud raises concerns about reproducibility and credibility. In a recent study, we empirically quantified the impact of…
Ruzhang Zhao, Jiuyao Lu, Weiqiang Zhou, Ni Zhao + 1 more
Selecting highly variable features is a crucial step in most analysis pipelines of single-cell RNA-sequencing (scRNA-seq) data. Despite numerous methods proposed in recent years, a systematic understanding of the best solution is still lacking. Here, we systematically evaluate 47 highly variable gene (HVG) selection…
Kien-Tuan Ngo, Thu-Trang Nguyen, Son Nguyen, Hieu Dinh Vo
Software fault localization is one of the most expensive, tedious, and time-consuming activities in program debugging. This activity becomes even much more challenging in Software Product Line (SPL) systems due to the variability of failures in SPL systems. These unexpected behaviors are caused by variability faults…
Mostafa Dehghani, Yi Tay, Alexey A. Gritsenko, Zhe Zhao + 4 more
'Neil Houlsby' 'Fernando Díaz' 'Donald Metzler' 'Oriol Vinyals'] The world of empirical machine learning (ML) strongly relies on benchmarks in order to determine the relative effectiveness of different algorithms and methods. This paper proposes the notion of a benchmark lottery that describes the overall fragility of…
Michael Bentley, Ian Briggs, Ganesh Gopalakrishnan, Dong H. Ahn + 3 more
'Ignacio Laguna' 'Gregory L. Lee' 'Holger E. Jones'] Successful HPC software applications are long-lived. When ported across machines and their compilers, these applications often produce different numerical results, many of which are unacceptable. Such variability is also a concern while optimizing the code more…
Jonas Vester, David Carrasco-Busturia, Kenneth Ruud, Magnus Ringholm + 1 more
We present a workflow, benchmarks, and applications to provide a roadmap for simulating harmonic IR and Raman spectra for large solute-solvent systems by employing a polarizable-embedding quantum-mechanics (PE-QM) approach. This multiscale modeling scheme divides the system into a central core region described by…
Authors not listed
Optimizing the synthesis conditions of advanced materials is challenging, especially when outcomes are subject to inherent experimental uncertainties. Bayesian optimization is a popular tool for accelerating materials discovery, but its standard risk-neutral framework overlooks the variability of outcomes under…
Nahyun Kong, Zitian Tang, Andrew Ruttenberg, Juan F. Macias-Velasco + 24 more
Somatic mosaicism is essential in human biology and disease, yet robust benchmarks are scarce. The SMaHT Consortium mixed six HapMap cell lines to create artificial somatic variants spanning 0.25% to 16.5% variant allele fractions. We developed a technology-agnostic method that builds pangenome graphs from individual…
Xiaoqi Cabiria Liang, Nick Robertson, Marni Torkel, Sanghyun Kim + 3 more
The rapid growth of computational methods for the computational biology field highlights the critical role of benchmarking in guiding method selection. However, there is no standardised data structure that effectively links and stores datasets, performance metrics and available ground truth. Without such a unified and…
Authors not listed
Physics-based methods such as protein-ligand binding free energy calculations have been increasingly adopted in early-stage drug discovery to prioritize promising compounds for synthesis. However, the accuracy of these methods is highly dependent on details of the calculation and choices made while preparing the…
Scott Wolf, Diogo Melo, Kristina M. Garske, Luisa F. Pallares + 2 more
Gene expression variance has been linked to organismal function and fitness but remains a commonly ne-glected aspect of molecular research. As a result, we lack a comprehensive understanding of the patterns of transcriptional variance across genes, and how this variance is linked to context-specific gene regulation and…
Zhenghao Wu, Tianhang Zhou
In the realm of multiscale molecular simulations, structure-based coarse graining is a prominent approach for creating efficient coarse-grained (CG) representations of soft matter systems such as polymers. This involves optimizing CG interactions by matching static correlation functions of corresponding degrees of…
Vincent Dufour-Decieux, Brandi Ransom, Rodrigo Freitas, Jose Blanchet + 1 more
Molecular Dynamics (MD) simulations are a key tool to understand the mechanism of complex chemical system and observe their outcomes in different conditions. However, such simulations are computationally expensive, which limits their timescales to the nanoseconds. This limitation is inconsequential at high…
Authors not listed
The construction of large benchmark sets has accelerated advancement of quantum chemistry methods, especially in density functional theory and lower-cost methods. However, these large benchmark sets can be unsuitable for cutting-edge method development, because research codes developed for fundamentally new approaches…
Julien F. Ayroles, Sean M. Buchanan, Chelsea Jenney, Kyobi Skutt-Kakaria + 4 more
Variability is ubiquitous in nature and a fundamental feature of complex systems. Few studies, however, have investigated variance itself as a trait under genetic control. By focusing primarily on trait means and ignoring the effect of alternative alleles on trait variability, we may be missing an important axis of…