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Insufficient performance of optimization approaches for fitting of mathematical models is still a major bottleneck in systems biology. In this manuscript, the reasons and methodological challenges are summarized as well as their impact in…

Performance · Computer Science 2019-07-09 Clemens Kreutz

Benchmarking, which involves collecting reference datasets and demonstrating method performances, is a requirement for the development of new computational tools, but also becomes a domain of its own to achieve neutral comparisons of…

Other Quantitative Biology · Quantitative Biology 2025-07-24 Izaskun Mallona , Charlotte Soneson , Ben Carrillo , Almut Luetge , Daniel Incicau , Reto Gerber , Anthony Sonrel , Mark D. Robinson

I would like to share recommendations on how to do performance benchmarks for the purpose of computer science research evaluation. Research in my field (programming language research) often involves performance considerations, but it is…

Programming Languages · Computer Science 2026-05-05 Gabriel Scherer

Method comparisons are essential to provide recommendations and guidance for applied researchers, who often have to choose from a plethora of available approaches. While many comparisons exist in the literature, these are often not neutral…

Methodology · Statistics 2022-12-07 Sarah Friedrich , Tim Friede

Computational chemistry has become an important complement to experimental measurements. In order to choose among the multitude of the existing approximations, it is common to use benchmark data sets, and to issue recommendations based on…

Chemical Physics · Physics 2020-04-02 Andreas Savin , Pascal Pernot

Architectures for quantum computing can only be scaled up when they are accompanied by suitable benchmarking techniques. The document provides a comprehensive overview of the state and recommendations for systematic benchmarking of quantum…

For scientific software, especially those used for large-scale simulations, achieving good performance and efficiently using the available hardware resources is essential. It is important to regularly perform benchmarks to ensure the…

Citation recommendation systems have attracted much academic interest, resulting in many studies and implementations. These systems help authors automatically generate proper citations by suggesting relevant references based on the text…

Information Retrieval · Computer Science 2024-12-11 Puja Maharjan

The rapid pace of development in quantum computing technology has sparked a proliferation of benchmarks for assessing the performance of quantum computing hardware and software. Good benchmarks empower scientists, engineers, programmers,…

Quantum Physics · Physics 2026-02-17 Timothy Proctor , Kevin Young , Andrew D. Baczewski , Robin Blume-Kohout

Comparing, or benchmarking, of optimization algorithms is a complicated task that involves many subtle considerations to yield a fair and unbiased evaluation. In this paper, we systematically review the benchmarking process of optimization…

Optimization and Control · Mathematics 2017-09-26 Vahid Beiranvand , Warren Hare , Yves Lucet

This survey compiles ideas and recommendations from more than a dozen researchers with different backgrounds and from different institutes around the world. Promoting best practice in benchmarking is its main goal. The article discusses…

The growing interest in making use of Knowledge Graphs for developing explainable artificial intelligence, there is an increasing need for a comparable and repeatable comparison of the performance of Knowledge Graph-based systems. History…

Note: A revised version of this is now published. Please cite and read (it's open access): Van Mechelen, I., Boulesteix, A.-L., Dangl, R., Dean, N., Hennig, C., Leisch, F., Steinley, D., Warrens, M. J. (2023). A white paper on good research…

Recent advances in probabilistic modelling have led to a large number of simulation-based inference algorithms which do not require numerical evaluation of likelihoods. However, a public benchmark with appropriate performance metrics for…

Machine Learning · Statistics 2021-04-12 Jan-Matthis Lueckmann , Jan Boelts , David S. Greenberg , Pedro J. Gonçalves , Jakob H. Macke

Benchmarking functionalities in current commercial process mining tools allow organizations to contextualize their process performance through high-level performance indicators, such as completion rate or throughput time. However, they do…

Software Engineering · Computer Science 2025-04-24 Luka Abb , Majid Rafiei , Timotheus Kampik , Jana-Rebecca Rehse

Benchmarking plays an important role in the development of novel search algorithms as well as for the assessment and comparison of contemporary algorithmic ideas. This paper presents common principles that need to be taken into account when…

Neural and Evolutionary Computing · Computer Science 2018-10-08 Michael Hellwig , Hans-Georg Beyer

Novel reinforcement learning algorithms, or improvements on existing ones, are commonly justified by evaluating their performance on benchmark environments and are compared to an ever-changing set of standard algorithms. However, despite…

Machine Learning · Computer Science 2024-06-25 Scott M. Jordan , Adam White , Bruno Castro da Silva , Martha White , Philip S. Thomas

Benchmarking is how the performance of a computing system is determined. Surprisingly, even for classical computers this is not a straightforward process. One must choose the appropriate benchmark and metrics to extract meaningful results.…

Quantum Physics · Physics 2021-05-07 Salonik Resch , Ulya R. Karpuzcu

In a context where most published articles are devoted to the development of "new methods", comparison studies are generally appreciated by readers but surprisingly given poor consideration by many scientific journals. In connection with…

Computation · Statistics 2015-06-11 Anne-Laure Boulesteix , Manuel J. A. Eugster

The increasing attention on deep learning has tremendously spurred the design of intelligence processing hardware. The variety of emerging intelligence processors requires standard benchmarks for fair comparison and system optimization (in…

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