20 papers · ranked by Valyu relevance
David Hanson
As artificial intelligence (AI) becomes increasingly integrated into software development processes, the prevalence and sophistication of AI-generated code continue to expand rapidly. This study addresses the critical need for transparency and safety in AI-generated code by examining the current landscape, identifying…
Krzysztof J. Gorgolewski, Russell A. Poldrack
Recent years have seen an increase in alarming signals about the lack of replicability in neuroscience, psychology, and other related fields. To avoid a widespread crisis in our field and consequent loss of credibility in the public eye, we need to improve how we do science. This article aims to be a practical guide…
Shirley V Wang, Anton Pottegård
Real-world evidence (RWE) studies are increasingly used to inform policy and clinical decisions. However, there remain concerns about the credibility and reproducibility of RWE studies. While there is universal agreement on the critical importance of transparent and reproducible science, the building blocks of open…
Nitesh Kumar Sharma, Ram Ayyala, Dhrithi Deshpande, Yesha M Patel + 11 more
Data-driven computational analysis is becoming increasingly important in biomedical research, as the amount of data being generated continues to grow. However, the lack of practices of sharing research outputs, such as data, source code and methods, affects transparency and reproducibility of studies, which are…
Authors not listed
Scientific discovery relies on innovative software as much as experimental methods, especially in proteomics, where computational tools are essential for mass spectrometer setup, data analysis, and interpretation. Since the introduction of SEQUEST, proteomics software has grown into a complex ecosystem of algorithms…
Ceren Kocaoğullar, Tina Marjanov, Ivan Petrov, Ben Laurie + 4 more
'Al Cutter' 'Christoph Kern' 'Alice Hutchings' 'Alastair R. Beresford'] Confidential Computing is a security paradigm designed to protect data in-use by leveraging hardware-based Trusted Execution Environments (TEEs). While TEEs offer significant security benefits, the need for user trust remains a challenge, as…
Stylianos Serghiou, Despina G. Contopoulos-Ioannidis, Kevin W. Boyack, Nico Riedel + 3 more
'Nico Riedel' 'Joshua D. Wallach' 'John P. A. Ioannidis' 'Lisa Bero'] Recent concerns about the reproducibility of science have led to several calls for more open and transparent research practices and for the monitoring of potential improvements over time. However, with tens of thousands of new biomedical articles…
Balazs Aczel, Barnabas Szaszi, Alexandra Sarafoglou, Zoltan Kekecs + 63 more
'Šimon Kucharský' 'Daniel Benjamin' 'Christopher D. Chambers' 'Agneta Fisher' 'Andrew Gelman' 'Morton A. Gernsbacher' 'John P. Ioannidis' 'Eric Johnson' 'Kai Jonas' 'Stavroula Kousta' 'Scott O. Lilienfeld' 'D. Stephen Lindsay' 'Candice C. Morey' 'Marcus Munafò' 'Benjamin R. Newell' 'Harold Pashler' 'David R. Shanks'…
Stylianos Serghiou, Despina G. Contopoulos-Ioannidis, Kevin W. Boyack, Nico Riedel + 2 more
Recent concerns about the reproducibility of science have led to several calls for more open and transparent research practices and for the monitoring of potential improvements over time. However, with tens of thousands of new biomedical articles published per week, manually mapping and monitoring changes in…
Heike Felzmann, Eduard Fosch-Villaronga, Christoph Lutz, Aurelia Tamò-Larrieux
In this article, we develop the concept of Transparency by Design that serves as practical guidance in helping promote the beneficial functions of transparency while mitigating its challenges in automated-decision making (ADM) environments. With the rise of artificial intelligence (AI) and the ability of AI systems to…
Authors not listed
The increasing importance and predictive power of modern molecular modeling, driven by physics- and machine learning-based methods, necessitates a new collaborative architecture to replace the isolated, traditional model of software development. The traditional approach often led to redundant engineering effort, high…
Wei Jeng, Shih-Hung Wang, Hung-Wei Chen, Po-Wei Huang + 3 more
Research transparency has been advocated as a key means of addressing the current crisis of reproducibility. This article proposes an enhanced form of research transparency, termed lifecycle transparency. Over the entire lifecycle of a research effort, this approach captures the syntactical contexts of artifacts and…
Pedro Garcı́a-López, Aleksander Slominski, Simon Shillaker, Michael Behrendt + 1 more
'Michael Behrendt' 'Barnard Metzler'] For many years, the distributed systems community has struggled to smooth the transition from local to remote computing. Transparency means concealing the complexities of distributed programming like remote locations, failures or scaling. For us, full transparency implies that we…
Rishi Bommasani, Kevin Klyman, Shayne Longpre, Sayash Kapoor + 4 more
'Nestor Maslej' 'Betty Xiong' 'Daniel Zhang' 'Percy Liang'] Foundation models have rapidly permeated society, catalyzing a wave of generative AI applications spanning enterprise and consumer-facing contexts. While the societal impact of foundation models is growing, transparency is on the decline, mirroring the opacity…
V. L. Kalmykov, L. V. Kalmykov
Mathematical black box models, which hide the structure and behavior of the subsystems, currently dominate science. Errors and paradoxes, such as the biodiversity paradox and the limiting similarity hypothesis, often arise from subjective interpretations of these hidden mechanisms. To address these problems, we have…
Micha Horlboge, Erwin Quiring, Roland Meyer, Konrad Rieck
—The source code of a program not only defines its semantics but also contains subtle clues that can identify its author. Several studies have shown that these clues can be automatically extracted using machine learning and allow for determining a program's author among hundreds of programmers. This attribution poses a…
Authors not listed
Bayesian optimization (BO) has become increasingly important for experimental optimization across scientific domains, yet implementing BO pipelines requires significant programming expertise and familiarity with specialized frameworks. This creates a barrier for domain experts who could benefit from BO but lack the…
Charline Pinna, Maëlle Vilbert, Stephan Borensztajn, Willy Daney de Marcillac + 7 more
Müllerian mimicry is a positive interspecific interaction, whereby co-occurring defended prey species share a common aposematic signal that advertises their defences to predators. In Lepidoptera, aposematic species typically harbour conspicuous opaque wing colour pattern, which have convergent optical properties, as…
Mónica Arias, Johanna Mappes, Charlotte Desbois, Swanne Gordon + 4 more
1. Predation is an important selective pressure and some prey have evolved warning colour signals advertising unpalatability (i.e. aposematism) as an antipredator strategy. Unexpectedly, some butterfly species from the unpalatable tribe Ithomiini possess transparent wings, an adaptation rare on land but common in water…
Authors not listed
Step-by-step thinking is essential in all domains of chemical sciences and engineering. While machine learning tools are broadly used, algorithms that automate reasoning are far less common. We elaborate on seven categories of human reasoning activities and connect each to applications in chemical science and…