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…
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…
Rachel Kowert
So called “toxic behaviors” (e.g., hate speech, harassment, doxxing) are pervasive in online gaming communities, with research consistently documenting significant negative consequences for player wellbeing, community health, and industry revenue. While gaming studios and platforms have developed a range of reactive…
Nitesh Kumar Sharma, Ram Ayyala, Dhrithi Deshpande, Yesha Patel + 13 more
'Viorel Munteanu' 'Dumitru Ciorba' 'Viorel Bostan' 'Andrada Fiscutean' 'Mohammad Vahed' 'Aditya Sarkar' 'Ruiwei Guo' 'Andrew Moore' 'Nicholas Darci-Maher' 'Nicole Nogoy' 'Malak Abedalthagafi' 'Serghei Mangul' 'Harry Hochheiser'] Data-driven computational analysis is becoming increasingly important in biomedical…
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…
Brian Maitner, Paul Efren Santos Andrade, Luna Lei, Jamie Kass + 11 more
'Hannah L. Owens' 'George C. G. Barbosa' 'Brad Boyle' 'Matiss Castorena' 'Brian J. Enquist' 'Xiao Feng' 'Daniel S. Park' 'Andrea Paz' 'Gonzalo Pinilla‐Buitrago' 'Cory Merow' 'Adam Wilson'] Title: Abstract Biologists increasingly rely on computer code to collect and analyze their data, reinforcing the importance of…
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…
Emmanuel A. Zavalis, John P. A. Ioannidis, Chi-Hua Chen
Mathematical models have become very influential, especially during the COVID-19 pandemic. Data and code sharing are indispensable for reproducing them, protocol registration may be useful sometimes, and declarations of conflicts of interest (COIs) and of funding are quintessential for transparency. Here, we evaluated…
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…
Ahmad Sofi-Mahmudi, Eero Raittio, Sergio E. Uribe, Rut Lucas-Dominguez
We assessed articles’ adherence to five transparent practices: 1. data sharing, 2. code sharing, 3. COI disclosures, 4. funding disclosures, 5. protocol registration.We used a validated and automated tool developed by Serghiou et al. suitable to identify these five transparent practices from articles in XML format from…
Yalan Lin, Chengcheng Wan, Yichuan Fang, Xiaodong Gu
While code large language models have made significant strides in AI-assisted coding tasks, there are growing concerns about privacy challenges. The user code is transparent to the cloud LLM service provider, inducing risks of unauthorized training, reading, and execution of sensitive code. Such fear of data leaking…
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…
Partha P. Mitra, Clément Sire
Contemporary Artificial Intelligence (AI) stands on two legs: large training data corpora and many-parameter artificial neural networks (ANNs). The data corpora are needed to represent the complexity and heterogeneity of the world. The role of the networks is less transparent due to the obscure dependence of the…
Keith D. Harris, Guy Hadari, Gili Greenbaum
Modeling the dynamics of biological processes is ubiquitous across the ecological and evolutionary disciplines. However, the increasing complexity of these models poses a significant challenge to the dissemination of model-derived results. With the existing requirements of scientific publishing, most often only a small…
Alexander Schniedermann
What is scientific quality and how can it be achieved? Recent developments in clinical biomedicine gave prominence to transparency as a new core value for scientific research. Without transparency, other characteristics and values remain unknown. But how can abstract concepts and values be implemented in day-to-day…
Carl H.C. Keck, Elizabeth L. Schmidt, Richard H. Roth, Brendan M. Floyd + 28 more
Light scattering in biological tissue presents a significant challenge for deep in vivo imaging. Our previous work demonstrated the ability to achieve optical transparency in live mice using intensely absorbing dye molecules, which created transparency in the red spectrum while blocking shorter-wavelength photons. In…
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…