Related papers: ppiTrim: Constructing non-redundant and up-to-date…
Automating experimental protocol design and execution remains as a fundamental bottleneck in realizing self-driving laboratories. We introduce PRISM (Protocol Refinement through Intelligent Simulation Modeling), a framework that automates…
Non-determinism and non-reproducibility present significant challenges in deep learning, leading to inconsistent results across runs and platforms. These issues stem from two origins: random number generation and floating-point computation.…
Data analysis in fundamental sciences nowadays is an essential process that pushes frontiers of our knowledge and leads to new discoveries. At the same time we can see that complexity of those analyses increases fast due to a)~enormous…
There has recently been growing interest in the automatic generation of cooking recipes that satisfy some form of dietary restrictions, thanks in part to the availability of online recipe data. Prior studies have used pre-trained language…
Relation extraction is a fundamental task in information extraction. Most existing methods have heavy reliance on annotations labeled by human experts, which are costly and time-consuming. To overcome this drawback, we propose a novel…
Laboratory research is a complex, collaborative process that involves several stages, including hypothesis formulation, experimental design, data generation and analysis, and manuscript writing. Although reproducibility and data sharing are…
The ubiquity of computation in modern scientific research inflicts new challenges for reproducibility. While most journals now require code and data be made available, the standards for organization, annotation, and validation remain lax,…
Sequential recommendation aims to provide users with personalized suggestions based on their historical interactions. When training sequential models, padding is a widely adopted technique for two main reasons: 1) The vast majority of…
Ensuring consistency between research papers and their corresponding software code implementations is a fundamental prerequisite for guaranteeing the reproducibility of scientific findings and the reliability of software systems. However,…
Ensuring the reproducibility of scientific work is crucial as it allows the consistent verification of scientific claims and facilitates the advancement of knowledge by providing a reliable foundation for future research. However,…
Cellular functions are based on the complex interplay of proteins, therefore the structure and dynamics of these protein-protein interaction (PPI) networks are the key to the functional understanding of cells. In the last years, large-scale…
Recent advances in Large Language Models have led to Large Reasoning Models, which produce step-by-step reasoning traces. These traces offer insight into how models think and their goals, improving explainability and helping users follow…
Generative sequence modeling faces a fundamental tension between the expressivity of Transformers and the efficiency of linear sequence models. Existing efficient architectures are theoretically bounded by shallow, single-step linear…
Protein-protein interactions (PPIs) are crucial in various biological processes and their study has significant implications for drug development and disease diagnosis. Existing deep learning methods suffer from significant performance…
Instruments play an essential role in creating research data. Given the importance of instruments and associated metadata to the assessment of data quality and data reuse, globally unique, persistent and resolvable identification of…
Motivation: A major challenge in the development of machine learning based methods in computational biology is that data may not be accurately labeled due to the time and resources required for experimentally annotating properties of…
Federated recommendation provides a privacy-preserving solution for training recommender systems without centralizing user interactions. However, existing methods follow an ID-indexed communication paradigm that transmit whole item…
Reusable data/code and reproducible analyses are foundational to quality research. This aspect, however, is often overlooked when designing interactive stream analysis workflows for time-series data (e.g., eye-tracking data). A mechanism to…
Environment designers in the entertainment industry create imaginative 2D and 3D scenes for games, films, and television, requiring both fine-grained control of specific details and consistent global coherence. Designers have increasingly…
PhyloFrame is a Python library for phylogenetic computation targeting the gap between specialist, compiler-optimized operations and flexible, script-based workflows -- with emphasis on fast, memory-efficient operations for very large tree…