Related papers: An Open Framework for Extensible Multi-Stage Bioin…
The increasing risk of epidemics and a fast-growing world population has contributed to a great investment in phylogenetic analysis, in order to track numerous diseases and conceive effective medication and treatments. Phylogenetic analysis…
The phase-field method has become a useful tool for the simulation of classical metallurgical phase transformations as well as other phenomena related to materials science. The thermodynamic consistency that forms the basis of these…
Predicting phenotypes with complex genetic bases based on a small, interpretable set of variant features remains a challenging task. Conventionally, data-driven approaches are utilized for this task, yet the high dimensional nature of…
Biology is at the precipice of a new era where AI accelerates and amplifies the ability to study how cells operate, organize, and work as systems, revealing why disease happens and how to correct it. Organizations globally are prioritizing…
This paper aims at identifying emerging computational intelligence trends for the design and modeling of complex biometric-enabled infrastructure and systems. Biometric-enabled systems are evolving towards deep learning and deep inference…
Inspired by biological and cultural evolution, there have been many attempts to explore and elucidate the necessary conditions for open-endedness in artificial intelligence and artificial life. Using a continuous cellular automata called…
Computational methods are the most effective tools we have besides scientific experiments to explore the properties of complex biological systems. Progress is slowing because digital silicon computers have reached their limits in terms of…
Hierarchical models are a powerful tool for high-throughput data with a small to moderate number of replicates, as they allow sharing information across units of information, for example, genes. We propose two such models and show its…
Artificial Intelligence methods are powerful tools for biological image analysis and processing. High-quality annotated images are key to training and developing new methods, but access to such data is often hindered by the lack of…
Several algorithms for RNA inverse folding have been used to design synthetic riboswitches, ribozymes and thermoswitches, whose activity has been experimentally validated. The RNAiFold software is unique among approaches for inverse folding…
Foundational models (FMs) have made significant strides in the healthcare domain. Yet the data silo challenge and privacy concern remain in healthcare systems, hindering safe medical data sharing and collaborative model development among…
Characterizing quantum systems through experimental data is critical to applications as diverse as metrology and quantum computing. Analyzing this experimental data in a robust and reproducible manner is made challenging, however, by the…
Software is vital for the advancement of biology and medicine. Analysis of usage and impact metrics can help developers determine user and community engagement, justify additional funding, encourage additional use, identify unanticipated…
Living labs have been established across different countries to evaluate how the interaction between humans and buildings can be optimized to improve comfort, health, and energy savings. However, existing living labs can be too…
We present an open architecture for just-in-time code generation and dynamic code optimization that is flexible, customizable, and extensible. While previous research has primarily investigated functional aspects of such a system,…
High-performance computing platforms are becoming more and more heterogeneous, which makes it very difficult for researchers and scientific software developers to keep up with the rapid changes on the hardware market. In this paper, the…
Composition is a powerful principle for systems biology, focused on the interfaces, interconnections, and orchestration of distributed processes to enable integrative multiscale simulations. Whereas traditional models focus on the structure…
The performance and generalization of foundation models for interactive systems critically depend on the availability of large-scale, realistic training data. While recent advances in large language models (LLMs) have improved GUI…
The finite cell method is a highly flexible discretization technique for numerical analysis on domains with complex geometries. By using a non-boundary conforming computational domain that can be easily meshed, automatized computations on a…
Despite their potential to address crucial bottlenecks in computing architectures and contribute to the pool of biological inspiration for engineering, pathological biological mechanisms remain absent from computational theory. We hereby…