Related papers: MolSSI and BioExcel Workflow Workshop 2018 Report
In recent years, deep learning revolutionized machine learning and its applications, producing results comparable to human experts in several domains, including neuroscience. Each year, hundreds of scientific publications present…
Human-in-the-loop data analysis applications necessitate greater transparency in machine learning models for experts to understand and trust their decisions. To this end, we propose a visual analytics workflow to help data scientists and…
Program synthesis is an active research field in academia, national labs, and industry. Yet, work directly applicable to scientific computing, while having some impressive successes, has been limited. This report reviews the relevant areas…
In the world of science new technology have opened up the possibility to rely on advanced computational methods and models to conduct and produce scientific research. An important aspect of scientific and business workflows is provenance -…
The extraction of molecular structures and reaction data from scientific documents is challenging due to their varied, unstructured chemical formats and complex document layouts. To address this, we introduce MolMole, a vision-based deep…
Computational methods and associated software implementations are central to every field of scientific investigation. Modern biological research, particularly within systems biology, has relied heavily on the development of software tools…
Artificial intelligence is transforming molecular and materials science, but its growing computational and data demands raise critical sustainability challenges. In this Perspective, we examine resource considerations across the AI-driven…
The existing approaches for scientific workflows composition face the problems of domain knowledge integration. By this paper we summarize the results, which have been elaborated and implemented during the 2-year research concerning to…
Development and homeostasis in multicellular systems both require exquisite control over spatial molecular pattern formation and maintenance. Advances in spatially-resolved and high-throughput molecular imaging methods such as multiplexed…
For many macromolecular systems the accurate sampling of the relevant regions on the potential energy surface cannot be obtained by a single, long Molecular Dynamics (MD) trajectory. New approaches are required to promote more efficient…
Nextflow is a workflow management system commonly used in fields like bioinformatics and earth observation. It coordinates distributed data processing of various tools as an acyclic sequence of tasks while using, containerization (e.g.,…
Machine learning has been increasingly applied in climate modeling on system emulation acceleration, data-driven parameter inference, forecasting, and knowledge discovery, addressing challenges such as physical consistency, multi-scale…
Simulation has become an essential component of designing and developing scientific experiments. The conventional procedural approach to coding simulations of complex experiments is often error-prone, hard to interpret, and inflexible,…
The development and deployment of safe and dependable AI models is crucial in applications where functional safety is a key concern. Given the rapid advancement in AI research and the relative novelty of the safe-AI domain, there is an…
Agile software development principles and values have been widely adopted across various industries, influencing products and services globally. Despite its increasing popularity, a significant gap remains between research and practical…
Molecules play a crucial role in biomedical research and discovery, particularly in the field of small molecule drug development. Given the rapid advancements in large language models, especially the recent emergence of reasoning models, it…
Successful implementation of active learning strategies in the engineering classroom -- and in particular in certain subjects which are highly technological in nature such as, for instance, rocket engines and space propulsion -- means…
University research groups in Computational Science and Engineering (CSE) generally lack dedicated funding and personnel for Research Software Engineering (RSE), which, combined with the pressure to maximize the number of scientific…
Drying of biologically-relevant sessile droplets, including passive systems (like DNA and proteins), as well as active microbial systems comprising bacteria and algae, have garnered considerable attention over the last decades. Distinct…
Machine learning (ML) applications become increasingly common in many domains. ML systems to execute these workloads include numerical computing frameworks and libraries, ML algorithm libraries, and specialized systems for deep neural…