Related papers: PEtab-GUI: A graphical user interface to create, e…
Temporal graphs are graphs whose nodes and edges, together with their associated properties, continuously change over time. With the development of Internet of Things (IoT) systems, a subclass of the temporal graph, i.e., Property Evolution…
Product Data Management (PDM) desktop and web based systems maintain the organizational technical and managerial data to increase the quality of products by improving the processes of development, business process flows, change management,…
PACKMOL is a widely utilized molecular modeling tool within the computational chemistry community. However, its perceivable advantages have been impeded by the long-standing lack of a robust open-source graphical user interface (GUI) that…
Generative modelling of multi-user datasets has become prominent in science and engineering. Generating a data point for a given user requires employing user information, and conventional generative models, including variational…
Parameter-efficient fine-tuning (PEFT) techniques have emerged to address overfitting and high computational costs associated with fully fine-tuning in self-supervised learning. Mainstream PEFT methods add a few trainable parameters while…
Statistical analysis is the tool of choice to turn data into information, and then information into empirical knowledge. To be valid, the process that goes from data to knowledge should be supported by detailed, rigorous guidelines, which…
Despite data's crucial role in machine learning, most existing tools and research tend to focus on systems on top of existing data rather than how to interpret and manipulate data. In this paper, we propose DataLab, a unified data-oriented…
Instruction tuning has shown promising potential for developing general-purpose AI capabilities by using large-scale pre-trained models and boosts growing research to integrate multimodal information for creative applications. However,…
PLUMED-GUI is an interactive environment to develop and test complex PLUMED scripts within the Visual Molecular Dynamics (VMD) environment. Computational biophysicists can take advantage of both PLUMED's rich syntax to define collective…
Our modern world produces an increasing quantity of data, and especially geospatial data, with advance of sensing technologies, and growing complexity and organisation of vector data. Tools are needed to efficiently create and edit those…
The integration of deep learning approaches in biomedical research has been transformative, enabling breakthroughs in various applications. Despite these strides, its application in protein inference is impeded by the scarcity of…
Motivation: The visualization and analysis of high-dimensional data are essential in biomedical research. There is a need for secure, scalable, and reproducible tools to facilitate data exploration and interpretation. Results: We introduce…
The Simulation Environment for Atomistic and Molecular Modeling (SEAMM) is an open-source software package written in Python that provides a graphical interface for setting up, executing, and analyzing molecular and materials simulations.…
Networks provide a meaningful way to represent and analyze complex biological information, but the methodological details of network-based tools are often described for a technical audience. Graphery is a hands-on tutorial webserver…
There is an ongoing need for scalable tools to aid researchers in both retrospective and prospective standardization of discrete entity types -- such as disease names, cell types or chemicals -- that are used in metadata associated with…
The success of Graph Neural Networks (GNNs) has led to a need for understanding their decision-making process and providing explanations for their predictions, which has given rise to explainable AI (XAI) that offers transparent…
This survey delves into the realm of Parameter-Efficient Fine-Tuning (PEFT) within the context of Foundation Models (FMs). PEFT, a cost-effective fine-tuning technique, minimizes parameters and computational complexity while striving for…
The computer programs most users interact with daily are driven by a graphical user interface (GUI). However, many scientific applications are used with a command line interface (CLI) for the ease of development and increased flexibility…
The rise of deep learning has marked significant progress in fields such as computer vision, natural language processing, and medical imaging, primarily through the adaptation of pre-trained models for specific tasks. Traditional…
The increasing importance of Computational Science and Engineering has highlighted the need for high-quality scientific software. However, research software development is often hindered by limited funding, time, staffing, and technical…