Related papers: IMPi: An interactive homology modeling pipeline
While the demand for machine learning (ML) applications is booming, there is a scarcity of data scientists capable of building such models. Automatic machine learning (AutoML) approaches have been proposed that help with this problem by…
Motivation: Identifying the molecular pathways more prone to disruption during a pathological process is a key task in network medicine and, more in general, in systems biology. Results: In this work we propose a pipeline that couples a…
The availability of interaction devices has raised interest in techniques to support the user interface (UI). A UI specification describes the functions that a system provides to its users by capturing the interface details and includes…
Interpreting samples from likelihood or posterior probability density functions is rarely as straightforward as it seems it should be. Producing publication-quality graphics of these distributions is often similarly painful. In this short…
Visual programming has the potential of providing novice programmers with a low-code experience to build customized processing pipelines. Existing systems typically require users to build pipelines from scratch, implying that novice users…
Motivation: Bioinformatics software often lacks graphical user interfaces (GUIs), which can limit its adoption by non-technical members of the scientific community. Web interfaces are a common alternative for building cross-platform GUIs,…
Interactive portrait matting refers to extracting the soft portrait from a given image that best meets the user's intent through their inputs. Existing methods often underperform in complex scenarios, mainly due to three factors. (1) Most…
Integrated information theory provides a mathematical framework to fully characterize the cause-effect structure of a physical system. Here, we introduce PyPhi, a Python software package that implements this framework for causal analysis…
Weighted model integration (WMI) is a very appealing framework for probabilistic inference: it allows to express the complex dependencies of real-world hybrid scenarios where variables are heterogeneous in nature (both continuous and…
This paper aims to create a transition path from file-based IO to streaming-based workflows for scientific applications in an HPC environment. By using the openPMP-api, traditional workflows limited by filesystem bottlenecks can be overcome…
Comparing mathematical models offers a means to evaluate competing scientific theories. However, exact methods of model calibration are not applicable to many probabilistic models which simulate high-dimensional spatio-temporal data.…
PyMOLfold is a flexible and open-source plugin designed to seamlessly integrate AI-based protein structure prediction and visualization within the widely used PyMOL molecular graphics system. By leveraging state-of-the-art protein folding…
Since the C++ bindings were deleted in 2008, the Message Passing Interface (MPI) community has revived efforts in building high-level modern C++ interfaces. Such interfaces are either built to serve specific scientific application needs…
Supervised machine learning pipelines trained on features derived from persistent homology have been experimentally observed to ignore much of the information contained in a persistence diagram. Computing persistence diagrams is often the…
When developing a (web) interface for a deductive database, functionality required by the client is provided by means of HTTP handlers that wrap the logical data access predicates. These handlers are responsible for converting between…
Prompt engineering has made significant contributions to the era of large language models, yet its effectiveness depends on the skills of a prompt author. This paper introduces $\textit{iPrOp}$, a novel interactive prompt optimization…
Natural human interactions for Mixed Reality Applications are overwhelmingly multimodal: humans communicate intent and instructions via a combination of visual, aural and gestural cues. However, supporting low-latency and accurate…
Acquiring plausible pathways on high-dimensional structural distributions is beneficial in several domains. For example, in the drug discovery field, a protein conformational pathway, i.e. a highly probable sequence of protein structural…
The Agent Based Model community has a rich and diverse ecosystem of libraries, platforms, and applications to help modelers develop rigorous simulations. Despite this robust and diverse ecosystem, the complexity of life from microbial…
Traditional data processing pipelines are typically static and handcrafted for specific tasks, limiting their adaptability to evolving requirements. While general-purpose agents and coding assistants can generate code for well-understood…