Related papers: SBMLDiagrams: A python package to process and visu…
Authors of biomedical publications use gel images to report experimental results such as protein-protein interactions or protein expressions under different conditions. Gel images offer a concise way to communicate such findings, not all of…
Statistical Parametric Mapping (SPM) is an integrated set of methods for testing hypotheses about the brain's structure and function, using data from imaging devices. These methods are implemented in an open source software package, SPM,…
Cyber-physical systems (CPSs) integrate cyber and physical components and enable them to interact with each other to meet user needs. The needs for CPSs span rich application domains such as healthcare and medicine, smart home, smart…
Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer, and comparative-genomics…
In many safety-critical engineering domains, hazard analysis techniques are an essential part of requirement elicitation. Of the methods proposed for this task, STPA (System-Theoretic Process Analysis) represents a relatively recent…
Rule-based modeling is a powerful way to model kinetic interactions in biochemical systems. Rules enable a precise encoding of biochemical interactions at the resolution of sites within molecules, but obtaining an integrated global view…
Background: The inception of next generations sequencing technologies have exponentially increased the volume of biological sequence data. Protein sequences, being quoted as the `language of life', has been analyzed for a multitude of…
Large language models (LLMs) are powerful tools capable of handling diverse tasks. Comparing and selecting appropriate LLMs for specific tasks requires systematic evaluation methods, as models exhibit varying capabilities across different…
We introduce the BMRMM package implementing Bayesian inference for a class of Markov renewal mixed models which can characterize the stochastic dynamics of a collection of sequences, each comprising alternative instances of categorical…
Diagrams play a crucial role in visually conveying complex relationships and processes within business documentation. Despite recent advances in Vision-Language Models (VLMs) for various image understanding tasks, accurately identifying and…
Creating suitable diagrams for technical and scientific publications is challenging and time-consuming, as manual control over the layout is required to communicate information effectively. Existing diagramming tools usually allow modeling…
In this and the associated article 'BioBlender: Fast and Efficient All Atom Morphing of Proteins Using Blender Game Engine', by Zini et al., we present BioBlender, a complete instrument for the elaboration of motion (Zini et al.) and the…
Kernel methods have proven to be powerful techniques for pattern analysis and machine learning (ML) in a variety of domains. However, many of their original or advanced implementations remain in Matlab. With the incredible rise and adoption…
Software Defined Networking is currently revolutionizing computer networking by decoupling the network control (control plane) from the forwarding functions (data plane) enabling the network control to become directly programmable and the…
Systems biology is an inter-disciplinary field that studies systems of biological components at different scales, which may be molecules, cells or entire organism. In particular, systems biology methods are applied to understand functional…
We introduce VLM-Lens, a toolkit designed to enable systematic benchmarking, analysis, and interpretation of vision-language models (VLMs) by supporting the extraction of intermediate outputs from any layer during the forward pass of…
This guide introduces Large Language Models (LLM) as a highly versatile text analysis method within the social sciences. As LLMs are easy-to-use, cheap, fast, and applicable on a broad range of text analysis tasks, ranging from text…
Pre-trained language models (PLMs) have proven to be effective for document re-ranking task. However, they lack the ability to fully interpret the semantics of biomedical and health-care queries and often rely on simplistic patterns for…
Business Process Management (BPM) aims to improve organizational activities and their outcomes by managing the underlying processes. To achieve this, it is often necessary to consider information from various sources, including unstructured…
pyssam is a Python library for creating statistical shape and appearance models (SSAMs) for biological (and other) shapes such as bones, lungs or other organs. A point cloud best describing the anatomical 'landmarks' of the organ are…