Related papers: BioStatFlow -Statistical Analysis Workflow for "Om…
Streamflow, as a natural phenomenon, is continuous in time and so are the meteorological variables which influence its variability. In practice, it can be of interest to forecast the whole flow curve instead of points (daily or hourly). To…
Swim extends the actor model to support applications composed of linked distributed actors that continuously analyze boundless streams of events from millions of sources, to respond in-sync with the real-world. Swim builds a running…
Workflow support typically focuses on single simulation experiments. This is also the case for simulation based on finite element methods. If entire simulation studies shall be supported, flexible means for intertwining revising the model,…
The MAterials Simulation Toolkit (MAST) is a workflow manager and post-processing tool for ab initio defect and diffusion workflows. MAST codifies research knowledge and best practices for such workflows, and allows for the generation and…
13C-based metabolic flux analysis (13C-MFA) is a cornerstone of quantitative systems biology, yet its increasing data complexity and methodological diversity place high demands on simulation software. We introduce 13CFLUX(v3), a…
In recent years there has been widespread concern in the scientific community over a reproducibility crisis. Among the major causes that have been identified is statistical: In many scientific research the statistical analysis (including…
Flow matching is a scalable generative framework for characterizing continuous normalizing flows with wide-range applications. However, current state-of-the-art methods are not well-suited for modeling dynamical systems, as they construct…
The concept of "tidy data" offers a powerful framework for structuring data to ease manipulation, modeling and visualization. However, most R functions, both those built-in and those found in third-party packages, produce output that is not…
RooStats is a project to create advanced statistical tools required for the analysis of LHC data, with emphasis on discoveries, confidence intervals, and combined measurements. The idea is to provide the major statistical techniques as a…
Current automated machine learning (ML) tools are model-centric, focusing on model selection and parameter optimization. However, the majority of the time in data analysis is devoted to data cleaning and wrangling, for which limited tools…
Metabolic flux balance analyses are a standard tool in analysing metabolic reaction rates compatible with measurements, steady-state and the metabolic reaction network stoichiometry. Flux analysis methods commonly place unrealistic…
Histograms provide a powerful means of summarizing large data sets by representing their distribution in a compact, binned form. The HistogramTools R package enhances R built-in histogram functionality, offering advanced methods for…
The OSTSC package is a powerful oversampling approach for classifying univariant, but multinomial time series data in R. This article provides a brief overview of the oversampling methodology implemented by the package. A tutorial of the…
The analysis of biological networks is characterized by the definition of precise linear constraints used to cumulatively reduce the solution space of the computed states of a multi-omic (for instance metabolic, transcriptomic and…
Classification is one of the most important supervised machine learning tasks. During the training of a classification model, the training instances are fed to the model multiple times (during multiple epochs) in order to iteratively…
Methods: We have developed a software suite (DataSet Tracker) for real-time analysis designed to run on computers, smartphones, and smart glasses hardware and suitable for resource-constrained, on-the-fly computing in microscopes without…
Purpose: In this work, we present a collaboration to create a validation dataset of pathologist annotations for algorithms that process whole slide images (WSIs). We focus on data collection and evaluation of algorithm performance in the…
Inferring trajectories from longitudinal spatially-resolved omics data is fundamental to understanding the dynamics of structural and functional tissue changes in development, regeneration and repair, disease progression, and response to…
Information flow analysis has largely ignored the setting where the analyst has neither control over nor a complete model of the analyzed system. We formalize such limited information flow analyses and study an instance of it: detecting the…
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…