Related papers: SimOmics: A Simulation Toolkit for Multivariate an…
Functional data analysis has become a tool of interest in applied areas such as economics, medicine, and chemistry. Among the techniques developed in recent literature, functional semiparametric regression stands out for its balance between…
As genomic scale datasets motivate research on species tree inference, simulators of the multispecies coalescent (MSC) process are essential for the testing and evaluation of new inference methods. However, the simulators themselves must be…
MPAgenomics, standing for multi-patients analysis (MPA) of genomic markers, is an R-package devoted to: (i) efficient segmentation, and (ii) genomic marker selection from multi-patient copy number and SNP data profiles. It provides wrappers…
Multiplex tissue immunostaining is a technology of growing relevance as it can capture in situ the complex interactions existing between the elements of the tumor microenvironment. The existence and availability of large, annotated image…
Motivation: Accurate detection of sequence similarity and homologous recombination are essential parts of many evolutionary analyses. Results: We have developed SimPlot++, an open-source multiplatform application implemented in Python,…
MiMiC is a framework for modeling large-scale chemical processes that require treatment at multiple resolutions. It does not aim to implement single-handedly all methods required to treat individual subsystems, but instead, it relegates…
Simulating physical systems is a core component of scientific computing, encompassing a wide range of physical domains and applications. Recently, there has been a surge in data-driven methods to complement traditional numerical simulations…
In systems biology, it is common to measure biochemical entities at different levels of the same biological system. One of the central problems for the data fusion of such data sets is the heterogeneity of the data. This thesis discusses…
Recommender systems play a central role in numerous real-life applications, yet evaluating their performance remains a significant challenge due to the gap between offline metrics and online behaviors. Given the scarcity and limits (e.g.,…
The BeatBox simulation environment combines flexible script language user interface with the robust computational tools, in order to setup cardiac electrophysiology in-silico experiments without re-coding at low-level, so that cell…
This letter introduced a new R package 'coexist' which can perform species coexistence simulation and analysis. The package was initially developed for understanding the role of different combinations of varying species growth rates,…
Prescriptive Process Monitoring (PresPM) is an emerging area within Process Mining, focused on optimizing processes through real-time interventions for effective decision-making. PresPM holds significant promise for organizations seeking…
As perception models continue to develop, the need for large-scale datasets increases. However, data annotation remains far too expensive to effectively scale and meet the demand. Synthetic datasets provide a solution to boost model…
This article introduces the pammtools package, which facilitates data transformation, estimation and interpretation of Piece-wise exponential Additive Mixed Models. A special focus is on time-varying effects and cumulative effects of…
Simulation is a foundational tool for the analysis and testing of cyber-physical systems (CPS), underpinning activities such as algorithm development, runtime monitoring, and system verification. As CPS grow in complexity and scale,…
Computer-assisted surgical (CAS) systems enhance surgical execution and outcomes by providing advanced support to surgeons. These systems often rely on deep learning models trained on complex, challenging-to-annotate data. While synthetic…
Visualization of multidimensional, categorical data is a common challenge across scientific areas and, in particular, the life sciences. The goal is to create a comprehensive overview of the underlying data which allows to assess multiple…
We present the concept of a unified graphical environment for expressing the semantics of control systems. The graphical control system design environment in Simulink already allows engineers to insert a variety of assertions aimed the…
Ordinary differential equation models facilitate the understanding of cellular signal transduction and other biological processes. However, for large and comprehensive models, the computational cost of simulating or calibrating can be…
Numerical simulation codes are very common tools to study complex phenomena, but they are often time-consuming and considered as black boxes. For some statistical studies (e.g. asset management, sensitivity analysis) or optimization…