Related papers: PhysiBoSS-Models: A database for multiscale models
Multimodal Foundation Models (FMs) offer a path to learn general-purpose representations from heterogeneous ecological data, easily transferable to downstream tasks. However, practical biodiversity modelling remains fragmented; separate…
An agent-based model (ABM) is a computational model in which the local interactions of autonomous agents with each other and with their environment give rise to global properties within a given domain. As the detail and complexity of these…
In medical imaging, there is a growing interest to provide real-time images with good quality for large anatomical structures. To cope with this issue, we developed a library that allows to replace, for some specific clinical applications,…
Simflowny is an open platform which automatically generates parallel code of scientific dynamical models for different simulation frameworks. Here we present major upgrades on this software to support an extended set of families of models,…
Existing biomedical benchmarks do not provide end-to-end infrastructure for training, evaluation, and inference of models that integrate multimodal biological data and a broad range of machine learning tasks in therapeutics. We present…
To facilitate flexible and efficient structural bioinformatics analyses, new functionality for three-dimensional structure processing and analysis has been introduced into PyCogent -- a popular feature-rich framework for sequence-based…
Model selection methods are used in different scientific contexts to represent a characteristic data set in terms of a reduced number of parameters. Apparently, these methods have not found their way into the literature on multibody systems…
Skin contraction is an important biophysical process that takes place during and after the recovery of deep tissue injury. This process is mainly caused by fibroblasts (skin cells) and myofibroblasts (differentiated fibroblasts) that exert…
Synthetic data has emerged as a promising source for 3D human research as it offers low-cost access to large-scale human datasets. To advance the diversity and annotation quality of human models, we introduce a new synthetic dataset,…
In the past few decades, the life sciences have experienced an unprecedented accumulation of data, ranging from genomic sequences and proteomic profiles to heavy-content imaging, clinical assays, and commercial biological products for…
To model dense crowds, the usual recourse to oversimplified (circular) pedestrian shapes and contact forces shows limitations. To help modellers overcome these limitations, we propose an open-source numerical tool. It consists of a Python…
We present a new approach to the simulation and analysis of immune system behavior. The simulations that can be done with our software package called SIMMUNE are based on immunological data that describe the behavior of immune system agents…
Genetic interaction can be defined as a deviation of the phenotypic quantitative effect of a double gene mutation from the effect predicted from single mutations using a simple (e.g., multiplicative or linear additive) statistical model.…
A distinguishing feature of a multicellular living system is that it operates at various scales, from the intracellular to organismal. Very little is known at present on how tissue level properties are related to cell and subcellular…
As cities evolve toward more complex and multimodal transportation systems, the need for human-centered multi-agent simulation tools has never been more urgent. Yet most existing platforms remain limited - they often separate different…
The dynamics and processes of urban morphogenesis are a central issue regarding a long-term sustainability of urban systems. They however imply stakeholders and parameters at multiple temporal and spatial scales simultaneously, leading to…
Khiops is an open source machine learning tool designed for mining large multi-table databases. Khiops is based on a unique Bayesian approach that has attracted academic interest with more than 20 publications on topics such as variable…
Computer simulations have become an important tool across the biomedical sciences and beyond. For many important problems several different models or hypotheses exist and choosing which one best describes reality or observed data is not…
Proteins are polymers of amino acids. These macromolecules are synthesized by intracellular machines called ribosomes. Although the experimental investigation of protein synthesis has been a traditional area of research in molecular cell…
Neural MMO is a computationally accessible research platform that combines large agent populations, long time horizons, open-ended tasks, and modular game systems. Existing environments feature subsets of these properties, but Neural MMO is…