相关论文: MI-Sim: A MATLAB Package for the Numerical Analysi…
Studying the growth and metabolism of microbes provides critical insights into their evolutionary adaptations to harsh environments, which are essential for microbial research and biotechnology applications. In this study, we developed an…
Network inference is a major field of interest for the ecological community, especially in light of the high cost and difficulty of manual observation, and easy availability of remote, long term monitoring data. In addition, comparing…
Interpretable insights from predictive models remain critical in bio-statistics, particularly when assessing causality, where classical statistical and machine learning methods often provide inherent clarity. While Neural Networks (NNs)…
Process mining provides methods to analyse event logs generated by information systems during the execution of processes. It thereby supports the design, validation, and execution of processes in domains ranging from healthcare, through…
A principle of evolutionary adaptation is applied to the Lotka--Volterra models, in particular to the food webs. We present a relatively simple computational algorithm of optimization with respect to a given criterion. This algorithm boils…
Biofilms are complex structures which are inhabited by numerous amount of different species of microorganisms. Due to their ubiquity, they influence human life on an everyday basis. It is therefore important to understand the interactions…
Summary: The DynaSig-ML (Dynamical Signatures - Machine Learning) Python package allows the efficient, user-friendly exploration of 3D dynamics-function relationships in biomolecules, using datasets of experimental measures from large…
Social behavior is crucial for survival in many animal species, and a heavily investigated research subject. Current analysis methods generally rely on measuring animal interaction time or annotating predefined behaviors. However, these…
Ecological networks describe the interactions between different species, informing us of how they rely on one another for food, pollination and survival. If a species in an ecosystem is under threat of extinction, it can affect other…
16S-ribosomal sequencing and other metagonomic techniques provide snapshots of microbial communities, revealing phylogeny and the abundances of microbial populations across diverse ecosystems. While changes in microbial community structure…
Phytoplankton is the basis of marine food webs, driving both ecological processes and global biogeochemical cycles. Despite their ecological and climatic significance, accurately simulating phytoplankton dynamics remains a major challenge…
Motif discovery is a powerful and insightful method to quantify network structures and explore their function. As a case study, we present a comprehensive analysis of regulatory motifs in the connectome of the model organism Caenorhabditis…
Soil is a complex, dynamic material, with physical properties that depend on its biological content. We propose a cellular automaton model for self-organizing soil structure, where soil aggregates and serves as food for microbial species.…
Biological cortical networks are potentially fully recurrent networks without any distinct output layer, where recognition may instead rely on the distribution of activity across its neurons. Because such biological networks can have rich…
Cell cultures exhibit rich and complex behaviors driven by dynamic metabolic interactions among cells. In this work, we present a model that captures these interactions through a framework inspired by statistical mechanics. Using Monte…
We introduce the Dynamic Influence Network (DIN), a novel visual analytics technique for representing and analyzing rule-based models of protein-protein interaction networks. Rule-based modeling has proved instrumental in developing…
This work presents an omics-driven modeling pipeline that integrates machine-learning tools to facilitate the dynamic modeling of multiscale biological systems. Random forests and permutation feature importance are proposed to mine omics…
Network estimation and variable selection have been extensively studied in the statistical literature, but only recently have those two challenges been addressed simultaneously. In this paper, we seek to develop a novel method to…
We introduce and test the System Dynamics Bot, a computer program leveraging a large language model to automate the creation of causal loop diagrams from textual data. To evaluate its performance, we ensembled two distinct databases. The…
We start by discussing the link between ecosystem simulators and general AI. Then we present the open-source ecosystem simulator Ecotwin, which is based on the game engine Unity and operates on ecosystems containing inanimate objects like…