相关论文: Comment of Global dynamics of biological systems
The development of multicellular organisms entails a deep connection between time-dependent biochemical processes taking place at the subcellular level, and the resulting macroscopic phenotypes that arise in populations of up to trillions…
Due to the dynamic nature of biological systems, biological networks underlying temporal process such as the development of {\it Drosophila melanogaster} can exhibit significant topological changes to facilitate dynamic regulatory…
Generative models derived from large protein sequence alignments define complex fitness landscapes, but their utility for accurately modeling non-equilibrium evolutionary dynamics remains unclear. In this work, we perform a rigorous…
We have developed a novel Monte Carlo method for simulating the dynamical evolution of stellar systems in arbitrary geometry. The orbits of stars are followed in a smooth potential represented by a basis-set expansion and perturbed after…
Time series analysis has proven to be a powerful method to characterize several phenomena in biology, neuroscience and economics, and to understand some of their underlying dynamical features. Despite a plethora of methods have been…
Switching dynamical systems are an expressive model class for the analysis of time-series data. As in many fields within the natural and engineering sciences, the systems under study typically evolve continuously in time, it is natural to…
Precise temporal coordination of gene expression is crucial for many developmental processes. One central question in developmental biology is how such coordinated expression patterns are robustly controlled. During embryonic development of…
State-of-the-art methods for data-driven modelling of non-linear dynamical systems typically involve interactions with an expert user. In order to partially automate the process of modelling physical systems from data, many EA-based…
Mesoscopic bio-systems typically evolve towards functionally important target states, such as cell-cycle checkpoints or decision boundaries for the release of specific behaviors. For the data-driven inference of the underlying directional…
Many real-world systems studied are governed by complex, nonlinear dynamics. By modeling these dynamics, we can gain insight into how these systems work, make predictions about how they will behave, and develop strategies for controlling…
Even the simplest of animals exhibit behavioral sequences with complex temporal dynamics. Prominent amongst the proposed organizing principles for these dynamics has been the idea of a hierarchy, wherein the movements an animal makes can be…
The past decade has seen a revived interest in the unavoidable or intrinsic noise in biochemical and genetic networks arising from the finite copy number of the participating species. That is, rather than modeling regulatory networks in…
Motivation: Microarray experiments result in large scale data sets that require extensive mining and refining to extract useful information. We have been developing an efficient novel algorithm for nonmetric multidimensional scaling (nMDS)…
This article is a presentation of specific recent results describing scaling limits of individual-based models. Thanks to them, we wish to relate the time-scales typical of demographic dynamics and natural selection to the parameters of the…
Probabilistic approaches for handling count-valued time sequences have attracted amounts of research attentions because their ability to infer explainable latent structures and to estimate uncertainties, and thus are especially suitable for…
1. Temporal trends in species distributions are necessary for monitoring changes in biodiversity, which aids policymakers and conservationists in making informed decisions. Dynamic species distribution models are often fitted to ecological…
In the context of self-assembly, where complex structures can be assembled from smaller units, it is desirable to devise strategies towards disassembly and reassembly processes that reuse the constituent parts. A non-reciprocal multifarious…
Traditional spatio-temporal models for areal data typically begin with spatial structure imposed at the level of random effects and later extend to include temporal dynamics. We propose an alternative hierarchical modeling framework that…
N-body simulations provide most of our insight into the structure and evolution of galaxies, but our analyses of these are often heuristic and from simple statistics. We propose a method that discovers the dynamics in space and time…
We formulate a nonlinear synergistic theory of coevolutionary systems, disentangling and explaining dynamic complexity in terms of fundamental processes for optimised data analysis and dynamic model design: Dynamic Source Analysis (DSA).…