11 papers · ranked by Valyu relevance
Yuji Masutomi, Kazuhiko Kobayashi
The photosynthesis–transpiration–stomatal conductance (A_n_–E–g_s_) model framework is widely used for estimating photosynthesis, transpiration, and stomatal conductance in plants. The model equations are solved by numerical iteration, and the converged model values are deemed the solution. However, there has been no…
Philipp Städter, Yannik Schälte, Leonard Schmiester, Jan Hasenauer + 1 more
Ordinary differential equation (ODE) models are a key tool to understand complex mechanisms in systems biology. These models are studied using various approaches, including stability and bifurcation analysis, but most frequently by numerical simulations. The number of required simulations is often large, e.g., when…
Monika Justyna Nir, Sarangam Majumdar
In a closed eco-system, there are only two types of animals: the predator and the prey. They form a simple food-chain where the predator species hunts the prey species, while the prey grazes vegetation. The size of the two populations can be described by a simple system of two nonlinear first order differential…
Alexandr N. Tetearing
Numerical model of population behaviour under conditions of full-fed existence of mortal persons in the personal areas, simulated with use the function of age distribution of birth rate in the form of normal (gaussian) distribution. Graphs of historical changes in the function of age distribution of population.
Nikolai Baudis, Pierre Barbera, Sebastian Graf, Sarah Lutteropp + 3 more
In the context of a master level programming practical at the computer science department of the Karlsruhe Institute of Technology, we developed and make available two independent and highly optimized open-source implementations for the pair-wise statistical alignment model, also known as TKF91, that was developed by…
Mohammed Baragilly, Brian H Willis
Meta-analysis may be used to summarise a test’s accuracy. Often the sensitivity and specificity are the measures of interest and as these are correlated a bivariate random effects model is commonly used to fit the data. This model has five parameters and it may be optimised using a Newton-Raphson based algorithm…
Takashi Sato
Omics data and single-cell analyses have recently produced many biological informatics. These require simple, fast, and flexible numerical/analytical methods such as ordinary differential equations. However, formulating these equations and their computational processes can be expensive and imprecise for simulating…
Mina Alizadeh, Yohan Chatelain, Gregory Kiar, Tristan Glatard
Network neuroscience provides a powerful framework for studying the mechanisms underlying brain-related diseases. As analyses become increasingly computational, ensuring their numerical reliability has become a critical challenge. Small perturbations introduced during processing can propagate through complex pipelines…
Ming Yang, Louis Z. Yang
What values of relative numerical tolerance should be chosen in simulation of a deterministic model of a biochemical reaction is unclear, which impairs the modeling effort since the simulation outcomes of a model may depend on the relative numerical tolerance values. In an attempt to provide a guideline to selecting…
Changin Oh, Kathleen P. Wilkie
We present the Toroidal Search Algorithm (TSA), a novel population-based metaheuristic optimization method inspired by the topology of a torus. Conventional metaheuristics frequently suffer from boundary stagnation, a phenomenon that severely degrades performance in bounded and high-dimensional search spaces. TSA…
Mercedes Bengochea, Jacobo D. Sitt, Thomas Preat, Veronique Izard + 2 more
Sensitivity to numbers is a crucial and evolutionarily conserved cognitive ability. The lack of experimental models amenable to systematic genetic and neural manipulation has precluded discovering circuits required for numerical cognition. Here, we demonstrate that in a two-choice task Drosophila fruit flies…