12 papers · ranked by Valyu relevance
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…
Andrea Polo-Rodríguez, David R. Penas, Julio R. Banga
Parameter estimation is a central challenge in systems biology, particularly for large dynamic models described by nonlinear ordinary differential equations (ODEs). These global optimization problems exhibit landscapes which are topologically heterogeneous, often exhibiting a pathological mixture of stiff, smooth…
Dominic M Dunstan, Mark P Richardson, Jonathan E Fieldsend, Marc Goodfellow
Neural mass models (NMMs) are often used to help understand the circuitry that underpins observed brain dynamics in basic and clinical research. A key step is to fuse models with data so that model parameter values can be inferred for a given data set—a process called model fitting or model calibration. This can shed…
Máté Mohácsi, Márk Patrik Török, Sára Sáray, Luca Tar + 1 more
Finding optimal parameters for detailed neuronal models is a ubiquitous challenge in neuroscientific research. Recently, manual model tuning has been replaced by automated parameter search using a variety of different tools and methods. However, using most of these software tools and choosing the most appropriate…
Husanbir Singh Pannu, Douglas B. Kell
We analyse the effectiveness of differential evolution hyperparameters in large-scale search problems, i.e. those with very many variables or vector elements, using a novel objective function that is easily calculated from the vector/string itself. The objective function is simply the sum of the differences between…
Prasad U. Bandodkar, Razeen R. Shaikh, Gregory T. Reeves
Model development is essential to gain a mathematical understanding of the underlying phenomena in systems biology. In most models, it is typically hard to estimate the values of the biophysical/phenomenological parameters that characterize the model. The parameters are estimated by minimizing a function that reduces a…
Billy Tchounke, Leopoldo Sanchez, Joseph Martin Bell, David Cros
Genomic selection (GS) is the most effective method of marker-assisted selection for the genetic improvement of complex traits in plants and animals. Optimization approaches could be used in conjunction with GS to further increase its efficiency and to limit inbreeding, which can increase faster with GS. Mate selection…
Harini Narayanan, Joshua Hinckley, Rachel Barry, Brendan Dang + 4 more
Optimizing operational conditions for complex biological systems used in life sciences research and biotechnology is an arduous task. Here, we have applied a Bayesian Optimization-based iterative framework for experimental design to accelerate cell culture media development for two applications. First, we show this…
Jaehoon Shin, Jee Hang Lee, Sang Wan Lee
Human reward learning is constrained by environmental structure. Stable environments facilitate reward prediction but limit learning experiences^1–8^, while uncertain environments hinder predictability and learnability^9–12^. We propose a novel framework extending these boundaries through “meta-prediction” – predicting…
Olena Doroshenko
Pathfinding in complex topographies poses a challenge with applications extending from urban planning to autonomous navigation. While numerous algorithms offer potential solutions, their comparative efficiency and reliability when confronted with nonlinear terrains remain to be systematically evaluated. This study…
Lillian T. Tatka, Lucian P. Smith, Herbert M. Sauro
Evolutionary algorithms, a class of optimization techniques inspired by biological evolution, have emerged as powerful tools for the optimization of complex systems, including the evolution of mass-action chemical reaction networks. This work explores the application of evolutionary algorithms in this domain…
Amir Pandi, Christoph Diehl, Ali Yazdizadeh Kharrazi, Léon Faure + 10 more
The study, engineering and application of biological networks require practical and efficient approaches. Current optimization efforts of these systems are often limited by wet lab labor and cost, as well as the lack of convenient, easily adoptable computational tools. Aimed at democratization and standardization, we…