Related papers: Universality and predictability in molecular quant…
Biological evolution depends on the passing down to subsequent generations of genetic information encoding beneficial traits, and on the removal of unfit individuals by a selection mechanism. However, selection acts on phenotypes, and is…
Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of biological networks is believed to be their…
In many scientific and data-driven applications, machine learning models are increasingly used as measurement instruments, rather than merely as predictors of predefined labels. When the measurement function is learned from data, the…
A general population evolution model is considered. Any individual of the population is characterized by its score. Certain general conditions are assumed concerning the number of the individuals and their scores. Asymptotic theorems are…
Introduction: Computational modeling has rapidly advanced over the last decades, especially to predict molecular properties for chemistry, material science and drug design. Recently, machine learning techniques have emerged as a powerful…
This paper characterizes the inherent power of evolutionary algorithms. This power depends on the computational properties of the genetic encoding. With some encodings, two parents recombined with a simple crossover operator can sample from…
Numerous concise models such as preferential attachment have been put forward to reveal the evolution mechanisms of real-world networks, which show that real-world networks are usually jointly driven by a hybrid mechanism of multiplex…
Molecular modeling is an important topic in drug discovery. Decades of research have led to the development of high quality scalable molecular force fields. In this paper, we show that neural networks can be used to train a universal…
The problem of the rate and mechanisms of biological evolution was considered. It was shown that species could not be formed due to undirected mutations in characteristic times of about one million years. A mechanism of deterministic…
In the first part of this two-part article, we have introduced and analyzed a multidimensional model, called the 'general tension-reduction' (GTR) model, able to describe general quantum-like measurements with an arbitrary number of…
The evolution of cooperation often depends upon population structure, yet nearly all models of cooperation implicitly assume that this structure remains static. This is a simplifying assumption, because most organisms possess genetic traits…
A set of molecular descriptors whose length is independent of molecular size is developed for machine learning models that target thermodynamic and electronic properties of molecules. These features are evaluated by monitoring performance…
The study of common heritability, or co-heritability, among multiple traits has been widely established in quantitative and molecular genetics. However, in bacteria, genome-based estimation of heritability has only been considered very…
Genetic programming and artificial life systems commonly employ tag-matching schemes to determine interactions between model components. However, the implications of criteria used to determine affinity between tags with respect to…
Mutations in a microbial population can increase the frequency of a genotype not only by increasing its exponential growth rate, but also by decreasing its lag time or adjusting the yield (resource efficiency). The contribution of multiple…
Quantitatively predicting phenotype variables by the expression changes in a set of candidate genes is of great interest in molecular biology but it is also a challenging task for several reasons. First, the collected biological…
Ecological and evolutionary processes show various population dynamics depending on internal interactions and environmental changes. While crucial in predicting biological processes, discovering general relations for such nonlinear dynamics…
The unprecedented prowess of measurement techniques provides a detailed, multi-scale look into the depths of living systems. Understanding these avalanches of high-dimensional data -- by distilling underlying principles and mechanisms --…
Molecular assembly offers a promising path to detect life beyond Earth, while minimizing assumptions based on terrestrial life. As mass spectrometers will be central to upcoming Solar System missions, predicting molecular assembly from…
The classical infinitesimal model is a simple and robust model for the inheritance of quantitative traits. In this model, a quantitative trait is expressed as the sum of a genetic and a non-genetic (environmental) component and the genetic…