Related papers: Phenotypic landscape inference reveals multiple ev…
We consider evolution of a large population, where fitness of each organism is defined by many phenotypical traits. These traits result from expression of many genes. We propose a new model of gene regulation, where gene expression is…
The traditional paradigm of applying deep learning -- collect, annotate and train on data -- is not applicable to image-based plant phenotyping as almost 400,000 different plant species exists. Data costs include growing physical samples,…
Fisher's geometric model was originally introduced to argue that complex adaptations must occur in small steps because of pleiotropic constraints. When supplemented with the assumption of additivity of mutational effects on phenotypic…
Facial recognition using deep convolutional neural networks relies on the availability of large datasets of face images. Many examples of identities are needed, and for each identity, a large variety of images are needed in order for the…
The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…
Quantitative models of associative learning that explain the behavior of real animals with high precision have turned out very difficult to construct. We do this in the context of the dynamics of the thermal preference of C. elegans. For…
In general, cellular phenotypes, as measured by concentrations of cellular components, involve large degrees of freedom. However, recent measurement has demonstrated that phenotypic changes resulting from adaptation and evolution in…
Let $\mathbb{F}$ be a field and let $M_2(\mathbb{F})$ be the algebra of $2\times 2$ matrices endowed with an involution of the first kind. We study the image of multilinear $*$-polynomials evaluated on $M_2(\mathbb{F})$. For the transpose…
Recently it has been discovered---contrary to expectations of physicists as well as biologists---that the energy transport during photosynthesis, from the chlorophyll pigment that captures the photon to the reaction centre where glucose is…
Methods that generate networks sharing a given degree distribution and global clustering can induce changes in structural properties other than that controlled for. Diversity in structural properties, in turn, can affect the outcomes of…
Plants frequently contain numerous organs, organized in 3D branching systems defining the plant's architecture. Reconstructing the architecture of plants from unstructured observations is challenging because of self-occlusion and spatial…
Space-saving design is a requirement that is encountered in biological systems and the development of modern technological devices alike. Many living organisms dynamically pack their polymer chains, filaments or membranes inside of…
Phylogenetic mixture models are statistical models of character evolution allowing for heterogeneity. Each of the classes in some unknown partition of the characters may evolve by different processes, or even along different trees. The…
Bayesian phylogenetics is vital for understanding evolutionary dynamics, and requires accurate and efficient approximation of posterior distributions over trees. In this work, we develop a variational Bayesian approach for ultrametric…
Evolutionary adaptation is the process that increases the fit of a population to the fitness landscape it inhabits. As a consequence, evolutionary dynamics is shaped, constrained, and channeled, by that fitness landscape. Much work has been…
The field of landscape genomics aims to infer how landscape features affect gene flow across space. Most landscape genomic frameworks assume the isolation-by-distance and isolation-by-resistance hypotheses, which propose that genetic…
Deep learning techniques have been successfully deployed for automating plant stress identification and quantification. In recent years, there is a growing push towards training models that are interpretable -i.e. that justify their…
Most theories of evolutionary diversification are based on equilibrium assumptions: they are either based on optimality arguments involving static fitness landscapes, or they assume that populations first evolve to an equilibrium state…
Many biological systems regulate phenotypic heterogeneity as a fitness-maximising strategy in uncertain and dynamic environments. Analysis of such strategies is typically confined both to a discrete set of environmental conditions, and to a…
A variety of selection-mutation models for DNA (or RNA) sequences, well known in molecular evolution, can be translated into a model of coupled Ising quantum chains. This correspondence is used to investigate the genetic variability and…