Related papers: Phyllotaxis, a model
We define a new balance index for rooted phylogenetic trees based on the symmetry of the evolutive history of every set of 4 leaves. This index makes sense for multifurcating trees and it can be computed in time linear in the number of…
Inferring predictive maps between multiple input and multiple output variables or tasks has innumerable applications in data science. Multi-task learning attempts to learn the maps to several output tasks simultaneously with information…
The emergence of large scale structures in biological systems, and in particular the formation of lines of hierarchy, is observed in many scales, from collections of cells to groups of insects to herds of animals. Motivated by phenomena in…
What are the general principles that allow proper growth of a tissue or an organ? A growing leaf is an example of such a system: it increases its area by orders of magnitude, maintaining a proper (usually flat) shape. How can this be…
Simple stochastic models for phylogenetic trees on species have been well studied. But much paleontology data concerns time series or trees on higher-order taxa, and any broad picture of relationships between extant groups requires use of…
The displayed tree phylogenetic network model is shown to sit as a natural submodel of the graphical model associated to a directed acyclic graph (DAG). This representation allows to derive a number of results about the displayed tree…
Phylogenetic networks provide a means of describing the evolutionary history of sets of species believed to have undergone hybridization or gene flow during their evolution. The mutation process for a set of such species can be modeled as a…
Gene regulatory networks arise in all living cells, allowing the control of gene expression patterns. The study of their topology has revealed that certain subgraphs of interactions or "motifs" appear at anomalously high frequencies. We ask…
We model a plant leaf by using two-dimensional domain walls with internal structures. Such domain walls can be found as soliton solutions in field theory describing magnetic materials. The radiation scattered by such domain walls behaves…
A common metaphor for describing development is a rugged "epigenetic landscape" where cell fates are represented as attracting valleys resulting from a complex regulatory network. Here, we introduce a framework for explicitly constructing…
Joint species distribution models are popular in ecology for modeling covariate effects on species occurrence, while characterizing cross-species dependence. Data consist of multivariate binary indicators of the occurrences of different…
Recent experiments have exploited elastic instabilities in membranes to create complex patterns. However, the rational design of such structures poses many challenges, as they are products of nonlinear elastic behavior. We pose a simple…
We discuss the formation of graded morphogen profiles in a cell layer by nonlinear transport phenomena, important for patterning developing organisms. We focus on a process termed transcytosis, where morphogen transport results from binding…
Nonreciprocal interactions violating Newton's third law are common in a plethora of nonequilibrium situations ranging from predator-prey systems to the swarming of birds and effective colloidal interactions under flow. While many recent…
Development combines three basic processes asymmetric --- cell division, signaling and gene regulation --- in a multitude of ways to create an overwhelming diversity of multicellular life-forms. Here, we attempt to chart this diversity…
We consider an evolving network of a fixed number of nodes. The allocation of edges is a dynamical stochastic process inspired by biological reproduction dynamics, namely by deleting and duplicating existing nodes and their edges. The…
Signal transduction networks can form highly interconnected systems within cells due to network crosstalk, the sharing of input signals between multiple downstream responses. To better understand the evolutionary design principles…
In an upward planar 2-slope drawing of a digraph, edges are drawn as straight-line segments in the upward direction without crossings using only two different slopes. We investigate whether a given upward planar digraph admits such a…
Flocks of birds and schools of fish are familiar examples of spatial patterns formed by living organisms. In contrast to the patterns on the skins of, say, zebra and giraffe, the patterns of our interest are {\it transient} although…
Construction of phylogenetic trees has traditionally focused on binary trees where all species appear on leaves, a problem for which numerous efficient solutions have been developed. Certain application domains though, such as viral…