Related papers: Multi-type Galton-Watson processes with affinity-d…

We introduce AbBiBench (Antibody Binding Benchmarking), a benchmarking framework for antibody binding affinity maturation and design. Unlike previous strategies that evaluate antibodies in isolation, typically by comparing them to natural…

We are interested in the design of generative networks. The training of these mathematical structures is mostly performed with the help of adversarial (min-max) optimization problems. We propose a simple methodology for constructing such…

Reinforced Galton-Watson processes have been introduced in arxiv:2306.02476 as population models with non-overlapping generations, such that reproduction events along genealogical lines can be repeated at random. We investigate here some of…

Population genetic processes, such as the adaptation of a quantitative trait to directional selection, may occur on longer time scales than the sweep of a single advantageous mutation. To study such processes in finite populations,…

Stochastic models of sequential mutation acquisition are widely used to quantify cancer and bacterial evolution. Across manifold scenarios, recurrent research questions are: how many cells are there with $n$ alterations, and how long will…

Complex systems, in many different scientific sectors, show coarse-grain properties with simple growth laws with respect to fundamental microscopic algorithms. We propose a classification scheme of growth laws which includes human aging,…

The evolution model with parallel mutation-selection scheme is solved for the case when selection is accompanied by base substitutions, insertions, and deletions. The fitness is assumed to be either a single-peak function (i.e., having one…

Many mathematical models of evolution assume that all individuals experience the same environment. Here, we study the Moran process in heterogeneous environments. The population is of finite size with two competing types, which are exposed…

In this article, I develop a formal model of free will for complex systems based on emergent properties and adaptive selection. The model is based on a process ontology in which a free choice is a singular process that takes a system from…

We consider the problem of inference for the states and parameters of a continuous-time multitype branching process from partially observed time series data. Exact inference for this class of models, typically using sequential Monte Carlo,…

We consider branching random walks and contact processes on infinite, connected, locally finite graphs whose reproduction and infectivity rates across edges are inversely proportional to vertex degree. We show that when the ambient graph is…

Co-evolution of two coupled quasispecies is studied, motivated by the competition between viral evolution and adapting immune response. In this co-adaptive model, besides the classical error catastrophe for high virus mutation rates, a…

Scale-free configuration models are intimately connected to power law Galton-Watson trees. It is known that contact process epidemics can propagate on these trees and therefore these networks with arbitrarily small infection rate, and this…

Several genetic programming systems are created, each solving a different problem. In these systems, the median number of generations G needed to evolve a working program is measured. The behavior of G is observed as the difficulty of the…

Multitype branching processes are ideal for studying the population dynamics of stem cell populations undergoing mutation accumulation over the years following transplant. In such stochastic models, several quantities are of clinical…

We address the problem of parameter estimation in models of systems biology from noisy observations. The models we consider are characterized by simultaneous deterministic nonlinear differential equations whose parameters are either taken…

The inheritance of characteristics induced by the environment has often been opposed to the theory of evolution by natural selection. Yet, while evolution by natural selection requires new heritable traits to be produced and transmitted, it…

Investigating the emergence of a particular cell type is a recurring theme in models of growing cellular populations. The evolution of resistance to therapy is a classic example. Common questions are: when does the cell type first occur,…

In a previous paper the authors argued the case for incorporating ideas from innate immunity into articficial immune systems (AISs) and presented an outline for a conceptual framework for such systems. A number of key general properties…

This paper presents an analysis of the orientation selectivity properties of idealized models of complex cells in terms of affine quasi quadrature measures, which combine the responses of idealized models of simple cells in terms of affine…