Related papers: Addressing missing context in regulatory variation…
A class of evolution variational inequalities (EVIs), which comprises ordinary differential equations (ODEs) coupled with variational inequalities (VIs) associated with time-varying set-valued mappings, is proposed in this paper. We first…
We introduce and experimentally demonstrate the utility of tag-based genetic regulation, a new genetic programming (GP) technique that allows programs to dynamically adjust which code modules to express. Tags are evolvable labels that…
Dynamic software adaptability is one of the central features leveraged by autonomic computing. However, developing software that changes its behavior at run time adapting to the operational conditions is a challenging task. Several…
Eco-evolutionary frameworks can explain certain features of communities in which ecological and evolutionary processes occur over comparable timescales. Here, we investigate whether an evolutionary dynamics may interact with the spatial…
The environment in which a population evolves can have a crucial impact on selection. We study evolutionary dynamics in finite populations of fixed size in a changing environment. The population dynamics are driven by birth and death…
We study genetic networks that produce many species of non-coding RNA molecules that are present at a moderate density, as typically exists in the cell. The associations of the many species of these RNA are modeled physically, taking into…
Biological phenotypes are products of complex evolutionary processes in which selective forces influence multiple biological trait measurements in unknown ways. Phylogenetic factor analysis disentangles these relationships across the…
We study an abstract model for the co-evolution between mutating viruses and the adaptive immune system. In sequence space, these two populations are localized around transiently dominant strains. Delocalization or error thresholds exhibit…
Predicting the adaptation of populations to a changing environment is crucial to assess the impact of human activities on biodiversity. Many theoretical studies have tackled this issue by modeling the evolution of quantitative traits…
A key challenge in reward learning from human input is that desired agent behavior often changes based on context. For example, a robot must adapt to avoid a stove once it becomes hot. We observe that while high-level preferences (e.g.,…
Living organisms must respond to environmental changes. Generally, accurate and rapid responses are provided by simple, unidirectional networks that connect inputs with outputs. Besides accuracy and speed, biological responses should also…
We consider the problem of fitting a reinforcement learning (RL) model to some given behavioral data under a multi-armed bandit environment. These models have received much attention in recent years for characterizing human and animal…
One of the most intriguing questions in evolution is how organisms exhibit suitable phenotypic variation to rapidly adapt in novel selective environments which is crucial for evolvability. Recent work showed that when selective environments…
A macroscopic theory for describing cellular states during steady-growth is presented, which is based on the consistency between cellular growth and molecular replication, as well as the robustness of phenotypes against perturbations.…
Numerous traits under migration-selection balance are shown to exhibit complex patterns of genetic architecture with large variance in effect sizes. However, the conditions under which such genetic architectures are stable have yet to be…
Context-dependent nature of biological phenomena are well documented in every branch of biology. While there have been few previous attempts to (implicitly) model various facets of biological context-dependence, a formal and general…
We consider the task of detecting regulatory elements in the human genome directly from raw DNA. Past work has focused on small snippets of DNA, making it difficult to model long-distance dependencies that arise from DNA's 3-dimensional…
Significant fraction (98.5% in humans) of most animal genomes is non- coding dark matter. Its largely unknown function (1-5) is related to programming (rather than to spontaneous mutations) of accurate adaptation to rapidly changing…
Adaptive populations such as those in financial markets and distributed control can be modeled by the Minority Game. We consider how their dynamics depends on the agents' initial preferences of strategies, when the agents use linear or…
For robots to handle the numerous factors that can affect them in the real world, they must adapt to changes and unexpected events. Evolutionary robotics tries to solve some of these issues by automatically optimizing a robot for a specific…