Related papers: Evolutionary Advantage of Diversity-Generating Ret…
One important feature of complex systems are problem domains that have many local minima and substructure. Biological systems manage these local minima by switching between different subsystems depending on their environmental or…
We study a genetic regulatory network model developed to demonstrate that genetic robustness can evolve through stabilizing selection for optimal phenotypes. We report preliminary results on whether such selection could result in a…
Dynamic magnetic resonance image reconstruction from incomplete k-space data has generated great research interest due to its capability to reduce scan time. Never-theless, the reconstruction problem is still challenging due to its…
Reinforcement Learning with Verifiable Rewards (RLVR) has become the dominant paradigm for advanced reasoning in Large Language Models (LLMs), but rollout samples are expensive to obtain, making sample efficiency a critical bottleneck. A…
We propose Score-based Relaxation-guided Generation (SRG), a generative framework based on an approximate formulation of relaxation-guided stochastic differential equations (SDEs) for mixed-integer linear programming. SRG employs a…
Morphogenesis is central to biology but remains largely unexplored in chemistry. Reaction-diffusion (RD) mechanisms are, however, essential to understand how shape emerges in the living world. While numerical methods confirm the incredible…
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…
Most existing swarm pattern formation methods depend on a predefined gene regulatory network (GRN) structure that requires designers' priori knowledge, which is difficult to adapt to complex and changeable environments. To dynamically adapt…
Environmental heterogeneity can drive genetic heterogeneity in expanding populations; mutant strains may emerge that trade overall growth rate for an improved ability to survive in patches that are hostile to the wild type. This…
Spatial extent is a complicating factor in mathematical biology. The possibility that an action at point A cannot immediately affect what happens at point B creates the opportunity for spatial nonuniformity. This nonuniformity must change…
The functions of proteins and RNAs are determined by a myriad of interactions between their constituent residues, but most quantitative models of how molecular phenotype depends on genotype must approximate this by simple additive effects.…
Deep generative models (DGMs) and their conditional counterparts provide a powerful ability for general-purpose generative modeling of data distributions. However, it remains challenging for existing methods to address advanced conditional…
A central goal of evolutionary biology is to explain the origins and distribution of diversity across life. Beyond species or genetic diversity, we also observe diversity in the circuits (genetic or otherwise) underlying complex functional…
Emergence is a phenomenon taken for granted in science but also still not well understood. We have developed a model of artificial genetic evolution intended to allow for emergence on genetic, population and social levels. We present the…
Quality-Diversity (QD) algorithms aim to discover diverse, high-performing solutions across behavioral niches. However, QD search often stagnates as incremental variation operators struggle to propagate building blocks across large…
Proper parameter configuration is a prerequisite for the success of Evolutionary Algorithms (EAs). While various adaptive strategies have been proposed, it remains an open question whether all control dimensions contribute equally to…
The var genes of the human malaria parasite Plasmodium falciparum present a challenge to population geneticists due to their extreme diversity, which is generated by high rates of recombination. These genes encode a primary antigen protein…
We propose a general framework for computing Retarded Green's Functions (RGFs) on quantum computers by recasting their evaluation as a problem of circuit differentiation. Our proposal is based on real-time evolution and specifically…
Motile biological cells in tissue often display the phenomenon of durotaxis, i.e. they tend to move towards stiffer parts of substrate tissue. The mechanism for this behavior is not completely understood. We consider simplified models for…
The parallel mutation-selection evolutionary dynamics, in which mutation and replication are independent events, is solved exactly in the case that the Malthusian fitnesses associated to the genomes are described by the Random Energy Model…