Related papers: Argudas: arguing with gene expression information
We discuss how to use a Genetic Regulatory Network as an evolutionary representation to solve a typical GP reinforcement problem, the pole balancing. The network is a modified version of an Artificial Regulatory Network proposed a few years…
Homeostasis, the ability to maintain a stable internal environment in the face of perturbations, is essential for the functioning of living systems. Given observations of a system, or even a detailed model of one, it is both valuable and…
The reproduction and replication of research results has become a major issue for a number of scientific disciplines. In computer science and related computational disciplines such as systems biology, the challenges closely revolve around…
Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters,…
We examine the evolution of expression patterns and the organization of genetic information in populations of self-replicating digital organisms. Seeding the experiments with a linearly expressed ancestor, we witness the development of…
Networks of genetic expression can be modelled by hypergraphs with the additional structure that real coefficients are given to each vertex-edge incidence. The spectra, i.e. the multiset of the eigenvalues, of such hypergraphs, are known to…
The objective of automated Question Answering (QA) systems is to provide answers to user queries in a time efficient manner. The answers are usually found in either databases (or knowledge bases) or a collection of documents commonly…
Understanding the rules underlying organismal development is a major unsolved problem in biology. Each cell in a developing organism responds to signals in its local environment by dividing, excreting, consuming, or reorganizing, yet how…
Artificial Life provides the opportunity to study the emergence and evolution of simple ecosystems in real time. We give an overview of the advantages and limitations of such an approach, as well as its relation to individual-based modeling…
Coherence evaluation aims to assess the organization and structure of a discourse, which remains challenging even in the era of large language models. Due to the scarcity of annotated data, data augmentation is commonly used for training…
The lack of annotated data on professional argumentation and complete argumentative debates has led to the oversimplification and the inability of approaching more complex natural language processing tasks. Such is the case of the automatic…
Genetic algorithms are stochastic iterative algorithms in which a population of individuals evolve by emulating the process of biological evolution and natural selection. The R package GA provides a collection of general purpose functions…
Systems biology of plants offers myriad opportunities and many challenges in modeling. A number of technical challenges stem from paucity of computational methods for discovery of the most fundamental properties of complex dynamical…
A clinical artificial intelligence (AI) system is often validated on a held-out set of data which it has not been exposed to before (e.g., data from a different hospital with a distinct electronic health record system). This evaluation…
Epigenetics has captured the attention of scientists in the past decades, yet its scope has been continuously changing. In this paper, we give an overview on how and why its definition has evolved and suggest several clarification on the…
Deep research agents have achieved remarkable progress on complex information seeking tasks. Even long ReAct style rollouts explore only a single trajectory, while recent state of the art systems scale inference time compute via parallel…
Phase separation has emerged as an essential concept for the spatial organization inside biological cells. However, despite the clear relevance to virtually all physiological functions, we understand surprisingly little about what phases…
A distributed computing system is a collection of processors that communicate either by reading and writing from a shared memory or by sending messages over some communication network. Most prior biologically inspired distributed computing…
Recent developments in AI have reinvigorated pursuits to advance the (life) sciences using AI techniques, thereby creating a renewed opportunity to bridge different fields and find synergies. Headlines for AI and the life sciences have been…
Online scientific publications provide vast opportunities for researchers. Alas, the quantity and the rate of increase in the articles make the utilization of these resources very challenging. This work presents as inquiry-based approach to…