Related papers: Argudas: arguing with gene expression information
In the presence of recombination, the evolutionary relationships between a set of sampled genomes cannot be described by a single genealogical tree. Instead, the genomes are related by a complex, interwoven collection of genealogies…
Gene expression-based heterogeneity analysis has been extensively conducted. In recent studies, it has been shown that network-based analysis, which takes a system perspective and accommodates the interconnections among genes, can be more…
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…
We investigate the evolutionary processes behind the development and optimization of multiple threads of execution in digital organisms using the avida platform, a software package that implements Darwinian evolution on populations of…
Artificial intelligence is one of the drivers of modern technological development. The current approach to the development of intelligent systems is data-centric. It has several limitations: it is fundamentally impossible to collect data…
Genetic algorithms, computer programs that simulate natural evolution, are increasingly applied across many disciplines. They have been used to solve various optimisation problems from neural network architecture search to strategic games,…
Software is omnipresent within all factors of society. It is thus important to ensure that software are well tested to mitigate bad user experiences as well as the potential for severe financial and human losses. Software testing is however…
Inferring from inconsistency and making decisions are two problems which have always been treated separately by researchers in Artificial Intelligence. Consequently, different models have been proposed for each category. Different…
Knowledge-based or Artificial Intelligence techniques are used increasingly as alternatives to more classical techniques to model ENVIRONMENTAL SYSTEMS. Use of Artificial Intelligence (AI) in environmental modelling has increased with…
The vast amount of biomedical information available today presents a significant challenge for investigators seeking to digest, process, and understand these findings effectively. Large Language Models (LLMs) have emerged as powerful tools…
Epigenetics encompasses mechanisms that can alter the expression of genes without changing the underlying genetic sequence. The epigenetic regulation of gene expression is initiated and sustained by several mechanisms such as DNA…
Information can evolve as a physical consequence of non-equilibrium dynamics, even in the absence of genes, replication, or predefined fitness functions. We present Stability-Driven Assembly (SDA), a framework in which stochastic assembly…
Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…
This paper presents our computational methodology using Genetic Algorithms (GA) for exploring the nature of RNA editing. These models are constructed using several genetic editing characteristics that are gleaned from the RNA editing system…
We define a notion of coupling time with ambiguities for interacting particle systems, and show how this can be used to prove ergodicity and to bound the convergence time to equilibrium and the decay of correlations at equilibrium. A…
Retrieval augmented generation (RAG) systems provide a method for factually grounding the responses of a Large Language Model (LLM) by providing retrieved evidence, or context, as support. Guided by this context, RAG systems can reduce…
Asterias (\url{http://www.asterias.info}) is an integrated collection of freely-accessible web tools for the analysis of gene expression and aCGH data. Most of the tools use parallel computing (via MPI). Most of our applications allow the…
Phylogenetics is the study of the evolutionary relationships between organisms. One of the main challenges in the field is to take biological data for a group of organisms and to infer an evolutionary tree, a graph that represents these…
To tackle the challenge of producing tractable phylogenetic trees in contexts where complete information is available, we introduce APOGeT: an online, pluggable, clustering algorithm for a stream of genomes. It is designed to run alongside…
Argument summarization aims to generate concise, structured representations of complex, multi-perspective debates. While recent work has advanced the identification and clustering of argumentative components, the generation stage remains…