Related papers: Argudas: arguing with gene expression information

Modern AI systems are complex workflows containing multiple components and data sources. Data provenance provides the ability to interrogate and potentially explain the outputs of these systems. However, provenance is often too detailed and…

Much artificial intelligence research focuses on the problem of deducing the validity of unobservable propositions or hypotheses from observable evidence.! Many of the knowledge representation techniques designed for this problem encode the…

Product configuration systems are often based on a variability model. The development of a variability model is a time consuming and error-prone process. Considering the ongoing development of products, the variability model has to be…

Large language models show promise for knowledge-intensive domains, yet their use in agriculture is constrained by weak grounding, English-centric training data, and limited real-world evaluation. These issues are amplified for low-resource…

The interaction between natural selection and random mutation is frequently debated in recent years. Does similar dilemma also exist in the evolution of real networks such as biological networks? In this paper, we try to discuss this issue…

Changing base composition during the evolution of biological sequences can mislead some of the phylogenetic inference techniques in current use. However, detecting whether such a process has occurred may be difficult, since convergent…

The topology of artificial neural networks has a significant effect on their performance. Characterizing efficient topology is a field of promising research in Artificial Intelligence. However, it is not a trivial task and it is mainly…

One way to understand the role history plays on evolutionary trajectories is by giving ancient life a second opportunity to evolve. Our ability to empirically perform such an experiment, however, is limited by current experimental designs.…

Genetic regulatory networks enable cells to respond to the changes in internal and external conditions by dynamically coordinating their gene expression profiles. Our ability to make quantitative measurements in these biochemical circuits…

We propose a monitoring mechanism for recording the evolution of systems after certain computations, maintaining the history in a tree-like structure. Technically, we develop the monitoring mechanism in a variant of ADR (after Architectural…

Gene innovation is a key mechanism on the evolution and phenotypic diversity of life forms. There is a need for tools able to study gene innovation across an increasingly large number of genomic sequences to maximally capitalise our…

One of the biggest challenges that artificial intelligence (AI) research is facing in recent times is to develop algorithms and systems that are not only good at performing a specific intelligent task but also good at learning a very…

GeneVis is a web-based tool to visualize complementary data sets of different disciplines within the field of genetics. It overlays gene-cluster information, gene-interaction data and gene-disease association data by means of web-based…

A representation of the genetic code as a six-dimensional Boolean hypercube is proposed. It is assumed here that this structure is the result of the hierarchical order of the interaction energies of the bases in codon-anticodon recognition.…

Artificial life is a research field studying what processes and properties define life, based on a multidisciplinary approach spanning the physical, natural and computational sciences. Artificial life aims to foster a comprehensive study of…

Large language models (LLMs) in biomedicine face a fundamental conflict between static parameter knowledge and the dynamic nature of clinical evidence. Retrieval-Augmented Generation (RAG) addresses this by grounding generation in external…

The concept of extended cloud requires efficient network infrastructure to support ecosystems reaching form the edge to the cloud(s). Standard approaches to network load balancing deliver static solutions that are insufficient for the…

One of the defining features of living systems is their adaptability to changing environmental conditions. This requires organisms to extract temporal and spatial features of their environment, and use that information to compute the…

Neuroevolutionary algorithms, automatic searches of neural network structures by means of evolutionary techniques, are computationally costly procedures. In spite of this, due to the great performance provided by the architectures which are…

Robust Unsupervised Domain Adaptation (RoUDA) aims to achieve not only clean but also robust cross-domain knowledge transfer from a labeled source domain to an unlabeled target domain. A number of works have been conducted by directly…