Related papers: Finding New Order in Biological Functions from the…
Here a genetic algorithm (GA) is presented that creates a teaching schedule for a university physics department by algorithmically assigning ${\sim}200$ classes to ${\sim}50$ professors for each of three academic terms per year. The…
Retrieval-Augmented Generation (RAG) systems combine Large Language Models (LLMs) with external knowledge, and their performance depends heavily on how that knowledge is represented. This study investigates how different Knowledge Graph…
Comprehending the interplay between spatial and temporal characteristics of neural dynamics can contribute to our understanding of information processing in the human brain. Graph neural networks (GNNs) provide a new possibility to…
The Phylogenetic Genome Annotator (PGA) is a computer program that enables real-time comparison of 'gene trees' versus 'species trees' obtained from predicted open reading frames of whole genome data. The gene phylogenies are inferred for…
Ontologies are known for their ability to organize rich metadata, support the identification of novel insights via semantic queries, and promote reuse. In this paper, we consider the problem of automated planning, where the objective is to…
Graph-structured data ubiquitously appears in science and engineering. Graph neural networks (GNNs) are designed to exploit the relational inductive bias exhibited in graphs; they have been shown to outperform other forms of neural networks…
In this chapter we propose Generic Ontology Design Patterns, GODPs, as a methodology for representing and instantiating ontology design patterns in a way that is adaptable, and allows domain experts (and other users) to safely use them…
Generative artificial intelligence (AI), exemplified by the release of GPT-3.5 in 2022, has significantly advanced the potential applications of large language models (LLMs), including in the realms of ontology development and knowledge…
Complex networks encountered in biology are often characterized by significant structural diversity. Whether it be differences in the three-dimensional structure of allosteric proteins, or the variation among the micro-scale structures of…
Gene expression programming, a genotype/phenotype genetic algorithm (linear and ramified), is presented here for the first time as a new technique for the creation of computer programs. Gene expression programming uses character linear…
Oscillatory activity is ubiquitous in natural and engineered network systems. The interaction scheme underlying interdependent oscillatory components governs the emergence of network-wide patterns of synchrony that regulate and enable…
DNA rearrangement processes recombine gene segments that are organized on the chromosome in a variety of ways. The segments can overlap, interleave or one may be a subsegment of another. We use directed graphs to represent segment…
Generic ontologies were introduced as an extension (Generic DOL) of the Distributed Ontology, Modeling and Specification Language, DOL, with the aim to provide a language for Generic Ontology Design Patterns. In this paper we present a…
Objective: Human-curated disease ontologies are widely used for diagnostic evaluation, treatment and data comparisons over time, and clinical decision support. The classification principles underlying these ontologies are guided by the…
Node role explainability in complex networks is very difficult, yet is crucial in different application domains such as social science, neurosciences or computer science. Many efforts have been made on the quantification of hubs revealing…
It is evident that the current state of Large Language Models (LLMs) necessitates the incorporation of external tools. The lack of straightforward algebraic and logical reasoning is well documented and prompted researchers to develop…
Leveraging generative Artificial Intelligence (AI), we have transformed a dataset comprising 1,000 scientific papers into an ontological knowledge graph. Through an in-depth structural analysis, we have calculated node degrees, identified…
The engineered control of cellular function through the design of synthetic genetic networks is becoming plausible. Here we show how a naturally occurring network can be used as a parts list for artificial network design, and how model…
The importance of improving the FAIRness (findability, accessibility, interoperability, reusability) of research data is undeniable, especially in the face of large, complex datasets currently being produced by omics technologies.…
Genetic algorithms are considered as an original way to solve problems, probably because of their generality and of their "blind" nature. But GAs are also unusual since the features of many implementations (among all that could be thought…