Related papers: A framework for parsing heritable information
Understanding and modelling the complexity of the immune system is a challenge that is shared by the ImmunoComplexiT$^1$ thematic network from the RNSC. The immune system is a complex biological, adaptive, highly diversified, self-organized…
Sensing and communication are fundamental enablers of next-generation networks. While communication technologies have advanced significantly, sensing remains limited to conventional parameter estimation and is far from fully explored.…
Biological systems, from cells to organisms, must respond to the ever changing environment in order to survive and function. This is not a simple task given the often random nature of the signals they receive, as well as the intrinsically…
Rapid advance of experimental techniques provides an unprecedented in-depth view into complex developmental processes. Still, little is known on how the complexity of multicellular organisms evolved by elaborating developmental programs and…
Metabolism displays striking and robust regularities in the forms of modularity and hierarchy, whose composition may be compactly described. This renders metabolic architecture comprehensible as a system, and suggests the order in which…
Through in-depth thinking and reasoning about the conditions required for cells to maintain unchanged material distribution, it is concluded that life metabolic reactions require high information content. However, the self-replication of a…
Foundation models in genomics have shown mixed success compared to their counterparts in natural language processing. Yet, the reasons for their limited effectiveness remain poorly understood. In this work, we investigate the role of…
Many systems involve numerous interacting parts and the whole system can have properties that the individual parts do not. I take this novelty as the defining characteristic of an emergent property. Other characteristics associated with…
The regulatory mechanisms driving progression of the yeast cell cycle appears to be comprised of an interacting network of transcription factors (TFs), cyclin-dependent kinases (CDK) and ubiquitin ligases. From a systems perspective the…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
Semantic information in embodied AI is inherently multi-source and multi-stage, making it challenging to fully leverage for achieving stable perception-to-action loops in real-world environments. Early studies have combined manual…
Event scenarios are often complex and involve multiple event sequences connected through different entity participants. Exploring such complex scenarios requires an ability to branch through different sequences, something that is difficult…
We present a theoretical as well as experimental investigation of a population of self-replicating segments of code subject to random mutation and survival of the fittest. Under the assumption that such a system constitutes a minimal system…
Lots of bio-inspired research works have been conducted in self-adaptive software. They have focused on the external behavior of biological entities without their genetic material that causes this behavior and constitutes the challenge this…
Genetic and pharmacological perturbation experiments, such as deleting a gene and monitoring gene expression responses, are powerful tools for studying cellular signal transduction pathways. However, it remains a challenge to automatically…
Modeling environmental ecosystems is essential for effective resource management, sustainable development, and understanding complex ecological processes. However, traditional data-driven methods face challenges in capturing inherently…
Entity Matching (EM) aims at recognizing entity records that denote the same real-world object. Neural EM models learn vector representation of entity descriptions and match entities end-to-end. Though robust, these methods require many…
We investigate the self-organising behaviour of Digital Ecosystems, because a primary motivation for our research is to exploit the self-organising properties of biological ecosystems. We extended a definition for the complexity, grounded…
The question What is Complexity? has occupied a great deal of time and paper over the last 20 or so years. There are a myriad different perspectives and definitions but still no consensus. In this paper I take a phenomenological approach,…
This white paper lays out a vision of research and development in the field of artificial intelligence for the next decade (and beyond). Its denouement is a cyber-physical ecosystem of natural and synthetic sense-making, in which humans are…