Related papers: The immune system: look who's talking
A notion of biologic system or just a system implies a functional wholeness of comprising system components. Positive and negative feedback are the examples of how the idea to unite anatomical elements in the whole functional structure was…
Biological systems, from a cell to the human brain, are inherently complex. A powerful representation of such systems, described by an intricate web of relationships across multiple scales, is provided by complex networks. Recently, several…
This paper describes necessary elements for constructing theoretical models of network and system administration. Armed with a theoretical model it becomes possible to determine best practices and optimal strategies in a way which…
Organisms have evolved immune systems that can counter pathogenic threats. The adaptive immune system in vertebrates consists of a diverse repertoire of immune receptors that can dynamically reorganize to specifically target the…
We develop a system that formally represents spatial semantics concepts within natural language descriptions of spatial arrangements. The system builds on a model of spatial semantics representation according to which words in a sentence…
I examine how terminological languages can be used to manage linguistic data during NL research and development. In particular, I consider the lexical semantics task of characterizing semantic verb classes and show how the language can be…
This paper proposes a formal framework for modeling the interaction of causal and (qualitative) epistemic reasoning. To this purpose, we extend the notion of a causal model with a representation of the epistemic state of an agent. On the…
This paper describes a framework and a method with which speech communication can be analyzed. The framework consists of a set of low bit rate, short-range acoustic communication systems, such as speech, but that are quite different from…
Large language models (LLMs) are transforming cellular biology by enabling the development of "virtual cells"--computational systems that represent, predict, and reason about cellular states and behaviors. This work provides a comprehensive…
Human beings are talkative. What advantage did their ancestors find in communicating so much? Numerous authors consider this advantage to be "obvious" and "enormous". If so, the problem of the evolutionary emergence of language amounts to…
This article summarises a Web-book on "Complexity" that was developed to introduce undergraduate students to interesting complex systems in the biological, physical and social sciences, and the common tools, principles and concepts used for…
Theory based AI research has had a hard time recently and the aim here is to propose a model of what LLMs are actually doing when they impress us with their language skills. The model integrates three established theories of human…
In this work, we develop an intelligent user interface that allows users to enter biomedical queries in a natural language, and that presents the answers (possibly with explanations if requested) in a natural language. We develop a rule…
We examine a naming game with two agents trying to establish a common vocabulary for n objects. Such efforts lead to the emergence of language that allows for an efficient communication and exhibits some degree of homonymy and synonymy.…
The paper introduces a framework for the evaluation of the encoding of factual scientific knowledge, designed to streamline the manual evaluation process typically conducted by domain experts. Inferring over and extracting information from…
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…
This paper presents the research on the interdisciplinary research infrastructure for understanding human reasoning in game-theoretic terms. Strategic reasoning is considered to impact human decision making in social, economical and…
Recently, computational modelling became a very important research tool that enables us to study problems that for decades evaded scientific analysis. Evolutionary systems are certainly examples of such problems: they are composed of many…
Exhaled breath can be used in retrieving information and creating innovative communication systems. It contains several volatile organic compounds (VOCs) and biological entities that can act as health biomarkers. For instance, the breath of…
Large language models (LLMs) have shown significant potential to change how we write, communicate, and create, leading to rapid adoption across society. This dissertation examines how individuals and institutions are adapting to and…