Related papers: Bridging abstract dialectical argumentation and Bo…
Dialectical frameworks are a unifying model of formal argumentation, where argumentative relations between arguments are represented by assigning acceptance conditions to atomic arguments. Their generality allow them to cover a number of…
Among the most general structures extending the framework by Dung are the abstract dialectical frameworks (ADFs). They come equipped with various types of semantics, with the most prominent - the labeling-based one - analyzed in the context…
Abstract Dialectical Frameworks (ADFs) generalize Dung's argumentation frameworks allowing various relationships among arguments to be expressed in a systematic way. We further generalize ADFs so as to accommodate arbitrary acceptance…
The two most fundamental processes describing change in biology, development and evolu-tion, occur over drastically different timescales, difficult to reconcile within a unified framework. Development involves temporal sequences of cell…
Gene regulatory networks (GRNs) play a central role in cellular decision-making. Understanding their structure and how it impacts their dynamics constitutes thus a fundamental biological question. GRNs are frequently modeled as Boolean…
One of the most prominent tools for abstract argumentation is the Dung's framework, AF for short. It is accompanied by a variety of semantics including grounded, complete, preferred and stable. Although powerful, AFs have their…
We present BAss (BDD-based ADF symbolic solver), a novel analysis tool for Abstract Dialectical Frameworks (ADFs) based on Binary Decision Diagrams (BDDs). It supports the fully symbolic computation of all admissible, complete, and…
This thesis aims at the logical analysis of discrete processes, in particular of such generated by gene regulatory networks. States, transitions and operators from temporal logics are expressed in the language of Formal Concept Analysis. By…
Assumption-based Argumentation (ABA) is a well-known structured argumentation formalism, whereby arguments and attacks between them are drawn from rules, defeasible assumptions and their contraries. A common restriction imposed on ABA…
One of the characteristic features of genetic networks is their inherent robustness, that is, their ability to retain functionality in spite of the introduction of random errors. In this paper, we seek to better understand how robustness is…
Boolean Networks (BNs) describe the time evolution of binary states using logic functions on the nodes of a network. They are fundamental models for complex discrete dynamical systems, with applications in various areas of science and…
Boolean threshold networks have recently been proposed as useful tools to model the dynamics of genetic regulatory networks, and have been successfully applied to describe the cell cycles of \textit{S. cerevisiae} and \textit{S. pombe}.…
Dung's abstract argumentation theory is a widely used formalism to model conflicting information and to draw conclusions in such situations. Hereby, the knowledge is represented by so-called argumentation frameworks (AFs) and the reasoning…
For years, we have been building models of gene regulatory networks, where recent advances in molecular biology shed some light on new structural and dynamical properties of such highly complex systems. In this work, we propose a novel…
Random boolean networks are a model of genetic regulatory networks that has proven able to describe experimental data in biology. They not only reproduce important phenomena in cell dynamics, but they are also extremely interesting from a…
Realizability for knowledge representation formalisms studies the following question: given a semantics and a set of interpretations, is there a knowledge base whose semantics coincides exactly with the given interpretation set? We…
Methods of modeling cellular regulatory networks as diverse as differential equations and Boolean networks co-exist, however, without any closer correspondence to each other. With the example system of the fission yeast cell cycle control…
Genetic regulatory networks control ontogeny. For fifty years Boolean networks have served as models of such systems, ranging from ensembles of random Boolean networks as models for generic properties of gene regulation to working dynamical…
Abstract Dialectical Frameworks (ADFs) are argumentation frameworks where each node is associated with an acceptance condition. This allows us to model different types of dependencies as supports and attacks. Previous studies provided a…
As a discrete approach to genetic regulatory networks, Boolean models provide an essential qualitative description of the structure of interactions among genes and proteins. Boolean models generally assume only two possible states…