Related papers: Bridging abstract dialectical argumentation and Bo…
Boolean networks may be viewed as idealizations of biological genetic networks, where each node is represented by an on-off switch which is a function of the binary output from some other nodes. We evolve connectivity in a single Boolean…
Interactions between genes and gene products give rise to complex circuits that enable cells to process information and respond to external signals. Theoretical studies often describe these interactions using continuous, stochastic, or…
Our aim is to build a set of rules, such that reasoning over temporal dependencies within gene regulatory networks is possible. The underlying transitions may be obtained by discretizing observed time series, or they are generated based on…
In this paper, we propose a mean-field model which attempts to bridge the gap between random Boolean networks and more realistic stochastic modeling of genetic regulatory networks. The main idea of the model is to replace all regulatory…
The dynamic stability of the Boolean networks representing a model for the gene transcriptional regulation (Kauffman model) is studied by calculating analytically and numerically the Hamming distance between two evolving configurations.…
We report a scalable hybrid quantum-classical machine learning framework to build Bayesian networks (BN) that captures the conditional dependence and causal relationships of random variables. The generation of a BN consists of finding a…
Boolean networks have been proposed as potentially useful models for genetic control. An important aspect of these networks is the stability of their dynamics in response to small perturbations. Previous approaches to stability have assumed…
The structure and dynamics of a typical biological system are complex due to strong and inhomogeneous interactions between its constituents. The investigation of such systems with classical mathematical tools, such as differential equations…
Characterization of the differences between biological and random networks can reveal the design principles that enable the robust realization of crucial biological functions including the establishment of different cell types. Previous…
Dung's abstract argumentation frameworks model acceptability solely in terms of an attack relation, thereby conflating two conceptually distinct aspects of argumentative reasoning: direct conflict between arguments and the structural…
Datalog$^\neg$ is a central formalism used in a variety of domains ranging from deductive databases and abstract argumentation frameworks to answer set programming. Its model theory is the finite counterpart of the logical semantics…
The editing of transcribed RNA by other molecules such that the form of the final product differs from that specified in the corresponding DNA sequence is ubiquitous. This paper uses an abstract, tunable Boolean genetic regulatory network…
Understanding design principles of molecular interaction networks is an important goal of molecular systems biology. Some insights have been gained into features of their network topology through the discovery of graph theoretic patterns…
We investigate the dynamical behavior of simple modules composed of two genes with two or three regulating connections. Continuous dynamics for mRNA and protein concentrations is compared to a Boolean model for gene activity. Using a…
Gene regulatory networks exhibit remarkable stability, maintaining functional phenotypes despite genetic and environmental perturbations. Discrete dynamical models, such as Boolean networks, provide systems biologists with a tractable…
This short paper presents an abstract, tunable model of genomic structural change within the cell lifecycle and explores its use with simulated evolution. A well-known Boolean model of genetic regulatory networks is extended to include…
Biological networks such as gene regulatory networks possess desirable properties. They are more robust and controllable than random networks. This motivates the search for structural and dynamical features that evolution has incorporated…
The dynamics of Boolean networks (BN) with quenched disorder and thermal noise is studied via the generating functional method. A general formulation, suitable for BN with any distribution of Boolean functions, is developed. It provides…
To model biological systems using networks, it is desirable to allow more than two levels of expression for the nodes and to allow the introduction of parameters. Various modeling and simulation methods addressing these needs using Boolean…
Cycles of attacking arguments pose non-trivial issues in Dung style argumentation theory, apparent behavioural difference between odd and even length cycles being a notable one. While a few methods were proposed for treating them, to - in…