Related papers: An ASP-based Approach for Attractor Enumeration in…
Different Boolean networks may reveal similar dynamics although their definition differs, then preventing their distinction from the observations. This raises the question about the sufficiency of a particular Boolean network for properly…
Dynamic models of signaling networks allow the formulation of hypotheses on the topology and kinetic rate laws characterizing a given molecular network, in-depth exploration and confrontation with kinetic biological data. Despite its…
Biological systems are driven by intricate interactions among the complex array of molecules that comprise the cell. Many methods have been developed to reconstruct network models of those interactions. These methods often draw on large…
Answer set programming (ASP) is a logic programming paradigm that can be used to solve complex combinatorial search problems. Aggregates are an ASP construct that plays an important role in many applications. Defining a satisfactory…
A Pseudo-Boolean (PB) constraint is a linear inequality constraint over Boolean literals. One of the popular, efficient ideas used to solve PB-problems (a set of PB-constraints) is to translate them to SAT instances (encodings) via, for…
Understanding control mechanisms in biological systems plays a crucial role in important applications, for instance in cell reprogramming. Boolean modeling allows the identification of possible efficient strategies, helping to reduce the…
We present the hybrid ASP solver clingcon, combining the simple modeling language and the high performance Boolean solving capacities of Answer Set Programming (ASP) with techniques for using non-Boolean constraints from the area of…
Detecting small sets of relevant patterns from a given dataset is a central challenge in data mining. The relevance of a pattern is based on user-provided criteria; typically, all patterns that satisfy certain criteria are considered…
Network embedding has recently emerged as a promising technique to embed nodes of a network into low-dimensional vectors. While fairly successful, most existing works focus on the embedding techniques for static networks. But in practice,…
Modeling the dynamics of biological networks introduces many challenges, among them the lack of first principle models, the size of the networks, and difficulties with parameterization. Discrete time Boolean networks and related continuous…
We report a new experimental approach using an optoelectronic feedback loop to investigate the dynamics of oscillators coupled on large complex networks with arbitrary topology. Our implementation is based on a single optoelectronic…
In this paper, we address the formal characterization of targets triggering cellular trans-differentiation in the scope of Boolean networks with asynchronous dynamics. Given two fixed points of a Boolean network, we are interested in all…
Answer Set Programming (ASP) is a powerful modeling formalism for combinatorial problems. However, writing ASP models is not trivial. We propose a novel method, called Sketched Answer Set Programming (SkASP), aiming at supporting the user…
We present an explanation system for applications that leverage Answer Set Programming (ASP). Given a program P, an answer set A of P, and an atom a in the program P, our system generates all explanation graphs of a which help explain why a…
The generating functional method is employed to investigate the synchronous dynamics of Boolean networks, providing an exact result for the system dynamics via a set of macroscopic order parameters. The topology of the networks studied and…
Within the area of computational models of argumentation, the instantiation-based approach is gaining more and more attention, not at least because meaningful input for Dung's abstract frameworks is provided in that way. In a nutshell, the…
Answer Set Programming (ASP) is a popular declarative reasoning and problem solving approach in symbolic AI. Its rule-based formalism makes it inherently attractive for explainable and interpretive reasoning, which is gaining importance…
Serial pattern mining consists in extracting the frequent sequential patterns from a unique sequence of itemsets. This paper explores the ability of a declarative language, such as Answer Set Programming (ASP), to solve this issue…
Effective control of biological systems can often be achieved through the control of a surprisingly small number of distinct variables. We bring clarity to such results using the formalism of Boolean dynamical networks, analyzing the…
In this paper, we propose a novel framework for dynamical analysis of human actions from 3D motion capture data using topological data analysis. We model human actions using the topological features of the attractor of the dynamical system.…