Belaid Benhamou

Graphical conditions for the existence, unicity and number of regular models

The regular models of a normal logic program are a particular type of partial (i.e. 3-valued) models which correspond to stable partial models with minimal undefinedness. In this paper, we explore graphical conditions on the dependency graph of a finite ground normal logic program to analyze the existence, unicity and number of regular models for the program […]

Tue, Oct 1, 2024

Scalable Enumeration of Trap Spaces in Boolean Networks via Answer Set Programming

Boolean Networks (BNs) are widely used as a modeling formalism in several domains, notably systems biology and computer science. A fundamental problem in BN analysis is the enumeration of trap spaces, which are hypercubes in the state space that cannot be escaped once entered. Several methods have been proposed for enumerating trap spaces, however they often suffer from scalability and efficiency issues, particularly for large and complex models […]

Thu, Feb 1, 2024

Trap spaces of Boolean networks are conflict-free siphons of their Petri net encoding

Boolean network modeling of gene regulation but also of post-transcriptomic systems has proven over the years that it can bring powerful analyses and corresponding insight to the many cases where precise biological data is not sufficiently available to build a detailed quantitative model. Besides simulation, the analysis of such models is mostly based on attractor computation, since those correspond roughly to observable biological phenotypes. The recent use of trap spaces made a real breakthrough in that field allowing to consider medium-sized models that used to be out of reach […]

Fri, Sep 1, 2023

Efficient Enumeration of Fixed Points in Complex Boolean Networks Using Answer Set Programming

Boolean Networks (BNs) are an efficient modeling formalism with applications in various research fields such as mathematics, computer science, and more recently systems biology. One crucial problem in the BN research is to enumerate all fixed points, which has been proven crucial in the analysis and control of biological systems. Indeed, in that field, BNs originated from the pioneering work of R […]

Tue, Aug 1, 2023

Minimal trap spaces of Logical models are maximal siphons of their Petri net encoding

Boolean modelling of gene regulation but also of post-transcriptomic systems has proven over the years that it can bring powerful analyses and corresponding insight to the many cases where precise biological data is not sufficiently available to build a detailed quantitative model. This is even more true for very large models where such data is frequently missing and led to a constant increase in size of logical models à la Thomas. Besides simulation, the analysis of such models is mostly based on attractor computation, since those correspond roughly to observable biological phenotypes […]

Thu, Sep 1, 2022