6 papers
BAss: Symbolic Reasoning in Abstract Dialectical Frameworks
Samuel Pastva, Van-Giang Trinh
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 sy…
SMT with Uninterpreted Functions and Monotonicity Constraints in Systems Biology
Ondřej Huvar, Martin Jonáš, Samuel Pastva
The theory of uninterpreted functions is a key modeling tool for systems with unknown or abstracted components. Some domains such as systems biology impose further restrictions reg…
Relating biomarkers and phenotypes using dynamical trap spaces
Samuel Pastva, Kyu Hyong Park, Jordan C. Rozum +2
Connecting the dynamics of biomolecular networks to experimentally measurable cell phenotypes remains a central challenge in systems biology. Here we introduce a model-based defini…
Scalable Counting of Minimal Trap Spaces and Fixed Points in Boolean Networks
Mohimenul Kabir, Van-Giang Trinh, Samuel Pastva +1
Boolean Networks (BNs) serve as a fundamental modeling framework for capturing complex dynamical systems across various domains, including systems biology, computational logic, and…
On the number of asynchronous attractors in AND-NOT Boolean networks
Van-Giang Trinh, Samuel Pastva, Jordan Rozum +2
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 syst…
An open problem: Why are motif-avoidant attractors so rare in asynchronous Boolean networks?
Samuel Pastva, Kyu Hyong Park, Ondrej Huvar +2
Asynchronous Boolean networks are a type of discrete dynamical system in which each variable can take one of two states, and a single variable state is updated in each time step ac…