4 papers · 1 filter
Inference of Qualitative Models from Steady-State Data via Weighted MaxSMT
Ondřej Huvar, Nikola Beneš, Martin Jonáš +2
Qualitative models provide crucial instruments for modelling complex biological systems. While advances in automated reasoning and symbolic encodings have enabled rigorous inferenc…
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…