Nikola Beneš

Ondřej Huvar, Nikola Beneš, Martin Jonáš et al.

Qualitative models provide crucial instruments for modelling complex biological systems. While advances in automated reasoning and symbolic encodings have enabled rigorous inference of these models from data, the process remains highly fragile. First, biological measurement errors inevitably propagate into formal model specifications. Second, when a specification becomes unsatisfiable, distinguishing between fundamental design flaws and minor technical errors is notoriously difficult. This uncertainty often leads to under-specification, as it is unclear which observations are still ``safe'' to incorporate. To overcome these challenges, we introduce a robust inference method based on weighted MaxSMT. By encoding uncertain biological observations as weighted soft constraints, our approach enables the solver to identify a model best reflecting the observations, even with some conflicting constraints. Our method allows for Boolean and multi-valued variable domains, alongside observations derived from discretisation (level constraints) and differential expression (ordering constraints). We show our approach can be used to successfully infer neural cell differentiation models from prior-knowledge networks with 200--1300 genes using ordering constraints on all included genes.

Jiří Barnat, Petr Bauch, Nikola Beneš et al.

In the last decade it became a common practice to formalise software requirements to improve the clarity of users' expectations. In this work we build on the fact that functional requirements can be expressed in temporal logic and we propose new sanity checking techniques that automatically detect flaws and suggest improvements of given requirements. Specifically, we describe and experimentally evaluate approaches to consistency and redundancy checking that identify all inconsistencies and pinpoint their exact source (the smallest inconsistent set). We further report on the experience obtained from employing the consistency and redundancy checking in an industrial environment. To complete the sanity checking we also describe a semi-automatic completeness evaluation that can assess the coverage of user requirements and suggest missing properties the user might have wanted to formulate. The usefulness of our completeness evaluation is demonstrated in a case study of an aeroplane control system.