Related papers: A Logical Framework for Systems Biology
Formally verifying properties of software code has been a highly desirable task, especially with the emergence of LLM-generated code. In the same vein, they provide an interesting avenue for the exploration of formal verification and…
Dynamic logic is a modal logic for reasoning about programs. A cyclic proof system is a proof system that allows proofs containing cycles and is an alternative to a proof system containing (co-)induction. This paper introduces a sequent…
We propose a general framework to allow: (a) specifying the operational semantics of a programming language; and (b) stating and proving properties about program correctness. Our framework is based on a many-sorted system of hybrid modal…
Logics and model-checking have been successfully used in the last decades for modeling and verification of various types of hardware (and software) systems. While most languages and techniques emerged in a context of monolithic systems with…
Matching logic is a logical framework for specifying and reasoning about programs using pattern matching semantics. A pattern is made up of a number of structural components and constraints. Structural components are syntactically matched,…
As large language models (LLMs) are increasing integrated into fact-checking pipelines, formal logic is often proposed as a rigorous means by which to mitigate bias, errors and hallucinations in these models' outputs. For example, some…
Verification of biomedical claims is critical for healthcare decision-making, public health policy and scientific research. We present an interactive biomedical claim verification system by integrating LLMs, transparent model explanations,…
We consider the problem of mining signal temporal logical requirements from a dataset of regular (good) and anomalous (bad) trajectories of a dynamical system. We assume the training set to be labeled by human experts and that we have…
Dynamically Adaptive Systems modify their behav- ior and structure in response to changes in their surrounding environment and according to an adaptation logic. Critical sys- tems increasingly incorporate dynamic adaptation capabilities;…
This article examines two approaches to verification, one based on using a logic for expressing properties of a system, and one based on showing the system equivalent to a simpler system that obviously has whatever property is of interest.…
The design of genetic networks with specific functions is one of the major goals of synthetic biology. However, constructing biological devices that work "as required" remains challenging, while the cost of uncovering flawed designs…
Large Language Models demonstrate substantial promise for advancing scientific discovery, yet their deployment in disciplines demanding factual precision and specialized domain constraints presents significant challenges. Within molecular…
We present a new approach for the design of a synthetic biological circuit whose behaviour is specified in terms of signal temporal logic (STL) formulae. We first show how to characterise with STL formulae the input/output behaviour of…
The verification of Multi-Agent Systems (MAS) poses a significant challenge. Various approaches and methodologies exist to address this challenge; however, tools that support them are not always readily available. Even when such tools are…
We introduce a technology to formally verify that a software system satisfies a temporal specification of functional correctness, without revealing the system itself. Our method combines a deductive approach to model checking to obtain a…
The problem of mechanically formalizing and proving metatheoretic properties of programming language calculi, type systems, operational semantics, and related formal systems has received considerable attention recently. However, the dual…
Metabolic networks, formed by a series of metabolic pathways, are made of intracellular and extracellular reactions that determine the biochemical properties of a cell, and by a set of interactions that guide and regulate the activity of…
Rule-based models are attractive for various tasks because they inherently lead to interpretable and explainable decisions and can easily incorporate prior knowledge. However, such systems are difficult to apply to problems involving…
Linear implication can represent state transitions, but real transition systems operate under temporal, stochastic or probabilistic constraints that are not directly representable in ordinary linear logic. We propose a general modal…
This paper motivates why Real-Time Maude should be well suited to provide a formal semantics and formal analysis capabilities to modeling languages for embedded systems. One can then use the code generation facilities of the tools for the…