Related papers: Experimental Biological Protocols with Formal Sema…
Formal Methods are mathematically-based techniques for software design and engineering, which enable the unambiguous description of and reasoning about a system's behaviour. Autonomous systems use software to make decisions without human…
Ordinary differential equation models are nowadays widely used for the mechanistic description of biological processes and their temporal evolution. These models typically have many unknown and non-measurable parameters, which have to be…
Stochastic models of biochemical reaction networks are widely used to capture intrinsic noise in cellular systems. The typical formulation of these models are based on Markov processes for which there is extensive research on efficient…
A new tool for modeling electrochemical kinetics is presented. An extension of the Stochastic Simulation Algorithm framework to electrochemical systems is proposed. The physical justifications and constraints for the derivation of a…
Many interesting and useful symbolic computation algorithms manipulate mathematical expressions in mathematically meaningful ways. Although these algorithms are commonplace in computer algebra systems, they can be surprisingly difficult to…
Mathematical theorems are human knowledge able to be accumulated in the form of symbolic representation, and proving theorems has been considered intelligent behavior. Based on the BHK interpretation and the Curry-Howard isomorphism, proof…
In the biotechnology and biomedical domains, recent text mining efforts advocate for machine-interpretable, and preferably, semantified, documentation formats of laboratory processes. This includes wet-lab protocols, (in)organic materials…
Computer systems can be found everywhere: in space, in our homes, in our cars, in our pockets, and sometimes even in our own bodies. For concerns of safety, economy, and convenience, it is important that such systems work correctly.…
Those seeking to reproduce a computational experiment often need to manually look at the code to see how to build necessary libraries, configure parameters, find data, and invoke the experiment; it is not automatic. Automatic…
Many universities have courses and projects revolving around compiler or interpreter implementation as part of their degree programmes in computer science. In such teaching activities, tool support can be highly beneficial. While there are…
This paper is a reflexion on the computability of natural language semantics. It does not contain a new model or new results in the formal semantics of natural language: it is rather a computational analysis of the logical models and…
We establish fundamental and general techniques for formal verification of quantum protocols. Quantum protocols are novel communication schemes involving the use of quantum-mechanical phenomena for representation, storage and transmission…
Concolic testing is a popular dynamic validation technique that can be used for both model checking and automatic test case generation. We have recently introduced concolic testing in the context of logic programming. In contrast to…
Probabilistic specifications are fast gaining ground as a tool for statistical modeling of probabilistic systems. One of the main goals of formal methods in this domain is to ensure that specific behavior is present or absent in the system,…
Stochastic hybrid systems have received significant attentions as a relevant modelling framework describing many systems, from engineering to the life sciences: they enable the study of numerous applications, including transportation…
An algorithm for computing the stable model semantics of logic programs is developed. It is shown that one can extend the semantics and the algorithm to handle new and more expressive types of rules. Emphasis is placed on the use of…
The foundation of reproducible science lies in protocols that are precise, logically ordered, and executable. The autonomous generation of these protocols through natural language queries could greatly improve the efficiency of the…
Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a…
To unleash the full potential of AI for Science, we must untether the agents from a purely digital environment. The agent's ability to control and explore in real-world labs is essential because the physical lab remains foundational to…
In order to work with mathematical content in computer systems, it is necessary to represent it in formal languages. Ideally, these are supported by tools that verify the correctness of the content, allow computing with it, and produce…