Related papers: Experimental Biological Protocols with Formal Sema…
The steadily increasing size of scientific Monte Carlo simulations and the desire for robust, correct, and reproducible results necessitates rigorous testing procedures for scientific simulations in order to detect numerical problems and…
Compartmentalization of biochemical processes underlies all biological systems, from the organelle to the tissue scale. Theoretical models to study the interplay between noisy reaction dynamics and compartmentalization are sparse, and…
Formal language techniques have been used in the past to study autonomous dynamical systems. However, for controlled systems, new features are needed to distinguish between information generated by the system and input control. We show how…
While generative methods have progressed rapidly in recent years, generating expressive prosody for an utterance remains a challenging task in text-to-speech synthesis. This is particularly true for systems that model prosody explicitly…
For cellular biochemical reaction systems where the numbers of molecules is small, significant noise is associated with chemical reaction events. This molecular noise can give rise to behavior that is very different from the predictions of…
Semantic typing has become a powerful tool for program verification, applying the technique of logical relations as not only a proof method, but also a device for prescribing program behavior. In recent work, Yao et al. scaled semantic…
The stochastic simulation of biological systems is an increasingly popular technique in bioinformatics. It often is an enlightening technique, which may however result in being computational expensive. We discuss the main opportunities to…
Biological data and knowledge bases increasingly rely on Semantic Web technologies and the use of knowledge graphs for data integration, retrieval and federated queries. We propose a solution for automatically semantifying biological…
Understanding the behaviour of biological systems requires a complex setting of in vitro and in vivo experiments, which attracts high costs in terms of time and resources. The use of mathematical models allows researchers to perform…
A recent study of bugs in real-world concurrent and distributed systems found that, while implementations of individual protocols tend to be robust, the composition of multiple protocols and its interplay with internal computation is the…
Matching logic is a formalism for specifying, and reasoning about, mathematical structures, using patterns and pattern matching. Growing in popularity, it has been used to define many logical systems such as separation logic with recursive…
Today's probabilistic language generators fall short when it comes to producing coherent and fluent text despite the fact that the underlying models perform well under standard metrics, e.g., perplexity. This discrepancy has puzzled the…
Complex behaviour in many systems arises from the stochastic interactions of spatially distributed particles or agents. Stochastic reaction-diffusion processes are widely used to model such behaviour in disciplines ranging from biology to…
The formalization of process knowledge using ontologies enables consistent modeling of parameter interdependencies in manufacturing. These interdependencies are typically represented as mathematical expressions that define relations between…
Normative non-functional requirements specify constraints that a system must observe in order to avoid violations of social, legal, ethical, empathetic, and cultural norms. As these requirements are typically defined by non-technical system…
Formal, mathematically rigorous programming language semantics are the essential prerequisite for the design of logics and calculi that permit automated reasoning about concurrent programs. We propose a novel modular semantics designed to…
Autonomous scientific research, capable of independently conducting complex experiments and serving non-specialists, represents a long-held aspiration. Achieving it requires a fundamental paradigm shift driven by artificial intelligence…
Synthetic Biology is an interdisciplinary field that utilizes well-established engineering principles, ranging from electrical, control and computer systems, for analyzing the biological systems, such as biological circuits, enzymes,…
In this paper we survey recent work on the use of statistical model checking techniques for biological applications. We begin with an overview of the basic modelling techniques for biochemical reactions and their corresponding stochastic…
The goal of this lecture is to show how modern theorem provers---in this case, the Coq proof assistant---can be used to mechanize the specification of programming languages and their semantics, and to reason over individual programs and…